references.bib

@article{grewal_migration_1992,
	title = {Migration of Caenorhabditis {elegans(Nematoda:} Rhabditidae) larvae towards bacteria and the nature of the bacterial stimulus.},
	volume = {15},
	shorttitle = {Migration of Caenorhabditis {elegans(Nematoda}},
	number = {2},
	journal = {{FUND.} {APPL.} {NEMATOL.}},
	author = {Grewal, P. S. and Wright, D. J.},
	year = {1992},
	pages = {159--166},
	file = {36448.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/NWWZ2VDQ/36448.pdf:application/pdf;Google Scholar Linked Page:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/7FBXQIKB/viewrecord.html:text/html}
},

@article{chalfie_organization_1979,
	title = {Organization of neuronal microtubules in the nematode Caenorhabditis elegans},
	volume = {82},
	issn = {0021-9525},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/479300},
	abstract = {We have studied the organization of microtubules in neurons of the nematode Caenorhabditis elegans. Six neurons, which we call the microtubule cells, contain bundles of darkly staining microtubules which can be followed easily in serial-section electron micrographs. Reconstruction of individual microtubules in these cells indicate that most, if not all, microtubules are short compared with the length of the cell process. Average microtubule length varies characteristically with cell type. The arrangement of microtubules gives an overall polarity to each bundle: the distal ends of the microtubles are on the outside of the bundle, whereas the proximal ends are preferentially inside. The distal and proximal ends each have a characteristic appearance indicating that these microtubules may have a polarity of their own. Short microtubules in processes of other neurons in C. elegans have also been observed.},
	number = {1},
	journal = {The Journal of Cell Biology},
	author = {Chalfie, M and Thomson, J N},
	month = jul,
	year = {1979},
	note = {{PMID:} 479300},
	keywords = {Animals, Microtubules, Nematoda, Neurons},
	pages = {278--289}
},

@article{sagan_case_2009,
	title = {The Case for No First Use},
	volume = {51},
	issn = {0039-6338},
	url = {http://www.informaworld.com.ezp-prod1.hul.harvard.edu/10.1080/00396330903011545},
	doi = {10.1080/00396330903011545},
	number = {3},
	journal = {Survival: Global Politics and Strategy},
	author = {Sagan, Scott D.},
	year = {2009},
	keywords = {Arms Control, Nukes, Policy, {ReadMe}},
	pages = {163}
},

@article{bradski_opencv_2000,
	title = {The {OpenCV} Library},
	volume = {25},
	issn = {{1044-789X}},
	abstract = {{OpenCV} is an open-source, computer-vision library for extracting and processing meaningful data from images.
 Additional resources include opencv.txt (listings).},
	number = {11},
	journal = {Dr. Dobb's Journal of Software Tools},
	author = {Bradski, Gary},
	month = nov,
	year = {2000},
	pages = {120, 122--125}
},

@book{rasband_image_1997,
	address = {Bethesda, Maryland, {USA}},
	title = {Image J},
	url = {http://imagej.nih.gov/ij/},
	publisher = {National Institutes of Health},
	author = {Rasband, W. S.},
	year = {1997}
},

@misc{kaplan_foraging_2008,
	title = {Foraging Information},
	author = {Kaplan, Joshua},
	month = dec,
	year = {2008},
	note = {At Mass General Hospital, Boston, {MA.}}
},

@article{rex_tyramine_2004,
	title = {Tyramine receptor {(SER-2)} isoforms are involved in the regulation of pharyngeal pumping and foraging behavior in Caenorhabditis elegans},
	volume = {91},
	issn = {0022-3042},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15569254},
	doi = {10.1111/j.1471-4159.2004.02787.x},
	abstract = {Octopamine regulates essential processes in nematodes; however, little is known about the physiological role of its precursor, tyramine. In the present study, we have characterized alternatively spliced Caenorhabditis elegans tyramine receptor isoforms {(SER-2} and {SER-2A)} that differ by 23 amino acids within the mid-region of the third intracellular loop. Membranes prepared from cells expressing either {SER-2} or {SER-2A} bind {[3H]lysergic} acid diethylamide {(LSD)} in the low nanomolar range and exhibit highest affinity for tyramine. Similarly, both isoforms exhibit nearly identical Ki values for a number of antagonists. In contrast, {SER-2A} exhibits a significantly lower affinity than {SER-2} for other physiologically relevant biogenic amines, including octopamine. Pertussis toxin treatment reduces affinity for both tyramine and octopamine, especially for octopamine in membranes from cells expressing {SER-2}, suggesting that the conformation of the mid-region of the third intracellular loop is dictated by G-protein interactions and is responsible for the differential tyramine/octopamine affinities of the two isoforms. Tyramine reduces forskolin-stimulated {cAMP} levels in {HEK293} cells expressing either isoform with nearly identical {IC50} values. Tyramine, but not octopamine, also elevates Ca2+ levels in cells expressing {SER-2} and to a lesser extent {SER-2A.} Most importantly, ser-2 null mutants (pk1357) fail to suppress head movements while reversing in response to nose-touch, suggesting a role for {SER-2} in the regulation of foraging behavior, and fail to respond to tyramine in assays measuring serotonin-dependent pharyngeal pumping. These are the first reported functions for {SER-2.} These results suggest that C. elegans contains tyramine receptors, that individual {SER-2} isoforms may differ significantly in their sensitivity to other physiologically relevant biogenic amines, such as octopamine {(OA)}, and that tyraminergic signaling may be important in the regulation of key processes in nematodes.},
	number = {5},
	journal = {Journal of Neurochemistry},
	author = {Rex, Elizabeth and Molitor, Scott C and Hapiak, Vera and Xiao, Hong and Henderson, Megan and Komuniecki, Richard},
	month = dec,
	year = {2004},
	note = {{PMID:} 15569254},
	keywords = {Adrenergic {alpha-Agonists}, Adrenergic Uptake Inhibitors, Amino Acid Sequence, Animals, Animals, Genetically Modified, Behavior, Animal, Biogenic Monoamines, Caenorhabditis elegans, Calcium, Cell Line, Cell Membrane, Cercopithecus aethiops, Cloning, Molecular, Cyclic {AMP}, Diagnostic Imaging, {DNA}, Recombinant, {Dose-Response} Relationship, Drug, Drug Interactions, Embryo, Mammalian, Embryo, Nonmammalian, Extracellular Space, Feeding Behavior, Gene Expression, Green Fluorescent Proteins, Humans, Lysergic Acid Diethylamide, Models, Molecular, Nose, Octopamine, Pertussis Toxin, Pharynx, Phenotype, Phosphatidylinositols, Protein Isoforms, Radioligand Assay, Receptors, Biogenic Amine, Reverse Transcriptase Polymerase Chain Reaction, {RNA}, Messenger, Serotonin, Time Factors, Transfection, Tritium, Tyramine},
	pages = {1104--1115},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/4MTUETQ7/15569254.html:text/html}
},

@article{__????
},

@article{seeman_nucleic_1982,
	title = {Nucleic acid junctions and lattices},
	volume = {99},
	issn = {0022-5193},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/6188926},
	number = {2},
	journal = {Journal of Theoretical Biology},
	author = {Seeman, N C},
	month = nov,
	year = {1982},
	note = {{PMID:} 6188926},
	keywords = {Base Composition, Base Sequence, {DNA}, Macromolecular Substances, Models, Molecular, {RNA}},
	pages = {237--247}
},

@article{clark_afd_2006,
	title = {The {AFD} sensory neurons encode multiple functions underlying thermotactic behavior in Caenorhabditis elegans},
	volume = {26},
	issn = {1529-2401},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16837592},
	doi = {10.1523/JNEUROSCI.1137-06.2006},
	abstract = {The thermotactic behaviors of Caenorhabditis elegans indicate that its thermosensory system exhibits exquisite temperature sensitivity, long-term plasticity, and the ability to transform thermosensory input into different patterns of motor output. Here, we study the physiological role of the {AFD} thermosensory neurons by quantifying intracellular calcium dynamics in response to defined temperature stimuli. We demonstrate that short-term adaptation allows {AFD} to sense temperature changes as small as 0.05 degrees C over temperature ranges as wide as 10 degrees C. We show that a bidirectional thermosensory response (increasing temperature raises and decreasing temperature lowers the level of intracellular calcium in {AFD)} allows the {AFD} neurons to phase-lock their calcium dynamics to oscillatory thermosensory inputs. By analyzing the thermosensory response of {AFD} dendrites severed from their cell bodies by femtosecond laser ablation, we show that long-term plasticity is encoded as shifts in the operating range of a putative thermoreceptor(s) in the {AFD} sensory endings. Finally, we demonstrate that {AFD} activity is directly coupled to stimulation of its postsynaptic partner {AIY.} These observations indicate that many functions underlying thermotactic behavior are properties of one sensory neuronal type. Encoding multiple functions in individual sensory neurons may enable C. elegans to perform complex behaviors with simple neuronal circuits.},
	number = {28},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Clark, Damon A and Biron, David and Sengupta, Piali and Samuel, Aravinthan D T},
	month = jul,
	year = {2006},
	note = {{PMID:} 16837592},
	keywords = {Adaptation, Physiological, Animals, Axons, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium, Dendrites, Homeodomain Proteins, Interneurons, Lasers, {Long-Term} Potentiation, Mutation, Neurons, Afferent, Neuropeptides, Receptors, Odorant, Synaptic Transmission, Temperature, Thermoreceptors},
	pages = {7444--7451}
},

@article{wilkening_modeling_2008,
	title = {Modeling the Incubation Period of Inhalational Anthrax},
	volume = {28},
	url = {http://mdm.sagepub.com.ezp-prod1.hul.harvard.edu/cgi/content/abstract/28/4/593},
	doi = {10.1177/0272989X08315245},
	abstract = {Ever since the pioneering work of Philip Sartwell, the incubation period distribution for infectious diseases is most often modeled using a lognormal distribution. Theoretical models based on underlying disease mechanisms in the host are less well developed. This article modifies a theoretical model originally developed by Brookmeyer and others for the inhalational anthrax incubation period distribution in humans by using a more accurate distribution to represent the in vivo bacterial growth phase and by extending the model to represent the time from exposure to death, thereby allowing the model to be fit to nonhuman primate time-to-death data. The resulting incubation period distribution and the dose dependence of the median incubation period are in good agreement with human data from the 1979 accidental atmospheric anthrax release in Sverdlovsk, Russia, and limited nonhuman primate data. The median incubation period for the Sverdlovsk victims is 9.05 (95\% confidence interval = 8.0-10.3) days, shorter than previous estimates, and it is predicted to drop to less than 2.5 days at doses above 106 spores. The incubation period distribution is important because the left tail determines the time at which clinical diagnosis or syndromic surveillance systems might first detect an anthrax outbreak based on early symptomatic cases, the entire distribution determines the efficacy of medical intervention--which is determined by the speed of the prophylaxis campaign relative to the incubation period--and the right tail of the distribution influences the recommended duration for antibiotic treatment.},
	number = {4},
	journal = {Med Decis Making},
	author = {Wilkening, Dean A.},
	month = jul,
	year = {2008},
	pages = {593--605}
},

@misc{_jorgensen_????,
	title = {Jorgensen Lab Publications},
	url = {http://www.biology.utah.edu/jorgnsen_cgi_bin/publications},
	howpublished = {http://www.biology.utah.edu/jorgnsen\_cgi\_bin/publications},
	file = {Jorgensen Lab Publications:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/WCTPK7KM/publications.html:text/html}
},

@article{miyawaki_fluorescent_1997,
	title = {Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin},
	volume = {388},
	issn = {0028-0836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9278050},
	doi = {10.1038/42264},
	abstract = {Important Ca2+ signals in the cytosol and organelles are often extremely localized and hard to measure. To overcome this problem we have constructed new fluorescent indicators for Ca2+ that are genetically encoded without cofactors and are targetable to specific intracellular locations. We have dubbed these fluorescent indicators 'cameleons'. They consist of tandem fusions of a blue- or cyan-emitting mutant of the green fluorescent protein {(GFP)}, calmodulin, the calmodulin-binding peptide M13, and an enhanced green- or yellow-emitting {GFP.} Binding of Ca2+ makes calmodulin wrap around the M13 domain, increasing the fluorescence resonance energy transfer {(FRET)} between the flanking {GFPs.} Calmodulin mutations can tune the Ca2+ affinities to measure free Ca2+ concentrations in the range 10(-8) to 10(-2) M. We have visualized free Ca2+ dynamics in the cytosol, nucleus and endoplasmic reticulum of single {HeLa} cells transfected with complementary {DNAs} encoding chimaeras bearing appropriate localization signals. Ca2+ concentration in the endoplasmic reticulum of individual cells ranged from 60 to 400 {microM} at rest, and 1 to 50 {microM} after Ca2+ mobilization. {FRET} is also an indicator of the reversible intermolecular association of {cyan-GFP-labelled} calmodulin with {yellow-GFP-labelled} M13. Thus {FRET} between {GFP} mutants can monitor localized Ca2+ signals and protein heterodimerization in individual live cells.},
	number = {6645},
	journal = {Nature},
	author = {Miyawaki, A and Llopis, J and Heim, R and {McCaffery}, J M and Adams, J A and Ikura, M and Tsien, R Y},
	month = aug,
	year = {1997},
	note = {{PMID:} 9278050},
	keywords = {Amino Acid Sequence, Calcium, Calmodulin, Cytosol, Energy Transfer, Fluorescence, Green Fluorescent Proteins, Hela Cells, Humans, Indicators and Reagents, Luminescent Proteins, Molecular Sequence Data, Mutagenesis, {Myosin-Light-Chain} Kinase, Peptide Fragments, Recombinant Fusion Proteins},
	pages = {882--887}
},

@article{steinhauer_superresolution_2008,
	title = {Superresolution microscopy on the basis of engineered dark states},
	volume = {130},
	issn = {1520-5126},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19053449},
	doi = {10.1021/ja806590m},
	abstract = {New concepts for superresolution fluorescence microscopy by subsequent localization of single molecules using photoswitchable or photoactivatable fluorophores are rapidly emerging and provide new ways to resolve structures beyond the diffraction limit. Here, we demonstrate that superresolution imaging can be carried out with practically every single-molecule compatible, synthetic fluorophore by controlling their emission properties. We prepare dark states by removing oxygen that extends the triplet state lifetime to several milliseconds. We further increase the duration of the off-states using electron transfer reactions to create radical ion states of severalfold longer lifetimes. Imaging single molecules, actin filaments, and microtubules in fixed cells as well as simulations demonstrate that the thus created dark states are sufficiently long for resolution of approximately 50 nm.},
	number = {50},
	journal = {Journal of the American Chemical Society},
	author = {Steinhauer, Christian and Forthmann, Carsten and Vogelsang, Jan and Tinnefeld, Philip},
	month = dec,
	year = {2008},
	note = {{PMID:} 19053449},
	keywords = {Actins, Microscopy, Fluorescence, Sensitivity and Specificity},
	pages = {16840--16841}
},

@article{marcon_--fly_2010,
	title = {{'On-the-fly'} optical encoding of combinatorial peptide libraries for profiling of protease specificity},
	volume = {6},
	issn = {1742-2051},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20024084},
	doi = {10.1039/b909087h},
	abstract = {Large solid-phase combinatorial libraries currently play an important role in areas such as infectious disease biomarker discovery, profiling of protease specificity and anticancer drug discovery. Because compounds on solid support beads are not positionally-encoded as they are in microarrays, innovative methods of encoding are required. There are many advantages associated with optical encoding and several strategies have been described in the literature to combine fluorescence encoding methods with solid-phase library synthesis. We have previously introduced an alternative fluorescence-based encoding method ("colloidal barcoding"), which involves encoding 10-20 mum support beads during a split-and-mix synthesis with smaller 0.6-0.8 mum silica colloids that contain specific and identifiable combinations of fluorescent dye. The power of this 'on-the-fly' encoding approach lies in the efficient use of a small number of fluorescent dyes to encode millions of compounds. Described herein, for the first time, is the use of a colloid-barcoded library in a biological assay (i.e., protease profiling) combined with the use of confocal microscopy to decode the colloidal barcode. In this proof-of-concept demonstration, a small focussed peptide library was optically-encoded during a combinatorial synthesis, incubated with a protease (trypsin), analysed by flow cytometry and decoded via confocal microscopy. During assay development, a range of parameters were investigated and optimised, including substrate (or probe) loading, barcode stability, characteristics of the peptide-tagging fluorophore, and spacer group configuration. Through successful decoding of the colloidal barcodes, it was confirmed that specific peptide sequences presenting one or two cleavage sites were recognised by trypsin while peptide sequences not cleavable by trypsin remained intact.},
	number = {1},
	journal = {Molecular {bioSystems}},
	author = {Marcon, Lionel and Battersby, Bronwyn J and Rühmann, Andreas and Ford, Kym and Daley, Matthew and Lawrie, Gwendolyn A and Trau, Matt},
	month = jan,
	year = {2010},
	note = {{PMID:} 20024084},
	keywords = {Combinatorial Chemistry Techniques, Flow Cytometry, Models, Theoretical, Peptide Hydrolases, Peptide Library, Substrate Specificity},
	pages = {225--233}
},

@article{tsien_green_1998,
	title = {The green fluorescent protein},
	volume = {67},
	issn = {0066-4154},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9759496},
	doi = {10.1146/annurev.biochem.67.1.509},
	abstract = {In just three years, the green fluorescent protein {(GFP)} from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a highly visible, efficiently emitting internal fluorophore is both intrinsically fascinating and tremendously valuable. High-resolution crystal structures of {GFP} offer unprecedented opportunities to understand and manipulate the relation between protein structure and spectroscopic function. {GFP} has become well established as a marker of gene expression and protein targeting in intact cells and organisms. Mutagenesis and engineering of {GFP} into chimeric proteins are opening new vistas in physiological indicators, biosensors, and photochemical memories.},
	journal = {Annual Review of Biochemistry},
	author = {Tsien, R Y},
	year = {1998},
	note = {{PMID:} 9759496},
	keywords = {Biological Markers, Genes, Reporter, Green Fluorescent Proteins, Indicators and Reagents, Luminescent Proteins},
	pages = {509--544},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/HGVKESEN/9759496.html:text/html}
},

@article{zheng_neuronal_1999,
	title = {Neuronal control of locomotion in C. elegans is modified by a dominant mutation in the {GLR-1} ionotropic glutamate receptor},
	volume = {24},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10571229},
	abstract = {How simple neuronal circuits control behavior is not well understood at the molecular or genetic level. In Caenorhabditis elegans, foraging behavior consists of long, forward movements interrupted by brief reversals. To determine how this pattern is generated and regulated, we have developed novel perturbation techniques that allow us to depolarize selected neurons in vivo using the dominant glutamate receptor mutation identified in the Lurcher mouse. Transgenic worms that expressed a mutated C. elegans glutamate receptor in interneurons that control locomotion displayed a remarkable and unexpected change in their behavior-they rapidly alternated between forward and backward coordinated movement. Our findings suggest that the gating of movement reversals is controlled in a partially distributed fashion by a small subset of interneurons and that this gating is modified by sensory input.},
	number = {2},
	journal = {Neuron},
	author = {Zheng, Y and Brockie, P J and Mellem, J E and Madsen, D M and Maricq, A V},
	month = oct,
	year = {1999},
	note = {{PMID:} 10571229},
	keywords = {Amino Acid Sequence, Animals, Animals, Genetically Modified, Apoptosis, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Caspase 1, Gene Expression, Genes, Dominant, Interneurons, Ion Channels, Mechanoreceptors, Membrane Proteins, Molecular Sequence Data, Motor Activity, Mutation, Nerve Tissue Proteins, Neural Pathways, Neurons, Phenotype, Promoter Regions, Genetic, Quan Recommends, Receptors, {AMPA}, Receptors, Glutamate, Sensation},
	pages = {347--361},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/KRR7HDVB/10571229.html:text/html;science.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/VPUSET9Z/science.pdf:application/pdf}
},

@article{piggott_neural_2011,
	title = {The Neural Circuits and Synaptic Mechanisms Underlying Motor Initiation in C. elegans},
	volume = {147},
	issn = {1097-4172},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22078887},
	doi = {10.1016/j.cell.2011.08.053},
	abstract = {C. elegans is widely used to dissect how neural circuits and genes generate behavior. During locomotion, worms initiate backward movement to change locomotion direction spontaneously or in response to sensory cues; however, the underlying neural circuits are not well defined. We applied a multidisciplinary approach to map neural circuits in freely behaving worms by integrating functional imaging, optogenetic interrogation, genetic manipulation, laser ablation, and electrophysiology. We found that a disinhibitory circuit and a stimulatory circuit together promote initiation of backward movement and that circuitry dynamics is differentially regulated by sensory cues. Both circuits require glutamatergic transmission but depend on distinct glutamate receptors. This dual mode of motor initiation control is found in mammals, suggesting that distantly related organisms with anatomically distinct nervous systems may adopt similar strategies for motor control. Additionally, our studies illustrate how a multidisciplinary approach facilitates dissection of circuit and synaptic mechanisms underlying behavior in a genetic model organism.},
	number = {4},
	journal = {Cell},
	author = {Piggott, Beverly J and Liu, Jie and Feng, Zhaoyang and Wescott, Seth A and Xu, X Z Shawn},
	month = nov,
	year = {2011},
	note = {{PMID:} 22078887},
	pages = {922--933},
	file = {science.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/V6FUUAQJ/science.pdf:application/pdf}
},

@article{kralj_electrical_2011,
	title = {Electrical spiking in Escherichia coli probed with a fluorescent voltage-indicating protein},
	volume = {333},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21764748},
	doi = {10.1126/science.1204763},
	abstract = {Bacteria have many voltage- and ligand-gated ion channels, and population-level measurements indicate that membrane potential is important for bacterial survival. However, it has not been possible to probe voltage dynamics in an intact bacterium. Here we developed a method to reveal electrical spiking in Escherichia coli. To probe bacterial membrane potential, we engineered a voltage-sensitive fluorescent protein based on green-absorbing proteorhodopsin. Expression of the proteorhodopsin optical proton sensor {(PROPS)} in E. coli revealed electrical spiking at up to 1 hertz. Spiking was sensitive to chemical and physical perturbations and coincided with rapid efflux of a small-molecule fluorophore, suggesting that bacterial efflux machinery may be electrically regulated.},
	number = {6040},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Kralj, Joel M and Hochbaum, Daniel R and Douglass, Adam D and Cohen, Adam E},
	month = jul,
	year = {2011},
	note = {{PMID:} 21764748},
	keywords = {Action Potentials, Escherichia coli, Fluorescence, Fluorescent Dyes, {Hydrogen-Ion} Concentration, Ion Channels, Ion Transport, Light, Membrane Potentials, Protons, Rhodamines, Rhodopsin, Spectrometry, Fluorescence, Stress, Physiological},
	pages = {345--348}
},

@article{hell_far-field_2007,
	title = {Far-field optical nanoscopy},
	volume = {316},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17525330},
	doi = {10.1126/science.1137395},
	abstract = {In 1873, Ernst Abbe discovered what was to become a well-known paradigm: the inability of a lens-based optical microscope to discern details that are closer together than half of the wavelength of light. However, for its most popular imaging mode, fluorescence microscopy, the diffraction barrier is crumbling. Here, I discuss the physical concepts that have pushed fluorescence microscopy to the nanoscale, once the prerogative of electron and scanning probe microscopes. Initial applications indicate that emergent far-field optical nanoscopy will have a strong impact in the life sciences and in other areas benefiting from nanoscale visualization.},
	number = {5828},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Hell, Stefan W},
	month = may,
	year = {2007},
	note = {{PMID:} 17525330},
	keywords = {Animals, Humans, Light, Microscopy, Fluorescence, Nanotechnology},
	pages = {1153--1158}
},

@article{ke_multilayer_2009,
	title = {Multilayer {DNA} origami packed on a square lattice},
	volume = {131},
	issn = {1520-5126},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19807088},
	doi = {10.1021/ja906381y},
	abstract = {Molecular self-assembly using {DNA} as a structural building block has proven to be an efficient route to the construction of nanoscale objects and arrays of increasing complexity. Using the remarkable "scaffolded {DNA} origami" strategy, Rothemund demonstrated that a long single-stranded {DNA} from a viral genome {(M13)} can be folded into a variety of custom two-dimensional {(2D)} shapes using hundreds of short synthetic {DNA} molecules as staple strands. More recently, we generalized a strategy to build custom-shaped, three-dimensional {(3D)} objects formed as pleated layers of helices constrained to a honeycomb lattice, with precisely controlled dimensions ranging from 10 to 100 nm. Here we describe a more compact design for {3D} origami, with layers of helices packed on a square lattice, that can be folded successfully into structures of designed dimensions in a one-step annealing process, despite the increased density of {DNA} helices. A square lattice provides a more natural framework for designing rectangular structures, the option for a more densely packed architecture, and the ability to create surfaces that are more flat than is possible with the honeycomb lattice. Thus enabling the design and construction of custom {3D} shapes from helices packed on a square lattice provides a general foundational advance for increasing the versatility and scope of {DNA} nanotechnology.},
	number = {43},
	journal = {Journal of the American Chemical Society},
	author = {Ke, Yonggang and Douglas, Shawn M and Liu, Minghui and Sharma, Jaswinder and Cheng, Anchi and Leung, Albert and Liu, Yan and Shih, William M and Yan, Hao},
	month = nov,
	year = {2009},
	note = {{PMID:} 19807088},
	keywords = {{DNA}, Nucleic Acid Conformation},
	pages = {15903--15908}
},

@article{white_structure_1976,
	title = {The Structure of the Ventral Nerve Cord of Caenorhabditis elegans},
	volume = {275},
	url = {http://rstb.royalsocietypublishing.org/content/275/938/327.abstract},
	doi = {10.1098/rstb.1976.0086},
	abstract = {The nervous system of Caenorhabditis elegans is arranged as a series of fibre bundles which run along internal hypodermal ridges. Most of the sensory integration takes place in a ring of nerve fibres which is wrapped round the pharynx in the head. The body muscles in the head are innervated by motor neurones in this nerve ring while those in the lower part of the body are innervated by a set of motor neurones in a longitudinal fibre bundle which joins the nerve ring, the ventral cord. These motor neurones can be put into five classes on the basis of their morphology and synaptic input. At any one point along the cord only one member from each class has neuromuscular junctions. Members of a given class are arranged in a regular linear sequence in the cord and have non-overlapping fields of motor synaptic activity, the transition between fields of adjacent neurones being sharp and well defined. Members of a given class form gap junctions with neighbouring members of the same class but never to motor neurones of another class. Three of the motor neurone classes receive their synaptic input from a set of interneurones coming from the nerve ring. These interneurones can in turn be grouped into four classes and each of the three motor neurone classes receives its synaptic input from a unique combination of interneurone classes. The possible developmental and functional significance of these observations is discussed.},
	number = {938},
	journal = {Philosophical Transactions of the Royal Society of London. B, Biological Sciences},
	author = {White, J. G. and Southgate, Eileen and Thomson, J. N. and Brenner, S.},
	year = {1976},
	pages = {327 --348},
	file = {Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/R4K57MBU/327.html:text/html}
},

@article{nagel_light_2005,
	title = {Light Activation of Channelrhodopsin-2 in Excitable Cells of Caenorhabditis elegans Triggers Rapid Behavioral Responses},
	volume = {15},
	issn = {0960-9822},
	url = {http://www.sciencedirect.com/science/article/B6VRT-4HV7CDJ-W/2/c2d98908e8dbee2808aa298cf3c7e0d2},
	doi = {10.1016/j.cub.2005.11.032},
	abstract = {Summary
For studying the function of specific neurons in their native circuitry, it is desired to precisely control their activity. This often requires dissection to allow accurate electrical stimulation [1] or neurotransmitter application [2], and it is thus inherently difficult in live animals, especially in small model organisms. Here, we employed channelrhodopsin-2 {(ChR2)}, a directly light-gated cation channel from the green alga Chlamydomonas reinhardtii [3], in excitable cells of the nematode Caenorhabditis elegans, to trigger specific behaviors, simply by illumination. Channelrhodopsins 3 and 4 are 7-transmembrane-helix proteins that resemble the light-driven proton pump bacteriorhodopsin [5], and they also utilize the chromophore all-trans retinal, but to open an intrinsic cation pore. In muscle cells, light-activated {ChR2} evoked strong, simultaneous contractions, which were reduced in the background of mutated L-type, voltage-gated Ca2+-channels {(VGCCs)} and ryanodine receptors {(RyRs).} Electrophysiological analysis demonstrated rapid inward currents that persisted as long as the illumination. When {ChR2} was expressed in mechanosensory neurons, light evoked withdrawal behaviors that are normally elicited by mechanical stimulation. Furthermore, {ChR2} enabled activity of these neurons in mutants lacking the {MEC-4/MEC-10} mechanosensory ion channel [6]. Thus, specific neurons or muscles expressing {ChR2} can be quickly and reversibly activated by light in live and behaving, as well as dissected, animals.},
	number = {24},
	journal = {Current Biology},
	author = {Nagel, Georg and Brauner, Martin and Liewald, Jana F. and Adeishvili, Nona and Bamberg, Ernst and Gottschalk, Alexander},
	month = dec,
	year = {2005},
	keywords = {Caenorhabditis elegans, {MOLNEURO}, optogenics, {SIGNALING}},
	pages = {2279--2284}
},

@article{boyden_history_2011,
	title = {A history of optogenetics: the development of tools for controlling brain circuits with light},
	volume = {3},
	issn = {{1757594X}},
	shorttitle = {A history of optogenetics},
	url = {http://f1000.com/reports/b/3/11/},
	doi = {10.3410/B3-11},
	journal = {F1000 Biology Reports},
	author = {Boyden, Edward},
	month = may,
	year = {2011}
},

@article{park_analysis_2007,
	title = {Analysis of nematode mechanics by piezoresistive displacement clamp},
	volume = {104},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17962419},
	doi = {10.1073/pnas.0702138104},
	abstract = {Studying animal mechanics is critical for understanding how signals in the neuromuscular system give rise to behavior and how force-sensing organs and sensory neurons work. Few techniques exist to provide forces and displacements appropriate for such studies. To address this technological gap, we developed a metrology using piezoresistive cantilevers as force-displacement sensors coupled to a feedback system to apply and maintain defined load profiles to micrometer-scale animals. We show that this system can deliver forces between 10(-8) and 10(-3) N across distances of up to 100 mum with a resolution of 12 {nN} between 0.1 Hz and 100 {kHz.} We use this new metrology to show that force-displacement curves of wild-type nematodes {(Caenorhabditis} elegans) are linear. Because nematodes have approximately cylindrical bodies, this finding demonstrates that nematode body mechanics can be modeled as a cylindrical shell under pressure. Little is known about the relative importance of hydrostatic pressure and shell mechanics, however. We show that dissipating pressure by cuticle puncture or decreasing it by hyperosmotic shock has only a modest effect on stiffness, whereas defects in the dpy-5 and lon-2 genes, which alter body shape and cuticle proteins, decrease and increase stiffness by 25\% and 50\%, respectively. This initial analysis of C. elegans body mechanics suggests that shell mechanics dominates stiffness and is a first step in understanding how body mechanics affect locomotion and force sensing.},
	number = {44},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Park, {Sung-Jin} and Goodman, Miriam B and Pruitt, Beth L},
	month = oct,
	year = {2007},
	note = {{PMID:} 17962419},
	keywords = {Animals, Biomechanics, Caenorhabditis elegans, Microscopy, Electron, Transmission, Models, Biological, Sepharose},
	pages = {17376--17381},
	file = {Analysis of nematode mechanics by piezoresistive displacement clamp — PNAS:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/N3IMRCKI/17376.full.html:text/html;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/852TM379/17962419.html:text/html}
},

@article{long_support_2010,
	title = {Support for a synaptic chain model of neuronal sequence generation},
	volume = {468},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20972420},
	doi = {10.1038/nature09514},
	abstract = {In songbirds, the remarkable temporal precision of song is generated by a sparse sequence of bursts in the premotor nucleus {HVC.} To distinguish between two possible classes of models of neural sequence generation, we carried out intracellular recordings of {HVC} neurons in singing zebra finches {(Taeniopygia} guttata). We found that the subthreshold membrane potential is characterized by a large, rapid depolarization 5-10 ms before burst onset, consistent with a synaptically connected chain of neurons in {HVC.} We found no evidence for the slow membrane potential modulation predicted by models in which burst timing is controlled by subthreshold dynamics. Furthermore, bursts ride on an underlying depolarization of ∼10-ms duration, probably the result of a regenerative calcium spike within {HVC} neurons that could facilitate the propagation of activity through a chain network with high temporal precision. Our results provide insight into the fundamental mechanisms by which neural circuits can generate complex sequential behaviours.},
	number = {7322},
	journal = {Nature},
	author = {Long, Michael A and Jin, Dezhe Z and Fee, Michale S},
	month = nov,
	year = {2010},
	note = {{PMID:} 20972420},
	keywords = {Animals, Calcium Channels, {L-Type}, Calcium Signaling, Finches, Male, Membrane Potentials, Models, Neurological, Neural Pathways, Neurons, Sleep, Synapses, Vocalization, Animal},
	pages = {394--399}
},

@article{chow_high-performance_2010,
	title = {High-performance genetically targetable optical neural silencing by light-driven proton pumps},
	volume = {463},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20054397},
	doi = {10.1038/nature08652},
	abstract = {The ability to silence the activity of genetically specified neurons in a temporally precise fashion would provide the opportunity to investigate the causal role of specific cell classes in neural computations, behaviours and pathologies. Here we show that members of the class of light-driven outward proton pumps can mediate powerful, safe, multiple-colour silencing of neural activity. The gene archaerhodopsin-3 {(Arch)} from Halorubrum sodomense enables near-100\% silencing of neurons in the awake brain when virally expressed in the mouse cortex and illuminated with yellow light. Arch mediates currents of several hundred picoamps at low light powers, and supports neural silencing currents approaching 900 {pA} at light powers easily achievable in vivo. Furthermore, Arch spontaneously recovers from light-dependent inactivation, unlike light-driven chloride pumps that enter long-lasting inactive states in response to light. These properties of Arch are appropriate to mediate the optical silencing of significant brain volumes over behaviourally relevant timescales. Arch function in neurons is well tolerated because {pH} excursions created by Arch illumination are minimized by self-limiting mechanisms to levels comparable to those mediated by channelrhodopsins or natural spike firing. To highlight how proton pump ecological and genomic diversity may support new innovation, we show that the blue-green light-drivable proton pump from the fungus Leptosphaeria maculans {(Mac)} can, when expressed in neurons, enable neural silencing by blue light, thus enabling alongside other developed reagents the potential for independent silencing of two neural populations by blue versus red light. Light-driven proton pumps thus represent a high-performance and extremely versatile class of 'optogenetic' voltage and ion modulator, which will broadly enable new neuroscientific, biological, neurological and psychiatric investigations.},
	number = {7277},
	journal = {Nature},
	author = {Chow, Brian Y and Han, Xue and Dobry, Allison S and Qian, Xiaofeng and Chuong, Amy S and Li, Mingjie and Henninger, Michael A and Belfort, Gabriel M and Lin, Yingxi and Monahan, Patrick E and Boyden, Edward S},
	month = jan,
	year = {2010},
	note = {{PMID:} 20054397},
	keywords = {Action Potentials, Animals, Ascomycota, Color, Electric Conductivity, Euryarchaeota, Genetic Engineering, {Hydrogen-Ion} Concentration, Mice, Molecular Sequence Data, Neocortex, Neurons, Proton Pumps, Rhodopsins, Microbial, Wakefulness},
	pages = {98--102}
},

@article{shih_knitting_2010,
	title = {Knitting complex weaves with {DNA} origami},
	volume = {20},
	issn = {{1879-033X}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20456942},
	doi = {10.1016/j.sbi.2010.03.009},
	abstract = {The past three decades have witnessed steady growth in our ability to harness {DNA} branched junctions as building blocks for programmable self-assembly of diverse supramolecular architectures. The {DNA-origami} method, which exploits the availability of long {DNA} sequences to template sophisticated nanostructures, has played a major role in extending this trend through the past few years. Today, two-dimensional and three-dimensional custom-shaped nanostructures comparable in mass to a small virus can be designed, assembled, and characterized with a prototyping cycle on the order of a couple of weeks.},
	number = {3},
	journal = {Current Opinion in Structural Biology},
	author = {Shih, William M and Lin, Chenxiang},
	month = jun,
	year = {2010},
	note = {{PMID:} 20456942},
	keywords = {Base Sequence, {DNA}, Nanostructures, Nanotechnology},
	pages = {276--282}
},

@article{hart_synaptic_1995,
	title = {Synaptic code for sensory modalities revealed by C. elegans {GLR-1} glutamate receptor},
	volume = {378},
	url = {http://dx.doi.org/10.1038/378082a0},
	doi = {10.1038/378082a0},
	number = {6552},
	journal = {Nature},
	author = {Hart, Anne C. and Sims, Shannon and Kaplan, Joshua M.},
	month = nov,
	year = {1995},
	keywords = {{PQE}  - definite citation, Sniffing / Foraging},
	pages = {82--85},
	file = {378082a0.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/UTTGHAPB/378082a0.pdf:application/pdf}
},

@article{naumann_monitoring_2010,
	title = {Monitoring neural activity with bioluminescence during natural behavior},
	volume = {13},
	issn = {1546-1726},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20305645},
	doi = {10.1038/nn.2518},
	abstract = {Existing techniques for monitoring neural activity in awake, freely behaving vertebrates are invasive and difficult to target to genetically identified neurons. We used bioluminescence to non-invasively monitor the activity of genetically specified neurons in freely behaving zebrafish. Transgenic fish with the Ca(2+)-sensitive photoprotein green fluorescent protein {(GFP)-Aequorin} in most neurons generated large and fast bioluminescent signals that were related to neural activity, neuroluminescence, which could be recorded continuously for many days. To test the limits of this technique, we specifically targeted {GFP-Aequorin} to the hypocretin-positive neurons of the hypothalamus. We found that neuroluminescence generated by this group of approximately 20 neurons was associated with periods of increased locomotor activity and identified two classes of neural activity corresponding to distinct swim latencies. Our neuroluminescence assay can report, with high temporal resolution and sensitivity, the activity of small subsets of neurons during unrestrained behavior.},
	number = {4},
	journal = {Nature Neuroscience},
	author = {Naumann, Eva A and Kampff, Adam R and Prober, David A and Schier, Alexander F and Engert, Florian},
	month = apr,
	year = {2010},
	note = {{PMID:} 20305645},
	keywords = {Aequorin, Animals, Animals, Genetically Modified, Behavior, Animal, Green Fluorescent Proteins, Intracellular Signaling Peptides and Proteins, Luminescent Proteins, Motor Activity, Nerve Net, Neuropeptides, Zebrafish},
	pages = {513--520}
},

@article{rust_sub-diffraction-limit_2006,
	title = {Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy {(STORM)}},
	volume = {3},
	issn = {1548-7091},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16896339},
	doi = {10.1038/nmeth929},
	abstract = {We have developed a high-resolution fluorescence microscopy method based on high-accuracy localization of photoswitchable fluorophores. In each imaging cycle, only a fraction of the fluorophores were turned on, allowing their positions to be determined with nanometer accuracy. The fluorophore positions obtained from a series of imaging cycles were used to reconstruct the overall image. We demonstrated an imaging resolution of 20 nm. This technique can, in principle, reach molecular-scale resolution.},
	number = {10},
	journal = {Nature Methods},
	author = {Rust, Michael J and Bates, Mark and Zhuang, Xiaowei},
	month = oct,
	year = {2006},
	note = {{PMID:} 16896339},
	keywords = {{DNA}, Fluorescent Dyes, Image Interpretation, {Computer-Assisted}, Microscopy, Fluorescence, Nanotechnology, Stochastic Processes},
	pages = {793--795}
},

@article{ryu_thermotaxis_2002,
	title = {Thermotaxis in Caenorhabditis elegans Analyzed by Measuring Responses to Defined Thermal Stimuli},
	volume = {22},
	url = {http://www.jneurosci.org/cgi/content/abstract/22/13/5727},
	doi = {20026542},
	abstract = {In a spatial thermal gradient, Caenorhabditis elegans migrates toward and then isothermally tracks near its cultivation temperature. A current model for thermotactic behavior involves a thermophilic drive (involving the neurons {AFD} and {AIY)} and cryophilic drive (involving the neuron {AIZ)} that balance at the cultivation temperature. Here, we analyze the movements of individual worms responding to defined thermal gradients. We found evidence for a mechanism for migration down thermal gradients that is active at temperatures above the cultivation temperature, and a mechanism for isothermal tracking that is active near the cultivation temperature. However, we found no evidence for a mechanism for migration up thermal gradients at temperatures below the cultivation temperature that might have supported the model of opposing drives. The mechanisms for migration down gradients and isothermal tracking control the worm's movements in different manners. Migration down gradients works by shortening (lengthening) the duration of forward movement in response to positive (negative) temperature changes. Isothermal tracking works by orienting persistent forward movement to offset temperature changes. We believe preference for the cultivation temperature is not at the balance between two drives. Instead, the worm activates the mechanism for isothermal tracking near the cultivation temperature and inactivates the mechanism for migration down gradients near or below the cultivation temperature. Inactivation of the mechanism for migration down gradients near or below the cultivation temperature requires the neurons {AFD} and {AIY.}},
	number = {13},
	journal = {Jounral of Neuroscience},
	author = {Ryu, William S. and Samuel, Aravinthan D. T.},
	month = jul,
	year = {2002},
	pages = {5727--5733},
	file = {HighWire Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/MBAAG2VT/Ryu and Samuel - 2002 - Thermotaxis in Caenorhabditis elegans Analyzed by .pdf:application/pdf;HighWire Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/IJET2I6W/5727.html:text/html}
},

@article{boyden_millisecond-timescale_2005,
	title = {Millisecond-timescale, genetically targeted optical control of neural activity},
	volume = {8},
	issn = {1097-6256},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16116447},
	doi = {10.1038/nn1525},
	abstract = {Temporally precise, noninvasive control of activity in well-defined neuronal populations is a long-sought goal of systems neuroscience. We adapted for this purpose the naturally occurring algal protein Channelrhodopsin-2, a rapidly gated light-sensitive cation channel, by using lentiviral gene delivery in combination with high-speed optical switching to photostimulate mammalian neurons. We demonstrate reliable, millisecond-timescale control of neuronal spiking, as well as control of excitatory and inhibitory synaptic transmission. This technology allows the use of light to alter neural processing at the level of single spikes and synaptic events, yielding a widely applicable tool for neuroscientists and biomedical engineers.},
	number = {9},
	journal = {Nature Neuroscience},
	author = {Boyden, Edward S and Zhang, Feng and Bamberg, Ernst and Nagel, Georg and Deisseroth, Karl},
	month = sep,
	year = {2005},
	note = {{PMID:} 16116447},
	keywords = {Action Potentials, Algal Proteins, Animals, Animals, Newborn, Cells, Cultured, {Dose-Response} Relationship, Radiation, Electric Stimulation, Electrophysiology, Excitatory Amino Acid Antagonists, {GABA} Antagonists, Green Fluorescent Proteins, Hippocampus, Ion Channel Gating, Ion Channels, Neural Inhibition, Neurons, Optics and Photonics, Photobiology, Pyridazines, Quinoxalines, Rats, Rats, {Sprague-Dawley}, Reaction Time, Reproducibility of Results, Rhodopsin, Synaptic Transmission, Time Factors, Transfection},
	pages = {1263--1268}
},

@article{liu_crystalline_2011,
	title = {Crystalline two-dimensional {DNA-origami} arrays},
	volume = {50},
	issn = {1521-3773},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21053236},
	doi = {10.1002/anie.201005911},
	number = {1},
	journal = {Angewandte Chemie {(International} Ed. in English)},
	author = {Liu, Wenyan and Zhong, Hong and Wang, Risheng and Seeman, Nadrian C},
	month = jan,
	year = {2011},
	note = {{PMID:} 21053236},
	keywords = {Crystallization, {DNA}, Microscopy, Electron, Scanning, Nanostructures, Nucleic Acid Conformation, Oligonucleotide Array Sequence Analysis},
	pages = {264--267}
},

@article{szobota_remote_2007,
	title = {Remote control of neuronal activity with a light-gated glutamate receptor},
	volume = {54},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17521567},
	doi = {10.1016/j.neuron.2007.05.010},
	abstract = {The ability to stimulate select neurons in isolated tissue and in living animals is important for investigating their role in circuits and behavior. We show that the engineered light-gated ionotropic glutamate receptor {(LiGluR)}, when introduced into neurons, enables remote control of their activity. Trains of action potentials are optimally evoked and extinguished by 380 nm and 500 nm light, respectively, while intermediate wavelengths provide graded control over the amplitude of depolarization. Light pulses of 1-5 ms in duration at approximately 380 nm trigger precisely timed action potentials and {EPSP-like} responses or can evoke sustained depolarizations that persist for minutes in the dark until extinguished by a short pulse of approximately 500 nm light. When introduced into sensory neurons in zebrafish larvae, activation of {LiGluR} reversibly blocks the escape response to touch. Our studies show that {LiGluR} provides robust control over neuronal activity, enabling the dissection and manipulation of neural circuitry in vivo.},
	number = {4},
	journal = {Neuron},
	author = {Szobota, Stephanie and Gorostiza, Pau and Del Bene, Filippo and Wyart, Claire and Fortin, Doris L and Kolstad, Kathleen D and Tulyathan, Orapim and Volgraf, Matthew and Numano, Rika and Aaron, Holly L and Scott, Ethan K and Kramer, Richard H and Flannery, John and Baier, Herwig and Trauner, Dirk and Isacoff, Ehud Y},
	month = may,
	year = {2007},
	note = {{PMID:} 17521567},
	keywords = {Action Potentials, Animals, Animals, Genetically Modified, Animals, Newborn, Behavior, Animal, Cells, Cultured, Cysteine, {Dose-Response} Relationship, Radiation, Electric Stimulation, Excitatory Postsynaptic Potentials, Hippocampus, Larva, Leucine, Lighting, Mutation, Neurons, {Patch-Clamp} Techniques, Physical Stimulation, Rats, Receptors, Kainic Acid, Transfection, Zebrafish},
	pages = {535--545}
},

@article{suzuki_topological_1985,
	title = {Topological structural analysis of digitized binary images by border following},
	volume = {30},
	issn = {{0734-189X}},
	url = {http://www.sciencedirect.com.ezp-prod1.hul.harvard.edu/science/article/B7GXG-4D8FS1C-M/2/a8579386448407d3a26b09845e194acc},
	doi = {10.1016/0734-189X(85)90016-7},
	abstract = {Two border following algorithms are proposed for the topological analysis of digitized binary images. The first one determines the surroundness relations among the borders of a binary image. Since the outer borders and the hole borders have a one-to-one correspondence to the connected components of 1-pixels and to the holes, respectively, the proposed algorithm yields a representation of a binary image, from which one can extract some sort of features without reconstructing the image. The second algorithm, which is a modified version of the first, follows only the outermost borders (i.e., the outer borders which are not surrounded by holes). These algorithms can be effectively used in component counting, shrinking, and topological structural analysis of binary images, when a sequential digital computer is used.},
	number = {1},
	journal = {Computer Vision, Graphics, and Image Processing},
	author = {Suzuki, Satoshi and be, {KeiichiA}},
	month = apr,
	year = {1985},
	pages = {32--46}
},

@article{bui_programmable_2010,
	title = {Programmable periodicity of quantum dot arrays with {DNA} origami nanotubes},
	volume = {10},
	issn = {1530-6992},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20681601},
	doi = {10.1021/nl101079u},
	abstract = {To fabricate quantum dot arrays with programmable periodicity, functionalized {DNA} origami nanotubes were developed. Selected {DNA} staple strands were biotin-labeled to form periodic binding sites for streptavidin-conjugated quantum dots. Successful formation of arrays with periods of 43 and 71 nm demonstrates precise, programmable, large-scale nanoparticle patterning; however, limitations in array periodicity were also observed. Statistical analysis of {AFM} images revealed evidence for steric hindrance or site bridging that limited the minimum array periodicity.},
	number = {9},
	journal = {Nano Letters},
	author = {Bui, Hieu and Onodera, Craig and Kidwell, Carson and Tan, {YerPeng} and Graugnard, Elton and Kuang, Wan and Lee, Jeunghoon and Knowlton, William B and Yurke, Bernard and Hughes, William L},
	month = sep,
	year = {2010},
	note = {{PMID:} 20681601},
	keywords = {{DNA}, Microscopy, Atomic Force, Nanotubes, Quantum Dots},
	pages = {3367--3372}
},

@article{feng_imaging_2004,
	title = {An imaging system for standardized quantitative analysis of C. elegans behavior},
	volume = {5},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=517925},
	doi = {10.1186/1471-2105-5-115},
	journal = {{BMC} Bioinformatics},
	author = {Feng, Zhaoyang and Cronin, Christopher J and Jr, John H Wittig, and Sternberg, Paul W and Schafer, William R},
	year = {2004},
	note = {{PMC517925}},
	keywords = {Direct Competitor, Image Processing, {PQE}  - definite citation},
	pages = {115},
	file = {PubMed Central Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/JRWI8JAP/articlerender.html:text/html}
},

@phdthesis{chen_neuronal_2007,
	address = {Cold Sporing Harbor Laboratory,: Cold Spring Harbor},
	type = {Thesis},
	title = {Neuronal Network of C. elegans: from Anatomy to Behavior},
	school = {Watson School of Biological Sciences},
	author = {Chen, Beth L},
	year = {2007},
	note = {p. 96}
},

@misc{_yongshin_????,
	title = {Yongshin Yu's Blog: {HOW} {TO:} Use {CDT} and {MinGW} for Eclipse (i.e. develop {C/C++} applications in windows)},
	url = {http://yongshin.blogspot.com/2005/11/how-to-use-cdt-and-mingw-for-eclipse.html},
	keywords = {{OpenCV}, Programming},
	howpublished = {http://yongshin.blogspot.com/2005/11/how-to-use-cdt-and-mingw-for-eclipse.html}
},

@article{rothemund_folding_2006,
	title = {Folding {DNA} to create nanoscale shapes and patterns},
	volume = {440},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16541064},
	doi = {10.1038/nature04586},
	abstract = {{'Bottom-up} fabrication', which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of {DNA} molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded {DNA} molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting {DNA} structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual {DNA} structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).},
	number = {7082},
	journal = {Nature},
	author = {Rothemund, Paul W K},
	month = mar,
	year = {2006},
	note = {{PMID:} 16541064},
	keywords = {Art, Bacteriophage M13, Biopolymers, {DNA}, {DNA}, {Single-Stranded}, {DNA}, Viral, Microscopy, Atomic Force, Nanostructures, Nanotechnology, Nucleic Acid Conformation},
	pages = {297--302}
},

@misc{_mechanotransduction_????,
	title = {Mechanotransduction in the Nematode Caenorhabditis elegans},
	url = {http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mechano.chapter.182},
	keywords = {{PQE}  - definite citation, Re}
},

@article{baran_c._1999,
	title = {The C. elegans homeodomain gene unc-42 regulates chemosensory and glutamate receptor expression},
	volume = {126},
	url = {http://dev.biologists.org/cgi/content/abstract/126/10/2241},
	number = {10},
	journal = {Development},
	author = {Baran, R and Aronoff, R and Garriga, G},
	month = may,
	year = {1999},
	pages = {2241--2251},
	file = {HighWire Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/8JGBGHCK/Baran et al - 1999 - The C elegans homeodomain gene unc-42 regulates c.pdf:application/pdf;HighWire Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/JRVH3G8C/2241.html:text/html;The C. elegans homeodomain gene unc-42 regulates chemosensory and glutamate receptor expression -- Baran et al. 126 (10): 2241 -- Development:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/Z6HQ47NM/2241.html:text/html}
},

@misc{_fast20inverse20square20root.pdf_????,
	title = {{Fast20Inverse20Square20Root.pdf}},
	url = {http://mceniry.net/papers/Fast%20Inverse%20Square%20Root.pdf}
},

@book{kandel_essentials_1995,
	title = {Essentials of neural science and behavior},
	isbn = {9780838522455},
	abstract = {This book introduces undergraduate students to the fundamentals of biology in mental processes.},
	publisher = {{McGraw-Hill} Professional},
	author = {Kandel, Eric R. and Schwartz, James Harris and Jessell, Thomas M.},
	year = {1995},
	keywords = {Behavior, Medical / Mental Health, Medical / Neurology, Medical / Neuroscience, Nervous System/ physiology, Neurosciences, Psychology / Neuropsychology, Science / Life Sciences / Neuroscience}
},

@article{stephens_modes_2010,
	title = {From Modes to Movement in the Behavior of Caenorhabditis elegans},
	volume = {5},
	url = {http://dx.doi.org/10.1371/journal.pone.0013914},
	doi = {10.1371/journal.pone.0013914},
	abstract = {Organisms move through the world by changing their shape, and here we explore the mapping from shape space to movements in the nematode Caenorhabditis elegans as it crawls on an agar plate. We characterize the statistics of the trajectories through the correlation functions of the orientation angular velocity, orientation angle and the mean-squared displacement, and we find that the loss of orientational memory has significant contributions from both abrupt, large amplitude turning events and the continuous dynamics between these events. Further, we discover long-time persistence of orientational memory in the intervals between abrupt turns. Building on recent work demonstrating that C. elegans movements are restricted to a low-dimensional shape space, we construct a map from the dynamics in this shape space to the trajectory of the worm along the agar. We use this connection to illustrate that changes in the continuous dynamics reveal subtle differences in movement strategy that occur among mutants defective in two classes of dopamine receptors.},
	number = {11},
	journal = {{PLoS} {ONE}},
	author = {Stephens, Greg J. and {Johnson-Kerner}, Bethany and Bialek, William and Ryu, William S.},
	month = nov,
	year = {2010},
	pages = {e13914}
},

@article{jungmann_single-molecule_2010,
	title = {Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on {DNA} origami},
	volume = {10},
	issn = {1530-6992},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20957983},
	doi = {10.1021/nl103427w},
	abstract = {{DNA} origami is a powerful method for the programmable assembly of nanoscale molecular structures. For applications of these structures as functional biomaterials, the study of reaction kinetics and dynamic processes in real time and with high spatial resolution becomes increasingly important. We present a single-molecule assay for the study of binding and unbinding kinetics on {DNA} origami. We find that the kinetics of hybridization to single-stranded extensions on {DNA} origami is similar to isolated substrate-immobilized {DNA} with a slight position dependence on the origami. On the basis of the knowledge of the kinetics, we exploit reversible specific binding of labeled oligonucleotides to {DNA} nanostructures for {PAINT} (points accumulation for imaging in nanoscale topography) imaging with {\textless}30 nm resolution. The method is demonstrated for flat monomeric {DNA} structures as well as multimeric, ribbon-like {DNA} structures.},
	number = {11},
	journal = {Nano Letters},
	author = {Jungmann, Ralf and Steinhauer, Christian and Scheible, Max and Kuzyk, Anton and Tinnefeld, Philip and Simmel, Friedrich C},
	month = nov,
	year = {2010},
	note = {{PMID:} 20957983},
	keywords = {Binding Sites, {DNA}, Image Enhancement, Kinetics, Microscopy, Fluorescence, Molecular Probe Techniques},
	pages = {4756--4761}
},

@misc{_mcintire_????,
	title = {{McIntire} Lab - Steve {McIntire}, {M.D.}, {Ph.D.}},
	url = {http://www.galloresearch.org/index.php/investigators/mcintirelab}
},

@article{liedl_self-assembly_2010,
	title = {Self-assembly of three-dimensional prestressed tensegrity structures from {DNA}},
	volume = {5},
	issn = {1748-3395},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20562873},
	doi = {10.1038/nnano.2010.107},
	abstract = {Tensegrity, or tensional integrity, is a property of a structure indicating a reliance on a balance between components that are either in pure compression or pure tension for stability. Tensegrity structures exhibit extremely high strength-to-weight ratios and great resilience, and are therefore widely used in engineering, robotics and architecture. Here, we report nanoscale, prestressed, three-dimensional tensegrity structures in which rigid bundles of {DNA} double helices resist compressive forces exerted by segments of single-stranded {DNA} that act as tension-bearing cables. Our {DNA} tensegrity structures can self-assemble against forces up to 14 {pN}, which is twice the stall force of powerful molecular motors such as kinesin or myosin. The forces generated by this molecular prestressing mechanism can be used to bend the {DNA} bundles or to actuate the entire structure through enzymatic cleavage at specific sites. In addition to being building blocks for nanostructures, tensile structural elements made of single-stranded {DNA} could be used to study molecular forces, cellular mechanotransduction and other fundamental biological processes.},
	number = {7},
	journal = {Nature Nanotechnology},
	author = {Liedl, Tim and Högberg, Björn and Tytell, Jessica and Ingber, Donald E and Shih, William M},
	month = jul,
	year = {2010},
	note = {{PMID:} 20562873},
	keywords = {{DNA}, Nucleic Acid Conformation, Physicochemical Phenomena, Stress, Mechanical},
	pages = {520--524}
},

@article{ramot_bidirectional_2008,
	title = {Bidirectional temperature-sensing by a single  thermosensory neuron in C. elegans},
	volume = {11},
	issn = {1546-1726},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/18660808},
	doi = {10.1038/nn.2157},
	abstract = {Humans and other animals can sense temperature changes as small as 0.1 degree C. How animals achieve such exquisite sensitivity is poorly understood. By recording from the C. elegans thermosensory neurons {AFD} in vivo, we found that cooling closes and warming opens ion channels. We found that {AFD} thermosensitivity, which exceeds that of most biological processes by many orders of magnitude, is achieved by nonlinear signal amplification. Mutations in genes encoding subunits of a cyclic guanosine monophosphate {(cGMP)-gated} ion channel (tax-4 and tax-2) and transmembrane guanylate cyclases (gcy-8, gcy-18 and gcy-23) eliminated both cooling- and warming-activated thermoreceptor currents, indicating that a {cGMP-mediated} pathway links variations in temperature to changes in ionic currents. The resemblance of C. elegans thermosensation to vertebrate photosensation and the sequence similarity between {TAX-4} and {TAX-2} and subunits of the rod phototransduction channel raise the possibility that nematode thermosensation and vertebrate vision are linked by conserved evolution.},
	number = {8},
	journal = {Nature Neuroscience},
	author = {Ramot, Daniel and {MacInnis}, Bronwyn L and Goodman, Miriam B},
	month = aug,
	year = {2008},
	note = {{PMID:} 18660808},
	keywords = {Adaptation, Physiological, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium Signaling, Cold Temperature, Cyclic {GMP}, Guanylate Cyclase, Hot Temperature, Ion Channels, Membrane Potentials, Mutagenesis, {Site-Directed}, Neurons, Afferent, {Patch-Clamp} Techniques, Protein Subunits, Reaction Time, Temperature, Thermosensing},
	pages = {908--915}
},

@phdthesis{luo_thermotactic_2009,
	title = {Thermotactic behavior in C. elegans and Drosophila larvae},
	school = {Harvard University},
	author = {Luo, Linjiao},
	year = {2009}
},

@misc{wormbase_wormbase_2009,
	title = {{WormBase}, release {WS201}},
	author = {{WormBase}},
	month = may,
	year = {2009}
},

@article{han_dna_2011,
	title = {{DNA} origami with complex curvatures in three-dimensional space},
	volume = {332},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21493857},
	doi = {10.1126/science.1202998},
	abstract = {We present a strategy to design and construct self-assembling {DNA} nanostructures that define intricate curved surfaces in three-dimensional {(3D)} space using the {DNA} origami folding technique. Double-helical {DNA} is bent to follow the rounded contours of the target object, and potential strand crossovers are subsequently identified. Concentric rings of {DNA} are used to generate in-plane curvature, constrained to {2D} by rationally designed geometries and crossover networks. Out-of-plane curvature is introduced by adjusting the particular position and pattern of crossovers between adjacent {DNA} double helices, whose conformation often deviates from the natural, B-form twist density. A series of {DNA} nanostructures with high curvature--such as {2D} arrangements of concentric rings and {3D} spherical shells, ellipsoidal shells, and a nanoflask--were assembled.},
	number = {6027},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Han, Dongran and Pal, Suchetan and Nangreave, Jeanette and Deng, Zhengtao and Liu, Yan and Yan, Hao},
	month = apr,
	year = {2011},
	note = {{PMID:} 21493857},
	keywords = {{DNA}, Models, Molecular, Nanostructures, Nanotechnology, Nucleic Acid Conformation},
	pages = {342--346}
},

@article{vilardaga_gpcr_2009,
	title = {{GPCR} and G proteins: drug efficacy and activation in live cells},
	volume = {23},
	issn = {1944-9917},
	shorttitle = {{GPCR} and G proteins},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19196832},
	doi = {10.1210/me.2008-0204},
	abstract = {Many biochemical pathways are driven by G protein-coupled receptors, cell surface proteins that convert the binding of extracellular chemical, sensory, and mechanical stimuli into cellular signals. Their interaction with various ligands triggers receptor activation that typically couples to and activates heterotrimeric G proteins, which in turn control the propagation of secondary messenger molecules (e.g. {cAMP)} involved in critically important physiological processes (e.g. heart beat). Successful transfer of information from ligand binding events to intracellular signaling cascades involves a dynamic interplay between ligands, receptors, and G proteins. The development of Förster resonance energy transfer and bioluminescence resonance energy transfer-based methods has now permitted the kinetic analysis of initial steps involved in G protein-coupled receptor-mediated signaling in live cells and in systems as diverse as neurotransmitter and hormone signaling. The direct measurement of ligand efficacy at the level of the receptor by Förster resonance energy transfer is also now possible and allows intrinsic efficacies of clinical drugs to be linked with the effect of receptor polymorphisms.},
	number = {5},
	journal = {Molecular Endocrinology {(Baltimore}, Md.)},
	author = {Vilardaga, {Jean-Pierre} and Bünemann, Moritz and Feinstein, Timothy N and Lambert, Nevin and Nikolaev, Viacheslav O and Engelhardt, Stefan and Lohse, Martin J and Hoffmann, Carsten},
	month = may,
	year = {2009},
	note = {{PMID:} 19196832},
	keywords = {Animals, Fluorescence Resonance Energy Transfer, {GTP-Binding} Proteins, Humans, Kinetics, Luminescent Measurements, Models, Biological, Receptors, {G-Protein-Coupled}, Signal Transduction},
	pages = {590--599}
},

@article{chen_wiring_2006,
	title = {Wiring optimization can relate neuronal structure and function},
	volume = {103},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16537428},
	doi = {10.1073/pnas.0506806103},
	abstract = {We pursue the hypothesis that neuronal placement in animals minimizes wiring costs for given functional constraints, as specified by synaptic connectivity. Using a newly compiled version of the Caenorhabditis elegans wiring diagram, we solve for the optimal layout of 279 nonpharyngeal neurons. In the optimal layout, most neurons are located close to their actual positions, suggesting that wiring minimization is an important factor. Yet some neurons exhibit strong deviations from "optimal" position. We propose that biological factors relating to axonal guidance and command neuron functions contribute to these deviations. We capture these factors by proposing a modified wiring cost function.},
	number = {12},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Chen, Beth L and Hall, David H and Chklovskii, Dmitri B},
	month = mar,
	year = {2006},
	note = {{PMID:} 16537428},
	keywords = {Animals, Caenorhabditis elegans, Models, Neurological, Neurons, Synapses},
	pages = {4723--4728}
},

@article{kristan_rhythmic_1976,
	title = {Rhythmic swimming activity in neurones of the isolated nerve cord of the leech},
	volume = {65},
	issn = {0022-0949},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/1018167},
	abstract = {1. Repeating bursts of motor neurone impulses have been recorded from the nerves of completely isolated nerve cords of the medicinal leech. The salient features of this burst rhythm are similar to those obtained in the semi-intact preparation during swimming. Hence the basic swimming rhythm is generated by a central oscillator. 2. Quantitative comparisons between the impulse patterns obtained from the isolated nerve cord and those obtained from a semi-intact preparation show that the variation in both dorsal to ventral motor neurone phasing and burst duration with swim cycle period differ in these two preparations. 3. The increase of intersegmental delay with period, which is a prominent feature of swimming behaviour of the intact animal, is not seen in either the semi-intact or isolated cord preparations. 4. In the semi-intact preparation, stretching the body wall or depolarizing an inhibitory motor neurone changes the burst duration of excitatory motor neurones in the same segment. In the isolated nerve cord, these manipulations also change the period of the swim cycle in the entire cord. 5. These comparisons suggest that sensory input stabilizes the centrally generated swimming rhythm, determines the phasing of the bursts of impulses from dorsal and ventral motor neurones, and matches the intersegmental delay to the cycle period so as to maintain a constant body shape at all rates of swimming.},
	number = {3},
	journal = {The Journal of Experimental Biology},
	author = {Kristan, W B, Jr and Calabrese, R L},
	month = dec,
	year = {1976},
	note = {{PMID:} 1018167},
	keywords = {Action Potentials, Animals, Ganglia, Leeches, Motor Neurons, Movement, Muscles, Nervous System, Nervous System Physiological Phenomena, Periodicity, Proprioception},
	pages = {643--668}
},

@book{dawes_advances_????,
	address = {London},
	title = {Advances in Parasitology},
	publisher = {Academic Press},
	author = {Dawes, Ben},
	keywords = {Parasitology}
},

@article{ohagan_mec-4_2005,
	title = {The {MEC-4} {DEG/ENaC} channel of Caenorhabditis elegans touch receptor neurons transduces mechanical signals},
	volume = {8},
	issn = {1097-6256},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15580270},
	doi = {10.1038/nn1362},
	abstract = {Transformation of mechanical energy into ionic currents is essential for touch, hearing and nociception. Although {DEG/ENaC} proteins are believed to form sensory mechanotransduction channels, the evidence for this role remains indirect. By recording from C. elegans touch receptor neurons in vivo, we found that external force evokes rapidly activating mechanoreceptor currents {(MRCs)} carried mostly by Na(+) and blocked by amiloride-characteristics consistent with direct mechanical gating of a {DEG/ENaC} channel. Like mammalian Pacinian corpuscles, these neurons depolarized with both positive and negative changes in external force but not with sustained force. Null mutations in the {DEG/ENaC} gene mec-4 and in the accessory ion channel subunit genes mec-2 and mec-6 eliminated {MRCs.} In contrast, the genetic elimination of touch neuron-specific microtubules reduced, but did not abolish, {MRCs.} Our findings link the application of external force to the activation of a molecularly defined metazoan sensory transduction channel.},
	number = {1},
	journal = {Nature Neuroscience},
	author = {{O'Hagan}, Robert and Chalfie, Martin and Goodman, Miriam B},
	month = jan,
	year = {2005},
	note = {{PMID:} 15580270},
	keywords = {Amiloride, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Electric Conductivity, Mechanoreceptors, Mechanotransduction, Cellular, Membrane Proteins, Mutation, Physical Stimulation, Print Me!, Sodium, Sodium Channels, Touch},
	pages = {43--50},
	file = {nn1362.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/E53CEMII/nn1362.pdf:application/pdf;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/IUWTAI52/15580270.html:text/html}
},

@misc{evans_official_2011,
	title = {The Official {YAML} Web Site},
	url = {http://yaml.org/},
	journal = {{YAML:} {YAML} Ain't Markup Language},
	author = {Evans, Clarkj},
	year = {2011},
	howpublished = {http://yaml.org/},
	file = {The Official YAML Web Site:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/KJ6GFZ6I/yaml.org.html:text/html}
},

@article{livolsi_projectors_2008,
	title = {Projectors and {PC} Gaming},
	shorttitle = {Projectors and {PC} Gaming},
	url = {http://web.archive.org/web/20110104033820/http://www.projectorcentral.com/pc_gaming_projectors.htm},
	journal = {{ProjectorCentral.com}},
	author = {Livolsi, Bill},
	month = aug,
	year = {2008},
	file = {Projectors and PC Gaming:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/ZAT6A9HH/pc_gaming_projectors.html:text/html}
},

@article{troemel_divergent_1995,
	title = {Divergent seven transmembrane receptors are candidate chemosensory receptors in C. elegans},
	volume = {83},
	issn = {0092-8674},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7585938},
	abstract = {Using their senses of taste and smell, animals recognize a wide variety of chemicals. The nematode C. elegans has only fourteen types of chemosensory neurons, but it responds to dozens of chemicals, because each chemosensory neuron detects several stimuli. Here we describe over 40 highly divergent members of the G protein-coupled receptor family that could contribute to this functional diversity. Most of these candidate receptor genes are in clusters of two to nine similar genes. Eleven of fourteen tested genes appear to be expressed in small subsets of chemosensory neurons. A single type of chemosensory neuron can potentially express at least four different receptor genes. Some of these genes might encode receptors for water-soluble attractants, repellents, and pheromones.},
	number = {2},
	journal = {Cell},
	author = {Troemel, E R and Chou, J H and Dwyer, N D and Colbert, H A and Bargmann, C I},
	month = oct,
	year = {1995},
	note = {{PMID:} 7585938},
	keywords = {{1-Octanol}, Amino Acid Sequence, Animals, Animals, Genetically Modified, Behavior, Animal, Benzaldehydes, Caenorhabditis elegans, Chemoreceptor Cells, Female, Gene Expression, Genes, Helminth, Genes, Reporter, Male, Molecular Sequence Data, Multigene Family, Octanols, Receptors, Cell Surface, Recombinant Fusion Proteins, Sequence Analysis, {DNA}, Sequence Homology, Amino Acid, Sex Characteristics, Smell, Tissue Distribution},
	pages = {207--18},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/7PUCEAWD/7585938.html:text/html}
},

@article{huang_breaking_2010,
	title = {Breaking the diffraction barrier: super-resolution imaging of cells},
	volume = {143},
	issn = {1097-4172},
	shorttitle = {Breaking the diffraction barrier},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21168201},
	doi = {10.1016/j.cell.2010.12.002},
	abstract = {Anyone who has used a light microscope has wished that its resolution could be a little better. Now, after centuries of gradual improvements, fluorescence microscopy has made a quantum leap in its resolving power due, in large part, to advancements over the past several years in a new area of research called super-resolution fluorescence microscopy. In this Primer, we explain the principles of various super-resolution approaches, such as {STED}, {(S)SIM}, and {STORM/(F)PALM.} Then, we describe recent applications of super-resolution microscopy in cells, which demonstrate how these approaches are beginning to provide new insights into cell biology, microbiology, and neurobiology.},
	number = {7},
	journal = {Cell},
	author = {Huang, Bo and Babcock, Hazen and Zhuang, Xiaowei},
	month = dec,
	year = {2010},
	note = {{PMID:} 21168201},
	keywords = {Animals, Cytological Techniques, Humans, Microscopy, Fluorescence},
	pages = {1047--1058}
},

@article{dejneka_rare_2003,
	title = {Rare earth-doped glass microbarcodes},
	volume = {100},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12515864},
	doi = {10.1073/pnas.0236044100},
	abstract = {The development of ultraminiaturized identification tags has applications in fields ranging from advanced biotechnology to security. This paper describes micrometer-sized glass barcodes containing a pattern of different fluorescent materials that are easily identified by using a {UV} lamp and an optical microscope. A model {DNA} hybridization assay using these "microbarcodes" is described. Rare earth-doped glasses were chosen because of their narrow emission bands, high quantum efficiencies, noninterference with common fluorescent labels, and inertness to most organic and aqueous solvents. These properties and the large number ({\textgreater}1 million) of possible combinations of these microbarcodes make them attractive for use in multiplexed bioassays and general encoding.},
	number = {2},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Dejneka, Matthew J and Streltsov, Alexander and Pal, Santona and Frutos, Anthony G and Powell, Christy L and Yost, Kevin and Yuen, Po Ki and Müller, Uwe and Lahiri, Joydeep},
	month = jan,
	year = {2003},
	note = {{PMID:} 12515864},
	keywords = {Biotechnology, {DNA}, Fluorescent Dyes, Metals, Rare Earth, Nucleic Acid Hybridization},
	pages = {389--393}
},

@article{tavernarakis_molecular_1997,
	title = {Molecular modeling of mechanotransduction in the nematode Caenorhabditis elegans},
	volume = {59},
	issn = {0066-4278},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9074782},
	doi = {10.1146/annurev.physiol.59.1.659},
	abstract = {Genetic and molecular studies of touch avoidance in the nematode Caenorhabditis elegans have resulted in a molecular model for a mechanotransducing complex. mec-4 and mec-10 encode proteins hypothesized to be subunits of a mechanically gated ion channel that are related to subunits of the vertebrate amiloride-sensitive epithelial Na+ channel. Products of mec-5, a novel collagen, and mec-9, a protein that includes multiple Kunitz-type protease inhibitor repeats and {EGF} repeats, may interact with the channel in the extracellular matrix. Inside the cell, specialized 15-protofilament microtubules composed of mec-12 alpha-tubulin and mec-7 beta-tubulin may be linked to the mechanosensitive channel by stomatin-homologous {MEC-2.} {MEC-4} and {MEC-10} are members of a large family of C. elegans proteins, the degenerins. Two other degenerins, {UNC-8} and {DEL-1}, are candidate components of a stretch-sensitive channel in motor neurons. Implications for advancing understanding of mechanotransduction in other systems are discussed.},
	journal = {Annual Review of Physiology},
	author = {Tavernarakis, N and Driscoll, M},
	year = {1997},
	note = {{PMID:} 9074782},
	keywords = {Animals, Caenorhabditis elegans, Humans, Mechanoreceptors, Models, Molecular, Physical Stimulation, Signal Transduction, Touch},
	pages = {659--689},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/QV2BT6PF/entrez.html:text/html}
},

@article{aldaye_assembling_2008,
	title = {Assembling materials with {DNA} as the guide},
	volume = {321},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18818351},
	doi = {10.1126/science.1154533},
	abstract = {{DNA's} remarkable molecular recognition properties and structural features make it one of the most promising templates to pattern materials with nanoscale precision. The emerging field of {DNA} nanotechnology strips this molecule from any preconceived biological role and exploits its simple code to generate addressable nanostructures in one, two, and three dimensions. These structures have been used to precisely position proteins, nanoparticles, transition metals, and other functional components into deliberately designed patterns. They can also act as templates for the growth of nanowires, aid in the structural determination of proteins, and provide new platforms for genomics applications. The field of {DNA} nanotechnology is growing in a number of directions, carrying with it the promise to substantially affect materials science and biology.},
	number = {5897},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Aldaye, Faisal A and Palmer, Alison L and Sleiman, Hanadi F},
	month = sep,
	year = {2008},
	note = {{PMID:} 18818351},
	keywords = {Biotechnology, {DNA}, Genomics, Metal Nanoparticles, Nanostructures, Nanotechnology, Nucleic Acid Conformation, Proteomics},
	pages = {1795--1799}
},

@article{peng_straightening_2008,
	title = {Straightening Caenorhabditis elegans images},
	volume = {24},
	number = {2},
	journal = {Bioinformatics},
	author = {Peng, H. and Long, F. and Liu, X. and Kim, S. K and Myers, E. W},
	year = {2008},
	pages = {234},
	file = {worm.straighten.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TICKWIIU/worm.straighten.pdf:application/pdf}
},

@article{curtis_seeing_2006,
	title = {Seeing what the mouse sees with its vibrissae: a matter of behavioral state},
	volume = {50},
	issn = {0896-6273},
	shorttitle = {Seeing what the mouse sees with its vibrissae},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16701202},
	doi = {10.1016/j.neuron.2006.05.004},
	abstract = {The behavioral state of an animal is accompanied by ongoing brain activity that primes neuronal circuitry to sensory inputs. While it should come as no surprise that the pattern of cortical activation is tied to behavioral states, only now has this dependence been imaged. In this issue of Neuron, Ferezou, Bolea, and Petersen show that the level and spatial extent of activation of vibrissa sensory cortex critically depend on behavioral context and mode of stimulation, i.e., passive versus active contact.},
	number = {4},
	journal = {Neuron},
	author = {Curtis, John C and Kleinfeld, David},
	month = may,
	year = {2006},
	note = {{PMID:} 16701202},
	keywords = {Anesthesia, General, Animals, Behavior, Animal, Brain Mapping, Mice, Research Design, Somatosensory Cortex, Touch, Vibrissae, Wakefulness},
	pages = {524--526},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/MI4V4R22/16701202.html:text/html}
},

@article{hilliard_c._2002,
	title = {C. elegans responds to chemical repellents by integrating sensory inputs from the head and the tail},
	volume = {12},
	issn = {0960-9822},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/12007416},
	abstract = {The phasmids are bilateral sensory organs located in the tail of Caenorhabditis elegans and other nematodes. The similar structures of the phasmids and the amphid chemosensory organs in the head have long suggested a chemosensory function for the phasmids. However, the {PHA} and {PHB} phasmid neurons are not required for chemotaxis or for dauer formation, and no direct proof of a chemosensory function of the phasmids has been obtained. C. elegans avoids toxic chemicals by reversing its movement, and this behavior is mediated by sensory neurons of the amphid, particularly, the {ASH} neurons. Here we show that the {PHA} and {PHB} phasmid neurons function as chemosensory cells that negatively modulate reversals to repellents. The antagonistic activity of head and tail sensory neurons is integrated to generate appropriate escape behaviors: detection of a repellent by head neurons mediates reversals, which are suppressed by antagonistic inputs from tail neurons. Our results suggest that C. elegans senses repellents by defining a head-to-tail spatial map of the chemical environment.},
	number = {9},
	journal = {Current Biology: {CB}},
	author = {Hilliard, Massimo A and Bargmann, Cornelia I and Bazzicalupo, Paolo},
	month = apr,
	year = {2002},
	note = {{PMID:} 12007416},
	keywords = {Animals, Caenorhabditis elegans, Chemoreceptor Cells, Chemotaxis, Head, Movement, Neurons, Afferent, Signal Transduction, Tail},
	pages = {730--734}
},

@article{yu_sensory_1999,
	title = {Sensory feedback can coordinate the swimming activity of the leech},
	volume = {19},
	issn = {1529-2401},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10341261},
	abstract = {Previous studies showed that sensory feedback from the body wall is important and sometimes critical for generating normal, robust swimming activity in leeches. In this paper, we evaluate the role of sensory feedback in intersegmental coordination using both behavioral and physiological measurements. We severed the ventral nerve cord of leeches in midbody and then made video and in situ extracellular recordings from swimming animals. Our electrophysiological recordings unequivocally demonstrate that active intersegmental coordination occurs in leeches with severed nerve cords, refuting earlier conclusions that sensory feedback cannot coordinate swimming activity. Intersegmental coordination can in fact be achieved by sensory feedback alone, without the intersegmental interactions conveyed by the nerve cord.},
	number = {11},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Yu, X and Nguyen, B and Friesen, W O},
	month = jun,
	year = {1999},
	note = {{PMID:} 10341261},
	keywords = {Animals, Feedback, Ganglia, Invertebrate, Leeches, Sensation, Swimming, Video Recording},
	pages = {4634--4643}
},

@misc{__????-1,
	url = {http://www.pnas.org/content/102/9/3184.full.pdf+html}
},

@article{zhang_multimodal_2007,
	title = {Multimodal fast optical interrogation of neural circuitry},
	volume = {446},
	issn = {0028-0836},
	url = {http://dx.doi.org/10.1038/nature05744},
	doi = {10.1038/nature05744},
	abstract = {Our understanding of the cellular implementation of systems-level neural processes like action, thought and emotion has been limited by the availability of tools to interrogate specific classes of neural cells within intact, living brain tissue. Here we identify and develop an archaeal light-driven chloride pump {(NpHR)} from Natronomonas pharaonis for temporally precise optical inhibition of neural activity. {NpHR} allows either knockout of single action potentials, or sustained blockade of spiking. {NpHR} is compatible with {ChR2}, the previous optical excitation technology we have described, in that the two opposing probes operate at similar light powers but with well-separated action spectra. {NpHR}, like {ChR2}, functions in mammals without exogenous cofactors, and the two probes can be integrated with calcium imaging in mammalian brain tissue for bidirectional optical modulation and readout of neural activity. Likewise, {NpHR} and {ChR2} can be targeted together to Caenorhabditis elegans muscle and cholinergic motor neurons to control locomotion bidirectionally. {NpHR} and {ChR2} form a complete system for multimodal, high-speed, genetically targeted, all-optical interrogation of living neural circuits.},
	number = {7136},
	journal = {Nature},
	author = {Zhang, Feng and Wang, {Li-Ping} and Brauner, Martin and Liewald, Jana F. and Kay, Kenneth and Watzke, Natalie and Wood, Phillip G. and Bamberg, Ernst and Nagel, Georg and Gottschalk, Alexander and Deisseroth, Karl},
	month = apr,
	year = {2007},
	keywords = {{FromChris}, Print Me!, {ReadMe}},
	pages = {633--639}
},

@article{allard_bisphenol_2010,
	title = {Bisphenol A impairs the double-strand break repair machinery in the germline and causes chromosome abnormalities},
	volume = {107},
	issn = {1091-6490},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/21059909},
	doi = {10.1073/pnas.1010386107},
	abstract = {Bisphenol A {(BPA)} is a highly prevalent constituent of plastics that has been associated with diabetes, cardiovascular disease, and an increased risk of miscarriages in humans. In mice, {BPA} exposure disrupts the process of meiosis; however, analysis of the affected molecular pathways is lagging and has been particularly challenging. Here we show that exposure of the nematode Caenorhabditis elegans to {BPA}, at internal concentrations consistent with mammalian models, causes increased sterility and embryonic lethality. {BPA} exposure results in impaired chromosome synapsis and disruption of meiotic double-strand break repair {(DSBR)} progression. {BPA} carries an anti-estrogenic activity in the germline and results in germline-specific down-regulation of {DSBR} genes, thereby impairing maintenance of genomic integrity during meiosis. C. elegans therefore constitutes a model of remarkable relevance to mammals with which to assess how our chemical landscape affects germ cells and meiosis.},
	number = {47},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Allard, Patrick and Colaiácovo, Monica P},
	month = nov,
	year = {2010},
	note = {{PMID:} 21059909},
	keywords = {Journal Club},
	pages = {20405--20410}
},

@article{song_peripheral_2007,
	title = {Peripheral multidendritic sensory neurons are necessary for rhythmic locomotion behavior in Drosophila larvae},
	volume = {104},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17360325},
	doi = {10.1073/pnas.0700895104},
	abstract = {From breathing to walking, rhythmic movements encompass physiological processes important across the entire animal kingdom. It is thought by many that the generation of rhythmic behavior is operated by a central pattern generator {(CPG)} and does not require peripheral sensory input. Sensory feedback is, however, required to modify or coordinate the motor activity in response to the circumstances of actual movement. In contrast to this notion, we report here that sensory input is necessary for the generation of Drosophila larval locomotion, a form of rhythmic behavior. Blockage of all peripheral sensory inputs resulted in cessation of larval crawling. By conditionally silencing various subsets of larval peripheral sensory neurons, we identified the multiple dendritic {(MD)} neurons as the neurons essential for the generation of rhythmic peristaltic locomotion. By recording the locomotive motor activities, we further demonstrate that removal of {MD} neuron input disrupted rhythmic motor firing pattern in a way that prolonged the stereotyped segmental motor firing duration and prevented the propagation of posterior to anterior segmental motor firing. These findings reveal that {MD} sensory neuron input is a necessary component in the neural circuitry that generates larval locomotion.},
	number = {12},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Song, Wei and Onishi, Maika and Jan, Lily Yeh and Jan, Yuh Nung},
	month = mar,
	year = {2007},
	note = {{PMID:} 17360325},
	keywords = {Action Potentials, Animals, Behavior, Animal, Dendrites, Drosophila melanogaster, Larva, Locomotion, Neurons, Afferent, Recombinant Fusion Proteins},
	pages = {5199--5204}
},

@incollection{driscoll_mechanotransduction_1998,
	edition = {1},
	series = {Cold Spring Harbor Monograph},
	title = {Mechanotransduction},
	isbn = {0879695323},
	shorttitle = {C. Elegans {II}},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/books/bv.fcgi?rid=ce2.chapter.777},
	number = {33},
	booktitle = {C. Elegans {II}},
	publisher = {Cold Spring Harbor Laboratory Press},
	author = {Driscoll, M and Kaplan, J M},
	month = jan,
	year = {1998},
	keywords = {{PQE}  - definite citation, Sniffing / Foraging}
},

@article{livet_transgenic_2007,
	title = {Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system},
	volume = {450},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17972876},
	doi = {10.1038/nature06293},
	abstract = {Detailed analysis of neuronal network architecture requires the development of new methods. Here we present strategies to visualize synaptic circuits by genetically labelling neurons with multiple, distinct colours. In Brainbow transgenes, Cre/lox recombination is used to create a stochastic choice of expression between three or more fluorescent proteins {(XFPs).} Integration of tandem Brainbow copies in transgenic mice yielded combinatorial {XFP} expression, and thus many colours, thereby providing a way to distinguish adjacent neurons and visualize other cellular interactions. As a demonstration, we reconstructed hundreds of neighbouring axons and multiple synaptic contacts in one small volume of a cerebellar lobe exhibiting approximately 90 colours. The expression in some lines also allowed us to map glial territories and follow glial cells and neurons over time in vivo. The ability of the Brainbow system to label uniquely many individual cells within a population may facilitate the analysis of neuronal circuitry on a large scale.},
	number = {7166},
	journal = {Nature},
	author = {Livet, Jean and Weissman, Tamily A and Kang, Hyuno and Draft, Ryan W and Lu, Ju and Bennis, Robyn A and Sanes, Joshua R and Lichtman, Jeff W},
	month = nov,
	year = {2007},
	note = {{PMID:} 17972876},
	keywords = {Animals, Attachment Sites, Microbiological, Axons, Cell Communication, Cell Line, Cerebellum, Color, Gene Expression, Genetic Engineering, Humans, Integrases, Luminescent Proteins, Mice, Mice, Transgenic, Nervous System, Neural Pathways, Neuroglia, Recombination, Genetic, Stochastic Processes, Synapses, Time Factors, Transgenes},
	pages = {56--62}
},

@article{goodman_transducing_2003,
	title = {Transducing touch in Caenorhabditis elegans},
	volume = {65},
	issn = {0066-4278},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12524464},
	doi = {10.1146/annurev.physiol.65.092101.142659},
	abstract = {Mechanosensation has been studied for decades, but understanding of its molecular mechanism is only now emerging from studies in Caenorhabditis elegans and Drosophila melanogaster. In both cases, the entry point proved to be genetic screens that allowed molecules needed for mechanosensation to be identified without any prior understanding of the likely components. In C. elegans, genetic screens revealed molecules needed for touch sensation along the body wall and other regions of force sensitivity. Members of two extensive membrane protein families have emerged as candidate sensory mechanotransduction channels: mec-4 and mec-10, which encode amiloride-sensitive channels {(ASCs} or {DEG/ENaCs)}, and osm-9, which encodes a {TRP} ion channel. There are roughly 50 other members of these families whose functions in C. elegans are unknown. This article classifies these channels in C. elegans, with an emphasis on insights into their function derived from mutation. We also review the neuronal cell types in which these channels might be expressed and mediate mechanotransduction.},
	journal = {Annual Review of Physiology},
	author = {Goodman, Miriam B and Schwarz, Erich M},
	year = {2003},
	note = {{PMID:} 12524464},
	keywords = {Amino Acid Sequence, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Mechanotransduction, Cellular, Molecular Sequence Data, Touch},
	pages = {429--452},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/K58UAJ2K/12524464.html:text/html}
},

@article{miesenbock_genetic_2004,
	title = {Genetic methods for illuminating the function of neural circuits},
	volume = {14},
	issn = {0959-4388},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15194122},
	doi = {10.1016/j.conb.2004.05.004},
	abstract = {Guided by the notion that biology itself offers some of the most incisive tools for studying biological systems, neurophysiologists rely increasingly on cell biological mechanisms and materials encoded in {DNA} to visualize and control the activity of neurons in functional circuits. Optical reporter proteins can broadcast the operational states of genetically designated cells and synapses; remote-controlled effectors can suppress or induce electrical activity. Many challenges, however, remain. These include the development of novel gene expression systems that target reporters and effectors to functionally relevant neuronal ensembles, the capacity to monitor and manipulate multiple populations of neurons in parallel, the ability to observe and elicit precisely timed action potentials, and the power to communicate with genetically designated target neurons through electromagnetic signals other than light.},
	number = {3},
	journal = {Current Opinion in Neurobiology},
	author = {Miesenböck, Gero},
	month = jun,
	year = {2004},
	note = {{PMID:} 15194122},
	keywords = {Action Potentials, Animals, Central Nervous System, Genes, Reporter, Humans, Magnetics, Molecular Biology, Neural Pathways, Neurons, Signal Transduction, Synaptic Transmission},
	pages = {395--402},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TF96P3PH/15194122.html:text/html}
},

@article{baccus_retinal_2008,
	title = {A retinal circuit that computes object motion},
	volume = {28},
	issn = {1529-2401},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18596156},
	doi = {10.1523/JNEUROSCI.4206-07.2008},
	abstract = {Certain ganglion cells in the retina respond sensitively to differential motion between the receptive field center and surround, as produced by an object moving over the background, but are strongly suppressed by global image motion, as produced by the observer's head or eye movements. We investigated the circuit basis for this object motion sensitive {(OMS)} response by recording intracellularly from all classes of retinal interneurons while simultaneously recording the spiking output of many ganglion cells. Fast, transient bipolar cells respond linearly to motion in the receptive field center. The synaptic output from their terminals is rectified and then pooled by the {OMS} ganglion cell. A type of polyaxonal amacrine cell is driven by motion in the surround, again via pooling of rectified inputs, but from a different set of bipolar cell terminals. By direct intracellular current injection, we found that these polyaxonal amacrine cells selectively suppress the synaptic input of {OMS} ganglion cells. A quantitative model of these circuit elements and their interactions explains how an important visual computation is accomplished by retinal neurons and synapses.},
	number = {27},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Baccus, Stephen A and Olveczky, Bence P and Manu, Mihai and Meister, Markus},
	month = jul,
	year = {2008},
	note = {{PMID:} 18596156},
	keywords = {Action Potentials, Amacrine Cells, Ambystoma, Animals, Computer Simulation, Motion Perception, Nerve Net, Neural Inhibition, Neural Pathways, Neurons, Organ Culture Techniques, Retina, Retinal Bipolar Cells, Retinal Ganglion Cells, Synapses, Synaptic Transmission, Visual Pathways},
	pages = {6807--6817}
},

@article{landro_role_1994,
	title = {The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by {(R)-alpha-phenylglycidate}},
	volume = {33},
	issn = {0006-2960},
	shorttitle = {The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8292591},
	abstract = {The mechanism of irreversible inactivation of mandelate racemase {(MR)} from Pseudomonas putida by alpha-phenylglycidate (alpha {PGA)} has been investigated stereochemically and crystallographically. The {(R)} and {(S)} enantiomers of alpha {PGA} were synthesized in high enantiomeric excess (81\% ee and 83\% ee, respectively) using Sharpless epoxidation chemistry. {(R)-alpha} {PGA} was determined to be a stereospecific and stoichiometric irreversible inactivator of {MR.} {(S)-alpha} {PGA} does not inactivate {MR} and appears to bind noncovalently to the active site of {MR} with less affinity than that of {(R)-alpha} {PGA.} The X-ray crystal structure {(2.0-A} resolution) of {MR} inactivated by {(R)-alpha} {PGA} revealed the presence of a covalent adduct formed by nucleophilic attack of the epsilon-amino group of Lys 166 on the distal carbon on the epoxide ring of {(R)-alpha} {PGA.} The proximity of the alpha-proton of {(S)-mandelate} to Lys 166 [configurationally equivalent to {(R)-alpha} {PGA]} was corroborated by the crystal structure {(2.1-A} resolution) of {MR} complexed with the substrate analog/competitive inhibitor, {(S)-atrolactate} {[(S)-alpha-methylmandelate].} These results support the proposal that Lys 166 is the polyvalent acid/base responsible for proton transfers on the {(S)} face of mandelate. In addition, the high-resolution structures also provide insight into the probable interactions of mandelate with the essential Mg2+ and functional groups in the active site.},
	number = {3},
	journal = {Biochemistry},
	author = {Landro, J A and Gerlt, J A and Kozarich, J W and Koo, C W and Shah, V J and Kenyon, G L and Neidhart, D J and Fujita, S and Petsko, G A},
	month = jan,
	year = {1994},
	note = {{PMID:} 8292591},
	keywords = {Alkylation, Crystallography, {X-Ray}, Epoxy Compounds, {Hydrogen-Ion} Concentration, Ligands, Lysine, Models, Molecular, Phenylpropionates, Protein Conformation, Pseudomonas putida, Racemases and Epimerases, Stereoisomerism},
	pages = {635--643},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/MXB86D57/8292591.html:text/html}
},

@misc{fang-yen_cold_????,
	title = {Cold Spring Harbor C. Elegans Course Email},
	url = {https://mail.google.com/mail/?shva=1#inbox/121d594850194dab},
	author = {{Fang-Yen}, Chris},
	keywords = {{CSHL}, {FromChris}},
	howpublished = {https://mail.google.com/mail/?shva=1\#inbox/121d594850194dab}
},

@article{szobota_remote_2007-1,
	title = {Remote Control of Neuronal Activity with a {Light-Gated} Glutamate Receptor},
	volume = {54},
	issn = {0896-6273},
	url = {http://www.sciencedirect.com.ezp-prod1.hul.harvard.edu/science/article/B6WSS-4NT3W06-9/2/72a0b62930590dc9fcfa3624d9fe34d5},
	doi = {10.1016/j.neuron.2007.05.010},
	abstract = {Summary
The ability to stimulate select neurons in isolated tissue and in living animals is important for investigating their role in circuits and behavior. We show that the engineered light-gated ionotropic glutamate receptor {(LiGluR)}, when introduced into neurons, enables remote control of their activity. Trains of action potentials are optimally evoked and extinguished by 380 nm and 500 nm light, respectively, while intermediate wavelengths provide graded control over the amplitude of depolarization. Light pulses of 1-5 ms in duration at {\textasciitilde}380 nm trigger precisely timed action potentials and {EPSP-like} responses or can evoke sustained depolarizations that persist for minutes in the dark until extinguished by a short pulse of {\textasciitilde}500 nm light. When introduced into sensory neurons in zebrafish larvae, activation of {LiGluR} reversibly blocks the escape response to touch. Our studies show that {LiGluR} provides robust control over neuronal activity, enabling the dissection and manipulation of neural circuitry in vivo.},
	number = {4},
	journal = {Neuron},
	author = {Szobota, Stephanie and Gorostiza, Pau and Del Bene, Filippo and Wyart, Claire and Fortin, Doris L. and Kolstad, Kathleen D. and Tulyathan, Orapim and Volgraf, Matthew and Numano, Rika and Aaron, Holly L. and Scott, Ethan K. and Kramer, Richard H. and Flannery, John and Baier, Herwig and Trauner, Dirk and Isacoff, Ehud Y.},
	month = may,
	year = {2007},
	keywords = {{CELLBIO}, {MOLNEURO}, {SYSNEURO}},
	pages = {535--545}
},

@article{karbowski_systems_2008,
	title = {Systems level circuit model of C. elegans undulatory locomotion: mathematical modeling and molecular genetics},
	volume = {24},
	issn = {1573-6873},
	shorttitle = {Systems level circuit model of C. elegans undulatory locomotion},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17768672},
	doi = {10.1007/s10827-007-0054-6},
	abstract = {To establish the relationship between locomotory behavior and dynamics of neural circuits in the nematode C. elegans we combined molecular and theoretical approaches. In particular, we quantitatively analyzed the motion of C. elegans with defective synaptic {GABA} and acetylcholine transmission, defective muscle calcium signaling, and defective muscles and cuticle structures, and compared the data with our systems level circuit model. The major experimental findings are: (1) anterior-to-posterior gradients of body bending flex for almost all strains both for forward and backward motion, and for neuronal mutants, also analogous weak gradients of undulatory frequency, (2) existence of some form of neuromuscular (stretch receptor) feedback, (3) invariance of neuromuscular wavelength, (4) biphasic dependence of frequency on synaptic signaling, and (5) decrease of frequency with increase of the muscle time constant. Based on (1) we hypothesize that the Central Pattern Generator {(CPG)} is located in the head both for forward and backward motion. Points (1) and (2) are the starting assumptions for our theoretical model, whose dynamical patterns are qualitatively insensitive to the details of the {CPG} design if stretch receptor feedback is sufficiently strong and slow. The model reveals that stretch receptor coupling in the body wall is critical for generation of the neuromuscular wave. Our model agrees with our behavioral data (3), (4), and (5), and with other pertinent published data, e.g., that frequency is an increasing function of muscle gap-junction coupling.},
	number = {3},
	journal = {Journal of Computational Neuroscience},
	author = {Karbowski, Jan and Schindelman, Gary and Cronin, Christopher J and Seah, Adeline and Sternberg, Paul W},
	month = jun,
	year = {2008},
	note = {{PMID:} 17768672},
	keywords = {Animals, Caenorhabditis elegans, Locomotion, Mechanoreceptors, Models, Biological, Models, Genetic, Motor Activity, Mutation, Signal Transduction, Synapses},
	pages = {253--276}
},

@article{roghani_molecular_1994,
	title = {Molecular cloning of a putative vesicular transporter for acetylcholine},
	volume = {91},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7938002},
	abstract = {Classical neurotransmitters such as acetylcholine {(ACh)} require transport into synaptic vesicles for regulated exocytotic release. The Caenorhabditis elegans gene unc-17 encodes a protein with homology to mammalian transporters that concentrate monoamine neurotransmitters into synaptic vesicles. Mutations in unc-17 protect against organophosphorus toxicity, indicating a role in cholinergic neurotransmission. Using the relationship of unc-17 to the vesicular amine transporters, we first isolated a related sequence from the electric ray Torpedo californica {[Torpedo} vesicular {ACh} transporter {(TorVAChT)]} that is expressed by the electric lobe but not by peripheral tissues. Using the relationship of the Torpedo sequence to unc-17, we then isolated the {cDNA} for a rat homologue {(rVAChT).} Northern blot analysis shows expression of these sequences in the basal forebrain, basal ganglia, and spinal cord but not cerebellum or peripheral tissues. In situ hybridization shows expression of {rVAChT} {mRNA} in all cholinergic cell groups, including those in the basal forebrain, brainstem, and spinal cord that previously have been shown to express choline acetyltransferase {mRNA.} The human {VAChT} gene also localizes to chromosome 10 near the gene for choline acetyltransferase. Taken together, these observations support a role for {rVAChT} in vesicular {ACh} transport and indicate its potential as a novel marker for cholinergic neurons.},
	number = {22},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Roghani, A and Feldman, J and Kohan, S A and Shirzadi, A and Gundersen, C B and Brecha, N and Edwards, R H},
	month = oct,
	year = {1994},
	note = {{PMID:} 7938002},
	keywords = {Acetylcholine, Amino Acid Sequence, Animals, Base Sequence, Blotting, Northern, Brain, Brain Stem, Caenorhabditis elegans, Carrier Proteins, Choline {O-Acetyltransferase}, Cloning, Molecular, {DNA} Primers, {DNA}, Complementary, In Situ Hybridization, Membrane Transport Proteins, Models, Structural, Molecular Sequence Data, Mutagenesis, Organ Specificity, Polymerase Chain Reaction, Prosencephalon, Protein Conformation, Rats, Sequence Homology, Amino Acid, Spinal Cord, Torpedo, Transcription, Genetic, Vesicular Acetylcholine Transport Proteins, Vesicular Transport Proteins},
	pages = {10620--10624}
},

@misc{vialux_vialux_2009,
	title = {{ViALUX} Messtechnik + Bildverarbeitung {GmbH}, Products, {DLP®} Technology, {ALP} Controller},
	shorttitle = {{ViaLUX} {DLP} Discovery {ALP-4} Controller Suite},
	url = {http://www.vialux.de/HTML/en_alpcontr.htm},
	journal = {{ViALUX} {DLP} Discovery {ALP-4} Controller Suite},
	author = {{ViaLUX}},
	year = {2009},
	howpublished = {{http://www.vialux.de/HTML/en\_alpcontr.htm}},
	file = {ViALUX Messtechnik + Bildverarbeitung GmbH | Products | DLP® Technology | ALP Controller:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/JAP7RN6M/en_alpcontr.html:text/html}
},

@article{yamada_quantitative_2011,
	title = {Quantitative comparison of genetically encoded ca indicators in cortical pyramidal cells and cerebellar purkinje cells},
	volume = {5},
	issn = {1662-5102},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21994490},
	doi = {10.3389/fncel.2011.00018},
	abstract = {Genetically encoded Ca(2+) indicators {(GECIs)} are promising tools for cell type-specific and chronic recording of neuronal activity. In the mammalian central nervous system, however, {GECIs} have been tested almost exclusively in cortical and hippocampal pyramidal cells, and the usefulness of recently developed {GECIs} has not been systematically examined in other cell types. Here we expressed the latest series of {GECIs}, yellow cameleon {(YC)} 2.60, {YC3.60}, {YC-Nano15}, and {GCaMP3}, in mouse cortical pyramidal cells as well as cerebellar Purkinje cells using in utero injection of recombinant adenoviral vectors. We characterized the performance of the {GECIs} by simultaneous two-photon imaging and whole-cell patch-clamp recording in acute brain slices at 33 ± {2°C.} The fluorescent responses of {GECIs} to action potentials {(APs)} evoked by somatic current injection or to synaptic stimulation were examined using rapid dendritic imaging. In cortical pyramidal cells, {YC2.60} showed the largest responses to single {APs}, but its decay kinetics were slower than {YC3.60} and {GCaMP3}, while {GCaMP3} showed the largest responses to 20 {APs} evoked at 20 Hz. In cerebellar Purkinje cells, only {YC2.60} and {YC-Nano15} could reliably report single complex spikes {(CSs)}, and neither showed signal saturation over the entire stimulus range tested (1-10 {CSs} at 10 Hz). The expression and response of {YC2.60} in Purkinje cells remained detectable and comparable for at least over 100 days. These results provide useful information for selecting an optimal {GECI} depending on the experimental requirements: in cortical pyramidal cells, {YC2.60} is suitable for detecting sparse firing of {APs}, whereas {GCaMP3} is suitable for detecting burst firing of {APs;} in cerebellar Purkinje cells, {YC2.60} as well as {YC-Nano15} is suitable for detecting {CSs.}},
	journal = {Frontiers in Cellular Neuroscience},
	author = {Yamada, Yoshiyuki and Michikawa, Takayuki and Hashimoto, Mitsuhiro and Horikawa, Kazuki and Nagai, Takeharu and Miyawaki, Atsushi and Häusser, Michael and Mikoshiba, Katsuhiko},
	year = {2011},
	note = {{PMID:} 21994490},
	pages = {18}
},

@incollection{mango_c._2007,
	title = {The C. elegans pharynx: a model for oganogenesis},
	url = {http://dev.wormbook.org/chapters/www_organformation/organformation.html},
	abstract = {The C. elegans foregut (pharynx) has emerged as a powerful system to study organ formation during embryogenesis. Here I review recent advances regarding cell-fate specification and epithelial morphogenesis during pharynx development. Maternally-supplied gene products function prior to gastrulation to establish pluripotent blastomeres. As gastrulation gets under way, pharyngeal precursors become committed to pharyngeal fate in a process that requires {PHA-4/FoxA} and the Tbox transcription factors {TBX-2}, {TBX-35}, {TBX-37} and {TBX-38.} Subsequent waves of gene expression depend on the affinity of {PHA-4} for its target promoters, coupled with combinatorial strategies such as feed-forward and positive-feedback loops. During later embryogenesis, pharyngeal precursors undergo reorganization and a mesenchymal-to-epithelial transition to form the linear gut tube. Surprisingly, epithelium formation does not depend on cadherins, catenins or integrins. Rather, the kinesin {ZEN-4/MKLP1} and {CYK-4/RhoGAP} are critical to establish the apical domain during epithelial polarization. Finally, I discuss similarities and differences between the nematode pharynx and the vertebrate heart.},
	booktitle = {Wormbook},
	publisher = {{WormBook}},
	author = {Mango, Susan E.},
	editor = {The C. Elegans Research Community},
	month = jan,
	year = {2007}
},

@article{kitamura_contribution_2001,
	title = {Contribution of neurons to habituation to mechanical stimulation in Caenorhabditis elegans},
	volume = {46},
	url = {http://dx.doi.org/10.1002/1097-4695(200101)46:1%3C29::AID-NEU3%3E3.0.CO;2-8},
	doi = {10.1002/1097-4695(200101)46:1<29::AID-NEU3>3.0.CO;2-8},
	abstract = {In Caenorhabditis elegans, a light touch induces a locomotor response. Repeated touches, however, result in an attenuation of response, that is, habituation. Withdrawal responses elicited by anterior touch are controlled by anterior mechanosensory neurons {(AVM} and {ALMs)}, and by four pairs of interneurons {(AVA}, {AVB}, {AVD}, and {PVC)} {(Chalfie} et al., 1985; White et al., 1986). To identify the neurons that participate in habituation, we ablated these neurons with a laser microbeam and investigated the resulting habituation of the operated animals. The animals lacking both left and right homologues {AVDLR} were habituated more rapidly than intact animals. We propose that chemical synapses at {AVD} play a critical role in the habituation of intact animals. © 2000 John Wiley \& Sons, Inc. J Neurobiol 46: 29-40, 2001},
	number = {1},
	journal = {Journal of Neurobiology},
	author = {Kitamura, Kei-ichiro and Amano, Shigetoyo and Hosono, Ryuji},
	year = {2001},
	pages = {29--40}
},

@article{braeckmans_encoding_2003,
	title = {Encoding microcarriers by spatial selective photobleaching},
	volume = {2},
	issn = {1476-1122},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12612674},
	doi = {10.1038/nmat828},
	abstract = {Bead-based assays on very large numbers of molecules in gene expression studies, drug screening and clinical diagnostics, require the encoding of each of the microspheres according to the particular ligand bound to its surface. This allows mixing the uniquely encoded microspheres and subjecting them to an assay simultaneously. When a particular microsphere gives a positive reaction, the substance on its surface can be identified by reading the code. Previously reported techniques for colour encoding polymer microspheres only allow for a limited number of unique codes. Graphical encoding methods use metallic particles, which are rather uncommon in screening applications. Here, we demonstrate a new approach to encode polymer microspheres that are commonly used in screening applications, such as polystyrene microspheres, with a method that provides a virtually unlimited number of unique codes. Patterns can be written in fluorescently dyed microspheres by 'spatial selective photobleaching' and can be identified by confocal microscopy. Such encoded microparticles can find broad application in the collection and analysis of genetic information, high-throughput screening, medical diagnostics and combinatorial chemistry, and can also be used for labelling of consumer goods or as security labels to prevent counterfeiting.},
	number = {3},
	journal = {Nature Materials},
	author = {Braeckmans, Kevin and De Smedt, Stefaan C and Roelant, Chris and Leblans, Marc and Pauwels, Rudi and Demeester, Joseph},
	month = mar,
	year = {2003},
	note = {{PMID:} 12612674},
	keywords = {Microspheres, Nanotechnology, Photobleaching},
	pages = {169--173}
},

@misc{center_for_history_and_new_media_zotero_????,
	title = {Zotero Quick Start Guide},
	url = {http://zotero.org/support/quick_start_guide},
	author = {{{Center} for History and New Media}},
	howpublished = {http://zotero.org/support/quick\_start\_guide}
},

@book{roberts_programming_1997,
	title = {Programming Abstractions in C: A Second Course in Computer Science},
	isbn = {0201545411},
	shorttitle = {Programming Abstractions in C},
	publisher = {Addison Wesley},
	author = {Roberts, Eric S.},
	month = aug,
	year = {1997}
},

@article{white_structure_1986,
	title = {The Structure of the Nervous System of the Nematode Caenorhabditis elegans},
	volume = {314},
	issn = {00804622},
	url = {http://www.jstor.org/stable/2990196},
	number = {1165},
	journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
	author = {White, J. G. and Southgate, E. and Thomson, J. N. and Brenner, S.},
	month = nov,
	year = {1986},
	keywords = {circuitry, {PQE}  - definite citation},
	pages = {1--340}
},

@article{wyart_optogenetic_2009,
	title = {Optogenetic dissection of a behavioural module in the vertebrate spinal cord},
	volume = {461},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19759620},
	doi = {10.1038/nature08323},
	abstract = {Locomotion relies on neural networks called central pattern generators {(CPGs)} that generate periodic motor commands for rhythmic movements. In vertebrates, the excitatory synaptic drive for inducing the spinal {CPG} can originate from either supraspinal glutamatergic inputs or from within the spinal cord. Here we identify a spinal input to the {CPG} that drives spontaneous locomotion using a combination of intersectional gene expression and optogenetics in zebrafish larvae. The photo-stimulation of one specific cell type was sufficient to induce a symmetrical tail beating sequence that mimics spontaneous slow forward swimming. This neuron is the {Kolmer-Agduhr} cell, which extends cilia into the central cerebrospinal-fluid-containing canal of the spinal cord and has an ipsilateral ascending axon that terminates in a series of consecutive segments. Genetically silencing {Kolmer-Agduhr} cells reduced the frequency of spontaneous free swimming, indicating that activity of {Kolmer-Agduhr} cells provides necessary tone for spontaneous forward swimming. {Kolmer-Agduhr} cells have been known for over 75 years, but their function has been mysterious. Our results reveal that during early development in zebrafish these cells provide a positive drive to the spinal {CPG} for spontaneous locomotion.},
	number = {7262},
	journal = {Nature},
	author = {Wyart, Claire and Del Bene, Filippo and Warp, Erica and Scott, Ethan K and Trauner, Dirk and Baier, Herwig and Isacoff, Ehud Y},
	month = sep,
	year = {2009},
	note = {{PMID:} 19759620},
	keywords = {Animals, Animals, Genetically Modified, Axons, Cilia, Female, Larva, Light, Locomotion, Male, Models, Neurological, Neurons, Spinal Cord, Swimming, Tail, Zebrafish},
	pages = {407--410}
},

@article{cohen_neuronal_1980,
	title = {The neuronal correlate of locomotion in fish. {"Fictive} swimming" induced in an in vitro preparation of the lamprey spinal cord},
	volume = {41},
	issn = {0014-4819},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7461065},
	abstract = {An in vitro preparation of the lamprey spinal cord was developed to enable detailed studies of the neuronal organization of the central spinal network generating fish swimming movements, one basic type of vertebrate locomotion. 1. In the isolated lamprey spinal cord, stable bursting activity recorded in the ventral roots was initiated by adding, e.g., D-glutamate or {L-DOPA} to the bathing solution. Less stable rhythmic activity could also be induced by tonic electrical stimulation of the spinal cord. 2. The isolated spinal cord is capable of producing rhythmic activity with the same type of intra- and intersegmental coordination as in the swimming fish, i.e., with alternation between the two sides of the segment and and intersegmental phase coupling. Hence, the in vitro preparation of the lamprey spinal cord may be said to represent the neuronal correlate of the undulatory swimming movements of fish. 3. By performing spinal cord transections it was demonstrated that as few as four segments can produce rhythmic activity with maintained coordination. It was concluded that the capacity to produce coordinated burst activity is distributed throughout the lamprey spinal cord. 4. A longitudinal midline lesion as long as four segments did not prevent the ventral roots on each side from bursting with maintained coordination between adjacent hemisegments. Thus, one side of a segment can produce bursting without interaction with its opposite side, at least when connected to its rostral and caudal neighbors. 5. The rate of bursting was found to vary from one cycle to the next with the period length tending to oscillate about a mean value. Burst duration and intersegmental phase lag varied in the same manner.},
	number = {1},
	journal = {Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale},
	author = {Cohen, A H and Wallén, P},
	year = {1980},
	note = {{PMID:} 7461065},
	keywords = {Animals, Electric Conductivity, Lampreys, Locomotion, Neurons, Periodicity, Spinal Cord, Swimming},
	pages = {11--18}
},

@article{croll_behavoural_1975,
	title = {Behavoural analysis of nematode movement.},
	volume = {13},
	journal = {Advances in Parasitology},
	author = {Croll, {NA}},
	year = {1975},
	pages = {71--122},
	file = {Countway Public Scanner - 12-09-08 - BJUXEY6.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/CS24UGKE/Countway Public Scanner - 12-09-08 - BJUXEY6.pdf:application/pdf}
},

@article{kaplan_dual_1993,
	title = {A dual mechanosensory and chemosensory neuron in Caenorhabditis elegans},
	volume = {90},
	url = {http://www.pnas.org/content/90/6/2227.abstract},
	abstract = {After light touch to its nose, the nematode Caenorhabditis elegans halts forward locomotion and initiates backing. Here we show that three classes of neurons {(ASH}, {FLP}, and {OLQ)} sense touch to the nose and hence are required for this avoidance response. {ASH}, {FLP}, and {OLQ} have sensory endings that contain axonemal cilia. Mutant animals that have defective ciliated sensory endings as well as laser-operated animals that lack {ASH}, {FLP}, and {OLQ} fail to respond to touch to the nose. Together with the previous work of others, these results demonstrate that C. elegans has at least five morphologically distinct classes of mechanosensory neurons. Interestingly, the {ASH} neuron also acts as a chemosensory neuron; it mediates the avoidance of noxious chemicals. Since {ASH} possesses both chemosensory and mechanosensory modalities, this neuron might be functionally analogous to vertebrate nociceptors, which mediate the sensation of pain.},
	number = {6},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Kaplan, J M and Horvitz, H R},
	year = {1993},
	keywords = {{PQE}  - definite citation, Sniffing / Foraging},
	pages = {2227--2231},
	file = {A dual mechanosensory and chemosensory neuron in Caenorhabditis elegans — PNAS:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/T2S28A3R/2227.html:text/html}
},

@article{borner_fret_2011,
	title = {{FRET} measurements of intracellular {cAMP} concentrations and {cAMP} analog permeability in intact cells},
	volume = {6},
	copyright = {© 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1754-2189},
	url = {http://www.nature.com.ezp-prod1.hul.harvard.edu/nprot/journal/v6/n4/full/nprot.2010.198.html},
	doi = {10.1038/nprot.2010.198},
	abstract = {Real-time measurements of second messengers in living cells, such as {cAMP}, are usually performed by ratiometric fluorescence resonance energy transfer {(FRET)} imaging. However, correct calibration of {FRET} ratios, accurate calculations of absolute {cAMP} levels and actual permeabilities of different {cAMP} analogs have been challenging. Here we present a protocol that allows precise measurements of {cAMP} concentrations and kinetics by expressing {FRET-based} {cAMP} sensors in cells and modulating them with an inhibitor of adenylyl cyclase activity and a cell-permeable {cAMP} analog that fully inhibits and activates the sensors, respectively. Using this protocol, we observed different basal {cAMP} levels in primary mouse cardiomyocytes, thyroid cells and in {293A} cells. The protocol can be generally applied for calibration of second messenger or metabolite concentrations measured by {FRET}, and for studying kinetics and pharmacological properties of their membrane-permeable analogs. The complete procedure, including cell preparation and {FRET} measurements, takes 3–6 d.},
	number = {4},
	journal = {Nature Protocols},
	author = {Börner, Sebastian and Schwede, Frank and Schlipp, Angela and Berisha, Filip and Calebiro, Davide and Lohse, Martin J and Nikolaev, Viacheslav O},
	month = mar,
	year = {2011},
	keywords = {Cell biology, Imaging},
	pages = {427--438}
},

@misc{_arms_????,
	title = {Arms Control Wonk • an arms control blog network},
	url = {http://armscontrolwonk.com/},
	howpublished = {http://armscontrolwonk.com/}
},

@article{li_multiplexed_2005,
	title = {Multiplexed detection of pathogen {DNA} with {DNA-based} fluorescence nanobarcodes},
	volume = {23},
	issn = {1087-0156},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15951805},
	doi = {10.1038/nbt1106},
	abstract = {Rapid, multiplexed, sensitive and specific molecular detection is of great demand in gene profiling, drug screening, clinical diagnostics and environmental analysis. One of the major challenges in multiplexed analysis is to identify each specific reaction with a distinct label or 'code'. Two encoding strategies are currently used: positional encoding, in which every potential reaction is preassigned a particular position on a solid-phase support such as a {DNA} microarray, and reaction encoding, where every possible reaction is uniquely tagged with a code that is most often optical or particle based. The micrometer size, polydispersity, complex fabrication process and nonbiocompatibility of current codes limit their usability. Here we demonstrate the synthesis of dendrimer-like {DNA-based}, fluorescence-intensity-coded nanobarcodes, which contain a built-in code and a probe for molecular recognition. Their application to multiplexed detection of the {DNA} of several pathogens is first shown using fluorescence microscopy and dot blotting, and further demonstrated using flow cytometry that resulted in detection that was sensitive (attomole) and rapid.},
	number = {7},
	journal = {Nature Biotechnology},
	author = {Li, Yougen and Cu, Yen Thi Hong and Luo, Dan},
	month = jul,
	year = {2005},
	note = {{PMID:} 15951805},
	keywords = {Bacillus anthracis, Base Sequence, {DNA} Probes, {DNA}, Bacterial, {DNA}, Viral, Flow Cytometry, Fluorescence, Fluorescent Dyes, Francisella tularensis, Molecular Sequence Data, Nanostructures, Nanotechnology, Nucleic Acid Hybridization, {SARS} Virus},
	pages = {885--889}
},

@article{betzig_imaging_2006,
	title = {Imaging intracellular fluorescent proteins at nanometer resolution},
	volume = {313},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16902090},
	doi = {10.1126/science.1127344},
	abstract = {We introduce a method for optically imaging intracellular proteins at nanometer spatial resolution. Numerous sparse subsets of photoactivatable fluorescent protein molecules were activated, localized (to approximately 2 to 25 nanometers), and then bleached. The aggregate position information from all subsets was then assembled into a superresolution image. We used this method--termed photoactivated localization microscopy--to image specific target proteins in thin sections of lysosomes and mitochondria; in fixed whole cells, we imaged vinculin at focal adhesions, actin within a lamellipodium, and the distribution of the retroviral protein Gag at the plasma membrane.},
	number = {5793},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Betzig, Eric and Patterson, George H and Sougrat, Rachid and Lindwasser, O Wolf and Olenych, Scott and Bonifacino, Juan S and Davidson, Michael W and {Lippincott-Schwartz}, Jennifer and Hess, Harald F},
	month = sep,
	year = {2006},
	note = {{PMID:} 16902090},
	keywords = {Actins, Algorithms, Animals, Cell Line, Cell Membrane, Cercopithecus aethiops, {COS} Cells, Fluorescence, Focal Adhesions, Gene Products, gag, {HIV-1}, Light, Luminescent Proteins, Lysosomes, Microscopy, Mitochondria, Nanotechnology, Organelles, Photobleaching, Proteins, Pseudopodia, Recombinant Fusion Proteins, Vinculin},
	pages = {1642--1645}
},

@article{alavez_amyloid-binding_2011,
	title = {Amyloid-binding compounds maintain protein homeostasis during ageing and extend lifespan},
	volume = {advance online publication},
	issn = {1476-4687},
	url = {http://dx.doi.org/10.1038/nature09873},
	doi = {10.1038/nature09873},
	journal = {Nature},
	author = {Alavez, Silvestre and Vantipalli, Maithili C. and Zucker, David J. S. and Klang, Ida M. and Lithgow, Gordon J.},
	month = mar,
	year = {2011},
	file = {Nature Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/HSCDGKRG/nature09873.html:text/html}
},

@article{chalfie_green_1994,
	title = {Green fluorescent protein as a marker for gene expression},
	volume = {263},
	issn = {0036-8075},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8303295},
	abstract = {A complementary {DNA} for the Aequorea victoria green fluorescent protein {(GFP)} produces a fluorescent product when expressed in prokaryotic {(Escherichia} coli) or eukaryotic {(Caenorhabditis} elegans) cells. Because exogenous substrates and cofactors are not required for this fluorescence, {GFP} expression can be used to monitor gene expression and protein localization in living organisms.},
	number = {5148},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Chalfie, M and Tu, Y and Euskirchen, G and Ward, W W and Prasher, D C},
	month = feb,
	year = {1994},
	note = {{PMID:} 8303295},
	keywords = {Animals, Base Sequence, Caenorhabditis elegans, Cell Division, Cell Separation, Escherichia coli, Fluorescence, Gene Expression, Green Fluorescent Proteins, Luminescent Proteins, Microscopy, Fluorescence, Molecular Sequence Data, Neurons, Oligodeoxyribonucleotides, Recombinant Proteins, Spectrometry, Fluorescence, Transformation, Genetic},
	pages = {802--805}
},

@article{chalfie_neural_1985,
	title = {The neural circuit for touch sensitivity in Caenorhabditis elegans},
	volume = {5},
	issn = {0270-6474},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/3981252},
	doi = {3981252},
	abstract = {The neural pathways for touch-induced movement in Caenorhabditis elegans contain six touch receptors, five pairs of interneurons, and 69 motor neurons. The synaptic relationships among these cells have been deduced from reconstructions from serial section electron micrographs, and the roles of the cells were assessed by examining the behavior of animals after selective killing of precursors of the cells by laser microsurgery. This analysis revealed that there are two pathways for touch-mediated movement for anterior touch (through the {AVD} and {AVB} interneurons) and a single pathway for posterior touch (via the {PVC} interneurons). The anterior touch circuitry changes in two ways as the animal matures. First, there is the formation of a neural network of touch cells as the three anterior touch cells become coupled by gap junctions. Second, there is the addition of the {AVB} pathway to the pre-existing {AVD} pathway. The touch cells also synapse onto many cells that are probably not involved in the generation of movement. Such synapses suggest that stimulation of these receptors may modify a number of behaviors.},
	number = {4},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Chalfie, M and Sulston, J E and White, J G and Southgate, E and Thomson, J N and Brenner, S},
	month = apr,
	year = {1985},
	note = {{PMID:} 3981252},
	keywords = {Animals, Caenorhabditis, Interneurons, Lasers, Mechanoreceptors, Motor Neurons, Movement, Muscle Contraction, Nervous System Physiology, Neural Pathways, Synapses, Touch},
	pages = {956--64},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/85A7TITI/entrez.html:text/html}
},

@book{reif_fundamentals_1965,
	address = {New York},
	series = {{McGraw-Hill} series in fundamentals of physics},
	title = {Fundamentals of statistical and thermal physics},
	publisher = {{McGraw-Hill}},
	author = {Reif, F.},
	year = {1965}
},

@article{mank_genetically_2008,
	title = {Genetically encoded calcium indicators},
	volume = {108},
	issn = {1520-6890},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18447377},
	doi = {10.1021/cr078213v},
	number = {5},
	journal = {Chemical Reviews},
	author = {Mank, Marco and Griesbeck, Oliver},
	month = may,
	year = {2008},
	note = {{PMID:} 18447377},
	keywords = {Animals, Calcium, {Calcium-Binding} Proteins, Humans, Indicators and Reagents, Kinetics, Models, Genetic, Neurons},
	pages = {1550--1564}
},

@misc{_setting_????,
	title = {Setting up Eclipse For Using {OpenCV}},
	url = {http://www.jestinstoffel.com/?q=node/112},
	keywords = {{OpenCV}, Programming},
	howpublished = {http://www.jestinstoffel.com/?q=node/112}
},

@article{ohagan_mec-4_2004,
	title = {The {MEC-4} {DEG/ENaC} channel of Caenorhabditis elegans touch receptor neurons transduces mechanical signals},
	volume = {8},
	url = {http://www.nature.com.ezp-prod1.hul.harvard.edu/neuro/journal/v8/n1/full/nn1362.html},
	doi = {10.1038/nn1362},
	abstract = {Transformation of mechanical energy into ionic currents is essential for touch, hearing and nociception. Although {DEG/ENaC} proteins are believed to form sensory mechanotransduction channels, the evidence for this role remains indirect. By recording from C. elegans touch receptor neurons in vivo, we found that external force evokes rapidly activating mechanoreceptor currents {(MRCs)} carried mostly by Na+ and blocked by amiloride—characteristics consistent with direct mechanical gating of a {DEG/ENaC} channel. Like mammalian Pacinian corpuscles, these neurons depolarized with both positive and negative changes in external force but not with sustained force. Null mutations in the {DEG/ENaC} gene mec-4 and in the accessory ion channel subunit genes mec-2 and mec-6 eliminated {MRCs.} In contrast, the genetic elimination of touch neuron–specific microtubules reduced, but did not abolish, {MRCs.} Our findings link the application of external force to the activation of a molecularly defined metazoan sensory transduction channel.},
	number = {1},
	journal = {Nature Neuroscience},
	author = {{O'Hagan}, Robert and Chalfie, Martin and Goodman, Miriam B},
	month = dec,
	year = {2004},
	keywords = {astrocyte, Behavior, Brain, brain research, brain scientist, brainstem, Cerebellum, cognitive science, computation, content, cortex, functional imaging, glia, hypothalamus, journal, Learning, memory, model, Molecular Biology, nature, nature neuroscience, nature publishing group, Nervous System, neurodegeneration, neurodegenerative disease, neuron, neuroscience, neuroscientist, oligodendrocyte, physiology, Psychophysics, Retina, Spinal Cord, spinal cord injury, systems neuroscience, thalamus},
	pages = {43}
},

@article{castellucci_neuronal_1970,
	title = {Neuronal mechanisms of habituation and dishabituation of the gill-withdrawal reflex in Aplysia},
	volume = {167},
	issn = {0036-8075},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/5416543},
	abstract = {The cellular mechanisms of habituation and dishabituation of the gill-withdrawal reflex in Aplysia were studied with an isolated abdominal ganglion connected to a piece of skin from the tactile receptive field of the reflex. By obtaining simultaneous intracellular recordings from both the sensory neurons and one of the main identified motor neurons, we have been able to reduce the reflex to its monosynaptic components. The monosynaptic excitatory postsynaptic potentials showed a profound low-frequency depression when repeatedly elicited and showed heterosynaptic facilitation after application of a strong stimulus to another pathway. Thus, both habituation and dishabituation can be explained in part and perhaps entirely by changes in the efficacy of specific excitatory synapses.},
	number = {926},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Castellucci, V and Pinsker, H and Kupfermann, I and Kandel, E R},
	month = mar,
	year = {1970},
	note = {{PMID:} 5416543},
	keywords = {Animals, Evoked Potentials, Ganglia, Gills, Habituation, Psychophysiologic, Mollusca, Motor Neurons, Neurons, Neurons, Afferent, Reflex, Reflex, Monosynaptic, Synapses},
	pages = {1745--1748}
},

@article{kurien_extraction_2002,
	title = {Extraction of nucleic acid fragments from gels},
	volume = {302},
	issn = {0003-2697},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11846370},
	doi = {10.1006/abio.2001.5526},
	number = {1},
	journal = {Analytical Biochemistry},
	author = {Kurien, Biji T and Scofield, R Hal},
	month = mar,
	year = {2002},
	note = {{PMID:} 11846370},
	keywords = {Animals, Cloning, Molecular, {DNA}, Electrophoresis, Agar Gel, Electrophoresis, Polyacrylamide Gel, Humans},
	pages = {1--9}
},

@misc{_wormatlas:_????,
	title = {{WormAtlas:} {CEP} sensillaimagegallery},
	url = {http://www.wormatlas.org/handbook/hypodermis/CEPimage%20gallery.htm},
	keywords = {Caenorhabditis elegans, Neurons, Touch},
	howpublished = {{http://www.wormatlas.org/handbook/hypodermis/CEPimage\%20gallery.htm}},
	file = {CEP sensillaimagegallery:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/C3FCRCAR/CEPimage20gallery.html:text/html}
},

@article{morran_mutation_2009,
	title = {Mutation load and rapid adaptation favour outcrossing over self-fertilization},
	volume = {462},
	issn = {0028-0836},
	url = {http://dx.doi.org.ezp-prod1.hul.harvard.edu/10.1038/nature08496},
	doi = {10.1038/nature08496},
	number = {7271},
	journal = {Nature},
	author = {Morran, Levi T. and Parmenter, Michelle D. and Phillips, Patrick C.},
	month = nov,
	year = {2009},
	pages = {350--352}
},

@article{tavernarakis_molecular_1997-1,
	title = {Molecular modeling of mechanotransduction in the nematode Caenorhabditis elegans},
	volume = {59},
	issn = {0066-4278},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9074782},
	doi = {9074782},
	abstract = {Genetic and molecular studies of touch avoidance in the nematode Caenorhabditis elegans have resulted in a molecular model for a mechanotransducing complex. mec-4 and mec-10 encode proteins hypothesized to be subunits of a mechanically gated ion channel that are related to subunits of the vertebrate amiloride-sensitive epithelial Na+ channel. Products of mec-5, a novel collagen, and mec-9, a protein that includes multiple Kunitz-type protease inhibitor repeats and {EGF} repeats, may interact with the channel in the extracellular matrix. Inside the cell, specialized 15-protofilament microtubules composed of mec-12 alpha-tubulin and mec-7 beta-tubulin may be linked to the mechanosensitive channel by stomatin-homologous {MEC-2.} {MEC-4} and {MEC-10} are members of a large family of C. elegans proteins, the degenerins. Two other degenerins, {UNC-8} and {DEL-1}, are candidate components of a stretch-sensitive channel in motor neurons. Implications for advancing understanding of mechanotransduction in other systems are discussed.},
	journal = {Annual Review of Physiology},
	author = {Tavernarakis, N and Driscoll, M},
	year = {1997},
	note = {{PMID:} 9074782},
	keywords = {Animals, Caenorhabditis elegans, Humans, Mechanoreceptors, Models, Molecular, Physical Stimulation, {PQE}  - definite citation, Signal Transduction, Touch},
	pages = {659--89},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/RAPUXSZB/9074782.html:text/html}
},

@article{pierce-shimomura_fundamental_1999,
	title = {The Fundamental Role of Pirouettes in Caenorhabditis elegans Chemotaxis},
	volume = {19},
	url = {http://www.jneurosci.org/cgi/content/abstract/19/21/9557},
	abstract = {To investigate the behavioral mechanism of chemotaxis in Caenorhabditis elegans, we recorded the instantaneous position, speed, and turning rate of single worms as a function of time during chemotaxis in gradients of the attractants ammonium chloride or biotin. Analysis of turning rate showed that each worm track could be divided into periods of smooth swimming (runs) and periods of frequent turning (pirouettes). The initiation of pirouettes was correlated with the rate of change of concentration {(dC/dt)} but not with absolute concentration. Pirouettes were most likely to occur when a worm was heading down the gradient {(dC/dt} {\textless} 0) and least likely to occur when a worm was heading up the gradient {(dC/dt} {\textgreater} 0). Further analysis revealed that the average direction of movement after a pirouette was up the gradient. These observations suggest that chemotaxis is produced by a series of pirouettes that reorient the animal to the gradient. We tested this idea by imposing the correlation between pirouettes and {dC/dt} on a stochastic point model of worm motion. The model exhibited chemotaxis behavior in a radial gradient and also in a novel planar gradient. Thus, the pirouette model of C. elegans chemotaxis is sufficient and general.},
	number = {21},
	journal = {J. Neurosci.},
	author = {{Pierce-Shimomura}, Jonathan T. and Morse, Thomas M. and Lockery, Shawn R.},
	month = nov,
	year = {1999},
	keywords = {{PQE}  - definite citation, Print Me!},
	pages = {9557--9569},
	file = {HighWire Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/T7RPDMZ6/Pierce-Shimomura et al - 1999 - The Fundamental Role of Pirouettes in Caenorhabdit.pdf:application/pdf;HighWire Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/HD4ZMCA3/9557.html:text/html}
},

@article{han_folding_2010,
	title = {Folding and cutting {DNA} into reconfigurable topological nanostructures},
	volume = {5},
	issn = {1748-3395},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20890274},
	doi = {10.1038/nnano.2010.193},
	abstract = {Topology is the mathematical study of the spatial properties that are preserved through the deformation, twisting and stretching of objects. Topological architectures are common in nature and can be seen, for example, in {DNA} molecules that condense and relax during cellular events. Synthetic topological nanostructures, such as catenanes and rotaxanes, have been engineered using supramolecular chemistry, but the fabrication of complex and reconfigurable structures remains challenging. Here, we show that {DNA} origami can be used to assemble a Möbius strip, a topological ribbon-like structure that has only one side. In addition, we show that the {DNA} Möbius strip can be reconfigured through strand displacement to create topological objects such as supercoiled ring and catenane structures. This {DNA} fold-and-cut strategy, analogous to Japanese kirigami, may be used to create and reconfigure programmable topological structures that are unprecedented in molecular engineering.},
	number = {10},
	journal = {Nature Nanotechnology},
	author = {Han, Dongran and Pal, Suchetan and Liu, Yan and Yan, Hao},
	month = oct,
	year = {2010},
	note = {{PMID:} 20890274},
	keywords = {{DNA}, Models, Molecular, Nanostructures, Nanotechnology, Nucleic Acid Conformation},
	pages = {712--717}
},

@article{coates_antagonistic_2002,
	title = {Antagonistic pathways in neurons exposed to body fluid regulate social feeding in Caenorhabditis elegans},
	volume = {419},
	issn = {0028-0836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12410311},
	doi = {10.1038/nature01170},
	abstract = {Wild isolates of Caenorhabditis elegans can feed either alone or in groups. This natural variation in behaviour is associated with a single residue difference in {NPR-1}, a predicted G-protein-coupled neuropeptide receptor related to Neuropeptide Y receptors. Here we show that the {NPR-1} isoform associated with solitary feeding acts in neurons exposed to the body fluid to inhibit social feeding. Furthermore, suppressing the activity of these neurons, called {AQR}, {PQR} and {URX}, using an activated K(+) channel, inhibits social feeding. {NPR-1} activity in {AQR}, {PQR} and {URX} neurons seems to suppress social feeding by antagonizing signalling through a cyclic {GMP-gated} ion channel encoded by tax-2 and tax-4. We show that mutations in tax-2 or tax-4 disrupt social feeding, and that tax-4 is required in several neurons for social feeding, including one or more of {AQR}, {PQR} and {URX.} The {AQR}, {PQR} and {URX} neurons are unusual in C. elegans because they are directly exposed to the pseudocoelomic body fluid. Our data suggest a model in which these neurons integrate antagonistic signals to control the choice between social and solitary feeding behaviour.},
	number = {6910},
	journal = {Nature},
	author = {Coates, Juliet C and de Bono, Mario},
	month = oct,
	year = {2002},
	note = {{PMID:} 12410311},
	keywords = {Animals, Animals, Genetically Modified, Biological Factors, Body Fluids, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cyclic {GMP}, Feeding Behavior, Gene Deletion, Ion Channel Gating, Ion Channels, Neural Pathways, Neurons, Potassium Channels, Promoter Regions, Genetic, Receptors, Neuropeptide Y, Signal Transduction, Social Behavior},
	pages = {925--929},
	file = {nature01170.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/485NKG2I/nature01170.pdf:application/pdf;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TMK4KT6T/entrez.html:text/html}
},

@article{friesen_sensory_2001,
	title = {Sensory and central mechanisms control intersegmental coordination},
	volume = {11},
	issn = {0959-4388},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11741017},
	abstract = {Recent experiments on the sensory and central mechanisms that coordinate animal locomotory movements have advanced our understanding of the relative importance of these two components and overturned some previously held notions. In different experimental preparations, sensory inputs and central pattern generators have now been shown to play different roles in setting intersegmental phase lags.},
	number = {6},
	journal = {Current Opinion in Neurobiology},
	author = {Friesen, W O and Cang, J},
	month = dec,
	year = {2001},
	note = {{PMID:} 11741017},
	keywords = {Animals, Central Nervous System, Humans, Locomotion, Models, Neurological, Neurons, Afferent},
	pages = {678--683}
},

@book{holloway_stalin_1996,
	title = {Stalin and the Bomb: The Soviet Union and Atomic Energy, 1939-1956},
	isbn = {0300066643},
	shorttitle = {Stalin and the Bomb},
	publisher = {Yale University Press},
	author = {Holloway, Mr. David},
	month = mar,
	year = {1996}
},

@article{douglas_dna-nanotube-induced_2007,
	title = {{DNA-nanotube-induced} alignment of membrane proteins for {NMR} structure determination},
	volume = {104},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17404217},
	doi = {10.1073/pnas.0700930104},
	abstract = {Membrane proteins are encoded by 20-35\% of genes but represent {\textless}1\% of known protein structures to date. Thus, improved methods for membrane-protein structure determination are of critical importance. Residual dipolar couplings {(RDCs)}, commonly measured for biological macromolecules weakly aligned by liquid-crystalline media, are important global angular restraints for {NMR} structure determination. For alpha-helical membrane proteins {\textgreater}15 {kDa} in size, {Nuclear-Overhauser} effect-derived distance restraints are difficult to obtain, and {RDCs} could serve as the main reliable source of {NMR} structural information. In many of these cases, {RDCs} would enable full structure determination that otherwise would be impossible. However, none of the existing liquid-crystalline media used to align water-soluble proteins are compatible with the detergents required to solubilize membrane proteins. We report the design and construction of a detergent-resistant liquid crystal of 0.8-microm-long {DNA-nanotubes} that can be used to induce weak alignment of membrane proteins. The nanotubes are heterodimers of 0.4-microm-long six-helix bundles each self-assembled from a 7.3-kb scaffold strand and {\textgreater}170 short oligonucleotide staple strands. We show that the {DNA-nanotube} liquid crystal enables the accurate measurement of backbone {N(H)} and {C(alpha)H(alpha)} {RDCs} for the detergent-reconstituted zeta-zeta transmembrane domain of the T cell receptor. The measured {RDCs} validate the high-resolution structure of this transmembrane dimer. We anticipate that this medium will extend the advantages of weak alignment to {NMR} structure determination of a broad range of detergent-solubilized membrane proteins.},
	number = {16},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Douglas, Shawn M and Chou, James J and Shih, William M},
	month = apr,
	year = {2007},
	note = {{PMID:} 17404217},
	keywords = {Bacteriophage M13, {DNA}, {Single-Stranded}, {DNA}, Viral, Liquid Crystals, Magnetic Resonance Spectroscopy, Membrane Proteins, Nanotechnology, Nanotubes, Receptors, Antigen, {T-Cell}},
	pages = {6644--6648}
},

@article{zhang_optogenetic_2010,
	title = {Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures},
	volume = {5},
	issn = {1754-2189},
	shorttitle = {Optogenetic interrogation of neural circuits},
	url = {http://dx.doi.org.ezp-prod1.hul.harvard.edu/10.1038/nprot.2009.226},
	doi = {10.1038/nprot.2009.226},
	number = {3},
	journal = {Nat. Protocols},
	author = {Zhang, Feng and Gradinaru, Viviana and Adamantidis, Antoine R and Durand, Remy and Airan, Raag D and de Lecea, Luis and Deisseroth, Karl},
	month = mar,
	year = {2010},
	pages = {439--456}
},

@article{rajendran_photo-cross-linking-assisted_2011,
	title = {Photo-cross-linking-assisted thermal stability of {DNA} origami structures and its application for higher-temperature self-assembly},
	volume = {133},
	issn = {1520-5126},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21859143},
	doi = {10.1021/ja204546h},
	abstract = {Heat tolerance of {DNA} origami structures has been improved about 30 {°C} by photo-cross-linking of 8-methoxypsoralen. To demonstrate one of its applications, the cross-linked origami were used for higher-temperature self-assembly, which markedly increased the yield of the assembled product when compared to the self-assembly of non-cross-linked origami at lower-temperature. By contrast, at higher-temperature annealing, native non-cross-linked tiles did not self-assemble to yield the desired product; however, they formed a nonspecific broken structure.},
	number = {37},
	journal = {Journal of the American Chemical Society},
	author = {Rajendran, Arivazhagan and Endo, Masayuki and Katsuda, Yousuke and Hidaka, Kumi and Sugiyama, Hiroshi},
	month = sep,
	year = {2011},
	note = {{PMID:} 21859143},
	pages = {14488--14491}
},

@article{dent_genetics_2000,
	title = {The genetics of ivermectin resistance in Caenorhabditis elegans},
	volume = {97},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10716995},
	abstract = {The ability of organisms to evolve resistance threatens the effectiveness of every antibiotic drug. We show that in the nematode Caenorhabditis elegans, simultaneous mutation of three genes, avr-14, avr-15, and glc-1, encoding glutamate-gated chloride channel {(GluCl)} alpha-type subunits confers high-level resistance to the antiparasitic drug ivermectin. In contrast, mutating any two channel genes confers modest or no resistance. We propose a model in which ivermectin sensitivity in C. elegans is mediated by genes affecting parallel genetic pathways defined by the family of {GluCl} genes. The sensitivity of these pathways is further modulated by unc-7, unc-9, and the Dyf (dye filling defective) genes, which alter the structure of the nervous system. Our results suggest that the evolution of drug resistance can be slowed by targeting antibiotic drugs to several members of a multigene family.},
	number = {6},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Dent, J A and Smith, M M and Vassilatis, D K and Avery, L},
	month = mar,
	year = {2000},
	note = {{PMID:} 10716995},
	keywords = {Animals, Antinematodal Agents, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Chloride Channels, Cloning, Molecular, Drug Resistance, Electrophysiology, Glutamic Acid, Helminth Proteins, Ivermectin, Models, Biological, Models, Genetic, Mutation, Pharynx, Protein Binding},
	pages = {2674--2679}
},

@article{bargmann_signal_1998,
	title = {Signal transduction in the Caenorhabditis elegans nervous system},
	volume = {21},
	issn = {{0147-006X}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9530498},
	doi = {9530498},
	abstract = {Caenorhabditis elegans interacts with its environment by sensing chemicals, touch, and temperature; genetic analysis of each of these responses has led to the identification of candidate signaling molecules within sensory neurons. A molecular model for touch sensation has emerged from studies of the mechanosensory response; the receptors and signal transduction mechanisms in olfactory neurons are being elucidated; and an unusual neuroendocrine role for a {TGF-beta-related} peptide in chemosensory neurons has been discovered. Presynaptic and postsynaptic components of neuronal synapses have been identified in behavioral and pharmacological mutant screens. Mutations have been found in multiple classes of nicotinic acetylcholine receptor genes, excitatory and inhibitory glutamate receptor genes, and candidate gap junction genes, allowing their function to be studied in vivo. Different G-protein signaling pathways have characteristic effects on behavior, neuronal degeneration, and embryonic development.},
	journal = {Annual Review of Neuroscience},
	author = {Bargmann, C I and Kaplan, J M},
	year = {1998},
	note = {{PMID:} 9530498},
	keywords = {Animals, Caenorhabditis elegans, Nervous System Physiology, Review, Signal Transduction},
	pages = {279--308},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/PTPBWXPF/9530498.html:text/html}
},

@article{kibler_role_2006,
	title = {The role of core stability in athletic function.},
	volume = {36},
	issn = {0112-1642},
	url = {http://ezp-prod1.hul.harvard.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=c8h&AN=2009161674&site=ehost-live&scope=site},
	abstract = {The importance of function of the central core of the body for stabilisation and force generation in all sports activities is being increasingly recognised. {'Core} stability' is seen as being pivotal for efficient biomechanical function to maximise force generation and minimise joint loads in all types of activities ranging from running to throwing. However, there is less clarity about what exactly constitutes 'the core', either anatomically or physiologically, and physical evaluation of core function is also {variable.'Core} stability' is defined as the ability to control the position and motion of the trunk over the pelvis to allow optimum production, transfer and control of force and motion to the terminal segment in integrated athletic activities. Core muscle activity is best understood as the pre-programmed integration of local, single-joint muscles and multi-joint muscles to provide stability and produce motion. This results in proximal stability for distal mobility, a proximal to distal patterning of generation of force, and the creation of interactive moments that move and protect distal joints. Evaluation of the core should be dynamic, and include evaluation of the specific functions (trunk control over the planted leg) and directions of motions (three-planar activity). Rehabilitation should include the restoring of the core itself, but also include the core as the base for extremity function.},
	number = {3},
	journal = {Sports Medicine},
	author = {Kibler, {WB} and Press, J and Sciascia, A},
	month = feb,
	year = {2006},
	keywords = {Abdomen, Abdominal Muscles -- Physiology, Balance, Postural, Biomechanics, Clinical Assessment Tools, Exercise Intensity, Exercise Physiology, Functional Status, Hip, Lower Extremity, Muscle Contraction -- Physiology, Muscle Strength, Muscle Strength -- Evaluation, Muscle Strengthening, Muscle Weakness, Pelvis, Physical Examination, Physical Performance, Pliability, Rehabilitation, Spine, Sports, Therapeutic Exercise, Torso, Torso -- Physiology},
	pages = {189--198}
},

@article{colbert_osm-9_1997,
	title = {{OSM-9}, a novel protein with structural similarity to channels, is required for olfaction, mechanosensation, and olfactory adaptation in Caenorhabditis elegans},
	volume = {17},
	issn = {0270-6474},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9334401},
	abstract = {Although cyclic nucleotide-gated channels mediate sensory transduction in olfaction and vision, other forms of sensory transduction are independent of these channels. Caenorhabditis elegans cyclic nucleotide-gated channel mutants respond normally to some olfactory stimuli and to osmotic stimuli, suggesting that these chemosensory responses use an alternative sensory transduction pathway. One gene that may act in this pathway is osm-9, which is required for each of these responses as well as a mechanosensory response to nose touch. osm-9 encodes a protein with ankyrin repeats and multiple predicted transmembrane domains that has limited similarity to the Drosophila phototransduction channels transient receptor potential {(TRP)} and {TRP-like} {(TRPL).} The sequence of {OSM-9} and other {TRP-like} genes reveals a previously unsuspected diversity of mammalian and invertebrate genes in this family. osm-9 is required for the activity of the predicted G-protein-coupled odorant receptor {ODR-10}, which acts in the {AWA} olfactory neurons; its similarity to other G-protein-regulated transduction channels suggests that {OSM-9} is involved in {AWA} signaling. osm-9:: {GFP} fusion genes are expressed in a subset of chemosensory, mechanosensory, and osmosensory neurons. osm-9 also affects olfactory adaptation within neurons that require the cyclic nucleotide-gated channel for olfaction; in these neurons, the gene has a regulatory function and not a primary role in sensory transduction.},
	number = {21},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Colbert, H A and Smith, T L and Bargmann, C I},
	month = nov,
	year = {1997},
	note = {{PMID:} 9334401},
	keywords = {Adaptation, Physiological, Amino Acid Sequence, Animals, Animals, Genetically Modified, Caenorhabditis elegans, Caenorhabditis elegans Proteins, {Calmodulin-Binding} Proteins, Cloning, Molecular, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, {GTP-Binding} Proteins, Helminth Proteins, Ion Channels, Mechanoreceptors, Membrane Proteins, Molecular Sequence Data, Nerve Tissue Proteins, Neurons, Afferent, Protein Conformation, Recombinant Fusion Proteins, Repetitive Sequences, Nucleic Acid, Sequence Alignment, Sequence Homology, Amino Acid, Signal Transduction, Smell, Species Specificity, {Structure-Activity} Relationship, Touch, Transient Receptor Potential Channels},
	pages = {8259--8269},
	file = {OSM-9, A Novel Protein with Structural Similarity to Channels, Is Required for Olfaction, Mechanosensation, and Olfactory Adaptation in Caenorhabditis elegans -- Colbert et al. 17 (21): 8259 -- Journal of Neuroscience:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/22RC4MNC/8259.html:text/html;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/7D6MHCTG/9334401.html:text/html}
},

@article{liu_low_2006,
	title = {Low conductance gap junctions mediate specific electrical coupling in body-wall muscle cells of Caenorhabditis elegans},
	volume = {281},
	issn = {0021-9258},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16434400},
	doi = {10.1074/jbc.M512382200},
	abstract = {Invertebrate innexins and their mammalian homologues, the pannexins, are gap junction proteins. Although a large number of such proteins have been identified, few of the gap junctions that they form have been characterized to provide combined information of biophysical properties, coupling pattern, and molecular compositions. We adapted the dual whole cell voltage clamp technique to in situ analysis of electrical coupling in Caenorhabditis elegans body-wall muscle. We found that body-wall muscle cells were electrically coupled in a highly organized and specific pattern. The coupling was characterized by small (350 {pS} or less) junctional conductance {(G(j))}, which showed a bell-shaped relationship with junctional potential {(V(j))} but was independent of membrane potential {(V(m)).} Injection of currents comparable to the junctional current {(I(j))} into body-wall muscle cells caused significant depolarization, suggesting important functional relevance. The innexin {UNC-9} appeared to be a key component of the gap junctions. Both Myc- and green fluorescent protein-tagged {UNC-9} was localized to muscle intercellular junctions. G(j) was greatly inhibited in unc-9(fc16), a putative null mutant. Specific inhibition of {UNC-9} function in muscle cells reduced locomotion velocity. Despite {UNC-9} expression in both motor neurons and body-wall muscle cells, analyses of miniature and evoked postsynaptic currents in the unc-9 mutant showed normal neuromuscular transmission. These analyses provide a relatively detailed description of innexin-based gap junctions in a native tissue and suggest that innexin-based small conductance gap junctions can play an important role in processes such as locomotion.},
	number = {12},
	journal = {The Journal of Biological Chemistry},
	author = {Liu, Qiang and Chen, Bojun and Gaier, Eric and Joshi, Jaya and Wang, {Zhao-Wen}},
	month = mar,
	year = {2006},
	note = {{PMID:} 16434400},
	keywords = {Animals, Biophysical Phenomena, Biophysics, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Electrophysiology, Gap Junctions, Membrane Potentials, Membrane Proteins, Models, Anatomic, Models, Biological, Motor Neurons, Movement, Muscles, Mutation, Oscillometry, {Patch-Clamp} Techniques, Protein Structure, Tertiary, Tissue Distribution},
	pages = {7881--7889}
},

@article{li_c._2006,
	title = {A C. elegans stretch receptor neuron revealed by a mechanosensitive {TRP} channel homologue},
	volume = {440},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16572173},
	doi = {10.1038/nature04538},
	abstract = {The nematode Caenorhabditis elegans is commonly used as a genetic model organism for dissecting integration of the sensory and motor systems. Despite extensive genetic and behavioural analyses that have led to the identification of many genes and neural circuits involved in regulating C. elegans locomotion behaviour, it remains unclear whether and how somatosensory feedback modulates motor output during locomotion. In particular, no stretch receptors have been identified in C. elegans, raising the issue of whether stretch-receptor-mediated proprioception is used by C. elegans to regulate its locomotion behaviour. Here we have characterized {TRP-4}, the C. elegans homologue of the mechanosensitive {TRPN} channel. We show that trp-4 mutant worms bend their body abnormally, exhibiting a body posture distinct from that of wild-type worms during locomotion, suggesting that {TRP-4} is involved in stretch-receptor-mediated proprioception. We show that {TRP-4} acts in a single neuron, {DVA}, to mediate its function in proprioception, and that the activity of {DVA} can be stimulated by body stretch. {DVA} both positively and negatively modulates locomotion, providing a unique mechanism whereby a single neuron can fine-tune motor activity. Thus, {DVA} represents a stretch receptor neuron that regulates sensory-motor integration during C. elegans locomotion.},
	number = {7084},
	journal = {Nature},
	author = {Li, Wei and Feng, Zhaoyang and Sternberg, Paul W and Xu, X Z Shawn},
	month = mar,
	year = {2006},
	note = {{PMID:} 16572173},
	keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium, Dopamine, Locomotion, Mechanoreceptors, Mechanotransduction, Cellular, Mutation, Neurons, Phenotype, {TRPC} Cation Channels},
	pages = {684--687}
},

@book{matlab_version_2010,
	title = {Version 7.11.0 {(R2010b)}},
	publisher = {The {MathWorks} Inc.},
	author = {{MATLAB}},
	year = {2010}
},

@article{schafer_mechanism_1996,
	title = {Mechanism of the Reaction Catalyzed by Mandelate Racemase: Structure and Mechanistic Properties of the {D270N} Mutant†,‡},
	volume = {35},
	shorttitle = {Mechanism of the Reaction Catalyzed by Mandelate Racemase},
	url = {http://dx.doi.org/10.1021/bi960174m},
	doi = {10.1021/bi960174m},
	abstract = {On the basis of the available high-resolution structures of mandelate racemase {(MR)} from Pseudomonas putida {[Landro}, J. A., Gerlt, J. A., Kozarich, J. W., Koo, C. W., Shah, V. J., Kenyon, G. L., Neidhart, D. J., Fujita, J., \& Petsko, G. A. (1994) Biochemistry 33, 635643], Lys 166 and His 297 are positioned appropriately to participate in catalysis as acid/base catalysts, with Lys 166 participating as the {(S)-specific} acid/base catalyst and His 297 participating as the {(R)-specific} acid/base catalyst. The dependence of kcat on {pH} for the racemization of both {(R)-} and {(S)-mandelates} suggests that the {pKas} of the conjugate acids of Lys 166 and His 297 are both 6.4 {[Landro}, J. A., Kallarakal, A. T., Ransom, S. C., Gerlt, J. A., Kozarich, J. W., Neidhart, D. J., \& Kenyon, G. L. (1991) Biochemistry 30, 92749281; Kallarakal, A. T., Mitra, B., Kozarich, J. W., Gerlt, J. A., Clifton, J. R., Petsko, G. A., \& Kenyon, G. L. (1995) Biochemistry 34, 27882797]. Both acid/base catalysts are in close proximity to and approximately equidistant to the epsilon-ammonium group of Lys 164 and the essential Mg2+. The positive electrostatic potential provided by these cationic groups might be expected to increase the acidities of the cationic conjugate acids of the acid/base catalysts, thereby explaining the depressed {pKa} of Lys 166 but not the normal {pKa} of His 297. Asp 270 is hydrogen bonded to Ndelta of His 297 and, therefore, may allow the {pKa} of His 297 to be normal. In this paper we report the structural and mechanistic properties of the mutant in which Asp 270 is replaced with asparagine {(D270N).} The structure of {D270N} with {(S)-atrolactate} bound in the active site reveals no geometric alterations in the active site when compared to the structure of wild-type {MR} complexed with {(S)-atrolactate}, with the exception that the side chain of His 297 is tilted and displaced 0.5 A away from Asn 270 and toward the {(S)-atrolactate.} The kcats for both {(R)-} and {(S)-mandelates} are reduced 104-fold. In accord with the proposal that Asp 270 influences the {pKa} of His 297, in the {(R)-} to {(S)-direction} no ascending limb is detected in the dependence of kcat on {pH;} instead, kcat decreases from a low {pH} plateau as described by a {pKa} of 10. In the {(S)-} to {(R)-direction} the dependence of kcat on {pH} is a bell-shaped curve that is described by {pKas} of 6.4 and 10. In analogy to the previously reported properties of the {H297N} mutant {[Landro}, J. A., Kallarakal, A. T., Ransom, S. C., Gerlt, J. A., Kozarich, J. W., Neidhart, D. J., \& Kenyon, G. L. (1991) Biochemistry 30, 92749281], {D270N} catalyzes both the facile exchange of the alpha-proton of {(S)-} but not {(R)-mandelate} with solvent and the stereospecific elimination of bromide ion from {(S)-p-(bromomethyl)mandelate.} These observations suggest that His 297 and Asp 270 function as a catalytic dyad, with Asp 270 being at least partially responsible for the normal {pKa} of His 297 in wild-type {MR.}},
	number = {18},
	journal = {Biochemistry},
	author = {Schafer, Susan L. and Barrett, William C. and Kallarakal, Abraham T. and Mitra, Bharati and Kozarich, John W. and Gerlt, John A. and Clifton, James G. and Petsko, Gregory A. and Kenyon, George L.},
	month = jan,
	year = {1996},
	pages = {5662--5669},
	file = {ACS Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/7FKHWNHZ/Schafer et al - 1996 - Mechanism of the Reaction Catalyzed by Mandelate R:;ACS Full Text Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/UKP5SVTR/Schafer et al - 1996 - Mechanism of the Reaction Catalyzed by Mandelate R:;Mechanism of the Reaction Catalyzed by Mandelate Racemase: Structure and Mechanistic Properties of the D270N Mutant†,‡ - Biochemistry (ACS Publications):/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/HPPSJJM9/bi960174m.html:text/html}
},

@article{hughes_sensory_2007,
	title = {A sensory feedback circuit coordinates muscle activity in Drosophila},
	volume = {35},
	issn = {1044-7431},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17498969},
	doi = {10.1016/j.mcn.2007.04.001},
	abstract = {Drosophila larval crawling is a simple behavior that allows us to dissect the functions of specific neurons in the intact animal and explore the roles of genes in the specification of those neurons. By inhibiting subsets of neurons in the {PNS}, we have found that two classes of multidendritic neurons play a major role in larval crawling. The bipolar dendrites and class I mds send a feedback signal to the {CNS} that keeps the contraction wave progressing quickly, allowing smooth forward movement. Genetic manipulation of the sensory neurons suggests that this feedback depends on proper dendritic morphology and axon pathfinding to appropriate synaptic target areas in the {CNS.} Our data suggest that coordination of muscle activity in larval crawling requires feedback from neurons acting as proprioceptors, sending a "mission accomplished" signal in response to segment contraction, and resulting in rapid relaxation of the segment and propagation of the wave.},
	number = {2},
	journal = {Molecular and Cellular Neurosciences},
	author = {Hughes, Cynthia L and Thomas, John B},
	month = jun,
	year = {2007},
	note = {{PMID:} 17498969},
	keywords = {Animals, Animals, Genetically Modified, Behavior, Animal, Dendrites, Drosophila, Drosophila Proteins, Embryo, Nonmammalian, Feedback, Green Fluorescent Proteins, Models, Biological, Movement, Muscles, Nerve Net, Neurons, Afferent, Videotape Recording},
	pages = {383--396}
},

@article{bellot_recovery_2011,
	title = {Recovery of intact {DNA} nanostructures after agarose gel-based separation},
	volume = {8},
	issn = {1548-7105},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21358621},
	doi = {10.1038/nmeth0311-192},
	number = {3},
	journal = {Nature Methods},
	author = {Bellot, Gaëtan and {McClintock}, Mark A and Lin, Chenxiang and Shih, William M},
	month = mar,
	year = {2011},
	note = {{PMID:} 21358621},
	keywords = {{DNA}, Electrophoresis, Agar Gel, Gels, Microscopy, Electron, Transmission, Nanostructures, Sepharose},
	pages = {192--194}
},

@article{ermentrout_frequency_1984,
	title = {Frequency Plateaus in a Chain of Weakly Coupled Oscillators, I.},
	volume = {15},
	issn = {00361410},
	url = {http://link.aip.org/link/SJMAAH/v15/i2/p215/s1&Agg=doi},
	doi = {10.1137/0515019},
	journal = {{SIAM} Journal on Mathematical Analysis},
	author = {Ermentrout, George Bard and Kopell, Nancy},
	year = {1984},
	pages = {215}
},

@article{jones_fast_2011,
	title = {Fast, three-dimensional super-resolution imaging of live cells},
	volume = {8},
	issn = {1548-7105},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21552254},
	doi = {10.1038/nmeth.1605},
	abstract = {We report super-resolution fluorescence imaging of live cells with high spatiotemporal resolution using stochastic optical reconstruction microscopy {(STORM).} By labeling proteins either directly or via {SNAP} tags with photoswitchable dyes, we obtained two-dimensional {(2D)} and {3D} super-resolution images of living cells, using clathrin-coated pits and the transferrin cargo as model systems. Bright, fast-switching probes enabled us to achieve {2D} imaging at spatial resolutions of ∼25 nm and temporal resolutions as fast as 0.5 s. We also demonstrated live-cell {3D} super-resolution imaging. We obtained {3D} spatial resolution of ∼30 nm in the lateral direction and ∼50 nm in the axial direction at time resolutions as fast as 1-2 s with several independent snapshots. Using photoswitchable dyes with distinct emission wavelengths, we also demonstrated two-color {3D} super-resolution imaging in live cells. These imaging capabilities open a new window for characterizing cellular structures in living cells at the ultrastructural level.},
	number = {6},
	journal = {Nature Methods},
	author = {Jones, Sara A and Shim, {Sang-Hee} and He, Jiang and Zhuang, Xiaowei},
	month = jun,
	year = {2011},
	note = {{PMID:} 21552254},
	keywords = {Animals, Cell Line, Clathrin, Coated Pits, {Cell-Membrane}, Endocytosis, Fluorescent Dyes, Image Processing, {Computer-Assisted}, Microscopy, Fluorescence, Transferrin},
	pages = {499--508}
},

@article{cronin_automated_2006,
	title = {Automated imaging of C. elegans behavior},
	volume = {351},
	issn = {1064-3745},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16988438},
	doi = {1-59745-151-7:241},
	abstract = {Automated systems for recording and analyzing behavior have many applications for the study of neurobiology in Caenorhabditis elegans. In particular, machine-based approaches allow for precise quantitative definitions of behavioral phenotypes that have traditionally been subjectively described by individual observers. Automated systems also facilitate the analysis of behaviors that occur over long time scales or are difficult to detect by eye. Here we describe the detailed methodology for the use of one recently described automated tracking system for C. elegans. These protocols make it possible to measure a wide range of parameters related to the morphology, body posture, and locomotion patterns of individual wild-type and mutant nematodes.},
	journal = {Methods in Molecular Biology {(Clifton}, {N.J.)}},
	author = {Cronin, Christopher J and Feng, Zhaoyang and Schafer, William R},
	year = {2006},
	note = {{PMID:} 16988438},
	keywords = {Algorithms, Animals, Behavior, Animal, Caenorhabditis elegans, Image Interpretation, {Computer-Assisted}, Locomotion, Microscopy, Video, Motor Activity, Mutation, Software},
	pages = {241--51},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/FUKBHD8U/16988438.html:text/html}
},

@article{alkema_tyramine_2005,
	title = {Tyramine Functions independently of octopamine in the Caenorhabditis elegans nervous system},
	volume = {46},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15848803},
	doi = {10.1016/j.neuron.2005.02.024},
	abstract = {Octopamine biosynthesis requires tyrosine decarboxylase to convert tyrosine into tyramine and tyramine beta-hydroxylase to convert tyramine into octopamine. We identified and characterized a Caenorhabditis elegans tyrosine decarboxylase gene, tdc-1, and a tyramine beta-hydroxylase gene, tbh-1. The {TBH-1} protein is expressed in a subset of {TDC-1-expressing} cells, indicating that C. elegans has tyraminergic cells that are distinct from its octopaminergic cells. tdc-1 mutants have behavioral defects not shared by tbh-1 mutants. We show that tyramine plays a specific role in the inhibition of egg laying, the modulation of reversal behavior, and the suppression of head oscillations in response to anterior touch. We propose a model for the neural circuit that coordinates locomotion and head oscillations in response to anterior touch. Our findings establish tyramine as a neurotransmitter in C. elegans, and we suggest that tyramine is a genuine neurotransmitter in other invertebrates and possibly in vertebrates as well.},
	number = {2},
	journal = {Neuron},
	author = {Alkema, Mark J and {Hunter-Ensor}, Melissa and Ringstad, Niels and Horvitz, H Robert},
	month = apr,
	year = {2005},
	note = {{PMID:} 15848803},
	keywords = {Amino Acid Sequence, Animals, Blotting, Western, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Chromatography, High Pressure Liquid, Humans, Immunohistochemistry, Models, Neurological, Molecular Sequence Data, Nervous System Physiological Phenomena, Neurotransmitter Agents, Octopamine, Polymerase Chain Reaction, Sequence Homology, Amino Acid, Tyramine, Tyrosine {3-Monooxygenase}, Tyrosine Decarboxylase},
	pages = {247--260},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/KADF75TT/entrez.html:text/html;science.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/U6F6K88R/science.pdf:application/pdf}
},

@article{chalfie_developmental_1981,
	title = {Developmental genetics of the mechanosensory neurons of Caenorhabditis elegans},
	volume = {82},
	issn = {0012-1606},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7227647},
	number = {2},
	journal = {Developmental Biology},
	author = {Chalfie, M and Sulston, J},
	month = mar,
	year = {1981},
	note = {{PMID:} 7227647},
	keywords = {Alleles, Animals, Caenorhabditis, Chromosome Mapping, Genes, Microscopy, Electron, Mutation, Neurons, Species Specificity, Touch},
	pages = {358--370}
},

@article{khatri_rat_2006,
	title = {Rat whisker psychophysics},
	volume = {26},
	issn = {1529-2401},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17139795},
	number = {48},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Khatri, Vivek and Ramos, Raddy},
	month = nov,
	year = {2006},
	note = {{PMID:} 17139795},
	keywords = {Animals, Neural Pathways, Psychophysics, Rats, Sensory Deprivation, Vibrissae},
	pages = {12385--12386},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/T9MT8ETM/17139795.html:text/html}
},

@article{brockie_c._2001,
	title = {The C. elegans glutamate receptor subunit {NMR-1} is required for slow {NMDA-activated} currents that regulate reversal frequency during locomotion},
	volume = {31},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/11545720},
	abstract = {The {N-methyl-D-aspartate} {(NMDA)} subtype of glutamate receptor is important for synaptic plasticity and nervous system development and function. We have used genetic and electrophysiological methods to demonstrate that {NMR-1}, a Caenorhabditis elegans {NMDA-type} ionotropic glutamate receptor subunit, plays a role in the control of movement and foraging behavior. nmr-1 mutants show a lower probability of switching from forward to backward movement and a reduced ability to navigate a complex environment. Electrical recordings from the interneuron {AVA} show that {NMDA-dependent} currents are selectively disrupted in nmr-1 mutants. We also show that a slowly desensitizing variant of a {non-NMDA} receptor can rescue the nmr-1 mutant phenotype. We propose that {NMDA} receptors in C. elegans provide long-lived currents that modulate the frequency of movement reversals during foraging behavior.},
	number = {4},
	journal = {Neuron},
	author = {Brockie, P J and Mellem, J E and Hills, T and Madsen, D M and Maricq, A V},
	month = aug,
	year = {2001},
	note = {{PMID:} 11545720},
	keywords = {Animals, Animals, Genetically Modified, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Electrophysiology, Gene Deletion, Gene Expression, Interneurons, Locomotion, Maze Learning, Membrane Potentials, Molecular Sequence Data, Mutagenesis, Phenotype, Quan Recommends, Receptors, {AMPA}, Receptors, Glutamate, Receptors, {N-Methyl-D-Aspartate}, Sequence Homology, Amino Acid, Synaptic Transmission},
	pages = {617--630}
},

@article{wen_bending_2011,
	title = {Bending waves during Caenorhabditis elegans locomotion  are driven and organized by proprioceptive coupling},
	journal = {Nature (submitted)},
	author = {Wen, Quan and Hulme, Elizabeth and Chen, Sway and Liu, Xinyu and Gershow, Marc and Leifer, Andrew M and Butler, Victoria and {Fang-Yen}, Christopher and Schafer, William R and Whitesides, George and Wyart, Matthieu and Chklovskii, Dmitri B and Samuel, Aravinthan D T},
	year = {2011}
},

@article{esmaeili_c._2002,
	title = {The C. elegans even-skipped homologue, vab-7, specifies {DB} motoneurone identity and axon trajectory},
	volume = {129},
	issn = {0950-1991},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11861469},
	abstract = {Locomotory activity is defined by the specification of motoneurone subtypes. In the nematode, C. elegans, {DA} and {DB} motoneurones innervate dorsal muscles and function to induce movement in the backwards or forwards direction, respectively. These two neurone classes express separate sets of genes and extend axons with oppositely directed trajectories; anterior {(DA)} versus posterior {(DB).} The {DA-specific} homeoprotein {UNC-4} interacts with {UNC-37/Groucho} to repress the {DB} gene, acr-5 (nicotinic acetylcholine receptor subunit). We show that the C. elegans even-skipped-like homoedomain protein, {VAB-7}, coordinately regulates different aspects of the {DB} motoneurone fate, in part by repressing unc-4. Wild-type {DB} motoneurones express {VAB-7}, have posteriorly directed axons, express {ACR-5} and lack expression of the homeodomain protein {UNC-4.} In a vab-7 mutant, ectopic {UNC-4} represses acr-5 and induces an anteriorly directed {DB} axon trajectory. Thus, vab-7 indirectly promotes {DB-specific} gene expression and posteriorly directed axon outgrowth by preventing {UNC-4} repression of {DB} differentiation. Ectopic expression of {VAB-7} also induces {DB} traits in an unc-4-independent manner, suggesting that {VAB-7} can act through a parallel pathway. This work supports a model in which a complementary pair of homeodomain transcription factors {(VAB-7} and {UNC-4)} specifies differences between {DA} and {DB} neurones through inhibition of the alternative fates. The recent findings that Even-skipped transcriptional repressor activity specifies neurone identity and axon guidance in the mouse and Drosophila motoneurone circuit points to an ancient origin for homeoprotein-dependent mechanisms of neuronal differentiation in the metazoan nerve cord.},
	number = {4},
	journal = {Development {(Cambridge}, England)},
	author = {Esmaeili, Behrooz and Ross, Jennifer M and Neades, Cara and Miller, David M, 3rd and Ahringer, Julie},
	month = feb,
	year = {2002},
	note = {{PMID:} 11861469},
	keywords = {Animals, Axons, Bacterial Proteins, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Polarity, Drosophila Proteins, Gene Expression, Helminth Proteins, Homeodomain Proteins, Motor Neurons, Muscle Proteins, Mutagenesis, Nuclear Proteins, Protozoan Proteins, Transcription Factors},
	pages = {853--862}
},

@article{klein_live-cell_2011,
	title = {Live-cell {dSTORM} with {SNAP-tag} fusion proteins},
	volume = {8},
	issn = {1548-7105},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21191367},
	doi = {10.1038/nmeth0111-7b},
	number = {1},
	journal = {Nature Methods},
	author = {Klein, Teresa and Löschberger, Anna and Proppert, Sven and Wolter, Steve and van de Linde, Sebastian and Sauer, Markus},
	month = jan,
	year = {2011},
	note = {{PMID:} 21191367},
	keywords = {Animals, Cell Line, Histones, Humans, Image Interpretation, {Computer-Assisted}, Mice, Microscopy, Fluorescence, Recombinant Fusion Proteins, Stochastic Processes},
	pages = {7--9}
},

@article{steinhauer_dna_2009,
	title = {{DNA} origami as a nanoscopic ruler for super-resolution microscopy},
	volume = {48},
	issn = {1521-3773},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19830751},
	doi = {10.1002/anie.200903308},
	number = {47},
	journal = {Angewandte Chemie {(International} Ed. in English)},
	author = {Steinhauer, Christian and Jungmann, Ralf and Sobey, Thomas L and Simmel, Friedrich C and Tinnefeld, Philip},
	year = {2009},
	note = {{PMID:} 19830751},
	keywords = {Biotin, {DNA}, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, Microscopy, Fluorescence, Nanostructures},
	pages = {8870--8873}
},

@article{fenno_development_2011,
	title = {The development and application of optogenetics},
	volume = {34},
	issn = {1545-4126},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21692661},
	doi = {10.1146/annurev-neuro-061010-113817},
	abstract = {Genetically encoded, single-component optogenetic tools have made a significant impact on neuroscience, enabling specific modulation of selected cells within complex neural tissues. As the optogenetic toolbox contents grow and diversify, the opportunities for neuroscience continue to grow. In this review, we outline the development of currently available single-component optogenetic tools and summarize the application of various optogenetic tools in diverse model organisms.},
	journal = {Annual Review of Neuroscience},
	author = {Fenno, Lief and Yizhar, Ofer and Deisseroth, Karl},
	year = {2011},
	note = {{PMID:} 21692661},
	keywords = {Animals, Animals, Genetically Modified, Genetic Engineering, Humans, Light Signal Transduction, Models, Genetic, Nerve Net, Neural Inhibition, Neurons, Neurosciences, Opsins},
	pages = {389--412}
},

@article{friesen_neuronal_1978,
	title = {Neuronal control of swimming in the medicinal leech. {IV.} Identification of a network of oscillatory interneurones},
	volume = {75},
	issn = {0022-0949},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/702043},
	abstract = {Four oscillatory interneurones that appear to be the principal components of the central swim oscillator of Hirudo medicinalis have been identified on each side of the segmental ganglia of the ventral nerve cord. During 'swimming' episodes of an isolated nerve cord preparation each interneurone undergoes a polarization rhythm that is phase-locked with the impulse burst rhythm of the motor neurones known to drive the swimming movement. Passage of current into any of the interneurones can shift the phase of the swim rhythm. One of the interneurones projects its axon rearward to posterior ganglia and the other three project their axons frontward to anterior ganglia. The oscillatory interneurones are connected both intra- and interganglionically to form a topologically complex intersegmental network of concatenated ring circuits that possess the feature of recurrent cyclic inhibition. Theoretical analysis and electronic analogue models show that the network is inherently oscillatory and can produce both a cycle period and intra- and intersegmental phase relations of its elements that are appropriate for generating the body wave of the swimming movement.},
	journal = {The Journal of Experimental Biology},
	author = {Friesen, W O and Poon, M and Stent, G S},
	month = aug,
	year = {1978},
	note = {{PMID:} 702043},
	keywords = {Animals, Interneurons, Leeches, Locomotion, Swimming},
	pages = {25--43}
},

@book{hoffman_dead_2009,
	edition = {1},
	title = {The Dead Hand: The Untold Story of the Cold War Arms Race and its Dangerous Legacy},
	isbn = {0385524374},
	shorttitle = {The Dead Hand},
	publisher = {Doubleday},
	author = {Hoffman, David E.},
	month = sep,
	year = {2009}
},

@article{elkes_serotonin_1993,
	title = {Serotonin Modulates Foraging and Head Withdrawel Behaviors},
	volume = {12},
	url = {http://elegans.swmed.edu/wli/%5Bwbg12.5p66%5D/},
	abstract = {Foraging behavior consists of the rhythmic movements of the worm's nose, in an apparent attempt to explore the surrounding environment. We have found two environmental cues that modulate foraging behavior. Worms forage hyperactively both under starved conditions and after being touched with a platinum wire. To discover the mechanism of modulation we sought to identify the neurons and neurotransmitters involved in the control of foraging. {OLQ}, {IL1} ,and {RMD} neurons control foraging behavior. Laser ablation of any of these three classes of neurons results in an abnormally slow foraging rate, as well as an abnormal pattern of foraging movements. Laser operated animals bend their noses further dorsally and ventrally while foraging, which we call loopy foraging. This neural circuit formed of the mechanosensory neurons {IL1} and {OLQ}, and {RMD} motor neurons, also controls the head-withdrawal response. When a worm is touched on either the dorsal or ventral tip of its nose, it responds by an aversive head-withdrawal reflex (i.e., when touched ventrally, the head is pulled back dorsally). Laser ablation of the neurons {IL1} {,OLQ}, and {RMD} eliminate the head-withdrawal response, indicating that foraging and head-withdrawal are controlled by this single neural circuit. Serotonin modulates foraging and head-withdrawal behaviors. Three pieces of information supports this belief. first, cat-l mutants, which have low levels of endogenous serotonin, forage hyperactively. Secondly, wild type foraging can be restored to cat-l animals by adding either imipramine (a serotonin uptake inhibitor), serotonergic agonists, or S-hydroxytryptophan (a serotonin precursor). Finally, serotonergic agonists or imipramine cause wild type worms to forage slowly and to fail to exhibit the headwithdrawal response. These results suggest that serotonergic neurons modulate both foraging and the headwithdrawal behaviors. There are five classes of neurons that produce serotonin in C. elegans: {NSM}, {ADF}, {HSN}, {RIG}, and {RIH} {(G.} Garriga, personal communication). Laser ablation experiments should allow us to determine which specific serotonergic neurons modulate these behaviors. Genetic analysis of modulation. We decided to conduct a genetic screen for mutations that disrupt modulation by serotonin. We reasoned that mutants with defects in modulation should resemble cat-l animals. Therefore, we are screening for mutants that forage hyperactively. So far, 4 foraging abnormal (fab) mutants corresponding to four different genes were found in a preliminary screen and an additional 1650 haploid genomes have been screened systematically and the mutants from this latter screen are being characterized. The fab mutants fall into three categories. Presynaptic mutants The hyperforating mutants have been characterized pharmacologically using two drugs: imipramine, a serotonin re-uptake inhibitor, and {CGS12066} B,a serotonergic agonist. These drugs cause wild type worms to forage abnormally slowly and to forage in a loopy pattern. Presynaptic mutants are resistant to the imipramine, but sensitive to the agonist. cat-l, cat-4 ,fab-2 {(n2460)L} and fab-3 (n2462)m exhibit this presynaptic phenotype. Pootsynaptic mutants. Mutants that have defects in the postsynaptic neuron fail to respond to both serotonergic agonists and uptake inhibitors. So far, two postsynaptic mutants have been found, {3AA2} and {4E1.} The final class of mutants are sensitive to both drugs. This class may contain weak presynaptic or postsynaptic defects, or defects in other pathways that regulate foraging. Four have been isolated thus far: fab-1 {(ky2)I},fab-4 {(n2466)VR,2E1}, and {4H2.} We expect to screen between 10,000 - 15,000 haploid genomes in all. Hopefully, at that point we should have multiple alleles of these genes.},
	journal = {Worm Breeder's Gazette},
	author = {Elkes, D. A. and Kaplan, Joshua M.},
	year = {1993},
	keywords = {Caenorhabditis elegans, {IL1}, laser ablation, {OLQ}, {RMD}, Sniffing / Foraging},
	pages = {66},
	file = {Citation: Serotonin Modulates Foraging and Head Withdrawal Behaviors:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/ZUQE8SR2/paper.html:text/html;Serotonin Modulates Foraging and Head-Withdrawal Behaviors:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/V8DTTPRX/5Bwbg12.html:text/html}
},

@article{briggman_imaging_2006,
	title = {Imaging dedicated and multifunctional neural circuits generating distinct behaviors},
	volume = {26},
	issn = {1529-2401},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17050731},
	doi = {10.1523/JNEUROSCI.3265-06.2006},
	abstract = {Central pattern generators {(CPGs)} control both swimming and crawling in the medicinal leech. To investigate whether the neurons comprising these two {CPGs} are dedicated or multifunctional, we used voltage-sensitive dye imaging to record from approximately 80\% of the approximately 400 neurons in a segmental ganglion. By eliciting swimming and crawling in the same preparation, we were able to identify neurons that participated in either of the two rhythms, or both. More than twice as many cells oscillated in-phase with crawling (188) compared with swimming (90). Surprisingly, 84 of the cells (93\%) that oscillated with swimming also oscillated with crawling. We then characterized two previously unidentified interneurons, cells 255 and 257, that had interesting activity patterns based on the imaging results. Cell 255 proved to be a multifunctional interneuron that oscillates with and can perturb both rhythms, whereas cell 257 is an interneuron dedicated to crawling. These results show that the swimming and crawling networks are driven by both multifunctional and dedicated circuitry.},
	number = {42},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Briggman, Kevin L and Kristan, William B, Jr},
	month = oct,
	year = {2006},
	note = {{PMID:} 17050731},
	keywords = {Animals, Fluorescence Resonance Energy Transfer, Hirudo medicinalis, Interneurons, Motor Activity, Nerve Net, Swimming},
	pages = {10925--10933}
},

@article{chatzigeorgiou_specific_2010,
	title = {Specific roles for {DEG/ENaC} and {TRP} channels in touch and thermosensation in C. elegans nociceptors},
	volume = {13},
	issn = {1097-6256},
	url = {http://dx.doi.org.ezp-prod1.hul.harvard.edu/10.1038/nn.2581},
	doi = {10.1038/nn.2581},
	number = {7},
	journal = {Nat Neurosci},
	author = {Chatzigeorgiou, Marios and Yoo, Sungjae and Watson, Joseph D and Lee, {Wei-Hsiang} and Spencer, W Clay and Kindt, Katie S and Hwang, Sun Wook and Miller {III}, David M and Treinin, Millet and Driscoll, Monica and Schafer, William R},
	month = jul,
	year = {2010},
	pages = {861--868}
},

@article{de_bono_natural_1998,
	title = {Natural variation in a neuropeptide Y receptor homolog modifies social behavior and food response in C. elegans},
	volume = {94},
	issn = {0092-8674},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9741632},
	abstract = {Natural isolates of C. elegans exhibit either solitary or social feeding behavior. Solitary foragers move slowly on a bacterial lawn and disperse across it, while social foragers move rapidly on bacteria and aggregate together. A loss-of-function mutation in the npr-1 gene, which encodes a predicted G protein-coupled receptor similar to neuropeptide Y receptors, causes a solitary strain to take on social behavior. Two isoforms of {NPR-1} that differ at a single residue occur in the wild. One isoform, {NPR-1} {215F}, is found exclusively in social strains, while the other isoform, {NPR-1} {215V}, is found exclusively in solitary strains. An {NPR-1} {215V} transgene can induce solitary feeding behavior in a wild social strain. Thus, isoforms of a putative neuropeptide receptor generate natural variation in C. elegans feeding behavior.},
	number = {5},
	journal = {Cell},
	author = {de Bono, M and Bargmann, C I},
	month = sep,
	year = {1998},
	note = {{PMID:} 9741632},
	keywords = {Amino Acid Sequence, Amino Acid Substitution, Animals, Caenorhabditis elegans, Feeding Behavior, Genetic Variation, {GTP-Binding} Proteins, Helminth Proteins, Models, Molecular, Molecular Sequence Data, Mutation, Receptors, Neuropeptide Y, Sequence Homology, Amino Acid, Social Behavior},
	pages = {679--689},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/MMZ226XU/entrez.html:text/html;sdarticle-5.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/XVDE7UG4/sdarticle-5.pdf:application/pdf}
},

@article{hwang_nociceptive_2007,
	title = {Nociceptive Neurons Protect Drosophila Larvae from Parasitoid Wasps},
	volume = {17},
	issn = {09609822},
	url = {http://www.cell.com/current-biology/retrieve/pii/S0960982207022683},
	doi = {10.1016/j.cub.2007.11.029},
	number = {24},
	journal = {Current Biology},
	author = {Hwang, Richard Y. and Zhong, Lixian and Xu, Yifan and Johnson, Trevor and Zhang, Feng and Deisseroth, Karl and Tracey, W. Daniel},
	month = dec,
	year = {2007},
	pages = {2105--2116}
},

@misc{hires_gcamp5_2011,
	title = {{GCaMP5} is out},
	url = {http://brainwindows.wordpress.com/2011/11/15/gcamp5-is-out/},
	journal = {Brain Windows: New tools for peering into the brain},
	author = {Hires, Andrew},
	month = nov,
	year = {2011}
},

@book{kamkin_mechanosensitive_2007,
	edition = {1},
	title = {Mechanosensitive Ion Channels {(Mechanosensitivity} in Cells and Tissues)},
	isbn = {{140206425X}},
	publisher = {Springer},
	author = {Kamkin, Andre and Kiseleva, Irina},
	month = dec,
	year = {2007},
	file = {Mechanotransduction in the Nematode Caenorhabditis elegans:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/7UHJKDRV/bv.html:text/html}
},

@article{stirman_real-time_2011,
	title = {Real-time multimodal optical control of neurons and muscles in freely behaving Caenorhabditis elegans},
	volume = {8},
	issn = {1548-7105},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21240278},
	doi = {10.1038/nmeth.1555},
	abstract = {The ability to optically excite or silence specific cells using optogenetics has become a powerful tool to interrogate the nervous system. Optogenetic experiments in small organisms have mostly been performed using whole-field illumination and genetic targeting, but these strategies do not always provide adequate cellular specificity. Targeted illumination can be a valuable alternative but it has only been shown in motionless animals without the ability to observe behavior output. We present a real-time, multimodal illumination technology that allows both tracking and recording the behavior of freely moving C. elegans while stimulating specific cells that express channelrhodopsin-2 or {MAC.} We used this system to optically manipulate nodes in the C. elegans touch circuit and study the roles of sensory and command neurons and the ultimate behavioral output. This technology enhances our ability to control, alter, observe and investigate how neurons, muscles and circuits ultimately produce behavior in animals using optogenetics.},
	number = {2},
	journal = {Nature methods},
	author = {Stirman, Jeffrey N and Crane, Matthew M and Husson, Steven J and Wabnig, Sebastian and Schultheis, Christian and Gottschalk, Alexander and Lu, Hang},
	month = feb,
	year = {2011},
	note = {{PMID:} 21240278},
	keywords = {Animals, Behavior, Animal, Caenorhabditis elegans, Muscles, Neurons, Optical Processes, Photobiology, Time Factors, Visual Perception},
	pages = {153--158}
},

@article{cao_light-sensitive_2011,
	title = {{Light-Sensitive} Coupling of Rhodopsin and Melanopsin to {Gi/O} and Gq Signal Transduction in Caenorhabditis Elegans},
	issn = {0892-6638, 1530-6860},
	url = {http://www.fasebj.org/content/early/2011/11/03/fj.11-197798},
	doi = {10.1096/fj.11-197798},
	abstract = {Activation of G-protein-coupled receptors {(GPCRs)} initiates signal transduction cascades that affect many physiological responses. The worm Caenorhabditis elegans expresses {\textgreater}1000 of these receptors along with their cognate heterotrimeric G proteins. Here, we report properties of 9-cis-retinal regenerated bovine opsin {[(b)isoRho]} and human melanopsin {[(h)Mo]}, two light-activated, heterologously expressed {GPCRs} in the nervous system of C. elegans with various genetically engineered alterations. Profound transient photoactivation of Gi/o signaling by {(b)isoRho} led to a sudden and transient loss of worm motility dependent on cyclic adenosine monophosphate, whereas transient photoactivation of Gq signaling by {(h)Mo} enhanced worm locomotion dependent on phospholipase Cβ. These transgenic C. elegans models provide a unique way to study the consequences of Gi/o and Gq signaling in vivo with temporal and spatial precision and, by analogy, their relationship to human neuromotor {function.—Cao}, P., Sun, W., Kramp, K., Zheng, M., Salom, D., Jastrzebska, B., Jin, H., Palczewski, K., Feng, Z. Light-sensitive coupling of rhodopsin and melanopsin to Gi/o and Gq signal transduction in Caenorhabditis elegans.},
	journal = {The {FASEB} Journal},
	author = {Cao, Pengxiu and Sun, Wenyu and Kramp, Kristopher and Zheng, Maohua and Salom, David and Jastrzebska, Beata and Jin, Hui and Palczewski, Krzysztof and Feng, Zhaoyang},
	month = nov,
	year = {2011},
	keywords = {G-protein signaling, optogenetics}
},

@incollection{hart_behavior_2006,
	edition = {The C. elegans Research Community},
	title = {Behavior},
	isbn = {1551-507},
	url = {http://www.wormbook.org/chapters/www_behavior/behavior.html},
	number = {82},
	booktitle = {{WormBook}},
	publisher = {{WormBook}},
	author = {Hart, A. C.},
	editor = {The C. elegans Research Community},
	month = jul,
	year = {2006},
	keywords = {behavior, hart, methods, Print Me!}
},

@article{edwards_novel_2008,
	title = {A Novel Molecular Solution for Ultraviolet Light Detection in Caenorhabditis elegans},
	volume = {6},
	url = {http://dx.doi.org/10.1371/journal.pbio.0060198},
	doi = {10.1371/journal.pbio.0060198},
	abstract = {An ultraviolet light receptor drives a robust locomotory response that restores normal levels of movement to paralyzed neuronal signaling mutants. This may {helpC.} elegans avoid lethal doses of sunlight.},
	number = {8},
	journal = {{PLoS} Biol},
	author = {Edwards, Stacey L and Charlie, Nicole K and Milfort, Marie C and Brown, Brandon S and Gravlin, Christen N and Knecht, Jamie E and Miller, Kenneth G},
	year = {2008},
	pages = {e198}
},

@article{briggman_optical_2005,
	title = {Optical imaging of neuronal populations during decision-making},
	volume = {307},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15705844},
	doi = {10.1126/science.1103736},
	abstract = {We investigated decision-making in the leech nervous system by stimulating identical sensory inputs that sometimes elicit crawling and other times swimming. Neuronal populations were monitored with voltage-sensitive dyes after each stimulus. By quantifying the discrimination time of each neuron, we found single neurons that discriminate before the two behaviors are evident. We used principal component analysis and linear discriminant analysis to find populations of neurons that discriminated earlier than any single neuron. The analysis highlighted the neuron cell 208. Hyperpolarizing cell 208 during a stimulus biases the leech to swim; depolarizing it biases the leech to crawl or to delay swimming.},
	number = {5711},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Briggman, K L and Abarbanel, H D I and Kristan, W B, Jr},
	month = feb,
	year = {2005},
	note = {{PMID:} 15705844},
	keywords = {Analysis of Variance, Animals, Central Nervous System, Coloring Agents, Decision Making, Discriminant Analysis, Electric Stimulation, Fluorescence Resonance Energy Transfer, Ganglia, Invertebrate, Interneurons, Leeches, Locomotion, Membrane Potentials, Microelectrodes, Motor Neurons, Neurons, Principal Component Analysis, Swimming},
	pages = {896--901}
},

@article{ben_arous_automated_2010,
	title = {Automated imaging of neuronal activity in freely behaving Caenorhabditis elegans},
	volume = {187},
	issn = {0165-0270},
	url = {http://www.sciencedirect.com/science/article/B6T04-4Y6S7GN-3/2/f80f32c2892d34b07f1db80b870e4b53},
	doi = {10.1016/j.jneumeth.2010.01.011},
	abstract = {In order to understand how neuronal circuits control locomotory patterns it is necessary to record neuronal activity of freely behaving animals. Here, using a new automated system for simultaneous recording of behavior and neuronal activity in freely moving Caenorhabditis elegans on standard agar plates, we show that spontaneous reversals from forward to backward locomotion reflect precisely the activity of the {AVA} command interneurons. We also witness spontaneous activity transients in the {PLM} sensory neurons during free behavior of the worm in standard conditions. We show that these activity transients are coupled to short spontaneous forward accelerations of the worm.},
	number = {2},
	journal = {Journal of Neuroscience Methods},
	author = {Ben Arous, Juliette and Tanizawa, Yoshinori and Rabinowitch, Ithai and Chatenay, Didier and Schafer, William R.},
	month = mar,
	year = {2010},
	keywords = {Behavior, C. elegans, Calcium imaging, Mechanosensory neurons, Tracking system},
	pages = {229--234},
	file = {ScienceDirect Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/694GX8VD/Ben Arous et al. - 2010 - Automated imaging of neuronal activity in freely b.pdf:application/pdf;ScienceDirect Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TKE66FJH/science.html:text/html}
},

@article{lohse_optical_2008,
	title = {Optical techniques to analyze real-time activation and signaling of G-protein-coupled receptors},
	volume = {29},
	issn = {0165-6147},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18262662},
	doi = {10.1016/j.tips.2007.12.002},
	abstract = {The activation of G-protein-coupled receptors {(GPCRs)} is traditionally measured either by monitoring downstream physiological events or by membrane-based biochemical assays. Neither of these approaches permits detailed kinetic or spatial analysis of receptor activation and signaling. Recently, several optical techniques have been developed to monitor receptor activation either by using purified reconstituted {GPCRs} or by observing {GPCRs}, G proteins and second messengers in intact cells. These techniques are providing, literally, new views on both the mechanistic basis of the signaling process and the kinetic and spatial properties of {GPCR-mediated} signals. They suggest that agonists can activate {GPCRs} within milliseconds, that different compounds can induce distinct active conformations of {GPCRs}, that G-protein activation is the rate-limiting step in {GPCR} signaling, and that cellular signals can be temporally and spatially confined. They are also raising controversial issues, such as whether or not receptors and G proteins are pre-coupled and whether G proteins dissociate during activation.},
	number = {3},
	journal = {Trends in Pharmacological Sciences},
	author = {Lohse, Martin J and Nikolaev, Viacheslav O and Hein, Peter and Hoffmann, Carsten and Vilardaga, {Jean-Pierre} and Bünemann, Moritz},
	month = mar,
	year = {2008},
	note = {{PMID:} 18262662},
	keywords = {Animals, Biosensing Techniques, Cells, Cultured, Fluorescence Resonance Energy Transfer, Luminescent Proteins, Microscopy, Fluorescence, Receptors, {G-Protein-Coupled}, Signal Transduction},
	pages = {159--165}
},

@article{lin_self-assembled_2007,
	title = {Self-assembled combinatorial encoding nanoarrays for multiplexed biosensing},
	volume = {7},
	issn = {1530-6984},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17298017},
	doi = {10.1021/nl062998n},
	abstract = {Multiplexed and sensitive detection of nucleic acids, proteins, or other molecules from a single solution and a small amount of sample is of great demand in biomarker profiling and disease diagnostics. Here we describe a new concept using combinatorial self-assembly of {DNA} nanotiles into micrometer-sized two-dimensional arrays that carry nucleic acid probes and barcoded fluorescent dyes to achieve multiplexed detection. We demonstrated the specificity and sensitivity of the arrays by detecting multiple {DNA} sequences and aptamer binding molecules. This {DNA} tile-array-based sensor platform can be constructed through {DNA} self-assembly. The attachment of different molecular probes can be achieved by simple {DNA} hybridization so bioconjugation is not necessary for the labeling. Accurate control of the interprobe distances and solution-based binding reactions ensures fast target binding kinetics.},
	number = {2},
	journal = {Nano Letters},
	author = {Lin, Chenxiang and Liu, Yan and Yan, Hao},
	month = feb,
	year = {2007},
	note = {{PMID:} 17298017},
	keywords = {Animals, Biosensing Techniques, Cattle, {DNA}, Equipment Design, Microarray Analysis, Nanotechnology, Oligonucleotide Array Sequence Analysis},
	pages = {507--512}
},

@article{schafer_neurophysiological_2006,
	title = {Neurophysiological methods in C. elegans: an introduction},
	issn = {15518507},
	shorttitle = {Neurophysiological methods in C. elegans},
	url = {http://www.wormbook.org/chapters/www_intromethodsneurophys/intromethodsneurophys.html},
	doi = {10.1895/wormbook.1.111.1},
	journal = {{WormBook}},
	author = {Schafer, William},
	year = {2006},
	file = {Neurophysiological methods in C. elegans: an introduction:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/MMEFBIJN/intromethodsneurophys.html:text/html}
},

@article{tian_imaging_2009,
	title = {Imaging neural activity in worms, flies and mice with improved {GCaMP} calcium indicators},
	volume = {6},
	issn = {1548-7105},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19898485},
	doi = {10.1038/nmeth.1398},
	abstract = {Genetically encoded calcium indicators {(GECIs)} can be used to image activity in defined neuronal populations. However, current {GECIs} produce inferior signals compared to synthetic indicators and recording electrodes, precluding detection of low firing rates. We developed a single-wavelength {GCaMP2-based} {GECI} {(GCaMP3)}, with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). We detected {GCaMP3} fluorescence changes triggered by single action potentials in pyramidal cell dendrites, with signal-to-noise ratio and photostability substantially better than those of {GCaMP2}, {D3cpVenus} and {TN-XXL.} In Caenorhabditis elegans chemosensory neurons and the Drosophila melanogaster antennal lobe, sensory stimulation-evoked fluorescence responses were significantly enhanced with {GCaMP3} (4-6-fold). In somatosensory and motor cortical neurons in the intact mouse, {GCaMP3} detected calcium transients with amplitudes linearly dependent on action potential number. Long-term imaging in the motor cortex of behaving mice revealed large fluorescence changes in imaged neurons over months.},
	number = {12},
	journal = {Nature Methods},
	author = {Tian, Lin and Hires, S Andrew and Mao, Tianyi and Huber, Daniel and Chiappe, M Eugenia and Chalasani, Sreekanth H and Petreanu, Leopoldo and Akerboom, Jasper and {McKinney}, Sean A and Schreiter, Eric R and Bargmann, Cornelia I and Jayaraman, Vivek and Svoboda, Karel and Looger, Loren L},
	month = dec,
	year = {2009},
	note = {{PMID:} 19898485},
	keywords = {Animals, Brain, Caenorhabditis elegans, Calcium, Cell Line, Drosophila melanogaster, Fluorescence Resonance Energy Transfer, Humans, Mice, Neurons},
	pages = {875--881}
},

@article{vogelsang_make_2010,
	title = {Make them Blink: Probes for {Super‐Resolution} Microscopy},
	volume = {11},
	issn = {1439-7641},
	shorttitle = {Make them Blink},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/cphc.201000189/abstract},
	doi = {10.1002/cphc.201000189},
	abstract = {In recent years, a number of approaches have emerged that enable far-field fluorescence imaging beyond the diffraction limit of light, namely super-resolution microscopy. These techniques are beginning to profoundly alter our abilities to look at biological structures and dynamics and are bound to spread into conventional biological laboratories. Nowadays these approaches can be divided into two categories, one based on targeted switching and readout, and the other based on stochastic switching and readout of the fluorescence information. The main prerequisite for a successful implementation of both categories is the ability to prepare the fluorescent emitters in two distinct states, a bright and a dark state. Herein, we provide an overview of recent developments in super-resolution microscopy techniques and outline the special requirements for the fluorescent probes used. In combination with the advances in understanding the photophysics and photochemistry of single fluorophores, we demonstrate how essentially any single-molecule compatible fluorophore can be used for super-resolution microscopy. We present examples for super-resolution microscopy with standard organic fluorophores, discuss factors that influence resolution and present approaches for calibration samples for super-resolution microscopes including {AFM-based} single-molecule assembly and {DNA} origami.},
	number = {12},
	journal = {{ChemPhysChem}},
	author = {Vogelsang, Jan and Steinhauer, Christian and Forthmann, Carsten and Stein, Ingo H and {Person‐Skegro}, Britta and Cordes, Thorben and Tinnefeld, Philip},
	month = aug,
	year = {2010},
	keywords = {electron transfer, molecular switches, photophysics, single‐molecule studies, super‐resolution microscopy},
	pages = {2475--2490},
	file = {Wiley Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TJGP5AP2/Vogelsang et al. - 2010 - Make them Blink Probes for Super‐Resolution Micro.pdf:application/pdf}
},

@book{rhodes_making_1995,
	title = {The Making of the Atomic Bomb},
	isbn = {0684813785},
	publisher = {Simon \& Schuster},
	author = {Rhodes, Richard},
	month = aug,
	year = {1995}
},

@article{arous_automated_2010,
	title = {Automated imaging of neuronal activity in freely behaving Caenorhabditis elegans},
	issn = {{1872-678X}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20096306},
	doi = {10.1016/j.jneumeth.2010.01.011},
	abstract = {In order to understand how neuronal circuits control locomotory patterns it is necessary to record neuronal activity of freely behaving animals. Here, using a new automated system for simultaneous recording of behavior and neuronal activity in freely moving Caenorhabditis elegans on standard agar plates, we show that spontaneous reversals from forward to backward locomotion reflect precisely the activity of the {AVA} command interneurons. We also witness spontaneous activity transients in the {PLM} sensory neurons during free behavior of the worm in standard conditions. We show that these activity transients are coupled to short spontaneous forward accelerations of the worm.},
	journal = {Journal of Neuroscience Methods},
	author = {Arous, Juliette Ben and Tanizawa, Yoshinori and Rabinowitch, Ithai and Chatenay, Didier and Schafer, William R},
	month = jan,
	year = {2010},
	note = {{PMID:} 20096306}
},

@article{clark_temporal_2007,
	title = {Temporal Activity Patterns in Thermosensory Neurons of Freely Moving Caenorhabditis elegans Encode Spatial Thermal Gradients},
	volume = {27},
	url = {http://www.jneurosci.org/cgi/content/abstract/27/23/6083},
	doi = {10.1523/JNEUROSCI.1032-07.2007},
	abstract = {Our understanding of the operation of neurons and neuronal circuits has come primarily from probing their activity in dissected, anesthetized, or restrained animals. However, the behaviorally relevant operation of neurons and neuronal circuits occurs within intact animals as they freely perform behavioral tasks. The small size and transparency of the nematode Caenorhabditis elegans make it an ideal system for noninvasive, optical measurements of neuronal activity. Here, we use a high signal-to-noise version of cameleon, a fluorescent calcium-binding protein, to quantify the activity of the {AFD} thermosensory neuron of individual worms freely navigating spatial thermal gradients. We find that {AFD} activity is directly coupled to the worm's exploratory movements in spatial thermal gradients. We show that the worm is able, in principle, to evaluate and guide its own thermotactic behaviors with respect to ambient spatial thermal gradients by monitoring the activity of this single thermosensory neuron.},
	number = {23},
	journal = {J. Neurosci.},
	author = {Clark, Damon A. and Gabel, Christopher V. and Gabel, Harrison and Samuel, Aravinthan D. T.},
	month = jun,
	year = {2007},
	keywords = {{PQE}  - definite citation},
	pages = {6083--6090},
	file = {6083.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/3G7B5KJ5/6083.pdf:application/pdf;HighWire Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TPTKU3CJ/6083.html:text/html}
},

@article{miyawaki_innovations_2005,
	title = {Innovations in the imaging of brain functions using fluorescent proteins},
	volume = {48},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16242400},
	doi = {10.1016/j.neuron.2005.10.003},
	abstract = {Fluorescence imaging has enabled us to decipher spatiotemporal information coded in complex tissues. Genetically encoded probes that enable fluorescence imaging of excitable cell activity have been constructed by fusing fluorescent proteins to functional proteins that are involved in physiological signaling. The probes are introduced into an intact organism and targeted to specific tissues, cell types, or subcellular compartments, thereby allowing specific signals to be extracted more efficiently than was previously possible. In this primer, I will describe how this approach has met neuroscientists' demands and desires.},
	number = {2},
	journal = {Neuron},
	author = {Miyawaki, Atsushi},
	month = oct,
	year = {2005},
	note = {{PMID:} 16242400},
	keywords = {Animals, Brain, Brain Mapping, Diagnostic Imaging, Humans, Luminescent Proteins, Neurons, Synapses},
	pages = {189--199},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/MJD7I5QZ/16242400.html:text/html}
},

@article{park_enhanced_2008,
	title = {Enhanced Caenorhabditis elegans Locomotion in a Structured Microfluidic Environment},
	volume = {3},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2430527},
	doi = {10.1371/journal.pone.0002550},
	abstract = {Background
Behavioral studies of Caenorhabditis elegans traditionally are done on the smooth surface of agar plates, but the natural habitat of C. elegans and other nematodes is the soil, a complex and structured environment. In order to investigate how worms move in such environments, we have developed a technique to study C. elegans locomotion in microstructures fabricated from agar.
{Methodology/Principal} Findings
When placed in open, liquid-filled, microfluidic chambers containing a square array of posts, we discovered that worms are capable of a novel mode of locomotion, which combines the fast gait of swimming with the more efficient movements of crawling. When the wavelength of the worms matched the periodicity of the post array, the microstructure directed the swimming and increased the speed of C. elegans ten-fold. We found that mutants defective in mechanosensation (mec-4, mec-10) or mutants with abnormal waveforms (unc-29) did not perform this enhanced locomotion and moved much more slowly than wild-type worms in the microstructure.
{Conclusion/Significance}
These results show that the microstructure can be used as a behavioral screen for mechanosensory and uncoordinated mutants. It is likely that worms use mechanosensation in the movement and navigation through heterogeneous environments.},
	number = {6},
	journal = {{PLoS} {ONE}},
	author = {Park, Sungsu and Hwang, Hyejin and Nam, {Seong-Won} and Martinez, Fernando and Austin, Robert H. and Ryu, William S.},
	year = {2008},
	note = {{PMC2430527}},
	keywords = {Caenorhabditis elegans, Locomotion, pdms, Touch},
	pages = {e2550}
},

@phdthesis{stavens_learning_2011,
	type = {{Ph.D.} Dissertation},
	title = {Learning to drive perception for autonomous cars.},
	school = {Stanford University},
	author = {Stavens, David Michael},
	year = {2011}
},

@article{cheng_role_2010,
	title = {The role of the {TRP} channel {NompC} in Drosophila larval and adult locomotion},
	volume = {67},
	issn = {1097-4199},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20696376},
	doi = {10.1016/j.neuron.2010.07.004},
	abstract = {The generation of coordinated body movements relies on sensory feedback from mechanosensitive proprioceptors. We have found that the proper function of {NompC}, a putative mechanosensitive {TRP} channel, is not only required for fly locomotion, but also crucial for larval crawling. Calcium imaging revealed that {NompC} is required for the activation of two subtypes of sensory neurons during peristaltic muscle contractions. Having isolated a full-length {nompC} {cDNA} with a protein coding sequence larger than previously predicted, we demonstrate its function by rescuing locomotion defects in {nompC} mutants, and further show that antibodies against the extended C terminus recognize {NompC} in chordotonal ciliary tips. Moreover, we show that the ankyrin repeats in {NompC} are required for proper localization and function of {NompC} in vivo and are required for association of {NompC} with microtubules. Taken together, our findings suggest that {NompC} mediates proprioception in locomotion and support its role as a mechanosensitive channel.},
	number = {3},
	journal = {Neuron},
	author = {Cheng, Li E and Song, Wei and Looger, Loren L and Jan, Lily Yeh and Jan, Yuh Nung},
	month = aug,
	year = {2010},
	note = {{PMID:} 20696376},
	keywords = {Age Factors, Amino Acid Sequence, Animals, Animals, Genetically Modified, Drosophila, Drosophila Proteins, Ion Channels, Larva, Locomotion, Molecular Sequence Data, Predictive Value of Tests, {TRPC} Cation Channels},
	pages = {373--380}
},

@article{zhang_pathogenic_2005,
	title = {Pathogenic bacteria induce aversive olfactory learning in Caenorhabditis elegans},
	volume = {438},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16281027},
	doi = {10.1038/nature04216},
	abstract = {Food can be hazardous, either through toxicity or through bacterial infections that follow the ingestion of a tainted food source. Because learning about food quality enhances survival, one of the most robust forms of olfactory learning is conditioned avoidance of tastes associated with visceral malaise. The nematode Caenorhabditis elegans feeds on bacteria but is susceptible to infection by pathogenic bacteria in its natural environment. Here we show that C. elegans modifies its olfactory preferences after exposure to pathogenic bacteria, avoiding odours from the pathogen and increasing its attraction to odours from familiar nonpathogenic bacteria. Particular bacteria elicit specific changes in olfactory preferences that are suggestive of associative learning. Exposure to pathogenic bacteria increases serotonin in {ADF} chemosensory neurons by transcriptional and post-transcriptional mechanisms. Serotonin functions through {MOD-1}, a serotonin-gated chloride channel expressed in sensory interneurons, to promote aversive learning. An increase in serotonin may represent the negative reinforcing stimulus in pathogenic infection.},
	number = {7065},
	journal = {Nature},
	author = {Zhang, Yun and Lu, Hang and Bargmann, Cornelia I},
	month = nov,
	year = {2005},
	note = {{PMID:} 16281027},
	keywords = {Animals, Bacteria, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Chloride Channels, Diet, Food Preferences, Interneurons, Learning, Maze Learning, Odors, Serotonin, Smell},
	pages = {179--184}
},

@article{niebur_theory_1991,
	title = {Theory of the locomotion of nematodes: Dynamics of undulatory progression on a surface},
	volume = {60},
	issn = {0006-3495},
	shorttitle = {Theory of the locomotion of nematodes},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19431807},
	abstract = {We develop a model of the undulatory locomotion of nematodes, in particular that of Caenorhabditis elegans, based on mechanics. The model takes into account the most important forces acting on a moving worm and allows the computer simulation of a creeping nematode. These forces are produced by the interior pressure in the liquid-filled body cavity, the elasticity of the cuticle, the excitation of certain sets of muscles and the friction between the body and its {support.We} propose that muscle excitation patterns can be generated by stretch receptor control. By solving numerically the equations of motion of the model of the nematode, we demonstrate that these muscle excitation patterns are suitable for the propulsion of the animal.},
	number = {5},
	journal = {Biophysical Journal},
	author = {Niebur, E and Erdös, P},
	month = nov,
	year = {1991},
	note = {{PMID:} 19431807},
	pages = {1132--1146}
},

@article{wicks_dynamic_1996,
	title = {A dynamic network simulation of the nematode tap withdrawal circuit: predictions concerning synaptic function using behavioral criteria},
	volume = {16},
	issn = {0270-6474},
	shorttitle = {A dynamic network simulation of the nematode tap withdrawal circuit},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8656295},
	abstract = {The nematode tap withdrawal reflex demonstrates several forms of behavioral plasticity. Although the neural connectivity that supports this behavior is identified {(Integration} of mechanosensory stimuli in Caenorhabditis elegans, Wicks and Rankin, 1995, J Neurosci 15:2434-2444), the neurotransmitter phenotypes, and hence whether the synapses in the circuit are excitatory or inhibitory, remain uncharacterized. Here we use a novel strategy to predict the polarity configuration, i.e., the array of excitatory and inhibitory connections, of the nematode tap withdrawal circuit using an anatomically and physiologically justifiable dynamic network simulation of that circuit. The output of the modeled circuit was optimized to the behavior of animals, which possessed circuits altered by surgical ablation by exhaustively enumerating an array of synaptic signs that constituted the modeled circuit. All possible polarity configurations were then compared, and a statistical analysis was used to determine whether, for a given synaptic class, a particular polarity was associated with a good fit to behavioral data. The results from four related experiments were used to predict the polarities of seven of the nine cell classes of the tap withdrawal circuit. In addition, the model was used to assess possible roles for two novel mechanosensory integration neurons: {DVA} and {PVD.}},
	number = {12},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Wicks, S R and Roehrig, C J and Rankin, C H},
	month = jun,
	year = {1996},
	note = {{PMID:} 8656295},
	keywords = {Animals, Behavior, Animal, Caenorhabditis elegans, Mechanoreceptors, Models, Neurological, Synapses},
	pages = {4017--4031}
},

@article{nicewarner-pena_submicrometer_2001,
	title = {Submicrometer metallic barcodes},
	volume = {294},
	issn = {0036-8075},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11588257},
	doi = {10.1126/science.294.5540.137},
	abstract = {We synthesized multimetal microrods intrinsically encoded with submicrometer stripes. Complex striping patterns are readily prepared by sequential electrochemical deposition of metal ions into templates with uniformly sized pores. The differential reflectivity of adjacent stripes enables identification of the striping patterns by conventional light microscopy. This readout mechanism does not interfere with the use of fluorescence for detection of analytes bound to particles by affinity capture, as demonstrated by {DNA} and protein bioassays.},
	number = {5540},
	journal = {Science {(New} York, {N.Y.)}},
	author = {{Nicewarner-Pena}, S R and Freeman, R G and Reiss, B D and He, L and Pena, D J and Walton, I D and Cromer, R and Keating, C D and Natan, M J},
	month = oct,
	year = {2001},
	note = {{PMID:} 11588257},
	keywords = {Animals, Biochemistry, Chemistry Techniques, Analytical, Electrochemistry, Fluorescence, Fluorescent Antibody Technique, Humans, Immunoassay, Immunoglobulin G, Metals, Microscopy, Miniaturization, Nucleic Acid Hybridization, Oligonucleotide Probes, Optics and Photonics, Rabbits, Templates, Genetic},
	pages = {137--141}
},

@article{chiu_flying_2008,
	title = {Flying in silence: Echolocating bats cease vocalizing to avoid sonar jamming},
	volume = {105},
	issn = {1091-6490},
	shorttitle = {Flying in silence},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18725624},
	doi = {10.1073/pnas.0804408105},
	abstract = {Although it has been recognized that echolocating bats may experience jamming from the signals of conspecifics, research on this problem has focused exclusively on time-frequency adjustments in the emitted signals to minimize interference. Here, we report a surprising new strategy used by bats to avoid interference, namely silence. In a quantitative study of flight and vocal behavior of the big brown bat {(Eptesicus} fuscus), we discovered that the bat spends considerable time in silence when flying with conspecifics. Silent behavior, defined here as at least one bat in a pair ceasing vocalization for more than 0.2 s (200 ms), occurred as much as 76\% of the time (mean of 40\% across 7 pairs) when their separation was shorter than 1 m, but only 0.08\% when a single bat flew alone. Spatial separation, heading direction, and similarity in call design of paired bats were related to the prevalence of this silent behavior. Our data suggest that the bat uses silence as a strategy to avoid interference from sonar vocalizations of its neighbor, while listening to conspecific-generated acoustic signals to guide orientation. Based on previous neurophysiological studies of the bat's auditory midbrain, we hypothesize that environmental sounds (including vocalizations produced by other bats) and active echolocation evoke neural activity in different populations of neurons. Our findings offer compelling evidence that the echolocating bat switches between active and passive sensing to cope with a complex acoustic environment, and these results hold broad implications for research on navigation and communication throughout the animal kingdom.},
	number = {35},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Chiu, Chen and Xian, Wei and Moss, Cynthia F},
	month = sep,
	year = {2008},
	note = {{PMID:} 18725624},
	keywords = {Animals, Chiroptera, Discriminant Analysis, Echolocation, Flight, Animal, Predatory Behavior, Sound, Time Factors, Vocalization, Animal},
	pages = {13116--13121},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TN5ARXC9/18725624.html:text/html}
},

@article{sharonov_wide-field_2006,
	title = {Wide-field subdiffraction imaging by accumulated binding of diffusing probes},
	volume = {103},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17142314},
	doi = {10.1073/pnas.0609643104},
	abstract = {A method is introduced for subdiffraction imaging that accumulates points by collisional flux. It is based on targeting the surface of objects by fluorescent probes diffusing in the solution. Because the flux of probes at the object is essentially constant over long time periods, the examination of an almost unlimited number of individual probe molecules becomes possible. Each probe that hits the object and that becomes immobilized is located with high precision by replacing its point-spread function by a point at its centroid. Images of lipid bilayers, contours of these bilayers, and large unilamellar vesicles are shown. A spatial resolution of approximately 25 nm is readily achieved. The ability of the method to effect rapid nanoscale imaging and spatial resolution below Rayleigh criterion and without the necessity for labeling with fluorescent probes is proven.},
	number = {50},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Sharonov, Alexey and Hochstrasser, Robin M},
	month = dec,
	year = {2006},
	note = {{PMID:} 17142314},
	keywords = {Diffusion, Fluorescent Dyes, Image Processing, {Computer-Assisted}, Software},
	pages = {18911--18916}
},

@article{al-rawi_improved_2007,
	title = {An improved matched filter for blood vessel detection of digital retinal images},
	volume = {37},
	issn = {0010-4825},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16697363},
	doi = {10.1016/j.compbiomed.2006.03.003},
	abstract = {The matched filter has been widely used in the detection of blood vessels of the human retina digital image. In this paper, the matched filter response to the detection of blood vessels is increased by proposing better filter parameters. These filter parameters are found by using an optimization procedure on 20 retina images of the {DRIVE} database. Comparisons with other approaches show that the matched filter that uses the newly found parameters outperforms the matched filter that uses the classical filter parameters as well as some vessel detection techniques. A technique is also discussed to find the best threshold value for the continuous matched filter output image and hence the best segmented vessel image.},
	number = {2},
	journal = {Computers in Biology and Medicine},
	author = {{Al-Rawi}, Mohammed and Qutaishat, Munib and Arrar, Mohammed},
	month = feb,
	year = {2007},
	note = {{PMID:} 16697363},
	keywords = {Database Management Systems, Humans, Retinal Vessels},
	pages = {262--267}
},

@article{levsky_single-cell_2002,
	title = {Single-cell gene expression profiling},
	volume = {297},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12161654},
	doi = {10.1126/science.1072241},
	abstract = {A key goal of biology is to relate the expression of specific genes to a particular cellular phenotype. However, current assays for gene expression destroy the structural context. By combining advances in computational fluorescence microscopy with multiplex probe design, we devised technology in which the expression of many genes can be visualized simultaneously inside single cells with high spatial and temporal resolution. Analysis of 11 genes in serum-stimulated cultured cells revealed unique patterns of gene expression within individual cells. Using the nucleus as the substrate for parallel gene analysis, we provide a platform for the fusion of genomics and cell biology: "cellular genomics."},
	number = {5582},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Levsky, Jeffrey M and Shenoy, Shailesh M and Pezo, Rossanna C and Singer, Robert H},
	month = aug,
	year = {2002},
	note = {{PMID:} 12161654},
	keywords = {Adenocarcinoma, Cell Nucleus, Cells, Colonic Neoplasms, Color, {DNA} Probes, Fibroblasts, Gene Expression Profiling, Gene Expression Regulation, Genes, Genomics, Humans, Microscopy, Fluorescence, Odds Ratio, {RNA}, Sensitivity and Specificity, Time Factors, Transcription, Genetic, Tumor Cells, Cultured},
	pages = {836--840}
},

@misc{ryu_ryu_????,
	title = {Ryu lab: movies},
	url = {http://www.genomics.princeton.edu/ryulab/movies/movies_v6.html},
	journal = {Ryu Lab Homepage},
	author = {Ryu, William S.},
	howpublished = {http://www.genomics.princeton.edu/ryulab/movies/movies\_v6.html},
	file = {Ryu lab: movies:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/3ZIN892Q/movies_v6.html:text/html}
},

@article{fields_electrokinetic_2011,
	title = {Electrokinetic trapping at the one nanometer limit},
	volume = {108},
	issn = {1091-6490},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21562206},
	doi = {10.1073/pnas.1103554108},
	abstract = {{Anti-Brownian} electrokinetic traps have been used to trap and study the free-solution dynamics of large protein complexes and long chains of {DNA.} Small molecules in solution have thus far proved too mobile to trap by any means. Here we explore the ultimate limits on trapping single molecules. We developed a feedback-based {anti-Brownian} electrokinetic trap in which classical thermal noise is compensated to the maximal extent allowed by quantum measurement noise. We trapped single fluorophores with a molecular weight of {\textless} 1 {kDa} and a hydrodynamic radius of 6.7 Å for longer than one second, in aqueous buffer at room temperature. This achievement represents an 800-fold decrease in the mass of objects trapped in solution, and opens the possibility to trap and manipulate any soluble molecule that can be fluorescently labeled. To illustrate the use of this trap, we studied the binding of unlabeled {RecA} to fluorescently labeled single-stranded {DNA.} Binding of {RecA} induced changes in the {DNA} diffusion coefficient, electrophoretic mobility, and brightness, all of which were measured simultaneously and on a molecule-by-molecule basis. This device greatly extends the size range of molecules that can be studied by room temperature feedback trapping, and opens the door to further studies of the binding of unmodified proteins to {DNA} in free solution.},
	number = {22},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Fields, Alexander P and Cohen, Adam E},
	month = may,
	year = {2011},
	note = {{PMID:} 21562206},
	keywords = {Algorithms, Diffusion, {DNA}, {DNA}, {Single-Stranded}, Electrochemistry, Fluorescent Dyes, Hot Temperature, Hydrodynamics, Kinetics, Lasers, Likelihood Functions, Models, Statistical, Nanotechnology, Optics and Photonics, Photons},
	pages = {8937--8942}
},

@article{simons_response_1978,
	title = {Response properties of vibrissa units in rat {SI} somatosensory neocortex},
	volume = {41},
	url = {http://jn.physiology.org/cgi/content/abstract/41/3/798},
	number = {3},
	journal = {J Neurophysiol},
	author = {Simons, D. J.},
	month = may,
	year = {1978},
	pages = {798--820},
	file = {798.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/K8X7TSDB/798.pdf:application/pdf;HighWire Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/BPSQTEFP/798.html:text/html;Response properties of vibrissa units in rat SI somatosensory neocortex -- Simons 41 (3): 798 -- Journal of Neurophysiology:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/23E4TDVE/798.html:text/html}
},

@article{croll_components_1975,
	title = {Components and patterns in the behavior of the nematode Caenorhabditis elegans},
	volume = {176},
	url = {http://www.wormbase.org/db/misc/biblio?name=BEHAV%2FMOVEMENT&category=&class=Keyword&abstract=WBPaper00000075#WBPaper00000075},
	abstract = {The behavioural activities during movement, feeding and defaecation have been recorded and measured in adult females of Caenorhabditis elegans. The postures and components of recognizable wave forms are described. Stress has been laid on the machanism of antagonistic interaction of backward and forward movement, and the rates and characteristics of "spontaneous" and "induced" reversal periods. During feeding, rapid rates of pharyngeal activity are invariably related to low rates of somatic muscle wave propagation. Head oscillations are considered to be separate events not directly linked with feeding or foraging. The combination of certain wave forms, together with other measurements have been used to develop a hypothesis to describe a co-ordinating mechanism to the nematode level of organization.},
	journal = {Journal of Zoology},
	author = {Croll, {NA}},
	year = {1975},
	keywords = {{PQE}  - definite citation, Sniffing / Foraging},
	pages = {159--176},
	file = {Croll001.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/DETQ3QWD/Croll001.pdf:application/pdf}
},

@article{zhang_red-shifted_2008,
	title = {Red-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri},
	volume = {11},
	issn = {1097-6256},
	shorttitle = {Red-shifted optogenetic excitation},
	url = {http://dx.doi.org.ezp-prod1.hul.harvard.edu/10.1038/nn.2120},
	doi = {10.1038/nn.2120},
	number = {6},
	journal = {Nat Neurosci},
	author = {Zhang, Feng and Prigge, Matthias and Beyriere, Florent and Tsunoda, Satoshi P and Mattis, Joanna and Yizhar, Ofer and Hegemann, Peter and Deisseroth, Karl},
	month = jun,
	year = {2008},
	pages = {631--633}
},

@book{kandel_search_2007,
	edition = {1},
	title = {In Search of Memory: The Emergence of a New Science of Mind},
	isbn = {0393329372},
	shorttitle = {In Search of Memory},
	publisher = {W. W. Norton \& Company},
	author = {Kandel, Eric R.},
	month = mar,
	year = {2007}
},

@article{kallarakal_mechanism_1995,
	title = {Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the {K166R} mutant},
	volume = {34},
	issn = {0006-2960},
	shorttitle = {Mechanism of the reaction catalyzed by mandelate racemase},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7893690},
	abstract = {On the basis of the available high-resolution structures of mandelate racemase {(MR)} from Pseudomonas putida {[Landro}, J. A., Gerlt, J. A., Kozarich, J. W., Koo, C. W., Shah, V. J., Kenyon, G. L., Neidhart, D. J., Fujita, J., \& Petsko, G. A. (1994) Biochemistry 33, 635-643], Lys 166 and His 297 are positioned appropriately to participate in catalysis as acid/base catalysts that either abstract the alpha-proton from the enantiomers of mandelate to form an enolic intermediate or protonate the enolic intermediate to form the enantiomers of mandelate, with Lys 166 participating as the {(S)-specific} acid/base catalyst and His 297 participating as the {(R)-specific} acid/base catalyst. In this paper we report the structural and mechanistic properties of the mutant in which Lys 166 has been replaced with arginine {(K166R).} The structure of {K166R} has been determined at 1.85 A resolution with the substrate {(S)-mandelate} bound in the active site. The structure of this complex reveals no geometric alterations in the active site, with the exception that the longer side chain of Arg 166 is necessarily displaced upward from the position occupied by Lys 166 by steric interactions with the bound substrate. In contrast to the {H297N} mutant of {MR} {[Landro}, J. A., Kallarakal, A. T., Ransom, S. C., Gerlt, J. A., Kozarich, J. W., Neidhart, D. J., \& Kenyon, G. L. (1991) Biochemistry 30, 9275-9281], the {K166R} exhibits low levels of racemase activity [kcat is reduced 5 x 10(3)-fold in the {(R)-} to {(S)-direction} and 1 x 10(3)-fold in the {(S)-} to {(R)-direction].} The substrate and solvent deuterium isotope effects support a reaction coordinate for the {K166R-catalyzed} reaction in which the transition state for interconversion of bound {(S)-mandelate} and the stabilized enolic intermediate is higher in energy that the transition state for interconversion of bound {(R)-mandelate} and the stabilized enolic intermediate. The solvent deuterium isotope effect when {(S)-mandelate} is substrate (2.2 +/- 0.3) supports the proposal that the formation of the enolic intermediate involves partial transfer of a solvent-derived proton from Glu 317 to the substrate as the alpha-proton is abstracted {[Mitra}, B., Kallarakal, A. T., Kozarich, J. W., Gerlt, J. A., Clifton, J. G., Petsko, G. A., \& Kenyon, G. L. (1995) Biochemistry 34, {2777-2787].(ABSTRACT} {TRUNCATED} {AT} 400 {WORDS)}},
	number = {9},
	journal = {Biochemistry},
	author = {Kallarakal, A T and Mitra, B and Kozarich, J W and Gerlt, J A and Clifton, J G and Petsko, G A and Kenyon, G L},
	month = mar,
	year = {1995},
	note = {{PMID:} 7893690},
	keywords = {Base Sequence, Binding Sites, Catalysis, Crystallography, {X-Ray}, {DNA}, Bacterial, Escherichia coli, Kinetics, Mandelic Acids, Models, Molecular, Molecular Sequence Data, Molecular Structure, Mutagenesis, {Site-Directed}, Mutation, Protein Conformation, Pseudomonas aeruginosa, Pseudomonas putida, Racemases and Epimerases, Stereoisomerism, Substrate Specificity, Thermodynamics},
	pages = {2788--2797},
	file = {Mechanism of the Reaction Catalyzed by Mandelate Racemase: Structure and Mechanistic Properties of the K166R Mutant - Biochemistry (ACS Publications):/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/U96H8PT9/bi00009a007.html:text/html;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/X5ZFFBFT/entrez.html:text/html}
},

@article{fournier-bidoz_facile_2008,
	title = {Facile and rapid one-step mass preparation of quantum-dot barcodes},
	volume = {47},
	issn = {1521-3773},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18613155},
	doi = {10.1002/anie.200800409},
	number = {30},
	journal = {Angewandte Chemie {(International} Ed. in English)},
	author = {{Fournier-Bidoz}, Sébastien and Jennings, Travis L and Klostranec, Jesse M and Fung, Winnie and Rhee, Alex and Li, David and Chan, Warren C W},
	year = {2008},
	note = {{PMID:} 18613155},
	keywords = {Automatic Data Processing, Quantum Dots, Spectrometry, Fluorescence},
	pages = {5577--5581}
},

@article{long_using_2008,
	title = {Using temperature to analyse temporal dynamics in the songbird motor pathway},
	volume = {456},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19005546},
	doi = {10.1038/nature07448},
	abstract = {Many complex behaviours, like speech or music, have a hierarchical organization with structure on many timescales, but it is not known how the brain controls the timing of behavioural sequences, or whether different circuits control different timescales of the behaviour. Here we address these issues by using temperature to manipulate the biophysical dynamics in different regions of the songbird forebrain involved in song production. We find that cooling the premotor nucleus {HVC} (formerly known as the high vocal centre) slows song speed across all timescales by up to 45 per cent but only slightly alters the acoustic structure, whereas cooling the downstream motor nucleus {RA} (robust nucleus of the arcopallium) has no observable effect on song timing. Our observations suggest that dynamics within {HVC} are involved in the control of song timing, perhaps through a chain-like organization. Local manipulation of brain temperature should be broadly applicable to the identification of neural circuitry that controls the timing of behavioural sequences and, more generally, to the study of the origin and role of oscillatory and other forms of brain dynamics in neural systems.},
	number = {7219},
	journal = {Nature},
	author = {Long, Michael A and Fee, Michale S},
	month = nov,
	year = {2008},
	note = {{PMID:} 19005546},
	keywords = {Animals, Cold Temperature, Efferent Pathways, Finches, High Vocal Center, Neurons, Prosencephalon, Time Factors, Vocalization, Animal},
	pages = {189--194}
},

@article{ulbrich_subunit_2007,
	title = {Subunit counting in membrane-bound proteins},
	volume = {4},
	issn = {1548-7091},
	url = {http://access.harvard.edu/10.1038/nmeth1024},
	doi = {10.1038/nmeth1024},
	number = {4},
	journal = {Nat Meth},
	author = {Ulbrich, Maximilian H and Isacoff, Ehud Y},
	month = apr,
	year = {2007},
	keywords = {{GFP}, {SubunitCounting}, Urea},
	pages = {319--321}
},

@article{troemel_divergent_1995-1,
	title = {Divergent seven transmembrane receptors are candidate chemosensory receptors in C. elegans},
	volume = {83},
	issn = {0092-8674},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7585938},
	abstract = {Using their senses of taste and smell, animals recognize a wide variety of chemicals. The nematode C. elegans has only fourteen types of chemosensory neurons, but it responds to dozens of chemicals, because each chemosensory neuron detects several stimuli. Here we describe over 40 highly divergent members of the G protein-coupled receptor family that could contribute to this functional diversity. Most of these candidate receptor genes are in clusters of two to nine similar genes. Eleven of fourteen tested genes appear to be expressed in small subsets of chemosensory neurons. A single type of chemosensory neuron can potentially express at least four different receptor genes. Some of these genes might encode receptors for water-soluble attractants, repellents, and pheromones.},
	number = {2},
	journal = {Cell},
	author = {Troemel, E R and Chou, J H and Dwyer, N D and Colbert, H A and Bargmann, C I},
	month = oct,
	year = {1995},
	note = {{PMID:} 7585938},
	keywords = {{1-Octanol}, Amino Acid Sequence, Animals, Animals, Genetically Modified, Behavior, Animal, Benzaldehydes, Caenorhabditis elegans, Chemoreceptor Cells, Female, Gene Expression, Genes, Helminth, Genes, Reporter, Male, Molecular Sequence Data, Multigene Family, Octanols, Receptors, Cell Surface, Recombinant Fusion Proteins, Sequence Analysis, {DNA}, Sequence Homology, Amino Acid, Sex Characteristics, Smell, Tissue Distribution},
	pages = {207--218},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/3FS8XQAF/7585938.html:text/html}
},

@misc{_rcsb_????,
	title = {{RCSB} {PDB} : {SecA} {SecY}},
	url = {http://www.rcsb.org/pdb/explore/explore.do?structureId=3DIN}
},

@misc{_little_????,
	title = {The Little Handbook of Statistical Practice},
	url = {http://www.tufts.edu/~gdallal/LHSP.HTM},
	howpublished = {{http://www.tufts.edu/{\textasciitilde}gdallal/LHSP.HTM}}
},

@book{the_c._elegans_research_community_wormbook_2011,
	title = {{WormBook}},
	url = {http://www.wormbook.org},
	editor = {{{The} C. Elegans Research Community}},
	year = {2011}
},

@article{saloner_old_1985,
	title = {Old Boy Networks as Screening Mechanisms},
	volume = {3},
	issn = {{0734306X}},
	url = {http://www.jstor.org.ezp-prod1.hul.harvard.edu/stable/2534841},
	abstract = {This paper studies a fulfilled-expectations equilibrium in situations in which intermediaries provide personal opinions on the likelihood of success of personnel, projects, or investments. Each referee must recommend some candidates from a group of people about whom he has private information. The employer uses the recommendations to choose the workers, using his expectations about the quality of the recommended and the nonrecommended applicants. Although the referees use their information strategically, the competition among them produces optimal use of the information in the sense that employers make the same choices in equilibrium as they would if they had the same information as the referees.},
	number = {3},
	journal = {Journal of Labor Economics},
	author = {Saloner, Garth},
	month = jul,
	year = {1985},
	note = {{ArticleType:} primary\_article / Full publication date: Jul., 1985 / Copyright © 1985 The University of Chicago Press},
	pages = {255--267}
},

@article{wilkening_sverdlovsk_2006,
	title = {Sverdlovsk revisited: Modeling human inhalation anthrax},
	volume = {103},
	shorttitle = {Sverdlovsk revisited},
	url = {http://www.pnas.org.ezp-prod1.hul.harvard.edu/content/103/20/7589.abstract},
	doi = {10.1073/pnas.0509551103},
	abstract = {Several models have been proposed for the dose–response function and the incubation period distribution for human inhalation anthrax. These models give very different predictions for the severity of a hypothetical bioterror attack, when an attack might be detected from clinical cases, the efficacy of medical intervention and the requirements for decontamination. Using data from the 1979 accidental atmospheric release of anthrax in Sverdlovsk, Russia, and limited nonhuman primate data, this paper eliminates two of the contending models and derives parameters for the other two, thereby narrowing the range of models that accurately predict the effects of human inhalation anthrax. Dose–response functions that exhibit a threshold for infectivity are contraindicated by the Sverdlovsk data. Dose-dependent incubation period distributions explain the 10-day median incubation period observed at Sverdlovsk and the 1- to 5-day incubation period observed in nonhuman primate experiments.},
	number = {20},
	author = {Wilkening, Dean A.},
	month = may,
	year = {2006},
	pages = {7589--7594}
},

@article{huang_gene_1994,
	title = {Gene interactions affecting mechanosensory transduction in Caenorhabditis elegans},
	volume = {367},
	issn = {0028-0836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7509039},
	doi = {10.1038/367467a0},
	abstract = {Genetic screening has identified a group of mec (mechanosensory) genes that are required for the function of a set of six touch-receptor neurons in the nematode Caenorhabditis elegans. Such genes potentially encode components of the mechanosensory apparatus. We have cloned one of these genes, mec-10, which is a member of the degenerin gene family (genes such as mec-4 and deg-1 that can be mutated to cause neurodegeneration). Because components of an amiloride-sensitive sodium channel (alpha, beta and gamma {rENaC)} from rat share considerable sequence similarity with the C. elegans genes, it is likely that degenerins may function as channel proteins. Here we show that two degenerin homologues (mec-4 and mec-10) are expressed in the same cells, although each provides a unique function. Based on genetic data of mutations affecting mec-10-induced degeneration, we propose that the products of three genes (mec-4, mec-10 and mec-6) form a complex needed for mechanosensation, and that several other mec genes may be important in regulating the putative channel complex.},
	number = {6462},
	journal = {Nature},
	author = {Huang, M and Chalfie, M},
	month = feb,
	year = {1994},
	note = {{PMID:} 7509039},
	keywords = {Amino Acid Sequence, Animals, Base Sequence, Caenorhabditis elegans, Caenorhabditis elegans Proteins, {DNA}, Genes, Helminth, Helminth Proteins, Ion Channels, Mechanoreceptors, Membrane Proteins, Molecular Sequence Data, Nerve Degeneration, Neural Conduction},
	pages = {467--470},
	file = {367467a0.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/SKHME3ES/367467a0.pdf:application/pdf;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/QP2HV8QB/entrez.html:text/html}
},

@misc{_steven_????,
	title = {Steven {McIntire} Home Page},
	url = {http://bms.ucsf.edu/faculty/mcintire.html}
},

@book{loeliger_version_2009,
	title = {Version Control with Git},
	isbn = {9780596520120},
	abstract = {Version Control with Git takes you step-by-step through ways to track, merge, and manage software projects, using this highly flexible, open source version control system. Git permits virtually an infinite variety of methods for development and collaboration. Created by Linus Torvalds to manage development of the Linux kernel, it's become the principal tool for distributed version control. But Git's flexibility also means that some users don't understand how to use it to their best advantage. Version Control with Git offers tutorials on the most effective ways to use it, as well as friendly yet rigorous advice to help you navigate Git's many functions. With this book, you will:  Learn how to use Git in several real-world development environments Gain insight into Git's common-use cases, initial tasks, and basic functions Understand how to use Git for both centralized and distributed version control Use Git to manage patches, diffs, merges, and conflicts Acquire advanced techniques such as rebasing, hooks, and ways to handle submodules (subprojects) Learn how to use Git with Subversion  Git has earned the respect of developers around the world. Find out how you can benefit from this amazing tool with Version Control with Git.},
	publisher = {{O'Reilly} Media, Inc.},
	author = {Loeliger, Jon},
	month = may,
	year = {2009},
	keywords = {Computer software, Computers / General, Computers / Operating Systems / General, Computers / Operating Systems / Linux, Computers / Operating Systems / {UNIX}, Computers / Programming / General, Computers / Software Development \& Engineering / General, Computers / Utilities, Git, Git {(Computer} file), Open source software, Software engineering}
},

@misc{karl_j._erlandson_role_2008,
	title = {A role for the two-helix finger of the {SecA} {ATPase} in protein translocation},
	copyright = {© 2008 Nature Publishing Group},
	url = {http://www.nature.com/nature/journal/v455/n7215/pdf/nature07439.pdf},
	author = {Karl J. Erlandson and Stephanie B. M. Miller and Yunsun Nam and Andrew R. Osborne and Jochen Zimmer and Tom A. Rapoport},
	month = oct,
	year = {2008},
	howpublished = {http://www.nature.com/nature/journal/v455/n7215/pdf/nature07439.pdf},
	file = {Access : A role for the two-helix finger of the SecA ATPase in protein translocation : Nature:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/I5V64WDK/nature07439.html:text/html}
},

@article{hughes_sensory_2007-1,
	title = {A sensory feedback circuit coordinates muscle activity in Drosophila},
	volume = {35},
	issn = {1044-7431},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/17498969},
	doi = {10.1016/j.mcn.2007.04.001},
	abstract = {Drosophila larval crawling is a simple behavior that allows us to dissect the functions of specific neurons in the intact animal and explore the roles of genes in the specification of those neurons. By inhibiting subsets of neurons in the {PNS}, we have found that two classes of multidendritic neurons play a major role in larval crawling. The bipolar dendrites and class I mds send a feedback signal to the {CNS} that keeps the contraction wave progressing quickly, allowing smooth forward movement. Genetic manipulation of the sensory neurons suggests that this feedback depends on proper dendritic morphology and axon pathfinding to appropriate synaptic target areas in the {CNS.} Our data suggest that coordination of muscle activity in larval crawling requires feedback from neurons acting as proprioceptors, sending a "mission accomplished" signal in response to segment contraction, and resulting in rapid relaxation of the segment and propagation of the wave.},
	number = {2},
	journal = {Molecular and Cellular Neurosciences},
	author = {Hughes, Cynthia L and Thomas, John B},
	month = jun,
	year = {2007},
	note = {{PMID:} 17498969},
	keywords = {Animals, Animals, Genetically Modified, Behavior, Animal, Dendrites, Drosophila, Drosophila Proteins, Embryo, Nonmammalian, Feedback, Green Fluorescent Proteins, Models, Biological, Movement, Muscles, Nerve Net, Neurons, Afferent, Videotape Recording},
	pages = {383--396}
},

@book{bretthorst_probability_2003,
	address = {Cambridge, {UK}},
	title = {Probability theory : the logic of science},
	isbn = {0521592712 (hardback)},
	shorttitle = {Probability theory},
	publisher = {Cambridge University Press},
	author = {Jaynes, E. T},
	editor = {Bretthorst, G. Larry},
	year = {2003}
},

@incollection{tantama_chapter_2012,
	title = {Chapter 12 - Optogenetic reporters: Fluorescent protein-based genetically encoded indicators of signaling and metabolism in the brain},
	volume = {Volume 196},
	isbn = {0079-6123},
	shorttitle = {Chapter 12 - Optogenetic reporters},
	url = {http://www.sciencedirect.com/science/article/pii/B9780444594266000124},
	abstract = {Abstract
Fluorescent protein technology has evolved to include genetically encoded biosensors that can monitor levels of ions, metabolites, and enzyme activities as well as protein conformation and even membrane voltage. They are well suited to live-cell microscopy and quantitative analysis, and they can be used in multiple imaging modes, including one- or two-photon fluorescence intensity or lifetime microscopy. Although not nearly complete, there now exists a substantial set of genetically encoded reporters that can be used to monitor many aspects of neuronal and glial biology, and these biosensors can be used to visualize synaptic transmission and activity-dependent signaling in vitro and in vivo. In this review, we present an overview of design strategies for engineering biosensors, including sensor designs using circularly permuted fluorescent proteins and using fluorescence resonance energy transfer between fluorescent proteins. We also provide examples of indicators that sense small ions (e.g., {pH}, chloride, zinc), metabolites (e.g., glutamate, glucose, {ATP}, {cAMP}, lipid metabolites), signaling pathways (e.g., G protein-coupled receptors, Rho {GTPases)}, enzyme activities (e.g., protein kinase A, caspases), and reactive species. We focus on examples where these genetically encoded indicators have been applied to brain-related studies and used with live-cell fluorescence microscopy.},
	booktitle = {Optogenetics: Tools for Controlling and Monitoring Neuronal Activity},
	publisher = {Elsevier},
	author = {Tantama, Mathew and Hung, Yin Pun and Yellen, Gary and Thomas Knöpfel and Edward S. Boyden},
	year = {2012},
	keywords = {biosensor, circularly permuted, fluorescent protein, {FRET}, genetically encoded, live-cell microscopy, resonance energy transfer},
	pages = {235--263},
	file = {ScienceDirect Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/VG6JGHEH/Tantama et al. - 2012 - Chapter 12 - Optogenetic reporters Fluorescent pr.pdf:application/pdf;ScienceDirect Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/IJMXE6E5/Tantama et al. - 2012 - Chapter 12 - Optogenetic reporters Fluorescent pr.html:text/html}
},

@article{cunin_biomolecular_2002,
	title = {Biomolecular screening with encoded porous-silicon photonic crystals},
	volume = {1},
	issn = {1476-1122},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12618846},
	doi = {10.1038/nmat702},
	abstract = {Strategies to encode or label small particles or beads for use in high-throughput screening and bioassay applications focus on either spatially differentiated, on-chip arrays or random distributions of encoded beads. Attempts to encode large numbers of polymeric, metallic or glass beads in random arrays or in fluid suspension have used a variety of entities to provide coded elements (bits)--fluorescent molecules, molecules with specific vibrational signatures, quantum dots, or discrete metallic layers. Here we report a method for optically encoding micrometre-sized nanostructured particles of porous silicon. We generate multilayered porous films in crystalline silicon using a periodic electrochemical etch. This results in photonic crystals with well-resolved and narrow optical reflectivity features, whose wavelengths are determined by the etching parameters. Millions of possible codes can be prepared this way. Micrometre-sized particles are then produced by ultrasonic fracture, mechanical grinding or by lithographic means. A simple antibody-based bioassay using fluorescently tagged proteins demonstrates the encoding strategy in biologically relevant media.},
	number = {1},
	journal = {Nature Materials},
	author = {Cunin, Frédérique and Schmedake, Thomas A and Link, Jamie R and Li, Yang Yang and Koh, Jennifer and Bhatia, Sangeeta N and Sailor, Michael J},
	month = sep,
	year = {2002},
	note = {{PMID:} 12618846},
	keywords = {Animals, Antibodies, Antigens, Biosensing Techniques, Cattle, Crystallization, Fluorescence, Goats, Immunoassay, Membranes, Artificial, Molecular Probes, Porosity, Rabbits, Rats, Serum Albumin, Silicon Compounds},
	pages = {39--41}
},

@book{oppenheim_digital_1975,
	address = {Englewood Cliffs, {N.J}},
	title = {Digital Signal Processing},
	isbn = {0132146355},
	lccn = {{TK5102.5} {.O245}},
	publisher = {{Prentice-Hall}},
	author = {Oppenheim, Alan V and Schafer, Ronald W},
	year = {1975},
	keywords = {Digital electronics, Signal theory {(Telecommunication)}}
},

@article{kawano_imbalancing_2011,
	title = {An Imbalancing Act: Gap Junctions Reduce the Backward Motor Circuit Activity to Bias C. elegans for Forward Locomotion},
	volume = {72},
	issn = {1097-4199},
	shorttitle = {An Imbalancing Act},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22099460},
	doi = {10.1016/j.neuron.2011.09.005},
	abstract = {A neural network can sustain and switch between different activity patterns to execute multiple behaviors. By monitoring the decision making for directional locomotion through motor circuit calcium imaging in behaving Caenorhabditis elegans {(C.} elegans), we reveal that C. elegans determines the directionality of movements by establishing an imbalanced output between the forward and backward motor circuits and that it alters directions by switching between these imbalanced states. We further demonstrate that premotor interneurons modulate endogenous motoneuron activity to establish the output imbalance. Specifically, the {UNC-7} and {UNC-9} innexin-dependent premotor interneuron-motoneuron coupling prevents a balanced output state that leads to movements without directionality. Moreover, they act as shunts to decrease the backward-circuit activity, establishing a persistent bias for the high forward-circuit output state that results in the inherent preference of C. elegans for forward locomotion. This study demonstrates that imbalanced motoneuron activity underlies directional movement and establishes gap junctions as critical modulators of the properties and outputs of neural circuits.},
	number = {4},
	journal = {Neuron},
	author = {Kawano, Taizo and Po, Michelle D and Gao, Shangbang and Leung, George and Ryu, William S and Zhen, Mei},
	month = nov,
	year = {2011},
	note = {{PMID:} 22099460},
	pages = {572--586},
	file = {zhen.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/6N2X3TG3/zhen.pdf:application/pdf}
},

@article{stirman_multispectral_2012,
	title = {A multispectral optical illumination system with precise spatiotemporal control for the manipulation of optogenetic reagents},
	volume = {7},
	issn = {1750-2799},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22240583},
	doi = {10.1038/nprot.2011.433},
	abstract = {Optogenetics is an excellent tool for noninvasive activation and silencing of neurons and muscles. Although they have been widely adopted, illumination techniques for optogenetic tools remain limited and relatively nonstandardized. We present a protocol for constructing an illumination system capable of dynamic multispectral optical targeting of micrometer-sized structures in both stationary and moving objects. The initial steps of the protocol describe how to modify an off-the-shelf video projector by insertion of optical filters and modification of projector optics. Subsequent steps involve altering the microscope's epifluorescence optical train as well as alignment and characterization of the system. When fully assembled, the illumination system is capable of dynamically projecting multispectral patterns with a resolution better than 10 μm at medium magnifications. Compared with other custom-assembled systems and commercially available products, this protocol allows a researcher to assemble the illumination system for a fraction of the cost and can be completed within a few days.},
	number = {2},
	journal = {Nature protocols},
	author = {Stirman, Jeffrey N and Crane, Matthew M and Husson, Steven J and Gottschalk, Alexander and Lu, Hang},
	month = feb,
	year = {2012},
	note = {{PMID:} 22240583},
	pages = {207--220}
},

@article{andersen_self-assembly_2009,
	title = {Self-assembly of a nanoscale {DNA} box with a controllable lid},
	volume = {459},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19424153},
	doi = {10.1038/nature07971},
	abstract = {The unique structural motifs and self-recognition properties of {DNA} can be exploited to generate self-assembling {DNA} nanostructures of specific shapes using a 'bottom-up' approach. Several assembly strategies have been developed for building complex three-dimensional {(3D)} {DNA} nanostructures. Recently, the {DNA} 'origami' method was used to build two-dimensional addressable {DNA} structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable {3D} {DNA} nanostructures. Here we extend the {DNA} origami method into three dimensions by creating an addressable {DNA} box 42 x 36 x 36 nm(3) in size that can be opened in the presence of externally supplied {DNA} 'keys'. We thoroughly characterize the structure of this {DNA} box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this {DNA} nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.},
	number = {7243},
	journal = {Nature},
	author = {Andersen, Ebbe S and Dong, Mingdong and Nielsen, Morten M and Jahn, Kasper and Subramani, Ramesh and Mamdouh, Wael and Golas, Monika M and Sander, Bjoern and Stark, Holger and Oliveira, Cristiano L P and Pedersen, Jan Skov and Birkedal, Victoria and Besenbacher, Flemming and Gothelf, Kurt V and Kjems, Jørgen},
	month = may,
	year = {2009},
	note = {{PMID:} 19424153},
	keywords = {Cryoelectron Microscopy, {DNA}, Imaging, {Three-Dimensional}, Microscopy, Atomic Force, Nanostructures, Nucleic Acid Conformation},
	pages = {73--76}
},

@incollection{bargmann_chemotaxis_1998,
	edition = {1},
	series = {Cold Spring Harbor Monograph Series},
	title = {Chemotaxis and Thermotaxis},
	isbn = {0879695323},
	shorttitle = {C. Elegans {II}},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/books/bv.fcgi?rid=ce2.chapter.860},
	number = {33},
	booktitle = {C. Elegans {II}},
	publisher = {Cold Spring Harbor Laboratory Press},
	author = {Bargmann, C I and Mori, I},
	month = jan,
	year = {1998},
	keywords = {Chemotaxis, {PQE}  - definite citation, thermosensing}
},

@misc{altun_wormatlas_2002,
	title = {{WormAtlas}},
	url = {http://www.wormatlas.org},
	author = {Altun, Z. F. and Herndon, L. A. and Crocker, C. and Lints, R. and Hall, D. H.},
	year = {2002}
},

@article{dietz_folding_2009,
	title = {Folding {DNA} into twisted and curved nanoscale shapes},
	volume = {325},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19661424},
	doi = {10.1126/science.1174251},
	abstract = {We demonstrate the ability to engineer complex shapes that twist and curve at the nanoscale from {DNA.} Through programmable self-assembly, strands of {DNA} are directed to form a custom-shaped bundle of tightly cross-linked double helices, arrayed in parallel to their helical axes. Targeted insertions and deletions of base pairs cause the {DNA} bundles to develop twist of either handedness or to curve. The degree of curvature could be quantitatively controlled, and a radius of curvature as tight as 6 nanometers was achieved. We also combined multiple curved elements to build several different types of intricate nanostructures, such as a wireframe beach ball or square-toothed gears.},
	number = {5941},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Dietz, Hendrik and Douglas, Shawn M and Shih, William M},
	month = aug,
	year = {2009},
	note = {{PMID:} 19661424},
	keywords = {Base Pairing, {DNA}, Nanostructures, Nanotechnology, Nucleic Acid Conformation},
	pages = {725--730}
},

@article{richmond_unc-13_1999,
	title = {{UNC-13} is required for synaptic vesicle fusion in C. elegans},
	volume = {2},
	issn = {1097-6256},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10526333},
	doi = {10.1038/14755},
	abstract = {We analyzed the synaptic physiology of unc-13 mutants in the nematode C. elegans. Mutants of unc-13 had normal nervous system architecture, and the densities of synapses and postsynaptic receptors were normal at the neuromuscular junction. However, the number of synaptic vesicles at neuromuscular junctions was two- to threefold greater in unc-13 mutants than in wild-type animals. Most importantly, evoked release at both {GABAergic} and cholinergic synapses was almost absent in unc-13 null alleles, as determined by whole-cell, voltage-clamp techniques. Although mutant synapses had morphologically docked vesicles, these vesicles were not competent for release as assayed by spontaneous release in calcium-free solution or by the application of hyperosmotic saline. These experiments support models in which {UNC-13} mediates either fusion of vesicles during exocytosis or priming of vesicles for fusion.},
	number = {11},
	journal = {Nature Neuroscience},
	author = {Richmond, J E and Davis, W S and Jorgensen, E M},
	month = nov,
	year = {1999},
	note = {{PMID:} 10526333},
	keywords = {Alleles, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Helminth Proteins, Mutation, Nerve Tissue Proteins, Neuromuscular Junction, Synaptic Transmission, Synaptic Vesicles},
	pages = {959--964}
},

@article{gloria-soria_npr-1_2008,
	title = {npr-1 Regulates foraging and dispersal strategies in Caenorhabditis elegans},
	volume = {18},
	issn = {0960-9822},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18993077},
	doi = {10.1016/j.cub.2008.09.043},
	abstract = {Wild isolates of Caenorhabditis elegans differ in their tendency to aggregate on food [1, 2]. Most quantitative variation in this behavior is explained by a polymorphism at a single amino acid in the G protein-coupled receptor {NPR-1:} gregarious strains carry the {215F} allele, and solitary strains carry the {215V} allele [2]. Although npr-1 regulates a behavioral syndrome with potential adaptive implications, the evolutionary causes and consequences of this natural polymorphism remain unclear. Here we show that npr-1 regulates two behaviors that can promote coexistence of the two alleles. First, gregarious and solitary worms differ in their responses to food such that they can partition a single, continuous patch of food. Second, gregarious worms disperse more readily from patch to patch than do solitary worms, which can cause partitioning of a fragmented resource. The dispersal propensity of both gregarious and solitary worms increases with density. npr-1-dependent dispersal is independent of aggregation and could be part of a food-searching strategy. The gregarious allele is favored in a fragmented relative to a continuous food environment in competition experiments. We conclude that the npr-1 polymorphism could be maintained by a trade-off between dispersal and competitive ability.},
	number = {21},
	journal = {Current Biology: {CB}},
	author = {{Gloria-Soria}, Andrea and Azevedo, Ricardo B R},
	month = nov,
	year = {2008},
	note = {{PMID:} 18993077},
	keywords = {Alleles, Amino Acid Substitution, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Environment, Feeding Behavior, Polymorphism, Genetic, Receptors, Neuropeptide Y, Selection {(Genetics)}},
	pages = {1694--1699},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/3ET2J7VS/18993077.html:text/html}
},

@article{woo_programmable_2011,
	title = {Programmable molecular recognition based on the geometry of {DNA} nanostructures},
	volume = {3},
	issn = {1755-4349},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21778982},
	doi = {10.1038/nchem.1070},
	abstract = {From ligand-receptor binding to {DNA} hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. {DNA} retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of {Watson-Crick} binding. Here we show that {DNA} can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct {DNA} origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond {DNA} nanostructures.},
	number = {8},
	journal = {Nature Chemistry},
	author = {Woo, Sungwook and Rothemund, Paul W K},
	month = aug,
	year = {2011},
	note = {{PMID:} 21778982},
	keywords = {{DNA}, Isomerism, Nanostructures, Nucleic Acid Hybridization, Thermodynamics},
	pages = {620--627}
},

@article{huang_automated_2008,
	title = {Automated detection and analysis of foraging behavior in Caenorhabditis elegans},
	volume = {171},
	issn = {0165-0270},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18342950},
	doi = {S0165-0270(08)00086-1},
	abstract = {Foraging is a rapid, side-to-side movement of the nose generated by Caenorhabditis elegans as it explores its environment. In this paper, we present an automated method to detect and analyze foraging behavior of C. elegans in a video sequence. Several morphological image-processing methods are used to locate the precise nose position of the worm in each image. Then foraging events are detected by measuring the bending angle of the nose and investigating the overall bending curve using periodograms. We measure foraging-related parameters which have not previously been studied. The algorithm has applications in classifying and characterizing genetic mutations associated with this behavior.},
	number = {1},
	journal = {Journal of Neuroscience Methods},
	author = {Huang, {Kuang-Man} and Cosman, Pamela and Schafer, William R},
	month = jun,
	year = {2008},
	note = {{PMID:} 18342950},
	keywords = {Algorithms, Animals, Behavior, Animal, Caenorhabditis elegans, Exploratory Behavior, Image Processing, {Computer-Assisted}, Motor Activity, {PQE}  - definite citation, Video Recording},
	pages = {153--64},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/T4B7B2ZF/18342950.html:text/html}
},

@article{chronis_microfluidics_2007,
	title = {Microfluidics for in vivo imaging of neuronal and behavioral activity in Caenorhabditis elegans},
	volume = {4},
	issn = {1548-7091},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17704783},
	doi = {10.1038/nmeth1075},
	abstract = {The nematode C. elegans is an excellent model organism for studying behavior at the neuronal level. Because of the organism's small size, it is challenging to deliver stimuli to C. elegans and monitor neuronal activity in a controlled environment. To address this problem, we developed two microfluidic chips, the 'behavior' chip and the 'olfactory' chip for imaging of neuronal and behavioral responses in C. elegans. We used the behavior chip to correlate the activity of {AVA} command interneurons with the worm locomotion pattern. We used the olfactory chip to record responses from {ASH} sensory neurons exposed to high-osmotic-strength stimulus. Observation of neuronal responses in these devices revealed previously unknown properties of {AVA} and {ASH} neurons. The use of these chips can be extended to correlate the activity of sensory neurons, interneurons and motor neurons with the worm's behavior.},
	number = {9},
	journal = {Nature Methods},
	author = {Chronis, Nikos and Zimmer, Manuel and Bargmann, Cornelia I},
	month = sep,
	year = {2007},
	note = {{PMID:} 17704783},
	keywords = {Animals, Behavior, Animal, Caenorhabditis elegans, Calcium, Green Fluorescent Proteins, Interneurons, Microfluidic Analytical Techniques, Motor Activity},
	pages = {727--731}
},

@misc{_introduction_????,
	title = {Introduction to C. elegans Anatomy},
	url = {http://wormatlas.org/handbook/anatomyintro/anatomyintro.htm},
	keywords = {Print Me!, Putative Slide},
	howpublished = {http://wormatlas.org/handbook/anatomyintro/anatomyintro.htm},
	file = {:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/F62BAHTB/anatomyintro.html:text/html}
},

@article{ahissar_object_2008,
	title = {Object localization with whiskers},
	volume = {98},
	issn = {0340-1200},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18491159},
	doi = {10.1007/s00422-008-0214-4},
	abstract = {Rats use their large facial hairs (whiskers) to detect, localize and identify objects in their proximal three-dimensional {(3D)} space. Here, we focus on recent evidence of how object location is encoded in the neural sensory pathways of the rat whisker system. Behavioral and neuronal observations have recently converged to the point where object location in {3D} appears to be encoded by an efficient orthogonal scheme supported by primary sensory-afferents: each primary-afferent can signal object location by a spatial (labeled-line) code for the vertical axis (along whisker arcs), a temporal code for the horizontal axis (along whisker rows), and an intensity code for the radial axis (from the face out). Neuronal evidence shows that (i) the identities of activated sensory neurons convey information about the vertical coordinate of an object, (ii) the timing of their firing, in relation to other reference signals, conveys information about the horizontal object coordinate, and (iii) the intensity of firing conveys information about the radial object coordinate. Such a triple-coding scheme allows for efficient multiplexing of {3D} object location information in the activity of single neurons. Also, this scheme provides redundancy since the same information may be represented in the activity of many neurons. These features of orthogonal coding increase accuracy and reliability. We propose that the multiplexed information is conveyed in parallel to different readout circuits, each decoding a specific spatial variable. Such decoding reduces ambiguity, and simplifies the required decoding algorithms, since different readout circuits can be optimized for a particular variable.},
	number = {6},
	journal = {Biological Cybernetics},
	author = {Ahissar, Ehud and Knutsen, Per Magne},
	month = jun,
	year = {2008},
	note = {{PMID:} 18491159},
	keywords = {Animals, Models, Neurological, Nerve Net, Neural Pathways, Perception, Physical Stimulation, Rats, Touch, Vibrissae},
	pages = {449--458},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/MTMKCMB6/18491159.html:text/html}
},

@article{drew_chronic_2010,
	title = {Chronic optical access through a polished and reinforced thinned skull},
	volume = {advance online publication},
	issn = {1548-7105},
	url = {http://dx.doi.org/10.1038/nmeth.1530},
	doi = {10.1038/nmeth.1530},
	journal = {Nat Meth},
	author = {Drew, Patrick J and Shih, Andy Y and Driscoll, Jonathan D and Knutsen, Per Magne and Blinder, Pablo and Davalos, Dimitrios and Akassoglou, Katerina and Tsai, Philbert S and Kleinfeld, David},
	month = oct,
	year = {2010}
},

@article{hell_microscopy_2009,
	title = {Microscopy and its focal switch},
	volume = {6},
	issn = {1548-7105},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19116611},
	doi = {10.1038/nmeth.1291},
	abstract = {Until not very long ago, it was widely accepted that lens-based (far-field) optical microscopes cannot visualize details much finer than about half the wavelength of light. The advent of viable physical concepts for overcoming the limiting role of diffraction in the early 1990s set off a quest that has led to readily applicable and widely accessible fluorescence microscopes with nanoscale spatial resolution. Here I discuss the principles of these methods together with their differences in implementation and operation. Finally, I outline potential developments.},
	number = {1},
	journal = {Nature Methods},
	author = {Hell, Stefan W},
	month = jan,
	year = {2009},
	note = {{PMID:} 19116611},
	keywords = {Animals, Microscopy, Fluorescence, Nanostructures, Nonlinear Dynamics},
	pages = {24--32}
},

@article{sulston_c._1992,
	title = {The C. elegans genome sequencing project: a beginning},
	volume = {356},
	issn = {0028-0836},
	shorttitle = {The C. elegans genome sequencing project},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/1538779},
	doi = {10.1038/356037a0},
	abstract = {The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.},
	number = {6364},
	journal = {Nature},
	author = {Sulston, J and Du, Z and Thomas, K and Wilson, R and Hillier, L and Staden, R and Halloran, N and Green, P and {Thierry-Mieg}, J and Qiu, L},
	month = mar,
	year = {1992},
	note = {{PMID:} 1538779},
	keywords = {Animals, Base Sequence, Caenorhabditis, Chromosome Mapping, Cosmids, Gene Library, Genome},
	pages = {37--41}
},

@article{gray_circuit_2005,
	title = {A circuit for navigation in Caenorhabditis elegans},
	volume = {102},
	shorttitle = {{INAUGURAL} {ARTICLE} by a Recently Elected Academy Member},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=546636},
	doi = {10.1073/pnas.0409009101},
	number = {9},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Gray, Jesse M. and Hill, Joseph J. and Bargmann, Cornelia I.},
	month = mar,
	year = {2005},
	note = {{PMC546636}},
	keywords = {Background, Navigation, {PQE}  - definite citation, {PQE} Specific Aim 3, Print Me!},
	pages = {3184–3191},
	file = {PubMed Central Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/D87TSGTV/Gray et al - 2005 - INAUGURAL ARTICLE by a Recently Elected Academy Me.pdf:application/pdf;PubMed Central Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/9CXSZJIR/articlerender.html:text/html}
},

@article{suzuki_vivo_2003,
	title = {In vivo imaging of C. elegans mechanosensory neurons demonstrates a specific role for the {MEC-4} channel in the process of gentle touch sensation},
	volume = {39},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12971899},
	abstract = {In the nematode C. elegans, genes encoding components of a putative mechanotransducing channel complex have been identified in screens for light-touch-insensitive mutants. A long-standing question, however, is whether identified {MEC} proteins act directly in touch transduction or contribute indirectly by maintaining basic mechanoreceptor neuron physiology. In this study, we used the genetically encoded calcium indicator cameleon to record cellular responses of mechanosensory neurons to touch stimuli in intact, behaving nematodes. We defined a gentle touch sensory modality that adapts with a time course of approximately 500 ms and primarily senses motion rather than pressure. The {DEG/ENaC} channel subunit {MEC-4} and channel-associated stomatin {MEC-2} are specifically required for neural responses to gentle mechanical stimulation, but do not affect the basic physiology of touch neurons or their in vivo responses to harsh mechanical stimulation. These results distinguish a specific role for the {MEC} channel proteins in the process of gentle touch mechanosensation.},
	number = {6},
	journal = {Neuron},
	author = {Suzuki, Hiroshi and Kerr, Rex and Bianchi, Laura and {Frøkjaer-Jensen}, Christian and Slone, Dan and Xue, Jian and Gerstbrein, Beate and Driscoll, Monica and Schafer, William R},
	month = sep,
	year = {2003},
	note = {{PMID:} 12971899},
	keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium Channels, {L-Type}, Cells, Cultured, Mechanoreceptors, Mechanotransduction, Cellular, Membrane Potentials, Membrane Proteins, Neurons, Touch},
	pages = {1005--1017}
},

@misc{_current_????,
	title = {Current Biology},
	url = {http://www.cell.com/current-biology/citationexport},
	howpublished = {http://www.cell.com/current-biology/citationexport},
	file = {Current Biology:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/4D2NFSPX/citationexport.html:text/html}
},

@misc{_mcintire_????-1,
	title = {{McIntire} Lab - Steve {McIntire}, {M.D.}, {Ph.D.}},
	url = {http://www.galloresearch.org/index.php/investigators/mcintirelab}
},

@book{zhang_drosophila_2010,
	title = {Drosophila neurobiology: a laboratory manual},
	isbn = {9780879699048},
	shorttitle = {Drosophila neurobiology},
	abstract = {Cold Spring Harbor Laboratorys long-running Neurobiology of Drosophila course has trained a generation of neuroscientists, many of whom have become leaders in the field. Drosophila Neurobiology: A Laboratory Manual offers the detailed protocols and background material developed by the course instructors to all researchers interested in using Drosophila as an experimental model for investigating the nervous system. The manual covers three approaches to the field: Analysis of Neural Development, Recording and Imaging Activities in the Nervous System, and Analyzing Behavior. Techniques described include molecular, genetic, electrophysiological, imaging, behavioral and developmental methods. Written by leading experts from the community, Drosophila Neurobiology: A Laboratory Manual is an essential guide for researchers at all levels, from the beginning graduate student through the established primary investigator. Related Titles from the Publisher Drosophila Protocols, Drosophila: A Laboratory Handbook, Second Edition, An Introduction to Nervous Systems Invertebrate Neurobiology {(Cold} Spring Harbor Monograph Series 49), Fly Pushing: The Theory and Practice of Drosophila Genetics, Second Edition},
	publisher = {Cold Spring Harbor Laboratory Press},
	author = {Zhang, Bing and Freeman, Marc R. and Waddell, Scott},
	month = may,
	year = {2010},
	keywords = {Drosophila, Drosophila - physiology, Drosophila/ Laboratory manuals, Medical / Laboratory Medicine, Medical / Neuroscience, Neurobiology, Neurobiology - methods, Neurobiology/ Laboratory manuals, Neurobiology/ methods/ Laboratory Manuals, Science / Life Sciences / Biology / General, Science / Life Sciences / Neuroscience, Science / Life Sciences / Zoology / Entomology, Science / Research \& Methodology}
},

@article{ringstad_fmrfamide_2008,
	title = {{FMRFamide} neuropeptides and acetylcholine synergistically inhibit egg-laying by C. elegans},
	volume = {11},
	issn = {1546-1726},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18806786},
	doi = {10.1038/nn.2186},
	abstract = {Egg-laying behavior of the Caenorhabditis elegans hermaphrodite is regulated by G protein signaling pathways. Here we show that the egg laying-defective mutant egl-6(n592) carries an activating mutation in a G protein-coupled receptor that inhibits C. elegans egg-laying motor neurons in a G(o)-dependent manner. Ligands for {EGL-6} are {Phe-Met-Arg-Phe-NH(2)} {(FMRFamide)-related} peptides encoded by the genes flp-10 and flp-17. flp-10 is expressed in both neurons and non-neuronal cells. The major source of flp-17 peptides is a pair of presumptive sensory neurons, the {BAG} neurons. Genetic analysis of the egl-6 pathway revealed that the {EGL-6} neuropeptide signaling pathway functions redundantly with acetylcholine to inhibit egg-laying. The retention of embryos in the uterus of the C. elegans hermaphrodite is therefore under the control of a presumptive sensory system and is inhibited by the convergence of signals from neuropeptides and the small-molecule neurotransmitter acetylcholine.},
	number = {10},
	journal = {Nature Neuroscience},
	author = {Ringstad, Niels and Horvitz, H Robert},
	month = oct,
	year = {2008},
	note = {{PMID:} 18806786},
	keywords = {Acetylcholine, Alanine, Animals, Animals, Genetically Modified, Behavior, Animal, Caenorhabditis elegans, Caenorhabditis elegans Proteins, egl-6, Female, {FMRFamide}, Gene Expression Regulation, Green Fluorescent Proteins, Membrane Potentials, Membrane Transport Modulators, Motor Neurons, Mutation, Neural Inhibition, {Patch-Clamp} Techniques, Peptides, Receptors, {G-Protein-Coupled}, Reproduction, Signal Transduction, Threonine},
	pages = {1168--1176}
},

@article{lund_molecular_2010,
	title = {Molecular robots guided by prescriptive landscapes},
	volume = {465},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20463735},
	doi = {10.1038/nature09012},
	abstract = {Traditional robots rely for their function on computing, to store internal representations of their goals and environment and to coordinate sensing and any actuation of components required in response. Moving robotics to the single-molecule level is possible in principle, but requires facing the limited ability of individual molecules to store complex information and programs. One strategy to overcome this problem is to use systems that can obtain complex behaviour from the interaction of simple robots with their environment. A first step in this direction was the development of {DNA} walkers, which have developed from being non-autonomous to being capable of directed but brief motion on one-dimensional tracks. Here we demonstrate that previously developed random walkers-so-called molecular spiders that comprise a streptavidin molecule as an inert 'body' and three deoxyribozymes as catalytic 'legs'-show elementary robotic behaviour when interacting with a precisely defined environment. Single-molecule microscopy observations confirm that such walkers achieve directional movement by sensing and modifying tracks of substrate molecules laid out on a two-dimensional {DNA} origami landscape. When using appropriately designed {DNA} origami, the molecular spiders autonomously carry out sequences of actions such as 'start', 'follow', 'turn' and 'stop'. We anticipate that this strategy will result in more complex robotic behaviour at the molecular level if additional control mechanisms are incorporated. One example might be interactions between multiple molecular robots leading to collective behaviour; another might be the ability to read and transform secondary cues on the {DNA} origami landscape as a means of implementing Turing-universal algorithmic behaviour.},
	number = {7295},
	journal = {Nature},
	author = {Lund, Kyle and Manzo, Anthony J and Dabby, Nadine and Michelotti, Nicole and {Johnson-Buck}, Alexander and Nangreave, Jeanette and Taylor, Steven and Pei, Renjun and Stojanovic, Milan N and Walter, Nils G and Winfree, Erik and Yan, Hao},
	month = may,
	year = {2010},
	note = {{PMID:} 20463735},
	keywords = {Algorithms, Computers, Molecular, {DNA}, Catalytic, {DNA}, {Single-Stranded}, Microscopy, Atomic Force, Microscopy, Fluorescence, Movement, Nanotechnology, Robotics, Streptavidin, Surface Plasmon Resonance, Time Factors, Zinc},
	pages = {206--210}
},

@article{xiao_direct_2009,
	title = {Direct determination of haplotypes from single {DNA} molecules},
	volume = {6},
	issn = {1548-7105},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19198595},
	doi = {10.1038/nmeth.1301},
	abstract = {Determining the long-range haplotypes in a diploid individual is a major technical challenge. Here we report a method of molecular haplotyping by directly imaging multiple polymorphic sites on individual human {DNA} molecules simultaneously. We demonstrate the utility of this technology by accurately determining the haplotypes consisting of up to 16 single-nucleotide polymorphisms in genomic regions up to 50 kilobases.},
	number = {3},
	journal = {Nature Methods},
	author = {Xiao, Ming and Wan, Eunice and Chu, Catherine and Hsueh, {Wen-Chi} and Cao, Yang and Kwok, {Pui-Yan}},
	month = mar,
	year = {2009},
	note = {{PMID:} 19198595},
	keywords = {Carbocyanines, Chromosomes, Human, Pair 17, Chromosomes, Human, Pair 7, Chromosomes, Human, Pair 8, {DNA}, {DNA} Primers, {DNA-Directed} {DNA} Polymerase, {DNA}, {Single-Stranded}, Exodeoxyribonucleases, Genetic Techniques, Haplotypes, Heterozygote, Homozygote, Humans, Microscopy, Fluorescence, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Sequence Analysis, {DNA}, Staining and Labeling, Tissue Plasminogen Activator},
	pages = {199--201}
},

@book{cajal_advice_1999,
	edition = {1},
	title = {Advice for a Young Investigator},
	isbn = {0262181916},
	publisher = {The {MIT} Press},
	author = {Cajal, Santiago Ramón y},
	month = feb,
	year = {1999}
},

@article{meister_synchronous_1991,
	title = {Synchronous bursts of action potentials in ganglion cells of the developing mammalian retina},
	volume = {252},
	issn = {0036-8075},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/2035024},
	abstract = {The development of orderly connections in the mammalian visual system depends on action potentials in the optic nerve fibers, even before the retina receives visual input. In particular, it has been suggested that correlated firing of retinal ganglion cells in the same eye directs the segregation of their synaptic terminals into eye-specific layers within the lateral geniculate nucleus. Such correlations in electrical activity were found by simultaneous recording of the extracellular action potentials of up to 100 ganglion cells in the isolated retina of the newborn ferret and the fetal cat. These neurons fired spikes in nearly synchronous bursts lasting a few seconds and separated by 1 to 2 minutes of silence. Individual bursts consisted of a wave of excitation, several hundred micrometers wide, sweeping across the retina at about 100 micrometers per second. These concerted firing patterns have the appropriate spatial and temporal properties to guide the refinement of connections between the retina and the lateral geniculate nucleus.},
	number = {5008},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Meister, M and Wong, R O and Baylor, D A and Shatz, C J},
	month = may,
	year = {1991},
	note = {{PMID:} 2035024},
	keywords = {Action Potentials, Aging, Animals, Animals, Newborn, Calcium, Cats, Electrophysiology, Ferrets, Retina, Retinal Ganglion Cells, Vision, Ocular},
	pages = {939--943}
},

@article{pirri_tyramine-gated_2009,
	title = {A tyramine-gated chloride channel coordinates distinct motor programs of a Caenorhabditis elegans escape response},
	volume = {62},
	issn = {0896-6273},
	doi = {10.1016/j.neuron.2009.04.013},
	abstract = {A key feature of escape responses is the fast translation of sensory information into a coordinated motor output. In C. elegans anterior touch initiates a backward escape response in which lateral head movements are suppressed. Here we show that tyramine inhibits head movements and forward locomotion through the activation of a tyramine-gated chloride channel, {LGC-55.} lgc-55 mutant animals have defects in reversal behavior and fail to suppress head oscillations in response to anterior touch. lgc-55 is expressed in neurons and muscle cells that receive direct synaptic inputs from tyraminergic motor neurons. Therefore, tyramine can act as a classical inhibitory neurotransmitter. Activation of {LGC-55} by tyramine coordinates the output of two distinct motor programs, locomotion and head movements that are critical for a C. elegans escape response.},
	number = {4},
	journal = {Neuron},
	author = {Pirri, Jennifer K. and {McPherson}, Adam D. and Donnelly, Jamie L. and Francis, Michael M. and Alkema, Mark J.},
	month = may,
	year = {2009},
	note = {{PMID:} 19477154
{PMCID:} 2804440},
	pages = {526--538}
},

@misc{bhatla_c._2009,
	title = {C. elegans - Interactive Neural Network},
	url = {http://wormweb.org/neuralnet},
	author = {Bhatla, Nikhil},
	month = jun,
	year = {2009},
	howpublished = {http://wormweb.org/neuralnet},
	file = {C. elegans - Interactive Neural Network - Details - by nikhil bhatla:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/2URK5S4K/details.html:text/html}
},

@article{bock_network_2011,
	title = {Network anatomy and in vivo physiology of visual cortical neurons},
	volume = {471},
	issn = {0028-0836},
	url = {http://dx.doi.org/10.1038/nature09802},
	doi = {10.1038/nature09802},
	number = {7337},
	journal = {Nature},
	author = {Bock, Davi D. and Lee, {Wei-Chung} Allen and Kerlin, Aaron M. and Andermann, Mark L. and Hood, Greg and Wetzel, Arthur W. and Yurgenson, Sergey and Soucy, Edward R. and Kim, Hyon Suk and Reid, R. Clay},
	month = mar,
	year = {2011},
	pages = {177--182}
},

@article{miesenbock_optical_2005,
	title = {Optical imaging and control of genetically designated neurons in functioning circuits},
	volume = {28},
	issn = {{0147-006X}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16022604},
	doi = {10.1146/annurev.neuro.28.051804.101610},
	abstract = {Proteins with engineered sensitivities to light are infiltrating the biological mechanisms by which neurons generate and detect electrochemical signals. Encoded in {DNA} and active only in genetically specified target cells, these proteins provide selective optical interfaces for observing and controlling signaling by defined groups of neurons in functioning circuits, in vitro and in vivo. Light-emitting sensors of neuronal activity (reporting calcium increase, neurotransmitter release, or membrane depolarization) have begun to reveal how information is represented by neuronal assemblies, and how these representations are transformed during the computations that inform behavior. Light-driven actuators control the electrical activities of central neurons in freely moving animals and establish causal connections between the activation of specific neurons and the expression of particular behaviors. Anchored within mathematical systems and control theory, the combination of finely resolved optical field sensing and finely resolved optical field actuation will open new dimensions for the analysis of the connectivity, dynamics, and plasticity of neuronal circuits, and perhaps even for replacing lost--or designing novel--functionalities.},
	journal = {Annual Review of Neuroscience},
	author = {Miesenböck, Gero and Kevrekidis, Ioannis G},
	year = {2005},
	note = {{PMID:} 16022604},
	keywords = {Animals, Biosensing Techniques, Calcium, Diagnostic Imaging, Genetic Engineering, Humans, Membrane Potentials, Models, Neurological, Neural Pathways, Neurons, Neurotransmitter Agents, Optics and Photonics, Photic Stimulation, Signal Transduction, Synapses, Vision, Ocular},
	pages = {533--563},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/WW2N8ZHQ/entrez.html:text/html}
},

@article{meselson_sverdlovsk_1994,
	series = {New Series},
	title = {The Sverdlovsk Anthrax Outbreak of 1979},
	volume = {266},
	issn = {00368075},
	url = {http://www.jstor.org.ezp-prod1.hul.harvard.edu/stable/2885382},
	abstract = {In April and May 1979, an unusual anthrax epidemic occurred in Sverdlovsk, Union of Soviet Socialist Republics. Soviet officials attributed it to consumption of contaminated meat. {U.S.} agencies attributed it to inhalation of spores accidentally released at a military microbiology facility in the city. Epidemiological data show that most victims worked or lived in a narrow zone extending from the military facility to the southern city limit. Farther south, livestock died of anthrax along the zone's extended axis. The zone paralleled the northerly wind that prevailed shortly before the outbreak. It is concluded that the escape of an aerosol of anthrax pathogen at the military facility caused the outbreak.},
	number = {5188},
	journal = {Science},
	author = {Meselson, Matthew and Guillemin, Jeanne and {Hugh-Jones}, Martin and Langmuir, Alexander and Popova, Ilona and Shelokov, Alexis and Yampolskaya, Olga},
	month = nov,
	year = {1994},
	note = {{ArticleType:} primary\_article / Full publication date: Nov. 18, 1994 / Copyright © 1994 American Association for the Advancement of Science},
	pages = {1202--1208}
},

@article{leifer_optogenetic_2011,
	title = {Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans},
	volume = {8},
	issn = {1548-7105},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21240279},
	doi = {10.1038/nmeth.1554},
	abstract = {We present an optogenetic illumination system capable of real-time light delivery with high spatial resolution to specified targets in freely moving Caenorhabditis elegans. A tracking microscope records the motion of an unrestrained worm expressing channelrhodopsin-2 or halorhodopsin in specific cell types. Image processing software analyzes the worm's position in each video frame, rapidly estimates the locations of targeted cells and instructs a digital micromirror device to illuminate targeted cells with laser light of the appropriate wavelengths to stimulate or inhibit activity. Because each cell in an unrestrained worm is a rapidly moving target, our system operates at high speed (∼50 frames per second) to provide high spatial resolution (∼30 μm). To test the accuracy, flexibility and utility of our system, we performed optogenetic analyses of the worm motor circuit, egg-laying circuit and mechanosensory circuits that have not been possible with previous methods.},
	number = {2},
	journal = {Nature Methods},
	author = {Leifer, Andrew M and {Fang-Yen}, Christopher and Gershow, Marc and Alkema, Mark J and Samuel, Aravinthan D T},
	month = feb,
	year = {2011},
	note = {{PMID:} 21240279},
	keywords = {Animals, Caenorhabditis elegans, Movement, Muscle Cells, Neurons, Optical Processes, Photobiology},
	pages = {147--152}
},

@misc{_red_????,
	title = {Red Hat updates real-time Linux • The Register},
	url = {http://www.theregister.co.uk/2009/02/10/redhat_mrg_fedora11/},
	howpublished = {http://www.theregister.co.uk/2009/02/10/redhat\_mrg\_fedora11/},
	file = {Red Hat updates real-time Linux • The Register:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/88TJXJ8D/redhat_mrg_fedora11.html:text/html}
},

@article{gautier_engineered_2008,
	title = {An engineered protein tag for multiprotein labeling in living cells},
	volume = {15},
	issn = {1074-5521},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18291317},
	doi = {10.1016/j.chembiol.2008.01.007},
	abstract = {The visualization of complex cellular processes involving multiple proteins requires the use of spectroscopically distinguishable fluorescent reporters. We have previously introduced the {SNAP-tag} as a general tool for the specific labeling of {SNAP-tag} fusion proteins in living cells. The {SNAP-tag} is derived from the human {DNA} repair protein {O6-alkylguanine-DNA} alkyltransferase {(AGT)} and can be covalently labeled in living cells using O6-benzylguanine derivatives bearing a chemical probe. Here we report the generation of an {AGT-based} tag, named {CLIP-tag}, which reacts specifically with O2-benzylcytosine derivatives. Because {SNAP-tag} and {CLIP-tag} possess orthogonal substrate specificities, {SNAP} and {CLIP} fusion proteins can be labeled simultaneously and specifically with different molecular probes in living cells. We furthermore show simultaneous pulse-chase experiments to visualize different generations of two different proteins in one sample.},
	number = {2},
	journal = {Chemistry \& Biology},
	author = {Gautier, Arnaud and Juillerat, Alexandre and Heinis, Christian and Corrêa, Ivan Reis, Jr and Kindermann, Maik and Beaufils, Florent and Johnsson, Kai},
	month = feb,
	year = {2008},
	note = {{PMID:} 18291317},
	keywords = {Animals, Binding Sites, Cell Survival, {CHO} Cells, Cricetinae, Cricetulus, Cytosine, Fluorescent Dyes, Models, Molecular, Mutation, {O(6)-Methylguanine-DNA} Methyltransferase, Protein Conformation, Proteins, Staining and Labeling, Substrate Specificity},
	pages = {128--136}
},

@article{lin_self-assembled_2007-1,
	title = {{Self-Assembled} Combinatorial Encoding Nanoarrays for Multiplexed Biosensing},
	volume = {7},
	issn = {1530-6984},
	doi = {10.1021/nl062998n},
	abstract = {Multiplexed and sensitive detection of nucleic acids, proteins, or other molecules from a single solution and a small amount of sample is of great demand in biomarker profiling and disease diagnostics. Here we describe a new concept using combinatorial self-assembly of {DNA} nanotiles into micrometer-sized two-dimensional arrays that carry nucleic acid probes and barcoded fluorescent dyes to achieve multiplexed detection. We demonstrated the specificity and sensitivity of the arrays by detecting multiple {DNA} sequences and aptamer binding molecules. This {DNA} tile-array-based sensor platform can be constructed through {DNA} self-assembly. The attachment of different molecular probes can be achieved by simple {DNA} hybridization so bioconjugation is not necessary for the labeling. Accurate control of the interprobe distances and solution-based binding reactions ensures fast target binding kinetics.},
	number = {2},
	journal = {Nano letters},
	author = {Lin, Chenxiang and Liu, Yan and Yan, Hao},
	month = feb,
	year = {2007},
	note = {{PMID:} 17298017
{PMCID:} 1963466},
	pages = {507--512}
},

@article{nagel_channelrhodopsin-2_2003,
	title = {Channelrhodopsin-2, a directly light-gated cation-selective membrane channel},
	volume = {100},
	url = {http://www.pnas.org/content/100/24/13940.abstract},
	doi = {10.1073/pnas.1936192100},
	abstract = {Microbial-type rhodopsins are found in archaea, prokaryotes, and eukaryotes. Some of them represent membrane ion transport proteins such as bacteriorhodopsin, a light-driven proton pump, or channelrhodopsin-1 {(ChR1)}, a recently identified light-gated proton channel from the green alga Chlamydomonas reinhardtii. {ChR1} and {ChR2}, a related microbial-type rhodopsin from C. reinhardtii, were shown to be involved in generation of photocurrents of this green alga. We demonstrate by functional expression, both in oocytes of Xenopus laevis and mammalian cells, that {ChR2} is a directly light-switched cation-selective ion channel. This channel opens rapidly after absorption of a photon to generate a large permeability for monovalent and divalent cations. {ChR2} desensitizes in continuous light to a smaller steady-state conductance. Recovery from desensitization is accelerated by extracellular H+ and negative membrane potential, whereas closing of the {ChR2} ion channel is decelerated by intracellular H+. {ChR2} is expressed mainly in C. reinhardtii under low-light conditions, suggesting involvement in photoreception in dark-adapted cells. The predicted seven-transmembrane α helices of {ChR2} are characteristic for G protein-coupled receptors but reflect a different motif for a cation-selective ion channel. Finally, we demonstrate that {ChR2} may be used to depolarize small or large cells, simply by illumination.},
	number = {24},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Nagel, Georg and Szellas, Tanjef and Huhn, Wolfram and Kateriya, Suneel and Adeishvili, Nona and Berthold, Peter and Ollig, Doris and Hegemann, Peter and Bamberg, Ernst},
	month = nov,
	year = {2003},
	pages = {13940 --13945}
},

@article{tavernarakis_unc-8_1997,
	title = {unc-8, a {DEG/ENaC} family member, encodes a subunit of a candidate mechanically gated channel that modulates C. elegans locomotion},
	volume = {18},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9010209},
	abstract = {Mechanically gated ion channels are important modulators of coordinated movement, yet little is known of their molecular properties. We report that C. elegans unc-8, originally identified by gain-of-function mutations that induce neuronal swelling and severe uncoordination, encodes a {DEG/ENaC} family member homologous to subunits of a candidate mechanically gated ion channel. unc-8 is expressed in several sensory neurons, interneurons, and motor neurons. unc-8 null mutants exhibit previously unrecognized but striking defects in the amplitude and wavelength of sinusoidal tracks inscribed as they move through an E. coli lawn. We hypothesize that {UNC-8} channels could modulate coordinated movement in response to body stretch. del-1, a second {DEG/ENaC} family member coexpressed with unc-8 in a subset of motor neurons, might also participate in a channel that contributes to nematode proprioception.},
	number = {1},
	journal = {Neuron},
	author = {Tavernarakis, N and Shreffler, W and Wang, S and Driscoll, M},
	month = jan,
	year = {1997},
	note = {{PMID:} 9010209},
	keywords = {Amino Acid Sequence, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, {DNA} Primers, Genes, Helminth, Helminth Proteins, Ion Channel Gating, Ion Channels, Molecular Sequence Data, Motor Activity, Mutagenesis, Polymerase Chain Reaction, Recombinant Proteins, Sequence Homology, Amino Acid},
	pages = {107--119},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/2DKHQAX7/9010209.html:text/html}
},

@article{goodman_mechanosensation_2006,
	title = {Mechanosensation},
	url = {http://www.wormbook.org/chapters/www_mechanosensation/mechanosensation.html},
	doi = {10.1895/wormbook.1.62.1},
	abstract = {Wild C. elegans and other nematodes live in dirt and eat bacteria, relying on mechanoreceptor neurons {(MRNs)} to detect collisions with soil particles and other animals as well as forces generated by their own movement. {MRNs} may also help animals detect bacterial food sources. Hermaphrodites and males have 22 putative {MRNs;} males have an additional 46 {MRNs}, most, if not all of which are needed for mating. This chapter reviews key aspects of C. elegans  mechanosensation, including {MRN} anatomy, what is known about their contributions to behavior as well as the neural circuits linking {MRNs} to movement. Emerging models of the mechanisms used to convert mechanical energy into electrical signals are also discussed. Prospects for future research include expanding our understanding of the molecular basis of mechanotransduction and how activation of {MRNs} guides and modulates behavior.},
	journal = {{WormBook}},
	author = {Goodman, Miriam B.},
	month = jan,
	year = {2006},
	file = {Mechanosensation:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/9P5X7STV/mechanosensation.html:text/html}
},

@article{goodman_active_1998,
	title = {Active currents regulate sensitivity and dynamic range in C. elegans neurons},
	volume = {20},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9581767},
	abstract = {Little is known about the physiology of neurons in Caenorhabditis elegans. Using new techniques for in situ patch-clamp recording in C. elegans, we analyzed the electrical properties of an identified sensory neuron {(ASER)} across four developmental stages and 42 unidentified neurons at one stage. We find that {ASER} is nearly isopotential and fails to generate classical Na+ action potentials. Rather, {ASER} displays a high sensitivity to input currents coupled to a depolarization-dependent reduction in sensitivity that may endow {ASER} with a wide dynamic range. Voltage clamp revealed depolarization-activated K+ and Ca2+ currents that contribute to high sensitivity near the zero-current potential. The depolarization-dependent reduction in sensitivity can be attributed to activation of K+ current at voltages where it dominates the net membrane current. The voltage dependence of membrane current was similar in all neurons examined, suggesting that C. elegans neurons share a common mechanism of sensitivity and dynamic range.},
	number = {4},
	journal = {Neuron},
	author = {Goodman, M B and Hall, D H and Avery, L and Lockery, S R},
	month = apr,
	year = {1998},
	note = {{PMID:} 9581767},
	keywords = {Animals, Caenorhabditis elegans, Chemoreceptor Cells, Cilia, Larva, Membrane Potentials, Neurons, Neurons, Afferent, {Patch-Clamp} Techniques, Signal Transduction, Synapses, Time Factors},
	pages = {763--772}
},

@article{geiss_direct_2008,
	title = {Direct multiplexed measurement of gene expression with color-coded probe pairs},
	volume = {26},
	issn = {1546-1696},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18278033},
	doi = {10.1038/nbt1385},
	abstract = {We describe a technology, the {NanoString} {nCounter} gene expression system, which captures and counts individual {mRNA} transcripts. Advantages over existing platforms include direct measurement of {mRNA} expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 {fM} and 0.5 {fM}, and a linear dynamic range of over 500-fold. Comparison of the {NanoString} {nCounter} gene expression system with microarrays and {TaqMan} {PCR} demonstrated that the {nCounter} system is more sensitive than microarrays and similar in sensitivity to real-time {PCR.} Finally, a comparison of transcript levels for 21 genes across seven samples measured by the {nCounter} system and {SYBR} Green real-time {PCR} demonstrated similar patterns of gene expression at all transcript levels.},
	number = {3},
	journal = {Nature Biotechnology},
	author = {Geiss, Gary K and Bumgarner, Roger E and Birditt, Brian and Dahl, Timothy and Dowidar, Naeem and Dunaway, Dwayne L and Fell, H Perry and Ferree, Sean and George, Renee D and Grogan, Tammy and James, Jeffrey J and Maysuria, Malini and Mitton, Jeffrey D and Oliveri, Paola and Osborn, Jennifer L and Peng, Tao and Ratcliffe, Amber L and Webster, Philippa J and Davidson, Eric H and Hood, Leroy and Dimitrov, Krassen},
	month = mar,
	year = {2008},
	note = {{PMID:} 18278033},
	keywords = {Cell Line, Color, {DNA} Probes, Gene Expression Profiling, Gene Library, Genes, Reporter, Humans, Image Processing, {Computer-Assisted}, Nanotechnology, Oligonucleotide Array Sequence Analysis, Poliovirus, Polymerase Chain Reaction, Reproducibility of Results, {RNA}, Messenger, Sensitivity and Specificity},
	pages = {317--325}
},

@article{ward_chemotaxis_1973,
	title = {Chemotaxis by the nematode Caenorhabditis elegans: identification of attractants and analysis of the response by use of mutants},
	volume = {70},
	issn = {0027-8424},
	shorttitle = {Chemotaxis by the nematode Caenorhabditis elegans},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/4351805},
	doi = {PMC433366},
	abstract = {The nematode Caenorhabditis elegans is attracted by at least four classes of attractants: by cyclic nucleotides, {cAMP} and {cGMP;} by anions, Cl(-), Br(-), I(-); by cations, Na(+), Li(+), K(+), Mg(+); and by alkaline {pH} values. The nematode's behavioral response to gradients of these attractants involves orientation and movement up the gradient, accumulation, and then habitutation. Comparison of the tracks of wild-type and mutant animals responding to gradients of attractants indicates that sensory receptors in the head alone mediate the orientation response and that the direction of orientation is determined by the lateral motion of the head. Therefore, the orientation response is a klinotaxis.},
	number = {3},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Ward, S},
	month = mar,
	year = {1973},
	note = {{PMID:} 4351805},
	keywords = {Acetates, Adenosine Monophosphate, Ammonia, Ammonium Chloride, Bromides, Chemotaxis, Chlorides, Cyclic {AMP}, Cyclic {GMP}, Cysteine, Histidine, {Hydrogen-Ion} Concentration, Iodides, Lithium, Lysine, Magnesium, Mutation, Nematoda, Potassium, {PQ}, {PQE}  - definite citation, {PQE} Specific Aim 2, Sodium},
	pages = {817--21}
},

@article{bryden_neural_2008,
	title = {Neural control of Caenorhabditis elegans forward locomotion: the role of sensory feedback},
	volume = {98},
	issn = {0340-1200},
	shorttitle = {Neural control of Caenorhabditis elegans forward locomotion},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18350313},
	doi = {10.1007/s00422-008-0212-6},
	abstract = {This paper presents a simple yet biologically-grounded model for the neural control of Caenorhabditis elegans forward locomotion. We identify a minimal circuit within the C. elegans ventral cord that is likely to be sufficient to generate and sustain forward locomotion in vivo. This limited subcircuit appears to contain no obvious central pattern generated control. For that subcircuit, we present a model that relies on a chain of oscillators along the body which are driven by local and proximate mechano-sensory input. Computer simulations were used to study the model under a variety of conditions and to test whether it is behaviourally plausible. Within our model, we find that a minimal circuit of {AVB} interneurons and B-class motoneurons is sufficient to generate and sustain fictive forward locomotion patterns that are robust to significant environmental perturbations. The model predicts speed and amplitude modulation by the {AVB} command interneurons. An extended model including D-class motoneurons is included for comparison.},
	number = {4},
	journal = {Biological Cybernetics},
	author = {Bryden, John and Cohen, Netta},
	month = apr,
	year = {2008},
	note = {{PMID:} 18350313},
	keywords = {Animals, Caenorhabditis elegans, Computer Simulation, Feedback, Locomotion, Models, Neurological, Nerve Net, Neural Networks {(Computer)}, Neurons, Sensation},
	pages = {339--351}
},

@article{sawin_c._2000,
	title = {C. elegans locomotory rate is modulated by the environment through a dopaminergic pathway and by experience through a serotonergic pathway},
	volume = {26},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10896158},
	abstract = {Caenorhabditis elegans modulates its locomotory rate in response to its food, bacteria, in two ways. First, well-fed wild-type animals move more slowly in the presence of bacteria than in the absence of bacteria. This basal slowing response is mediated by a dopamine-containing neural circuit that senses a mechanical attribute of bacteria and may be an adaptive mechanism that increases the amount of time animals spend in the presence of food. Second, food-deprived wild-type animals, when transferred to bacteria, display a dramatically enhanced slowing response that ensures that the animals do not leave their newly encountered source of food. This experience-dependent response is mediated by serotonergic neurotransmission and is potentiated by fluoxetine {(Prozac).} The basal and enhanced slowing responses are distinct and separable neuromodulatory components of a genetically tractable paradigm of behavioral plasticity.},
	number = {3},
	journal = {Neuron},
	author = {Sawin, E R and Ranganathan, R and Horvitz, H R},
	month = jun,
	year = {2000},
	note = {{PMID:} 10896158},
	keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Catalase, Dopamine, Environment, Escherichia coli, Fluoxetine, Food Deprivation, Fungal Proteins, Helminth Proteins, Mechanoreceptors, Mixed Function Oxygenases, Motor Activity, Mutation, Neurons, Serotonin, Serotonin Uptake Inhibitors, Time Factors, {Trans-Activators}},
	pages = {619--631},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/PE6R963U/entrez.html:text/html;science.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/U8T3P4S8/science.pdf:application/pdf}
},

@article{chang_hypoxia_2008,
	title = {Hypoxia and the {HIF-1} transcriptional pathway reorganize a neuronal circuit for oxygen-dependent behavior in Caenorhabditis elegans},
	volume = {105},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2438248},
	doi = {10.1073/pnas.0802164105},
	number = {20},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Chang, Andy J. and Bargmann, Cornelia I.},
	month = may,
	year = {2008},
	note = {{PMC2438248}},
	pages = {7321–7326},
	file = {PubMed Central Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/EQQ8EF5C/Chang and Bargmann - 2008 - Hypoxia and the HIF-1 transcriptional pathway reor.pdf:application/pdf;PubMed Central Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/56R3K76R/articlerender.html:text/html}
},

@article{lee_eat-4_1999,
	title = {{EAT-4}, a homolog of a mammalian sodium-dependent inorganic phosphate cotransporter, is necessary for glutamatergic neurotransmission in Caenorhabditis elegans},
	volume = {19},
	number = {1},
	journal = {Journal of Neuroscience},
	author = {Lee, R. {Y.N} and Sawin, E. R and Chalfie, M. and Horvitz, H. R and Avery, L.},
	year = {1999},
	pages = {159},
	file = {159.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/EQQRMQK2/159.pdf:application/pdf}
},

@book{helstrom_statistical_1968,
	address = {Oxford, New York},
	edition = {2d ed., rev. and enl},
	series = {International series of monographs in electronics and instrumentation, v. 9},
	title = {Statistical Theory of Signal Detection},
	isbn = {0080132650},
	lccn = {{TK5101} {.H39} 1968},
	publisher = {Pergamon Press},
	author = {Helstrom, Carl W},
	year = {1968},
	keywords = {Signal detection, Statistical communication theory}
},

@article{lis_size_1975,
	title = {Size fractionation of double-stranded {DNA} by precipitation with polyethylene glycol},
	volume = {2},
	issn = {0305-1048},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/236548},
	abstract = {We show that {DNA} molecules of differing molecular mass are separable by selective precipitation with polyethylene glycol {(PEG+..} Higher molecular mass {DNA} precipitates at lower {PEG} concentrations than lower molecular mass {DNA.} Double-stranded {DNA} can be fractionated at least in the range of 3 times 10-7 to 1 times 10-5 daltons. The effects on {PEG} concentration, sodium chloride concentration, {DNA} concentration, {pH}, divalent ions, precipitation time, and centrifugal force have been determined. These studies show {PEG} precipitation offers a size fractionation method for {DNA} which is convenient, of high capacity, and applicable over a wide range of conditions. However, resolution is not high and separation of two species approaches 100\% only if they differ in molecular mass by at least a factor of two.},
	number = {3},
	journal = {Nucleic Acids Research},
	author = {Lis, J T and Schleif, R},
	month = mar,
	year = {1975},
	note = {{PMID:} 236548},
	keywords = {Cations, Divalent, Coliphages, Deoxyribonucleases, {DNA} Viruses, {DNA}, Viral, Electrophoresis, Polyacrylamide Gel, Endonucleases, Haemophilus influenzae, {Hydrogen-Ion} Concentration, Methods, Molecular Weight, Osmolar Concentration, Polyethylene Glycols, Sodium Chloride, Time Factors, Ultracentrifugation},
	pages = {383--389}
},

@book{wainstein_extraction_1962,
	address = {Englewood Cliffs, N. J.},
	title = {Extraction of signals from noise},
	publisher = {{Prentice-Hall}},
	author = {Wainstein, L. A and Zubakov, V. D},
	year = {1962}
},

@book{bradski_learning_2008,
	edition = {1st},
	title = {Learning {OpenCV:} Computer Vision with the {OpenCV} Library},
	isbn = {0596516134},
	shorttitle = {Learning {OpenCV}},
	publisher = {{O'Reilly} Media, Inc.},
	author = {Bradski, Gary and Kaehler, Adrian},
	month = oct,
	year = {2008},
	file = {Bradski and Kaehler - 2008 - Learning OpenCV Computer Vision with the OpenCV L.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/3NBCMQ5K/Bradski and Kaehler - 2008 - Learning OpenCV Computer Vision with the OpenCV L.pdf:application/pdf}
},

@article{stephens_dimensionality_2008,
	title = {Dimensionality and Dynamics in the Behavior of C. elegans},
	volume = {4},
	url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1000028},
	doi = {10.1371/journal.pcbi.1000028},
	abstract = {A major challenge in analyzing animal behavior is to discover some underlying simplicity in complex motor actions. Here, we show that the space of shapes adopted by the nematode Caenorhabditis elegans is low dimensional, with just four dimensions accounting for 95\% of the shape variance. These dimensions provide a quantitative description of worm behavior, and we partially reconstruct “equations of motion” for the dynamics in this space. These dynamics have multiple attractors, and we find that the worm visits these in a rapid and almost completely deterministic response to weak thermal stimuli. Stimulus-dependent correlations among the different modes suggest that one can generate more reliable behaviors by synchronizing stimuli to the state of the worm in shape space. We confirm this prediction, effectively “steering” the worm in real time.},
	number = {4},
	journal = {{PLoS} Computational Biology},
	author = {Stephens, Greg J. and {Johnson-Kerner}, Bethany and Bialek, William and Ryu, William S.},
	month = apr,
	year = {2008},
	keywords = {{ImageProcessing}, {OpenCV}},
	pages = {e1000028}
},

@article{pearce_intersegmental_1984,
	title = {Intersegmental coordination of leech swimming: comparison of in situ and isolated nerve cord activity with body wall movement},
	volume = {299},
	issn = {0006-8993},
	shorttitle = {Intersegmental coordination of leech swimming},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/6733455},
	abstract = {Recordings of motoneuron activity during swimming, obtained from leech ventral nerve cords in situ, were compared with films of swimming leeches and with recordings of motoneuron activity from isolated nerve cords. It was found that the intersegmental phase lag in body movement is greater than the phase lag of in situ neuronal activity, which is in turn greater than the phase lag of isolated nerve cord activity. We conclude that peripheral neuronal or mechanical effects, as well as sensory feedback to the central pattern generator, contribute to the movement pattern of the intact swimming leech.},
	number = {2},
	journal = {Brain Research},
	author = {Pearce, R A and Friesen, W O},
	month = may,
	year = {1984},
	note = {{PMID:} 6733455},
	keywords = {Animals, Electrophysiology, Leeches, Motor Activity, Motor Neurons, Nervous System Physiological Phenomena},
	pages = {363--366}
},

@article{kuroyanagi_transgenic_2006,
	title = {Transgenic alternative-splicing reporters reveal tissue-specific expression profiles and regulation mechanisms in vivo},
	volume = {3},
	issn = {1548-7091},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17060915},
	doi = {10.1038/nmeth944},
	abstract = {Alternative splicing of {pre-mRNAs} allows multicellular organisms to create a huge diversity of proteomes from a finite number of genes. But extensive studies in vitro or in cultured cells have not fully explained the regulation mechanisms of tissue-specific or developmentally regulated alternative splicing in living organisms. Here we report a transgenic reporter system that allows visualization of expression profiles of mutually exclusive exons in Caenorhabditis elegans. Reporters for egl-15 exons {5A} and {5B} showed tissue-specific profiles, and we isolated mutants defective in the tissue specificity. We identified alternative-splicing defective-1 (asd-1), encoding a new {RNA-binding} protein of the evolutionarily conserved Fox-1 family, as a regulator of the egl-15 reporter. Furthermore, an asd-1;fox-1 double mutant was defective in the expression of endogenous egl-15 {(5A)} and phenocopied egl-15 {(5A)} mutant. This transgenic reporter system can be a powerful experimental tool for the comprehensive study of expression profiles and regulation mechanisms of alternative splicing in metazoans.},
	number = {11},
	journal = {Nature Methods},
	author = {Kuroyanagi, Hidehito and Kobayashi, Tetsuo and Mitani, Shohei and Hagiwara, Masatoshi},
	month = nov,
	year = {2006},
	note = {{PMID:} 17060915},
	keywords = {Alternative Splicing, Amino Acid Sequence, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Exons, Gene Expression Profiling, Genes, Reporter, Molecular Sequence Data, Mutation, Receptors, Fibroblast Growth Factor, Reverse Transcriptase Polymerase Chain Reaction, {RNA-Binding} Proteins, Transgenes},
	pages = {909--915}
},

@article{hwang_nociceptive_2007-1,
	title = {Nociceptive Neurons Protect Drosophila Larvae from Parasitoid Wasps},
	volume = {17},
	issn = {09609822},
	url = {http://www.cell.com.ezp-prod1.hul.harvard.edu/current-biology/retrieve/pii/S0960982207022683},
	doi = {10.1016/j.cub.2007.11.029},
	number = {24},
	journal = {Current Biology},
	author = {Hwang, Richard Y. and Zhong, Lixian and Xu, Yifan and Johnson, Trevor and Zhang, Feng and Deisseroth, Karl and Tracey, W. Daniel},
	month = dec,
	year = {2007},
	pages = {2105--2116}
},

@misc{_worm_????,
	title = {Worm Atlas: {AFD} Neuron},
	url = {http://www.wormatlas.org/neurons.htm/afd.htm}
},

@article{faumont_awake_2006,
	title = {The Awake Behaving Worm: Simultaneous Imaging of Neuronal Activity and Behavior in Intact Animals at Millimeter Scale},
	volume = {95},
	shorttitle = {The Awake Behaving Worm},
	url = {http://jn.physiology.org/cgi/content/abstract/95/3/1976},
	doi = {10.1152/jn.01050.2005},
	abstract = {Genetically encoded optical probes of neuronal activity offer the prospect of simultaneous recordings of neuronal activity and behavior in intact animals. A central problem in simultaneous imaging is that the field of view of the high-power objective required for imaging the neuron is often too small to allow the experimenter to assess the overall behavioral state of the animal. Here we present a method that solves this problem using a microscope with two objectives focused on the preparation: a high-power lens dedicated to imaging the neuron and low-power lens dedicated to imaging the behavior. Images of activity and behavior are acquired simultaneously but separately using different wavelengths of light. The new approach was tested using the cameleon calcium sensor expressed in Caenorhabditis elegans sensory neurons. We show that simultaneous recordings of neuronal activity and behavior are practical in C. elegans and, moreover, that such recordings can reveal subtle, transient correlations between calcium levels and behavior that may be missed in nonsimultaneous recordings. The new method is likely to be useful whenever it would be desirable to record simultaneously at two different spatial resolutions from a single location, or from two different locations in space.},
	number = {3},
	journal = {J Neurophysiol},
	author = {Faumont, Serge and Lockery, Shawn R.},
	month = mar,
	year = {2006},
	pages = {1976--1981},
	file = {HighWire Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/2EXA2AJZ/1976.html:text/html}
},

@article{lockery_artificial_2008,
	title = {Artificial Dirt: Microfluidic Substrates for Nematode Neurobiology and Behavior},
	volume = {99},
	shorttitle = {Artificial Dirt},
	url = {http://jn.physiology.org/cgi/content/abstract/99/6/3136},
	doi = {10.1152/jn.91327.2007},
	abstract = {With a nervous system of only 302 neurons, the free-living nematode Caenorhabditis elegans is a powerful experimental organism for neurobiology. However, the laboratory substrate commonly used in C. elegans research, a planar agarose surface, fails to reflect the complexity of this organism's natural environment, complicates stimulus delivery, and is incompatible with high-resolution optophysiology experiments. Here we present a new class of microfluidic devices for C. elegans neurobiology and behavior: agarose-free, micron-scale chambers and channels that allow the animals to crawl as they would on agarose. One such device mimics a moist soil matrix and facilitates rapid delivery of fluid-borne stimuli. A second device consists of sinusoidal channels that can be used to regulate the waveform and trajectory of crawling worms. Both devices are thin and transparent, rendering them compatible with high-resolution microscope objectives for neuronal imaging and optical recording. Together, the new devices are likely to accelerate studies of the neuronal basis of behavior in C. elegans.},
	number = {6},
	journal = {J Neurophysiol},
	author = {Lockery, S. R. and Lawton, K. J. and Doll, J. C. and Faumont, S. and Coulthard, S. M. and Thiele, T. R. and Chronis, N. and {McCormick}, K. E. and Goodman, M. B. and Pruitt, B. L.},
	month = jun,
	year = {2008},
	pages = {3136--3143},
	file = {3136.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/J4TF5WVN/3136.pdf:application/pdf;Artificial Dirt: Microfluidic Substrates for Nematode Neurobiology and Behavior -- Lockery et al. 99 (6): 3136 -- Journal of Neurophysiology:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/G8A6U9I2/3136.html:text/html}
},

@article{heilemann_subdiffraction-resolution_2008,
	title = {Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes},
	volume = {47},
	issn = {1521-3773},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18646237},
	doi = {10.1002/anie.200802376},
	number = {33},
	journal = {Angewandte Chemie {(International} Ed. in English)},
	author = {Heilemann, Mike and van de Linde, Sebastian and Schüttpelz, Mark and Kasper, Robert and Seefeldt, Britta and Mukherjee, Anindita and Tinnefeld, Philip and Sauer, Markus},
	year = {2008},
	note = {{PMID:} 18646237},
	keywords = {Animals, Carbocyanines, Cercopithecus aethiops, {COS} Cells, Cyclic {AMP}, Fluorescent Dyes, Microfilaments, Microscopy, Fluorescence, Microtubules, Phalloidine},
	pages = {6172--6176}
},

@article{ardiel_behavioral_2008,
	title = {Behavioral Plasticity in the C. elegans  Mechanosensory Circuit},
	volume = {22},
	issn = {0167-7063},
	shorttitle = {{\textless}title xmlns="http},
	url = {http://informahealthcare.com.ezp-prod1.hul.harvard.edu/doi/abs/10.1080/01677060802298509},
	doi = {10.1080/01677060802298509},
	number = {3},
	journal = {Journal of Neurogenetics},
	author = {Ardiel, Evan L. and Rankin, Catharine H.},
	month = jan,
	year = {2008},
	pages = {239--255}
},

@article{han_multiple-color_2007,
	title = {{Multiple-Color} Optical Activation, Silencing, and Desynchronization of Neural Activity, with {Single-Spike} Temporal Resolution},
	volume = {2},
	url = {http://dx.plos.org/10.1371/journal.pone.0000299},
	doi = {10.1371/journal.pone.0000299},
	abstract = {The quest to determine how precise neural activity patterns mediate computation, behavior, and pathology would be greatly aided by a set of tools for reliably activating and inactivating genetically targeted neurons, in a temporally precise and rapidly reversible fashion. Having earlier adapted a light-activated cation channel, channelrhodopsin-2 {(ChR2)}, for allowing neurons to be stimulated by blue light, we searched for a complementary tool that would enable optical neuronal inhibition, driven by light of a second color. Here we report that targeting the codon-optimized form of the light-driven chloride pump halorhodopsin from the archaebacterium Natronomas pharaonis (hereafter abbreviated Halo) to genetically-specified neurons enables them to be silenced reliably, and reversibly, by millisecond-timescale pulses of yellow light. We show that trains of yellow and blue light pulses can drive high-fidelity sequences of hyperpolarizations and depolarizations in neurons simultaneously expressing yellow light-driven Halo and blue light-driven {ChR2}, allowing for the first time manipulations of neural synchrony without perturbation of other parameters such as spiking rates. The {Halo/ChR2} system thus constitutes a powerful toolbox for multichannel photoinhibition and photostimulation of virally or transgenically targeted neural circuits without need for exogenous chemicals, enabling systematic analysis and engineering of the brain, and quantitative bioengineering of excitable cells.},
	number = {3},
	journal = {{PLoS} {ONE}},
	author = {Han, Xue and Boyden, Edward S.},
	year = {2007},
	pages = {e299},
	file = {PLoS Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/BVCVVFXD/Han and Boyden - 2007 - Multiple-Color Optical Activation, Silencing, and .pdf:application/pdf;PLoS Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/8JCPEWXW/infodoi10.1371journal.pone.html:text/html}
},

@article{zhang_channelrhodopsin-2_2006,
	title = {Channelrhodopsin-2 and optical control of excitable cells},
	volume = {3},
	issn = {1548-7091},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16990810},
	doi = {10.1038/nmeth936},
	abstract = {Electrically excitable cells are important in the normal functioning and in the pathophysiology of many biological processes. These cells are typically embedded in dense, heterogeneous tissues, rendering them difficult to target selectively with conventional electrical stimulation methods. The algal protein Channelrhodopsin-2 offers a new and promising solution by permitting minimally invasive, genetically targeted and temporally precise photostimulation. Here we explore technological issues relevant to the temporal precision, spatial targeting and physiological implementation of {ChR2}, in the context of other photostimulation approaches to optical control of excitable cells.},
	number = {10},
	journal = {Nature Methods},
	author = {Zhang, Feng and Wang, {Li-Ping} and Boyden, Edward S and Deisseroth, Karl},
	month = oct,
	year = {2006},
	note = {{PMID:} 16990810},
	keywords = {Algal Proteins, Cell Membrane, Eukaryota, Light, Photochemistry, Sensory Rhodopsins},
	pages = {785--792}
},

@article{yildiz_kinesin_2004,
	title = {Kinesin walks hand-over-hand},
	volume = {303},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/14684828},
	doi = {10.1126/science.1093753},
	abstract = {Kinesin is a processive motor that takes 8.3-nm center-of-mass steps along microtubules for each adenosine triphosphate hydrolyzed. Whether kinesin moves by a "hand-over-hand" or an "inchworm" model has been controversial. We have labeled a single head of the kinesin dimer with a Cy3 fluorophore and localized the position of the dye to within 2 nm before and after a step. We observed that single kinesin heads take steps of 17.3 +/- 3.3 nm. A kinetic analysis of the dwell times between steps shows that the 17-nm steps alternate with 0-nm steps. These results strongly support a hand-over-hand mechanism, and not an inchworm mechanism. In addition, our results suggest that kinesin is bound by both heads to the microtubule while it waits for adenosine triphosphate in between steps.},
	number = {5658},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Yildiz, Ahmet and Tomishige, Michio and Vale, Ronald D and Selvin, Paul R},
	month = jan,
	year = {2004},
	note = {{PMID:} 14684828},
	keywords = {Adenosine Triphosphate, Carbocyanines, Dimerization, Fluorescence, Fluorescent Dyes, Humans, Kinesin, Kinetics, Microtubules, Models, Biological, Models, Molecular, Molecular Motor Proteins, Mutation, Protein Conformation},
	pages = {676--678}
},

@article{gray_oxygen_2004,
	title = {Oxygen sensation and social feeding mediated by a C. elegans guanylate cyclase homologue},
	volume = {430},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15220933},
	doi = {10.1038/nature02714},
	abstract = {Specialized oxygen-sensing cells in the nervous system generate rapid behavioural responses to oxygen. We show here that the nematode Caenorhabditis elegans exhibits a strong behavioural preference for 5-12\% oxygen, avoiding higher and lower oxygen levels. 3',5'-cyclic guanosine monophosphate {(cGMP)} is a common second messenger in sensory transduction and is implicated in oxygen sensation. Avoidance of high oxygen levels by C. elegans requires the sensory {cGMP-gated} channel tax-2/tax-4 and a specific soluble guanylate cyclase homologue, gcy-35. The {GCY-35} haem domain binds molecular oxygen, unlike the haem domains of classical nitric-oxide-regulated guanylate cyclases. {GCY-35} and {TAX-4} mediate oxygen sensation in four sensory neurons that control a naturally polymorphic social feeding behaviour in C. elegans. Social feeding and related behaviours occur only when oxygen exceeds C. elegans' preferred level, and require gcy-35 activity. Our results suggest that {GCY-35} is regulated by molecular oxygen, and that social feeding can be a behavioural strategy for responding to hyperoxic environments.},
	number = {6997},
	journal = {Nature},
	author = {Gray, Jesse M and Karow, David S and Lu, Hang and Chang, Andy J and Chang, Jennifer S and Ellis, Ronald E and Marletta, Michael A and Bargmann, Cornelia I},
	month = jul,
	year = {2004},
	note = {{PMID:} 15220933},
	keywords = {Animals, Bacteria, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Aggregation, Cyclic {GMP}, Feeding Behavior, Food, Gases, Guanylate Cyclase, Heme, Hyperoxia, Ion Channels, Mutation, Neurons, Afferent, Nitric Oxide, Oxygen, Protein Binding, Protein Structure, Tertiary, Social Behavior},
	pages = {317--322},
	file = {nature02714.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/NVD4BRT3/nature02714.pdf:application/pdf;Oxygen sensation and social feeding mediated by a : C. elegans: guanylate cyclase homologue : Article : Nature:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/DZ9NKWMJ/nature02714.html:text/html;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/G3A42I3R/15220933.html:text/html}
},

@incollection{atlun_mesodermal_2006,
	title = {Mesodermal Organs: Body wall Muscle {(Muscle} Part {II)}},
	url = {http://www.wormatlas.org/handbook/mesodermal.htm/musclepartII.htm},
	booktitle = {{WormAtlas}},
	author = {Atlun, Z. F. and Hall, {D.H.}},
	year = {2006},
	keywords = {Print Me!},
	file = {:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/BNZ9WSVZ/musclepartII.html:text/html}
},

@article{yizhar_optogenetics_2011,
	title = {Optogenetics in neural systems},
	volume = {71},
	issn = {1097-4199},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21745635},
	doi = {10.1016/j.neuron.2011.06.004},
	abstract = {Both observational and perturbational technologies are essential for advancing the understanding of brain function and dysfunction. But while observational techniques have greatly advanced in the last century, techniques for perturbation that are matched to the speed and heterogeneity of neural systems have lagged behind. The technology of optogenetics represents a step toward addressing this disparity. Reliable and targetable single-component tools (which encompass both light sensation and effector function within a single protein) have enabled versatile new classes of investigation in the study of neural systems. Here we provide a primer on the application of optogenetics in neuroscience, focusing on the single-component tools and highlighting important problems, challenges, and technical considerations.},
	number = {1},
	journal = {Neuron},
	author = {Yizhar, Ofer and Fenno, Lief E and Davidson, Thomas J and Mogri, Murtaza and Deisseroth, Karl},
	month = jul,
	year = {2011},
	note = {{PMID:} 21745635},
	keywords = {Animals, Brain, Genetics, Neurons, Neurosciences, Opsins, Optics and Photonics, Photic Stimulation, Research},
	pages = {9--34}
},

@article{litke_retinal_1991,
	title = {The retinal readout array},
	volume = {310},
	issn = {01689002},
	url = {http://adsabs.harvard.edu/abs/1991NIMPA.310..389L},
	doi = {10.1016/0168-9002(91)91066-5},
	journal = {Nuclear Instruments and Methods in Physics Research Section A:  Accelerators, Spectrometers, Detectors and Associated Equipment},
	author = {Litke, A},
	month = dec,
	year = {1991},
	pages = {389--394}
},

@article{pregibon_multifunctional_2007,
	title = {Multifunctional encoded particles for high-throughput biomolecule analysis},
	volume = {315},
	issn = {1095-9203},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17347435},
	doi = {10.1126/science.1134929},
	abstract = {High-throughput screening for genetic analysis, combinatorial chemistry, and clinical diagnostics benefits from multiplexing, which allows for the simultaneous assay of several analytes but necessitates an encoding scheme for molecular identification. Current approaches for multiplexed analysis involve complicated or expensive processes for encoding, functionalizing, or decoding active substrates (particles or surfaces) and often yield a very limited number of analyte-specific codes. We present a method based on continuous-flow lithography that combines particle synthesis and encoding and probe incorporation into a single process to generate multifunctional particles bearing over a million unique codes. By using such particles, we demonstrate a multiplexed, single-fluorescence detection of {DNA} oligomers with encoded particle libraries that can be scanned rapidly in a flow-through microfluidic channel. Furthermore, we demonstrate with high specificity the same multiplexed detection using individual multiprobe particles.},
	number = {5817},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Pregibon, Daniel C and Toner, Mehmet and Doyle, Patrick S},
	month = mar,
	year = {2007},
	note = {{PMID:} 17347435},
	keywords = {Chemistry Techniques, Analytical, {DNA}, Fluorescence, Fluorescent Dyes, Microfluidic Analytical Techniques, Microfluidics, Molecular Probe Techniques, Particle Size, Reproducibility of Results, Sensitivity and Specificity},
	pages = {1393--1396}
},

@misc{intel_opencv_2009,
	title = {{OpenCV} Wiki},
	url = {http://opencv.willowgarage.com/wiki/},
	author = {Intel},
	year = {2009},
	howpublished = {http://opencv.willowgarage.com/wiki/},
	file = {Welcome - OpenCV Wiki:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/IRBFJ829/wiki.html:text/html}
},

@misc{alkema_personal_2009,
	title = {Personal Communication},
	abstract = {Mark suggested that perhaps foraging in C. elegans is used to sense chemical or thermal gradients.},
	author = {Alkema, Mark J.},
	month = may,
	year = {2009}
},

@article{von_stetina_motor_2006,
	title = {The motor circuit},
	volume = {69},
	issn = {0074-7742},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16492464},
	doi = {10.1016/S0074-7742(05)69005-8},
	abstract = {Caenorhabditis elegans motor neurons control a range of activities including locomotion, foraging, defecation, and gender-specific functions. In this chapter,we focus primarily on motor neurons that regulate body movement, with particular emphasis on those in the ventral nerve cord {(VNC).} We describe the basic architecture and development of the motor circuit, genes that specify motor neuron fates, and models of how the motor circuit controls locomotion. We identify surprising similarities between the structure and development of the nematode and vertebrate axial nerve cords and speculate about the potential roles of conserved families of transcription factors in the evolution of these motor circuits.},
	journal = {International Review of Neurobiology},
	author = {Von Stetina, Stephen E and Treinin, Millet and Miller, David M},
	year = {2006},
	note = {{PMID:} 16492464},
	keywords = {Animals, Caenorhabditis elegans, Cell Differentiation, Locomotion, Models, Neurological, Movement, Nerve Net, Neural Pathways, Neurons, Review},
	pages = {125--167}
},

@article{lin_designer_2009,
	title = {Designer {DNA} nanoarchitectures},
	volume = {48},
	issn = {1520-4995},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19199428},
	doi = {10.1021/bi802324w},
	abstract = {Naturally existing biological systems, from the simplest unicellular diatom to the most sophisticated organ such as the human brain, are functional self-assembled architectures. Scientists have long been dreaming about building artificial nanostructures that can mimic such elegance in nature. Structural {DNA} nanotechnology, which uses {DNA} as a blueprint and building material to organize matter with nanometer precision, represents an appealing solution to this challenge. On the basis of the knowledge of helical {DNA} structure and {Watson-Crick} base pairing rules, scientists have constructed a number of {DNA} nanoarchitectures with a large variety of geometries, topologies, and periodicities with considerably high yields. Modified by functional groups, those {DNA} nanostructures can serve as scaffolds to control the positioning of other molecular species, which opens opportunities to study intermolecular synergies, such as protein-protein interactions, as well as to build artificial multicomponent nanomachines. In this review, we summarize the principle of {DNA} self-assembly, describe the exciting progress of structural {DNA} nanotechnology in recent years, and discuss the current frontier.},
	number = {8},
	journal = {Biochemistry},
	author = {Lin, Chenxiang and Liu, Yan and Yan, Hao},
	month = mar,
	year = {2009},
	note = {{PMID:} 19199428},
	keywords = {{DNA}, Nanostructures, Nanotechnology, Nucleic Acid Conformation, Reproducibility of Results},
	pages = {1663--1674}
},

@article{hart_distinct_1999,
	title = {Distinct signaling pathways mediate touch and osmosensory responses in a polymodal sensory neuron},
	volume = {19},
	issn = {0270-6474},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10066248},
	abstract = {The Caenorhabditis elegans {ASH} sensory neurons mediate responses to nose touch, hyperosmolarity, and volatile repellent chemicals. We show here that distinct signaling pathways mediate the responses to touch and hyperosmolarity. {ASH} neurons distinguish between these stimuli because habituation to nose touch has no effect on the response to high osmolarity or volatile chemicals (1-octanol). Mutations in osm-10 eliminate the response to hyperosmolarity but have no effect on responses to nose touch or to volatile repellents. {OSM-10} is a novel cytosolic protein expressed in {ASH} and three other classes of sensory neurons. Mutations in two other osmosensory-defective genes, eos-1 and eos-2, interact genetically with osm-10. Our analysis suggests that nose touch sensitivity and osmosensation occur via distinct signaling pathways in {ASH} and that {OSM-10} is required for osmosensory signaling.},
	number = {6},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Hart, A C and Kass, J and Shapiro, J E and Kaplan, J M},
	month = mar,
	year = {1999},
	note = {{PMID:} 10066248},
	keywords = {Amino Acid Sequence, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Mechanoreceptors, Microtubules, Molecular Sequence Data, Nerve Tissue Proteins, Neurons, Afferent, Sensation, Signal Transduction, Touch, {Water-Electrolyte} Balance},
	pages = {1952--1958},
	file = {1952.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/UK4XICHK/1952.pdf:application/pdf;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/8XNMCPAZ/10066248.html:text/html}
},

@article{hein_dynamics_2005,
	title = {Dynamics of {receptor/G} protein coupling in living cells},
	volume = {24},
	issn = {0261-4189},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16292347},
	doi = {10.1038/sj.emboj.7600870},
	abstract = {The interaction of activated G protein-coupled receptors with G proteins is a key event in signal transduction. Here, using a fluorescence resonance energy transfer {(FRET)-based} assay, we measure directly and in living cells the interaction of {YFP-labeled} {alpha(2A)-adrenergic} receptors with {CFP-labeled} G proteins. Upon agonist stimulation, a small, concentration-dependent increase in {FRET} was observed. No specific basal {FRET} was detected in the absence of agonist. Kinetics of the onset of {receptor/G} protein interaction were {\textless}100 ms and depended on expression levels of Galpha. Simultaneously recorded G protein-regulated inwardly rectifying K(+) channel currents revealed a maximal current response already at agonist concentrations producing submaximal {FRET} amplitudes. By analyzing {FRET} signals in the presence of a Galpha mutant, which dissociates more slowly from activated receptors, it was demonstrated that only a fraction of wild-type G proteins interacts with the activated receptor at any time. Our data suggest that {alpha(2A)-adrenergic} receptors and G proteins interact by rapid collision coupling and indicate that there is no significant precoupling between these receptors and G proteins.},
	number = {23},
	journal = {The {EMBO} Journal},
	author = {Hein, Peter and Frank, Monika and Hoffmann, Carsten and Lohse, Martin J and Bünemann, Moritz},
	month = dec,
	year = {2005},
	note = {{PMID:} 16292347},
	keywords = {Adrenergic alpha-2 Receptor Agonists, Bacterial Proteins, Cell Line, Cell Membrane, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, {GTP-Binding} Proteins, Humans, Kinetics, Luminescent Proteins, Receptors, Adrenergic, alpha-2, Receptors, {G-Protein-Coupled}, Staining and Labeling},
	pages = {4106--4114}
},

@article{steinhauer_superresolution_2008-1,
	title = {Superresolution microscopy on the basis of engineered dark states},
	volume = {130},
	issn = {1520-5126},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19053449},
	doi = {10.1021/ja806590m},
	abstract = {New concepts for superresolution fluorescence microscopy by subsequent localization of single molecules using photoswitchable or photoactivatable fluorophores are rapidly emerging and provide new ways to resolve structures beyond the diffraction limit. Here, we demonstrate that superresolution imaging can be carried out with practically every single-molecule compatible, synthetic fluorophore by controlling their emission properties. We prepare dark states by removing oxygen that extends the triplet state lifetime to several milliseconds. We further increase the duration of the off-states using electron transfer reactions to create radical ion states of severalfold longer lifetimes. Imaging single molecules, actin filaments, and microtubules in fixed cells as well as simulations demonstrate that the thus created dark states are sufficiently long for resolution of approximately 50 nm.},
	number = {50},
	journal = {Journal of the American Chemical Society},
	author = {Steinhauer, Christian and Forthmann, Carsten and Vogelsang, Jan and Tinnefeld, Philip},
	month = dec,
	year = {2008},
	note = {{PMID:} 19053449},
	keywords = {Actins, Microscopy, Fluorescence, Sensitivity and Specificity},
	pages = {16840--16841}
},

@article{hedgecock_normal_1975,
	title = {Normal and mutant thermotaxis in the nematode Caenorhabditis elegans.},
	volume = {72},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=433138&amp;rendertype=abstract},
	abstract = {When grown at a temperature from 16 degrees to 25 degrees and placed on a thermal gradient, the nematode Caenorhabditis elegans migrates to its growth temperature and then moves isothermally. Behavioral adaptation to a new temperature takes several hours. Starved animals, in contrast, disperse from the growth temperature. Several mutants selected for chemotaxis defects have thermotaxis defects as well; these behaviors depend on some common gene products. New mutants selected directly for thermotaxis defects have unusual phenotypes which suggest mechanisms for thermotaxis.},
	number = {10},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Hedgecock, E M and Russell, R L},
	month = oct,
	year = {1975},
	note = {{PMC433138}},
	keywords = {{PQE}  - definite citation, {PQE} Specific Aim 1, Print Me!, thermosensing},
	pages = {4061–4065},
	file = {PubMed Central Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/CWTZBSTF/Hedgecock and Russell - 1975 - Normal and mutant thermotaxis in the nematode Caen.pdf:application/pdf}
},

@article{mclntire_gabaergic_1993,
	title = {The {GABAergic} nervous system of Caenorhabditis elegans},
	volume = {364},
	url = {http://dx.doi.org/10.1038/364337a0},
	doi = {10.1038/364337a0},
	number = {6435},
	journal = {Nature},
	author = {Mclntire, Steven L. and Jorgensen, Erik and Kaplan, Joshua and Horvitz, H. Robert},
	month = jul,
	year = {1993},
	keywords = {Important, {PQE}  - definite citation, Sniffing / Foraging},
	pages = {337--341},
	file = {364337a0-2.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/ZM2UI9UZ/364337a0-2.pdf:application/pdf;Nature Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/V3XUTQ85/364337a0.html:text/html}
},

@misc{the_video_lan_organization_videolan_2012,
	title = {{VideoLAN} - Official page for {VLC} media player, the Open Source video framework!},
	url = {http://www.videolan.org},
	journal = {{VLC} Media Player},
	author = {The Video Lan Organization},
	year = {2012},
	howpublished = {http://www.videolan.org},
	file = {VideoLAN - Official page for VLC media player, the Open Source video framework!:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/AESTU9U7/index.html:text/html}
},

@article{harris_wormbase:_2010,
	title = {{WormBase:} a comprehensive resource for nematode research},
	volume = {38},
	issn = {1362-4962},
	shorttitle = {{WormBase}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19910365},
	doi = {10.1093/nar/gkp952},
	abstract = {{WormBase} (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, {WormBase} has evolved into a powerful research tool in its own right. In the past 2 years, we expanded {WormBase} to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at {WormBase.} In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base.},
	number = {Database issue},
	journal = {Nucleic Acids Research},
	author = {Harris, Todd W and Antoshechkin, Igor and Bieri, Tamberlyn and Blasiar, Darin and Chan, Juancarlos and Chen, Wen J and De La Cruz, Norie and Davis, Paul and Duesbury, Margaret and Fang, Ruihua and Fernandes, Jolene and Han, Michael and Kishore, Ranjana and Lee, Raymond and Müller, {Hans-Michael} and Nakamura, Cecilia and Ozersky, Philip and Petcherski, Andrei and Rangarajan, Arun and Rogers, Anthony and Schindelman, Gary and Schwarz, Erich M and Tuli, Mary Ann and Van Auken, Kimberly and Wang, Daniel and Wang, Xiaodong and Williams, Gary and Yook, Karen and Durbin, Richard and Stein, Lincoln D and Spieth, John and Sternberg, Paul W},
	month = jan,
	year = {2010},
	note = {{PMID:} 19910365},
	keywords = {Alleles, Animals, Caenorhabditis, Caenorhabditis elegans, Computational Biology, Databases, Genetic, Databases, Nucleic Acid, Databases, Protein, Information Storage and Retrieval, Internet, Phenotype, Protein Structure, Tertiary, Software, Transcription Factors},
	pages = {D463--467}
},

@article{mclntire_genes_1993,
	title = {Genes required for {GABA} function in Caenorhabditis elegans},
	volume = {364},
	url = {http://dx.doi.org/10.1038/364334a0},
	doi = {10.1038/364334a0},
	number = {6435},
	journal = {Nature},
	author = {Mclntire, Steven L. and Jorgensen, Erik and Horvitz, H. Robert},
	month = jul,
	year = {1993},
	keywords = {Sniffing / Foraging},
	pages = {334--337},
	file = {Nature Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/Q6TQM8EW/364334a0.html:text/html}
},

@article{geldhof_combinatorial_2006,
	title = {Combinatorial {RNAi} on intestinal cathepsin B-like proteinases in Caenorhabditis elegans questions the perception of their role in nematode biology},
	volume = {145},
	issn = {0166-6851},
	url = {http://www.sciencedirect.com.ezp-prod1.hul.harvard.edu/science/article/B6T29-4HB5NDC-1/2/231c51eff724af73f13eded208e38a86},
	doi = {10.1016/j.molbiopara.2005.09.016},
	number = {1},
	journal = {Molecular and Biochemical Parasitology},
	author = {Geldhof, P. and Molloy, C. and Knox, {D.P.}},
	month = jan,
	year = {2006},
	keywords = {Caenorhabditis elegans, Cathepsin B-like cysteine proteinase, Combinatiorial {RNAi}, Nematode, Parasite},
	pages = {128--132},
	file = {ScienceDirect Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/4E88FIWX/Geldhof et al. - 2006 - Combinatorial RNAi on intestinal cathepsin B-like .pdf:application/pdf;ScienceDirect Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/38GK6H3S/science.html:text/html}
},

@misc{_rme_????,
	title = {{RME} {(Ring} Motor Neurons)},
	url = {http://www.wormatlas.org/neurons.htm/rme.htm}
},

@incollection{goodman_mechanosensation_2006-1,
	title = {Mechanosensation},
	url = {http://www.wormbook.org/chapters/www_mechanosensation/mechanosensation.html#figure2},
	publisher = {{WormBook}},
	author = {Goodman, {M.B.}},
	editor = {The C. elegans Research Community},
	month = jan,
	year = {2006},
	keywords = {Print Me!}
},

@article{keppler_general_2003,
	title = {A general method for the covalent labeling of fusion proteins with small molecules in vivo},
	volume = {21},
	issn = {1087-0156},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12469133},
	doi = {10.1038/nbt765},
	abstract = {Characterizing the movement, interactions, and chemical microenvironment of a protein inside the living cell is crucial to a detailed understanding of its function. Most strategies aimed at realizing this objective are based on genetically fusing the protein of interest to a reporter protein that monitors changes in the environment of the coupled protein. Examples include fusions with fluorescent proteins, the yeast two-hybrid system, and split ubiquitin. However, these techniques have various limitations, and considerable effort is being devoted to specific labeling of proteins in vivo with small synthetic molecules capable of probing and modulating their function. These approaches are currently based on the noncovalent binding of a small molecule to a protein, the formation of stable complexes between biarsenical compounds and peptides containing cysteines, or the use of biotin acceptor domains. Here we describe a general method for the covalent labeling of fusion proteins in vivo that complements existing methods for noncovalent labeling of proteins and that may open up new ways of studying proteins in living cells.},
	number = {1},
	journal = {Nature Biotechnology},
	author = {Keppler, Antje and Gendreizig, Susanne and Gronemeyer, Thomas and Pick, Horst and Vogel, Horst and Johnsson, Kai},
	month = jan,
	year = {2003},
	note = {{PMID:} 12469133},
	keywords = {Animals, Biotin, {CHO} Cells, Cricetinae, Escherichia coli, Fluorescein, Humans, Ligands, Macromolecular Substances, Microscopy, Confocal, Microscopy, Fluorescence, Molecular Weight, {O(6)-Methylguanine-DNA} Methyltransferase, Protein Binding, Recombinant Fusion Proteins, Staining and Labeling, Yeasts},
	pages = {86--89}
},

@article{ramot_bidirectional_2008-1,
	title = {Bidirectional temperature-sensing by a single thermosensory neuron in C. elegans},
	volume = {11},
	issn = {1097-6256},
	url = {http://dx.doi.org/10.1038/nn.2157},
	doi = {10.1038/nn.2157},
	number = {8},
	journal = {Nat Neurosci},
	author = {Ramot, Daniel and {MacInnis}, Bronwyn L and Goodman, Miriam B},
	year = {2008},
	keywords = {{FRET}, {PQE}  - definite citation},
	pages = {908--915},
	file = {Nature Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/WQSHMPTX/nn.2157.html:text/html}
},

@article{luo_sensorimotor_2006,
	title = {Sensorimotor control during isothermal tracking in Caenorhabditis elegans},
	volume = {209},
	url = {http://jeb.biologists.org/cgi/content/abstract/209/23/4652},
	doi = {10.1242/jeb.02590},
	abstract = {In order to purposefully navigate their environments, animals rely on precise coordination between their sensory and motor systems. The integrated performance of circuits for sensorimotor control may be analyzed by quantifying an animal's motile behavior in defined sensory environments. Here, we analyze the ability of the nematode C. elegans to crawl isothermally in spatial thermal gradients by quantifying the trajectories of individual worms responding to defined spatiotemporal thermal gradients. We show that sensorimotor control during isothermal tracking may be summarized as a strategy in which the worm changes the curvature of its propulsive undulations in response to temperature changes measured at its head. We show that a concise mathematical model for this strategy for sensorimotor control is consistent with the exquisite stability of the worm's isothermal alignment in spatial thermal gradients as well as its more complex trajectories in spatiotemporal thermal gradients.},
	number = {23},
	journal = {J Exp Biol},
	author = {Luo, Linjiao and Clark, Damon A. and Biron, David and Mahadevan, L. and Samuel, Aravinthan D. T.},
	month = dec,
	year = {2006},
	keywords = {{PQE}  - definite citation, thermosensing},
	pages = {4652--4662},
	file = {HighWire Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/SSRTMKP4/4652.html:text/html}
},

@article{chiu_adaptive_2009,
	title = {Adaptive echolocation behavior in bats for the analysis of auditory scenes},
	volume = {212},
	issn = {0022-0949},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19376960},
	doi = {10.1242/jeb.027045},
	abstract = {Echolocating bats emit sonar pulses and listen to returning echoes to probe their surroundings. Bats adapt their echolocation call design to cope with dynamic changes in the acoustic environment, including habitat change or the presence of nearby conspecifics/heterospecifics. Seven pairs of big brown bats, Eptesicus fuscus, were tested in this study to examine how they adjusted their echolocation calls when flying and competing with a conspecific for food. Results showed that differences in five call parameters, start/end frequencies, duration, bandwidth and sweep rate, significantly increased in the two-bat condition compared with the baseline data. In addition, the magnitude of spectral separation of calls was negatively correlated with the baseline call design differences in individual bats. Bats with small baseline call frequency differences showed larger increases in call frequency separation when paired than those with large baseline call frequency differences, suggesting that bats actively change their sonar call structure if pre-existing differences in call design are small. Call design adjustments were also influenced by physical spacing between two bats. Calls of paired bats exhibited the largest design separations when inter-bat distance was shorter than 0.5 m, and the separation decreased as the spacing increased. All individuals modified at least one baseline call parameter in response to the presence of another conspecific. We propose that dissimilarity between the time-frequency features of sonar calls produced by different bats aids each individual in segregating echoes of its own sonar vocalizations from the acoustic signals of neighboring bats.},
	number = {Pt 9},
	journal = {The Journal of Experimental Biology},
	author = {Chiu, Chen and Xian, Wei and Moss, Cynthia F},
	month = may,
	year = {2009},
	note = {{PMID:} 19376960},
	pages = {1392--1404},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/FFV67QRP/19376960.html:text/html}
},

@article{cully_cloning_1994,
	title = {Cloning of an avermectin-sensitive glutamate-gated chloride channel from Caenorhabditis elegans},
	volume = {371},
	issn = {0028-0836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7935817},
	doi = {10.1038/371707a0},
	abstract = {The avermectins are a family of macrocyclic lactones used in the control of nematode and arthropod parasites. Ivermectin (22,23-dihydroavermectin B1a) is widely used as an anthelmintic in veterinary medicine and is used to treat onchocerciasis or river blindness in humans. Abamectin (avermectin B1a) is a miticide and insecticide used in crop protection. Avermectins interact with vertebrate and invertebrate {GABA} receptors and invertebrate glutamate-gated chloride channels. The soil nematode Caenorhabditis elegans has served as a useful model to study the mechanism of action of avermectins. A C. elegans messenger {RNA} expressed in Xenopus oocytes encodes an avermectin-sensitive glutamate-gated chloride channel. To elucidate the structure and properties of this channel, we used Xenopus oocytes for expression cloning of two functional complementary {DNAs} encoding an avermectin-sensitive glutamate-gated chloride channel. We find that the electrophysiological and structural properties of these proteins indicate that they are new members of the ligand-gated ion channel superfamily.},
	number = {6499},
	journal = {Nature},
	author = {Cully, D F and Vassilatis, D K and Liu, K K and Paress, P S and Van der Ploeg, L H and Schaeffer, J M and Arena, J P},
	month = oct,
	year = {1994},
	note = {{PMID:} 7935817},
	keywords = {Amino Acid Sequence, Animals, Base Sequence, Caenorhabditis elegans, Cell Membrane Permeability, Cells, Cultured, Chloride Channels, Cloning, Molecular, {DNA}, Complementary, Electrophysiology, Escherichia coli, Glutamic Acid, Humans, Ion Channel Gating, Ivermectin, Molecular Sequence Data, Oocytes, Sequence Homology, Amino Acid, Xenopus},
	pages = {707--711}
},

@article{horvitz_serotonin_1982,
	title = {Serotonin and octopamine in the nematode Caenorhabditis elegans},
	volume = {216},
	url = {http://www.sciencemag.org.ezp-prod1.hul.harvard.edu/cgi/content/abstract/216/4549/1012},
	doi = {10.1126/science.6805073},
	abstract = {The biogenic amines serotonin and octopamine are present in the nematode Caenorhabditis elegans. Serotonin, detected histochemically in whole mounts, is localized in two pharyngeal neurons that appear to be neurosecretory. Octopamine, identified radioenzymatically in crude extracts, probably is also localized in a few neurons. Exogenous serotonin and octopamine elicit specific and opposite behavioral responses in Caenorhabditis elegans, suggesting that these compounds function physiologically as antagonists.},
	number = {4549},
	journal = {Science},
	author = {Horvitz, {HR} and Chalfie, M and Trent, C and Sulston, {JE} and Evans, {PD}},
	month = may,
	year = {1982},
	pages = {1012--1014}
},

@article{avery_pharyngeal_1989,
	title = {Pharyngeal pumping continues after laser killing of the pharyngeal nervous system of C. elegans},
	volume = {3},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/2642006},
	abstract = {Using a laser microbeam to kill specific subsets of the pharyngeal nervous system of C. elegans, we found that feeding was accomplished by two separately controlled muscle motions, isthmus peristalsis and pumping. The single neuron M4 was necessary and sufficient for isthmus peristalsis. The {MC} neurons were necessary for normal stimulation of pumping in response to food, but pumping continued and was functional in {MC-} worms. The remaining 12 neuron types were also unnecessary for functional pumping. No operation we did, including destruction of the entire pharyngeal nervous system, abolished pumping altogether. When we killed all pharyngeal neurons except M4, the worms were viable and fertile, although retarded and starved. Since feeding is one of the few known essential actions controlled by the nervous system, we suggest that most of the C. elegans nervous system is dispensable in hermaphrodites under laboratory conditions. This may explain the ease with which nervous system mutants are isolated and handled in C. elegans.},
	number = {4},
	journal = {Neuron},
	author = {Avery, L and Horvitz, H R},
	month = oct,
	year = {1989},
	note = {{PMID:} 2642006},
	keywords = {Animals, Caenorhabditis, Cell Survival, Immunohistochemistry, Lasers, Microscopy, Electron, Neurons, Pharynx, Serotonin},
	pages = {473--485}
},

@misc{chin-sang_c._????,
	title = {C. elegans wt {movement2.MOV} (video/quicktime Object)},
	url = {http://130.15.90.245/movies/C.%20elegans%20wt%20movement2.MOV},
	journal = {The {Chin-Sang} Lab},
	author = {{Chin-Sang}, Ian D.},
	howpublished = {{http://130.15.90.245/movies/C.\%20elegans\%20wt\%20movement2.MOV}},
	file = {C. elegans wt movement2.MOV:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/9UET2NC8/C.20elegans20wt20movement2.mov:video/quicktime}
},

@article{delcomyn_neural_1980,
	title = {Neural basis of rhythmic behavior in animals},
	volume = {210},
	issn = {0036-8075},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7423199},
	abstract = {Timing of the repetitive movements that constitute any rhythmic behavior is regulated by intrinsic properties of the central nervous system rather than by sensory feedback from moving parts of the body. Evidence of this permits resolution of the long-standing controversy over the neural basis of rhythmic behavior and aids in the identification of this mechanism as a general principle of neural organization applicable to all animals with central nervous systems.},
	number = {4469},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Delcomyn, F},
	month = oct,
	year = {1980},
	note = {{PMID:} 7423199},
	keywords = {Animals, Behavior, Animal, Biological Clocks, Central Nervous System, Feedback, Locomotion, Mastication, Nervous System Physiological Phenomena, Periodicity, Peripheral Nerves, Respiration, Vocalization, Animal},
	pages = {492--498}
},

@article{hilliard_c._2002-1,
	title = {C. elegans responds to chemical repellents by integrating sensory inputs from the head and the tail},
	volume = {12},
	issn = {0960-9822},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/12007416},
	abstract = {The phasmids are bilateral sensory organs located in the tail of Caenorhabditis elegans and other nematodes. The similar structures of the phasmids and the amphid chemosensory organs in the head have long suggested a chemosensory function for the phasmids. However, the {PHA} and {PHB} phasmid neurons are not required for chemotaxis or for dauer formation, and no direct proof of a chemosensory function of the phasmids has been obtained. C. elegans avoids toxic chemicals by reversing its movement, and this behavior is mediated by sensory neurons of the amphid, particularly, the {ASH} neurons. Here we show that the {PHA} and {PHB} phasmid neurons function as chemosensory cells that negatively modulate reversals to repellents. The antagonistic activity of head and tail sensory neurons is integrated to generate appropriate escape behaviors: detection of a repellent by head neurons mediates reversals, which are suppressed by antagonistic inputs from tail neurons. Our results suggest that C. elegans senses repellents by defining a head-to-tail spatial map of the chemical environment.},
	number = {9},
	journal = {Current Biology: {CB}},
	author = {Hilliard, Massimo A and Bargmann, Cornelia I and Bazzicalupo, Paolo},
	month = apr,
	year = {2002},
	note = {{PMID:} 12007416},
	keywords = {Animals, Caenorhabditis elegans, Chemoreceptor Cells, Chemotaxis, Head, Movement, Neurons, Afferent, Signal Transduction, Tail},
	pages = {730--734}
},

@article{rothemund_folding_2006-1,
	title = {Folding {DNA} to create nanoscale shapes and patterns},
	volume = {440},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16541064},
	doi = {10.1038/nature04586},
	abstract = {{'Bottom-up} fabrication', which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of {DNA} molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded {DNA} molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting {DNA} structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual {DNA} structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).},
	number = {7082},
	journal = {Nature},
	author = {Rothemund, Paul W K},
	month = mar,
	year = {2006},
	note = {{PMID:} 16541064},
	keywords = {Art, Bacteriophage M13, Biopolymers, {DNA}, {DNA}, {Single-Stranded}, {DNA}, Viral, Microscopy, Atomic Force, Nanostructures, Nanotechnology, Nucleic Acid Conformation},
	pages = {297--302}
},

@book{finger_origins_2001,
	title = {Origins of neuroscience: a history of explorations into brain function},
	isbn = {9780195146943},
	shorttitle = {Origins of neuroscience},
	abstract = {With over 350 illustrations, this impressive volume traces the rich history of ideas about the functioning of the brain from its roots in the ancient cultures of Egypt, Greece, and Rome through the centuries into relatively modern times. In contrast to biographically oriented accounts, this book is unique in its emphasis on the functions of the brain and how they came to be associated with specific brain regions and systems. Among the topics explored are vision, hearing, pain, motor control, sleep, memory, speech, and various other facets of intellect. The emphasis throughout is on presenting material in a very readable way, while describing with scholarly acumen the historical evolution of the field in all its amazing wealth and detail. From the opening introductory chapters to the concluding look at treatments and therapies, this monumental work will captivate readers from cover to cover. It will be valued as both an historical reference and as an exciting tale of scientific discovery. It is bound to attract a wide readership among students and professionals in the neural sciences as well as general readers interested in the history of science and medicine.},
	publisher = {Oxford University Press},
	author = {Finger, Stanley},
	month = sep,
	year = {2001},
	keywords = {Brain, Medical / History, Medical / Neurology, Medical / Neuroscience, Neurology, Neurosciences, Psychology / Neuropsychology, Science / Life Sciences / Neuroscience}
},

@article{xu_multiplexed_2003,
	title = {Multiplexed {SNP} genotyping using the Qbead system: a quantum dot-encoded microsphere-based assay},
	volume = {31},
	issn = {1362-4962},
	shorttitle = {Multiplexed {SNP} genotyping using the Qbead system},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12682378},
	abstract = {We have developed a new method using the Qbead system for high-throughput genotyping of single nucleotide polymorphisms {(SNPs).} The Qbead system employs fluorescent Qdot semiconductor nanocrystals, also known as quantum dots, to encode microspheres that subsequently can be used as a platform for multiplexed assays. By combining mixtures of quantum dots with distinct emission wavelengths and intensities, unique spectral 'barcodes' are created that enable the high levels of multiplexing required for complex genetic analyses. Here, we applied the Qbead system to {SNP} genotyping by encoding microspheres conjugated to allele-specific oligonucleotides. After hybridization of oligonucleotides to amplicons produced by multiplexed {PCR} of genomic {DNA}, individual microspheres are analyzed by flow cytometry and each {SNP} is distinguished by its unique spectral barcode. Using 10 model {SNPs}, we validated the Qbead system as an accurate and reliable technique for multiplexed {SNP} genotyping. By modifying the types of probes conjugated to microspheres, the Qbead system can easily be adapted to other assay chemistries for {SNP} genotyping as well as to other applications such as analysis of gene expression and protein-protein interactions. With its capability for high-throughput automation, the Qbead system has the potential to be a robust and cost-effective platform for a number of applications.},
	number = {8},
	journal = {Nucleic Acids Research},
	author = {Xu, Hongxia and Sha, Michael Y and Wong, Edith Y and Uphoff, Janet and Xu, Yanzhang and Treadway, Joseph A and Truong, Anh and {O'Brien}, Eamonn and Asquith, Steven and Stubbins, Michael and Spurr, Nigel K and Lai, Eric H and Mahoney, Walt},
	month = apr,
	year = {2003},
	note = {{PMID:} 12682378},
	keywords = {{DNA}, {DNA} Mutational Analysis, Female, Genotype, Humans, Male, Microspheres, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Sensitivity and Specificity},
	pages = {e43}
},

@article{atzmon_abrahams_2010,
	title = {Abraham's Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry},
	volume = {86},
	issn = {00029297},
	shorttitle = {Abraham's Children in the Genome Era},
	url = {http://www.cell.com/AJHG/abstract/S0002-9297(10)00246-6},
	doi = {10.1016/j.ajhg.2010.04.015},
	number = {6},
	journal = {The American Journal of Human Genetics},
	author = {Atzmon, Gil and Hao, Li and Pe'er, Itsik and Velez, Christopher and Pearlman, Alexander and Palamara, Pier Francesco and Morrow, Bernice and Friedman, Eitan and Oddoux, Carole and Burns, Edward},
	month = jun,
	year = {2010},
	pages = {850--859},
	file = {AJHG - Abraham's Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/38FGHG4U/S0002-9297(10)00246-6.html:text/html}
},

@article{hell_breaking_1994,
	title = {Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy},
	volume = {19},
	shorttitle = {Breaking the diffraction resolution limit by stimulated emission},
	url = {http://ol.osa.org/abstract.cfm?URI=ol-19-11-780},
	doi = {10.1364/OL.19.000780},
	abstract = {We propose a new type of scanning fluorescence microscope capable of resolving 35 nm in the far field. We overcome the diffraction resolution limit by employing stimulated emission to inhibit the fluorescence process in the outer regions of the excitation point-spread function. In contrast to near-field scanning optical microscopy, this method can produce three-dimensional images of translucent specimens.},
	number = {11},
	journal = {Optics Letters},
	author = {Hell, Stefan W. and Wichmann, Jan},
	month = jun,
	year = {1994},
	pages = {780--782},
	file = {Opt. Lett. Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/UHZB8HC2/Hell and Wichmann - 1994 - Breaking the diffraction resolution limit by stimu.pdf:application/pdf;Opt. Lett. Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/PKM68DXH/abstract.html:text/html}
},

@article{ando_optical_2002,
	title = {An optical marker based on the {UV-induced} green-to-red photoconversion of a fluorescent protein},
	volume = {99},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12271129},
	doi = {10.1073/pnas.202320599},
	abstract = {We have cloned a gene encoding a fluorescent protein from a stony coral, Trachyphyllia geoffroyi, which emits green, yellow, and red light. The protein, named Kaede, includes a tripeptide, {His-Tyr-Gly}, that acts as a green chromophore that can be converted to red. The red fluorescence is comparable in intensity to the green and is stable under usual aerobic conditions. We found that the green-red conversion is highly sensitive to irradiation with {UV} or violet light (350-400 nm), which excites the protonated form of the chromophore. The excitation lights used to elicit red and green fluorescence do not induce photoconversion. Under a conventional epifluorescence microscope, Kaede protein expressed in {HeLa} cells turned red in a graded fashion in response to {UV} illumination; maximal illumination resulted in a 2,000-fold increase in the ratio of red-to-green signal. These color-changing properties provide a simple and powerful technique for regional optical marking. A focused {UV} pulse creates an instantaneous plane source of red Kaede within the cytosol. The red spot spreads rapidly throughout the cytosol, indicating its free diffusibility in the compartment. The extensive diffusion allows us to delineate a single neuron in a dense culture, where processes originating from many different somata are present. Illumination of a focused {UV} pulse onto the soma of a Kaede-expressing neuron resulted in filling of all processes with red fluorescence, allowing visualization of contact sites between the red and green neurons of interest.},
	number = {20},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Ando, Ryoko and Hama, Hiroshi and {Yamamoto-Hino}, Miki and Mizuno, Hideaki and Miyawaki, Atsushi},
	month = oct,
	year = {2002},
	note = {{PMID:} 12271129},
	keywords = {Amino Acid Sequence, Animals, Anthozoa, Cloning, Molecular, Cytosol, Diffusion, {DNA}, Complementary, Electrophoresis, Polyacrylamide Gel, Green Fluorescent Proteins, Hela Cells, Hippocampus, Humans, {Hydrogen-Ion} Concentration, Light, Luminescent Proteins, Molecular Sequence Data, Neurons, Normal Distribution, Rats, Rats, Wistar, Scattering, Radiation, Sequence Homology, Amino Acid, Spectrum Analysis, Time Factors, Ultraviolet Rays},
	pages = {12651--12656}
},

@article{gollisch_eye_2010,
	title = {Eye smarter than scientists believed: neural computations in circuits of the retina},
	volume = {65},
	issn = {1097-4199},
	shorttitle = {Eye smarter than scientists believed},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20152123},
	doi = {10.1016/j.neuron.2009.12.009},
	abstract = {We rely on our visual system to cope with the vast barrage of incoming light patterns and to extract features from the scene that are relevant to our well-being. The necessary reduction of visual information already begins in the eye. In this review, we summarize recent progress in understanding the computations performed in the vertebrate retina and how they are implemented by the neural circuitry. A new picture emerges from these findings that helps resolve a vexing paradox between the retina's structure and function. Whereas the conventional wisdom treats the eye as a simple prefilter for visual images, it now appears that the retina solves a diverse set of specific tasks and provides the results explicitly to downstream brain areas.},
	number = {2},
	journal = {Neuron},
	author = {Gollisch, Tim and Meister, Markus},
	month = jan,
	year = {2010},
	note = {{PMID:} 20152123},
	keywords = {Animals, Computational Biology, Humans, Nerve Net, Neurology, Retina, Visual Pathways, Visual Perception},
	pages = {150--164}
},

@article{yildiz_myosin_2003,
	title = {Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization},
	volume = {300},
	issn = {1095-9203},
	shorttitle = {Myosin V walks hand-over-hand},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12791999},
	doi = {10.1126/science.1084398},
	abstract = {Myosin V is a dimeric molecular motor that moves processively on actin, with the center of mass moving approximately 37 nanometers for each adenosine triphosphate hydrolyzed. We have labeled myosin V with a single fluorophore at different positions in the light-chain domain and measured the step size with a standard deviation of {\textless}1.5 nanometers, with 0.5-second temporal resolution, and observation times of minutes. The step size alternates between 37 + 2x nm and 37 - 2x, where x is the distance along the direction of motion between the dye and the midpoint between the two heads. These results strongly support a hand-over-hand model of motility, not an inchworm model.},
	number = {5628},
	journal = {Science {(New} York, {N.Y.)}},
	author = {Yildiz, Ahmet and Forkey, Joseph N and {McKinney}, Sean A and Ha, Taekjip and Goldman, Yale E and Selvin, Paul R},
	month = jun,
	year = {2003},
	note = {{PMID:} 12791999},
	keywords = {Actins, Adenosine Triphosphate, Binding Sites, Calmodulin, Carbocyanines, Catalytic Domain, {DNA}, Fluorescence, Fluorescent Dyes, Kinetics, Mathematics, Microfilaments, Microscopy, Fluorescence, Models, Biological, Molecular Motor Proteins, Myosin Light Chains, Myosin Type V, Protein Structure, Tertiary, Rhodamines},
	pages = {2061--2065}
},

@misc{_wormatlas:_????-1,
	title = {{WormAtlas:} {CEP}},
	url = {http://www.wormatlas.org/neurons.htm/cep.htm},
	howpublished = {http://www.wormatlas.org/neurons.htm/cep.htm},
	file = {neuron pages.cep:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/MRHG473A/cep.html:text/html}
},

@misc{_real-time_????,
	title = {{REAL-TIME} {LINUX} {TUTORIAL}},
	url = {http://www.isd.mel.nist.gov/projects/rtlinux/rtutorial-2.0/doc/tutorial.htm}
},

@article{friesen_leech_2007,
	title = {Leech locomotion: swimming, crawling, and decisions},
	volume = {17},
	issn = {0959-4388},
	shorttitle = {Leech locomotion},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/18339544},
	doi = {10.1016/j.conb.2008.01.006},
	abstract = {Research on the neuronal control of locomotion in leeches spans almost four decades. Recent advances reviewed here include discoveries that: (1) interactions between multiple hormones modulate initiation of swimming; (2) stretch receptors associated with longitudinal muscles interact with the central oscillator circuit via electrical junctions; (3) intersegmental interactions, according to theoretical analyses, must be relatively weak compared to oscillator interactions within ganglia; and (4) multiple interacting neurons control the expression of alternative modes of locomotion. The innovative techniques that facilitated these advances include optical recording of membrane potential changes, simultaneous intracellular injection of high and low molecular weight fluorescent dyes, and detailed modeling via an input-output systems engineering approach.},
	number = {6},
	journal = {Current Opinion in Neurobiology},
	author = {Friesen, W Otto and Kristan, William B},
	month = dec,
	year = {2007},
	note = {{PMID:} 18339544},
	keywords = {Animals, Behavior, Animal, Decision Making, Leeches, Locomotion},
	pages = {704--711}
},

@article{walter_-it-yourself_2008,
	title = {Do-it-yourself guide: how to use the modern single-molecule toolkit},
	volume = {5},
	issn = {1548-7105},
	shorttitle = {Do-it-yourself guide},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18511916},
	doi = {10.1038/nmeth.1215},
	abstract = {Single-molecule microscopy has evolved into the ultimate-sensitivity toolkit to study systems from small molecules to living cells, with the prospect of revolutionizing the modern biosciences. Here we survey the current state of the art in single-molecule tools including fluorescence spectroscopy, tethered particle microscopy, optical and magnetic tweezers, and atomic force microscopy. We also provide guidelines for choosing the right approach from the available single-molecule toolkit for applications as diverse as structural biology, enzymology, nanotechnology and systems biology.},
	number = {6},
	journal = {Nature Methods},
	author = {Walter, Nils G and Huang, {Cheng-Yen} and Manzo, Anthony J and Sobhy, Mohamed A},
	month = jun,
	year = {2008},
	note = {{PMID:} 18511916},
	keywords = {Animals, Biotechnology, Equipment Design, Humans, Image Processing, {Computer-Assisted}, Microscopy, Microscopy, Atomic Force, Microscopy, Fluorescence, Models, Statistical, Nanotechnology, Optical Tweezers, Sensitivity and Specificity, Software, Spectrometry, Fluorescence},
	pages = {475--489}
},

@book{atlun_handbook_2005,
	series = {{WormAtlas}},
	title = {Handbook of C. elegans Anatomy},
	url = {http://www.wormatlas.org/handbook/content.htm},
	author = {Atlun, Z. F. and Hall, {D.H.}},
	year = {2005}
},

@misc{chin-sang_c._????-1,
	title = {C. elegans adult hermaphrodite.mov (video/quicktime Object)},
	url = {http://www.chin-sang.ca/movies/C.%20elegans%20adult%20hermaphrodite.mov},
	author = {{Chin-Sang}, Ian D.},
	howpublished = {{http://www.chin-sang.ca/movies/C.\%20elegans\%20adult\%20hermaphrodite.mov}},
	file = {C. elegans adult hermaphrodite.mov:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/DGHA3WQM/C.20elegans20adult20hermaphrodite.mov:video/quicktime}
},

@article{iino_parallel_2009,
	title = {Parallel use of two behavioral mechanisms for chemotaxis in Caenorhabditis elegans},
	volume = {29},
	issn = {1529-2401},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19403805},
	doi = {10.1523/JNEUROSCI.3633-08.2009},
	abstract = {Caenorhabditis elegans shows chemotaxis to various odorants and water-soluble chemoattractants such as {NaCl.} Previous studies described the pirouette mechanism for chemotaxis, in which C. elegans quickly changes the direction of locomotion by using a set of stereotyped behaviors, a pirouette, in response to a decrease in the concentration of the chemical. Here, we report the discovery of a second mechanism for chemotaxis, called the weathervane mechanism. In this strategy animals respond to a spatial gradient of chemoattractant and gradually curve toward higher concentration of the chemical. By computer simulation, we find that both of these mechanisms contribute to chemotaxis and both mechanisms need to act in parallel for efficient chemotaxis. Using laser ablation of individual neurons to examine the underlying neural circuit, we find the {ASE} sensory neurons and {AIZ} interneurons are essential for both the pirouette and weathervane mechanisms in chemotaxis to {NaCl.} Salt-conditioned animals show reversed responses in both of these behaviors, leading to avoidance of {NaCl.} These results provide a platform for detailed molecular and cellular analyses of chemotaxis and its plasticity in this model organism.},
	number = {17},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Iino, Yuichi and Yoshida, Kazushi},
	month = apr,
	year = {2009},
	note = {{PMID:} 19403805},
	keywords = {Animals, Behavior, Animal, Caenorhabditis elegans, Chemotaxis, Locomotion, Nerve Net, Sodium Chloride},
	pages = {5370--5380}
},

@misc{_restricted_????,
	title = {Restricted Data: The Nuclear Secrecy Blog},
	url = {http://nuclearsecrecy.com/blog/},
	howpublished = {http://nuclearsecrecy.com/blog/}
},

@article{haspel_motoneurons_2010,
	title = {Motoneurons dedicated to either forward or backward locomotion in the nematode Caenorhabditis elegans},
	volume = {30},
	issn = {1529-2401},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20720122},
	doi = {10.1523/JNEUROSCI.2244-10.2010},
	abstract = {Multifunctional motoneurons and muscles, which are active during forward and backward locomotion are ubiquitous in animal models. However, studies in the nematode Caenorhabditis elegans suggest that some locomotor motoneurons are necessary only for forward locomotion (dorsal B-motoneurons, {DB)}, while others (dorsal A-motoneurons, {DA)} are necessary only for backward locomotion. We tested this hypothesis directly by recording the activity of these motoneurons during semirestrained locomotion. For this purpose, we used epifluorescence imaging of the genetically encoded calcium sensor cameleon, expressed in specific motoneurons, while monitoring locomotor behavior through the microscope condenser using a second camera. We found that ventral and dorsal B-motoneurons {(DB} and {VB)} were coactive during forward locomotion while ventral A-motoneurons {(VA)} were only active during backward locomotion. The signals we recorded correlated with the direction of locomotion but not with the faster undulatory cycles. To our knowledge, these are the first recordings of motoneuron activity in C. elegans and the only direction-dedicated motoneurons described to date.},
	number = {33},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Haspel, Gal and {O'Donovan}, Michael J and Hart, Anne C},
	month = aug,
	year = {2010},
	note = {{PMID:} 20720122},
	keywords = {Animals, Caenorhabditis elegans, Dermoscopy, Larva, Locomotion, Motor Neurons, Muscles, Periodicity},
	pages = {11151--11156}
},

@article{marder_principles_1996,
	title = {Principles of rhythmic motor pattern generation},
	volume = {76},
	issn = {0031-9333},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8757786},
	abstract = {Rhythmic movements are produced by central pattern-generating networks whose output is shaped by sensory and neuromodulatory inputs to allow the animal to adapt its movements to changing needs. This review discusses cellular, circuit, and computational analyses of the mechanisms underlying the generation of rhythmic movements in both invertebrate and vertebrate nervous systems. Attention is paid to exploring the mechanisms by which synaptic and cellular processes interact to play specific roles in shaping motor patterns and, consequently, movement.},
	number = {3},
	journal = {Physiological Reviews},
	author = {Marder, E and Calabrese, R L},
	month = jul,
	year = {1996},
	note = {{PMID:} 8757786},
	keywords = {Animals, Circadian Rhythm, Motor Activity, Neural Networks {(Computer)}, Synaptic Transmission},
	pages = {687--717}
},

@article{goodman_active_1998-1,
	title = {Active currents regulate sensitivity and dynamic range in C. elegans neurons},
	volume = {20},
	issn = {0896-6273},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9581767},
	abstract = {Little is known about the physiology of neurons in Caenorhabditis elegans. Using new techniques for in situ patch-clamp recording in C. elegans, we analyzed the electrical properties of an identified sensory neuron {(ASER)} across four developmental stages and 42 unidentified neurons at one stage. We find that {ASER} is nearly isopotential and fails to generate classical Na+ action potentials. Rather, {ASER} displays a high sensitivity to input currents coupled to a depolarization-dependent reduction in sensitivity that may endow {ASER} with a wide dynamic range. Voltage clamp revealed depolarization-activated K+ and Ca2+ currents that contribute to high sensitivity near the zero-current potential. The depolarization-dependent reduction in sensitivity can be attributed to activation of K+ current at voltages where it dominates the net membrane current. The voltage dependence of membrane current was similar in all neurons examined, suggesting that C. elegans neurons share a common mechanism of sensitivity and dynamic range.},
	number = {4},
	journal = {Neuron},
	author = {Goodman, M B and Hall, D H and Avery, L and Lockery, S R},
	month = apr,
	year = {1998},
	note = {{PMID:} 9581767},
	keywords = {Animals, Caenorhabditis elegans, Chemoreceptor Cells, Cilia, Larva, Membrane Potentials, Neurons, Neurons, Afferent, {Patch-Clamp} Techniques, Signal Transduction, Synapses, Time Factors},
	pages = {763--772}
},

@article{fang-yen_biomechanical_2010,
	title = {Biomechanical analysis of gait adaptation in the nematode Caenorhabditis elegans},
	volume = {107},
	issn = {1091-6490},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21048086},
	doi = {10.1073/pnas.1003016107},
	abstract = {To navigate different environments, an animal must be able to adapt its locomotory gait to its physical surroundings. The nematode Caenorhabditis elegans, between swimming in water and crawling on surfaces, adapts its locomotory gait to surroundings that impose approximately 10,000-fold differences in mechanical resistance. Here we investigate this feat by studying the undulatory movements of C. elegans in Newtonian fluids spanning nearly five orders of magnitude in viscosity. In these fluids, the worm undulatory gait varies continuously with changes in external load: As load increases, both wavelength and frequency of undulation decrease. We also quantify the internal viscoelastic properties of the worm's body and their role in locomotory dynamics. We incorporate muscle activity, internal load, and external load into a biomechanical model of locomotion and show that (i) muscle power is nearly constant across changes in locomotory gait, and (ii) the onset of gait adaptation occurs as external load becomes comparable to internal load. During the swimming gait, which is evoked by small external loads, muscle power is primarily devoted to bending the worm's elastic body. During the crawling gait, evoked by large external loads, comparable muscle power is used to drive the external load and the elastic body. Our results suggest that C. elegans locomotory gait continuously adapts to external mechanical load in order to maintain propulsive thrust.},
	number = {47},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {{Fang-Yen}, Christopher and Wyart, Matthieu and Xie, Julie and Kawai, Risa and Kodger, Tom and Chen, Sway and Wen, Quan and Samuel, Aravinthan D T},
	month = nov,
	year = {2010},
	note = {{PMID:} 21048086},
	keywords = {Adaptation, Biological, Animals, Biomechanics, Caenorhabditis elegans, Gait, Locomotion, Models, Biological, Muscles, Viscosity},
	pages = {20323--20328}
},

@article{wicks_integration_1995,
	title = {Integration of mechanosensory stimuli in Caenorhabditis elegans},
	volume = {15},
	issn = {0270-6474},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/7891178},
	abstract = {The tap withdrawal reflex in Caenorhabditis elegans demonstrates various forms of nonassociative learning. A first step in determining the cellular mechanisms of this learning is to identify the neuronal circuitry that underlies this reflex. Studies by Chalfie et al. (1985) have defined the touch-circuit that mediates the response to a stimulus related to tap--a light touch. We used the touch circuit as a starting point in the identification of the tap withdrawal circuitry. Here we report the effects of lesions of identified neurons on the tap withdrawal reflex. Ablations of the sensory neurons and interneurons of the touch circuit produce effects on the tap withdrawal response that generally confirm and expand upon the roles of these cells in mechanosensory integration as proposed by Chalfie et al. (1985). However, no role for the {LUA} interneurons could be identified in the production of the tap withdrawal response. Furthermore, the effects of ablating some neurons outside the touch circuit suggest roles for two of these cells in the integration of the tap withdrawal response. Ablation of either the midline neuron {DVA} or the {PVD} neurons resulted in a decrease in both the frequency and magnitude of reversals that were elicited by tap. Additionally, the ablation of either cell decreased the magnitude of accelerations produced by animals in response to tap.},
	number = {3 Pt 2},
	journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience},
	author = {Wicks, S R and Rankin, C H},
	month = mar,
	year = {1995},
	note = {{PMID:} 7891178},
	keywords = {Animals, Caenorhabditis elegans, Habituation, Psychophysiologic, Interneurons, Learning, Locomotion, Mechanoreceptors, Neurons, Afferent, Reflex, Touch, Vibration},
	pages = {2434--2444}
},

@article{berri_forward_2009,
	title = {Forward locomotion of the nematode C. elegans is achieved through modulation of a single gait},
	volume = {3},
	issn = {1955-2068},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19639043},
	doi = {10.2976/1.3082260},
	abstract = {The ability of an animal to locomote through its environment depends crucially on the interplay between its active endogenous control and the physics of its interactions with the environment. The nematode worm Caenorhabditis elegans serves as an ideal model system for studying the respective roles of neural control and biomechanics, as well as the interaction between them. With only 302 neurons in a hard-wired neural circuit, the worm's apparent anatomical simplicity belies its behavioural complexity. Indeed, C. elegans exhibits a rich repertoire of complex behaviors, the majority of which are mediated by its adaptive undulatory locomotion. The conventional wisdom is that two kinematically distinct C. elegans locomotion behaviors-swimming in liquids and crawling on dense gel-like media-correspond to distinct locomotory gaits. Here we analyze the worm's motion through a series of different media and reveal a smooth transition from swimming to crawling, marked by a linear relationship between key locomotion metrics. These results point to a single locomotory gait, governed by the same underlying control mechanism. We further show that environmental forces play only a small role in determining the shape of the worm, placing conditions on the minimal pattern of internal forces driving locomotion.},
	number = {3},
	journal = {{HFSP} Journal},
	author = {Berri, Stefano and Boyle, Jordan H and Tassieri, Manlio and Hope, Ian A and Cohen, Netta},
	month = jun,
	year = {2009},
	note = {{PMID:} 19639043},
	pages = {186--193}
},

@article{liewald_optogenetic_2008,
	title = {Optogenetic analysis of synaptic function},
	volume = {5},
	issn = {1548-7091},
	url = {http://dx.doi.org/10.1038/nmeth.1252},
	doi = {10.1038/nmeth.1252},
	number = {10},
	journal = {Nat Meth},
	author = {Liewald, Jana F and Brauner, Martin and Stephens, Greg J and Bouhours, Magali and Schultheis, Christian and Zhen, Mei and Gottschalk, Alexander},
	month = oct,
	year = {2008},
	pages = {895--902}
},

@article{marder_principles_1996-1,
	title = {Principles of rhythmic motor pattern generation},
	volume = {76},
	issn = {0031-9333},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8757786},
	abstract = {Rhythmic movements are produced by central pattern-generating networks whose output is shaped by sensory and neuromodulatory inputs to allow the animal to adapt its movements to changing needs. This review discusses cellular, circuit, and computational analyses of the mechanisms underlying the generation of rhythmic movements in both invertebrate and vertebrate nervous systems. Attention is paid to exploring the mechanisms by which synaptic and cellular processes interact to play specific roles in shaping motor patterns and, consequently, movement.},
	number = {3},
	journal = {Physiological Reviews},
	author = {Marder, E and Calabrese, R L},
	month = jul,
	year = {1996},
	note = {{PMID:} 8757786},
	keywords = {Animals, Circadian Rhythm, Motor Activity, Neural Networks {(Computer)}, Synaptic Transmission},
	pages = {687--717}
},

@article{chiba_developmental_1990,
	title = {A developmental analysis of spontaneous and reflexive reversals in the {nematodeCaenorhabditis} elegans},
	volume = {21},
	issn = {0022-3034},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/neu.480210403/pdf},
	doi = {10.1002/neu.480210403},
	number = {4},
	journal = {Journal of Neurobiology},
	author = {Chiba, Catherine M. and Rankin, Catharine H.},
	month = jun,
	year = {1990},
	pages = {543--554}
},

@article{mehta_active_2007,
	title = {Active Spatial Perception in the Vibrissa Scanning Sensorimotor System},
	volume = {5},
	url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050015},
	doi = {10.1371/journal.pbio.0050015},
	abstract = {Haptic perception is an active process that provides an awareness of objects that are encountered as an organism scans its environment. In contrast to the sensation of touch produced by contact with an object, the perception of object location arises from the interpretation of tactile signals in the context of the changing configuration of the body. A discrete sensory representation and a low number of degrees of freedom in the motor plant make the ethologically prominent rat vibrissa system an ideal model for the study of the neuronal computations that underlie this perception. We found that rats with only a single vibrissa can combine touch and movement to distinguish the location of objects that vary in angle along the sweep of vibrissa motion. The patterns of this motion and of the corresponding behavioral responses show that rats can scan potential locations and decide which location contains a stimulus within 150 ms. This interval is consistent with just one to two whisk cycles and provides constraints on the underlying perceptual computation. Our data argue against strategies that do not require the integration of sensory and motor modalities. The ability to judge angular position with a single vibrissa thus connects previously described, motion-sensitive neurophysiological signals to perception in the behaving animal.},
	number = {2},
	journal = {{PLoS} Biology},
	author = {Mehta, Samar B. and Whitmer, Diane and Figueroa, Rodolfo and Williams, Ben A. and Kleinfeld, David},
	month = feb,
	year = {2007},
	pages = {e15 EP --},
	file = {Active Spatial Perception in the Vibrissa Scanning Sensorimotor System:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/QVAZ64WE/perlserv.html:text/html;PLoS Biology - Active Spatial Perception in the Vibrissa Scanning Sensorimotor System:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TZCSTQ4A/perlserv.html:text/html}
},

@article{stirman_high-throughput_2010,
	title = {High-throughput study of synaptic transmission at the neuromuscular junction enabled by optogenetics and microfluidics},
	volume = {191},
	issn = {{1872-678X}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20538016},
	doi = {10.1016/j.jneumeth.2010.05.019},
	abstract = {Over the past several years, optogenetic techniques have become widely used to help elucidate a variety of neuroscience problems. The unique optical control of neurons within a variety of organisms provided by optogenetics allows researchers to probe neural circuits and investigate neuronal function in a highly specific and controllable fashion. Recently, optogenetic techniques have been introduced to investigate synaptic transmission in the nematode Caenorhabditis elegans. For synaptic transmission studies, although quantitative, this technique is manual and very low-throughput. As it is, it is difficult to apply this technique to genetic studies. In this paper, we enhance this new tool by combining it with microfluidics technology and computer automation. This allows us to increase the assay throughput by several orders of magnitude as compared to the current standard approach, as well as improving standardization and consistency in data gathering. We also demonstrate the ability to infuse drugs to worms during optogenetic experiments using microfluidics. Together, these technologies will enable high-throughput genetic studies such as those of synaptic function.},
	number = {1},
	journal = {Journal of Neuroscience Methods},
	author = {Stirman, Jeffrey N and Brauner, Martin and Gottschalk, Alexander and Lu, Hang},
	month = aug,
	year = {2010},
	note = {{PMID:} 20538016},
	keywords = {Animals, Caenorhabditis elegans, Excitatory Postsynaptic Potentials, Image Processing, {Computer-Assisted}, Inhibitory Postsynaptic Potentials, Microfluidics, Microscopy, Video, Neuromuscular Junction, Pattern Recognition, Automated, Photic Stimulation, Rhodopsin, Synaptic Transmission},
	pages = {90--93}
},

@article{guo_optical_2009,
	title = {Optical interrogation of neural circuits in Caenorhabditis elegans},
	volume = {advance online publication},
	issn = {1548-7105},
	url = {http://dx.doi.org/10.1038/nmeth.1397},
	doi = {10.1038/nmeth.1397},
	journal = {Nat Meth},
	author = {Guo, Zengcai V and Hart, Anne C and Ramanathan, Sharad},
	month = nov,
	year = {2009},
	keywords = {Caenorhabditis elegans, {DLP}}
},

@article{faumont_image-free_2011,
	title = {An {Image-Free} {Opto-Mechanical} System for Creating Virtual Environments and Imaging Neuronal Activity in Freely Moving Caenorhabditis elegans},
	volume = {6},
	url = {http://dx.doi.org/10.1371/journal.pone.0024666},
	doi = {10.1371/journal.pone.0024666},
	abstract = {Non-invasive recording in untethered animals is arguably the ultimate step in the analysis of neuronal function, but such recordings remain elusive. To address this problem, we devised a system that tracks neuron-sized fluorescent targets in real time. The system can be used to create virtual environments by optogenetic activation of sensory neurons, or to image activity in identified neurons at high magnification. By recording activity in neurons of freely moving C. elegans, we tested the long-standing hypothesis that forward and reverse locomotion are generated by distinct neuronal circuits. Surprisingly, we found motor neurons that are active during both types of locomotion, suggesting a new model of locomotion control in C. elegans. These results emphasize the importance of recording neuronal activity in freely moving animals and significantly expand the potential of imaging techniques by providing a mean to stabilize fluorescent targets.},
	number = {9},
	journal = {{PLoS} {ONE}},
	author = {Faumont, Serge and Rondeau, Gary and Thiele, Tod R. and Lawton, Kristy J. and {McCormick}, Kathryn E. and Sottile, Matthew and Griesbeck, Oliver and Heckscher, Ellie S. and Roberts, William M. and Doe, Chris Q. and Lockery, Shawn R.},
	year = {2011},
	pages = {e24666},
	file = {PLoS Full Text PDF:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/ASTFVVVX/Faumont et al. - 2011 - An Image-Free Opto-Mechanical System for Creating .pdf:application/pdf;PLoS Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/3VMQPT4G/infodoi10.1371journal.pone.html:text/html}
},

@article{pal_dna-origami-directed_2010,
	title = {{DNA-origami-directed} self-assembly of discrete silver-nanoparticle architectures},
	volume = {49},
	issn = {1521-3773},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20235262},
	doi = {10.1002/anie.201000330},
	number = {15},
	journal = {Angewandte Chemie {(International} Ed. in English)},
	author = {Pal, Suchetan and Deng, Zhengtao and Ding, Baoquan and Yan, Hao and Liu, Yan},
	month = apr,
	year = {2010},
	note = {{PMID:} 20235262},
	keywords = {{DNA}, Gold, Metal Nanoparticles, Organometallic Compounds, Silver},
	pages = {2700--2704}
},

@article{nangreave_dna_2010,
	title = {{DNA} origami: a history and current perspective},
	volume = {14},
	issn = {1879-0402},
	shorttitle = {{DNA} origami},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20643573},
	doi = {10.1016/j.cbpa.2010.06.182},
	abstract = {Researchers have been using {DNA} for the rational design and construction of nanoscale objects for nearly 30 years. Recently, 'scaffolded {DNA} origami' has emerged as one of the most promising assembly techniques in {DNA} nanotechnology with a broad range of applications. In the past two years alone, {DNA} origami has been used to assemble water-soluble probe tiles for label-free {RNA} hybridization, to study single-molecule chemical reactions, to probe distance-dependent multivalent ligand-protein binding effects, and to organize a variety of relevant molecules including proteins, carbon nanotubes, and metal nanoparticles. This review will recount the origin, evolution, and current status of this extremely versatile assembly technique.},
	number = {5},
	journal = {Current Opinion in Chemical Biology},
	author = {Nangreave, Jeanette and Han, Dongran and Liu, Yan and Yan, Hao},
	month = oct,
	year = {2010},
	note = {{PMID:} 20643573},
	keywords = {{DNA}, Nanotechnology, Nucleic Acid Conformation},
	pages = {608--615}
},

@article{diamond_where_2008,
	title = {{'Where'} and 'what' in the whisker sensorimotor system},
	volume = {9},
	issn = {1471-0048},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18641667},
	doi = {10.1038/nrn2411},
	abstract = {In the visual system of primates, different neuronal pathways are specialized for processing information about the spatial coordinates of objects and their identity - that is, 'where' and 'what'. By contrast, rats and other nocturnal animals build up a neuronal representation of 'where' and 'what' by seeking out and palpating objects with their whiskers. We present recent evidence about how the brain constructs a representation of the surrounding world through whisker-mediated sense of touch. While considerable knowledge exists about the representation of the physical properties of stimuli - like texture, shape and position - we know little about how the brain represents their meaning. Future research may elucidate this and show how the transformation of one representation to another is achieved.},
	number = {8},
	journal = {Nature Reviews. Neuroscience},
	author = {Diamond, Mathew E and von Heimendahl, Moritz and Knutsen, Per Magne and Kleinfeld, David and Ahissar, Ehud},
	month = aug,
	year = {2008},
	note = {{PMID:} 18641667},
	keywords = {Action Potentials, Afferent Pathways, Animals, Behavior, Animal, Head Movements, Mechanoreceptors, Neurons, Afferent, Rats, Somatosensory Cortex, Space Perception, Touch, Trigeminal Nerve, Vibrissae},
	pages = {601--612},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/Z3UWK4RU/18641667.html:text/html}
},

@misc{_concerned_????,
	title = {Concerned About {BPA:} Check Your Receipts - Science News},
	url = {http://www.sciencenews.org/view/generic/id/48084/title/Science_%2B_the_Public__Concerned_about_BPA_Check_your_receipts},
	howpublished = {{http://www.sciencenews.org/view/generic/id/48084/title/Science\_\%2B\_the\_Public\_\_Concerned\_about\_BPA\_Check\_your\_receipts}}
},

@article{liedl_self-assembly_2010-1,
	title = {Self-assembly of three-dimensional prestressed tensegrity structures from {DNA}},
	volume = {5},
	issn = {1748-3395},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20562873},
	doi = {10.1038/nnano.2010.107},
	abstract = {Tensegrity, or tensional integrity, is a property of a structure indicating a reliance on a balance between components that are either in pure compression or pure tension for stability. Tensegrity structures exhibit extremely high strength-to-weight ratios and great resilience, and are therefore widely used in engineering, robotics and architecture. Here, we report nanoscale, prestressed, three-dimensional tensegrity structures in which rigid bundles of {DNA} double helices resist compressive forces exerted by segments of single-stranded {DNA} that act as tension-bearing cables. Our {DNA} tensegrity structures can self-assemble against forces up to 14 {pN}, which is twice the stall force of powerful molecular motors such as kinesin or myosin. The forces generated by this molecular prestressing mechanism can be used to bend the {DNA} bundles or to actuate the entire structure through enzymatic cleavage at specific sites. In addition to being building blocks for nanostructures, tensile structural elements made of single-stranded {DNA} could be used to study molecular forces, cellular mechanotransduction and other fundamental biological processes.},
	number = {7},
	journal = {Nature Nanotechnology},
	author = {Liedl, Tim and Högberg, Björn and Tytell, Jessica and Ingber, Donald E and Shih, William M},
	month = jul,
	year = {2010},
	note = {{PMID:} 20562873},
	keywords = {{DNA}, Nucleic Acid Conformation, Physicochemical Phenomena, Stress, Mechanical},
	pages = {520--524}
},

@article{li_controlled_2010,
	title = {Controlled fabrication of fluorescent barcode nanorods},
	volume = {4},
	issn = {{1936-086X}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20731421},
	doi = {10.1021/nn9017137},
	abstract = {We report a novel technique for generating polymer fluorescent barcode nanorods by reactive ion etching of polymer multilayer films using nonclose-packed (ncp) colloidal microsphere arrays as masks. The fluorescent polymer multilayer films were spin-coated on a substrate, and ncp microsphere arrays were transferred onto these films. The exposed polymers were then etched away selectively, leaving color-encoded nanorods with well-preserved fluorescent properties. By modifying the spin-coating procedure, the amount of polymer in each layer could be tuned freely, which determined the relative fluorescence intensity of the barcode nanorods. These nanorod arrays can be detached from the substrate to form dispersions of coding materials. Moreover, the shape of the nanorods is controllable according to the different etching speeds of various materials, which also endows the nanorods with shape-encoded characters. This method offers opportunities for the fabrication of novel fluorescent barcodes which can be used for detecting and tracking applications.},
	number = {8},
	journal = {{ACS} Nano},
	author = {Li, Xiao and Wang, Tieqiang and Zhang, Junhu and Zhu, Difu and Zhang, Xun and Ning, Yang and Zhang, Hao and Yang, Bai},
	month = aug,
	year = {2010},
	note = {{PMID:} 20731421},
	keywords = {Automatic Data Processing, Fluorescent Dyes, Microscopy, Electron, Scanning, Nanotechnology, Nanotubes, Polyvinyls, Spectrophotometry, Ultraviolet},
	pages = {4350--4360}
},

@unpublished{lin_sub-micrometer_2011,
	title = {Sub-micrometer Geometrically Encoded Fluorescent Barcodes {Self-Assembled} from {DNA}},
	author = {Lin, Chenxiang and Jungmann, Ralf and Leifer, Andrew M and Li, Chao and Levner, Daniel and Shih, William M and Yin, Peng},
	month = oct,
	year = {2011},
	note = {Submitted to Nature Nanotechnology}
},

@article{gudiksen_growth_2002,
	title = {Growth of nanowire superlattice structures for nanoscale photonics and electronics},
	volume = {415},
	issn = {0028-0836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11832939},
	doi = {10.1038/415617a},
	abstract = {The assembly of semiconductor nanowires and carbon nanotubes into nanoscale devices and circuits could enable diverse applications in nanoelectronics and photonics. Individual semiconducting nanowires have already been configured as field-effect transistors, photodetectors and bio/chemical sensors. More sophisticated light-emitting diodes {(LEDs)} and complementary and diode logic devices have been realized using both n- and p-type semiconducting nanowires or nanotubes. The n- and p-type materials have been incorporated in these latter devices either by crossing p- and n-type nanowires or by lithographically defining distinct p- and n-type regions in nanotubes, although both strategies limit device complexity. In the planar semiconductor industry, intricate n- and p-type and more generally compositionally modulated (that is, superlattice) structures are used to enable versatile electronic and photonic functions. Here we demonstrate the synthesis of semiconductor nanowire superlattices from group {III-V} and group {IV} materials. {(The} superlattices are created within the nanowires by repeated modulation of the vapour-phase semiconductor reactants during growth of the wires.) Compositionally modulated superlattices consisting of 2 to 21 layers of {GaAs} and {GaP} have been prepared. Furthermore, {n-Si/p-Si} and {n-InP/p-InP} modulation doped nanowires have been synthesized. Single-nanowire photoluminescence, electrical transport and electroluminescence measurements show the unique photonic and electronic properties of these nanowire superlattices, and suggest potential applications ranging from nano-barcodes to polarized nanoscale {LEDs.}},
	number = {6872},
	journal = {Nature},
	author = {Gudiksen, Mark S and Lauhon, Lincoln J and Wang, Jianfang and Smith, David C and Lieber, Charles M},
	month = feb,
	year = {2002},
	note = {{PMID:} 11832939},
	pages = {617--620}
},

@article{douglas_self-assembly_2009,
	title = {Self-assembly of {DNA} into nanoscale three-dimensional shapes},
	volume = {459},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19458720},
	doi = {10.1038/nature08016},
	abstract = {Molecular self-assembly offers a 'bottom-up' route to fabrication with subnanometre precision of complex structures from simple components. {DNA} has proved to be a versatile building block for programmable construction of such objects, including two-dimensional crystals, nanotubes, and three-dimensional wireframe nanopolyhedra. Templated self-assembly of {DNA} into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase 'scaffold strand' that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide 'staple strands'. Here we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six shapes-monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross-with precisely controlled dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and heterotrimeric wireframe icosahedra. Proper assembly requires week-long folding times and calibrated monovalent and divalent cation concentrations. We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometre scale.},
	number = {7245},
	journal = {Nature},
	author = {Douglas, Shawn M and Dietz, Hendrik and Liedl, Tim and Högberg, Björn and Graf, Franziska and Shih, William M},
	month = may,
	year = {2009},
	note = {{PMID:} 19458720},
	keywords = {{DNA}, Microscopy, Electron, Transmission, Nanostructures, Nanotechnology, Nucleic Acid Conformation},
	pages = {414--418}
},

@article{han_quantum-dot-tagged_2001,
	title = {Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules},
	volume = {19},
	issn = {1087-0156},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11433273},
	doi = {10.1038/90228},
	abstract = {Multicolor optical coding for biological assays has been achieved by embedding different-sized quantum dots (zinc sulfide-capped cadmium selenide nanocrystals) into polymeric microbeads at precisely controlled ratios. Their novel optical properties (e.g., size-tunable emission and simultaneous excitation) render these highly luminescent quantum dots {(QDs)} ideal fluorophores for wavelength-and-intensity multiplexing. The use of 10 intensity levels and 6 colors could theoretically code one million nucleic acid or protein sequences. Imaging and spectroscopic measurements indicate that the {QD-tagged} beads are highly uniform and reproducible, yielding bead identification accuracies as high as 99.99\% under favorable conditions. {DNA} hybridization studies demonstrate that the coding and target signals can be simultaneously read at the single-bead level. This spectral coding technology is expected to open new opportunities in gene expression studies, high-throughput screening, and medical diagnostics.},
	number = {7},
	journal = {Nature Biotechnology},
	author = {Han, M and Gao, X and Su, J Z and Nie, S},
	month = jul,
	year = {2001},
	note = {{PMID:} 11433273},
	keywords = {Biotechnology, {DNA}, Fluorescent Dyes, Genetic Techniques, Microscopy, Fluorescence, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Oligonucleotides, Spectrometry, Fluorescence},
	pages = {631--635}
},

@article{jones_bat_2007,
	title = {Bat echolocation calls: adaptation and convergent evolution},
	volume = {274},
	issn = {0962-8452},
	shorttitle = {Bat echolocation calls},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17251105},
	doi = {10.1098/rspb.2006.0200},
	abstract = {Bat echolocation calls provide remarkable examples of 'good design' through evolution by natural selection. Theory developed from acoustics and sonar engineering permits a strong predictive basis for understanding echolocation performance. Call features, such as frequency, bandwidth, duration and pulse interval are all related to ecological niche. Recent technological breakthroughs have aided our understanding of adaptive aspects of call design in free-living bats. Stereo videogrammetry, laser scanning of habitat features and acoustic flight path tracking permit reconstruction of the flight paths of echolocating bats relative to obstacles and prey in nature. These methods show that echolocation calls are among the most intense airborne vocalizations produced by animals. Acoustic tracking has clarified how and why bats vary call structure in relation to flight speed. Bats using broadband echolocation calls adjust call design in a range-dependent manner so that nearby obstacles are localized accurately. Recent phylogenetic analyses based on gene sequences show that particular types of echolocation signals have evolved independently in several lineages of bats. Call design is often influenced more by perceptual challenges imposed by the environment than by phylogeny, and provides excellent examples of convergent evolution. Now that whole genome sequences of bats are imminent, understanding the functional genomics of echolocation will become a major challenge.},
	number = {1612},
	journal = {Proceedings. Biological Sciences / The Royal Society},
	author = {Jones, Gareth and Holderied, Marc W},
	month = apr,
	year = {2007},
	note = {{PMID:} 17251105},
	keywords = {Adaptation, Biological, Animals, Chiroptera, Echolocation, Ecosystem, Flight, Animal, Phylogeny},
	pages = {905--912},
	file = {PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/R7KT3KPD/17251105.html:text/html}
},

@article{xu_early_2011,
	title = {The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit},
	volume = {12},
	issn = {1471-0064},
	shorttitle = {The early bird catches the worm},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21969037},
	doi = {10.1038/nrg3050},
	abstract = {The inherent simplicity of Caenorhabditis elegans and its extensive genetic toolkit make it ideal for studying complex biological processes. Recent developments further increase the usefulness of the worm, including new methods for: altering gene expression, altering physiology using optogenetics, manipulating large numbers of worms, automating laborious processes and processing high-resolution images. These developments both enhance the worm as a model for studying processes such as development and ageing and make it an attractive model in areas such as neurobiology and behaviour.},
	number = {11},
	journal = {Nature Reviews. Genetics},
	author = {Xu, Xiao and Kim, Stuart K},
	year = {2011},
	note = {{PMID:} 21969037},
	pages = {793--801}
},

@article{qin_maze_2007,
	title = {Maze exploration and learning in C. elegans},
	volume = {7},
	issn = {1473-0197},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17268620},
	doi = {10.1039/b613414a},
	abstract = {The soil dwelling nematode, Caenorhabditis {(C.)} elegans, is a popular model system for studying behavioral plasticity. Noticeably absent from the C. elegans literature, however, are studies evaluating worm behavior in mazes. Here, we report the use of microfluidic mazes to investigate exploration and learning behaviors in wild-type C. elegans, as well as in the dopamine-poor mutant, cat-2. The key research findings include: {(1)C.} elegans worms are motivated to explore complex spatial environments with or without the presence of food/reward, (2) wild-type worms exhibit a greater tendency to explore relative to mutant worms, (3) both wild-type and mutant worms can learn to make unconditioned responses to food/reward, and (4) wild-type worms are significantly more likely to learn to make conditioned responses linking reward to location than mutant worms. These results introduce microfluidic mazes as a valuable new tool for biological behavioral analysis.},
	number = {2},
	journal = {Lab on a Chip},
	author = {Qin, Jianhua and Wheeler, Aaron R},
	month = feb,
	year = {2007},
	note = {{PMID:} 17268620},
	keywords = {Animals, Behavior, Animal, Caenorhabditis elegans, Genotype, Maze Learning, Microfluidic Analytical Techniques, Models, Biological, Motor Activity, Movement, Mutation, Time Factors},
	pages = {186--192},
	file = {b613414a.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/W9HZUXWG/b613414a.pdf:application/pdf;Lab on a Chip Articles:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/TMAMMJ2F/article.html:text/html;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/J56KSIN4/17268620.html:text/html}
},

@article{mori_neural_1995,
	title = {Neural regulation of thermotaxis in Caenorhabditis elegans},
	volume = {376},
	issn = {0028-0836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7630402},
	doi = {10.1038/376344a0},
	abstract = {Thermal stimulus is an important environmental factor influencing animal behaviour. However, the mechanisms underlying thermosensation and thermal adaptation are poorly understood. The nematode Caenorhabditis elegans can sense a range of environmental temperatures and migrate towards the cultivation temperature on a thermal gradient. This modifiable thermotactic response provides an ideal system for studying the cellular and molecular processes involved in thermosensation and thermal information storage. We have identified neurons critical for thermotaxis by killing individual cells in live animals. The results indicate that an amphid sensory neuron, {AFD}, is a major thermosensory neuron. Some of the genetically defined cryophilic and thermophilic mutant phenotypes were mimicked when amphid interneurons {AIY} and {AIZ}, respectively, were killed, indicating that {AIY} is responsible for thermophilic movement and {AIZ} for cryophilic movement. We propose a neural model in which regulation of the activities of the two interneurons in opposite directions, depending on the cultivation temperature, is essential for thermotaxis.},
	number = {6538},
	journal = {Nature},
	author = {Mori, I and Ohshima, Y},
	month = jul,
	year = {1995},
	note = {{PMID:} 7630402},
	keywords = {Animals, Caenorhabditis elegans, Cell Death, Interneurons, Lasers, Models, Neurological, Movement, Mutation, Nerve Net, Neurons, Afferent, Temperature},
	pages = {344--348},
	file = {376344a0.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/UNT8A988/376344a0.pdf:application/pdf;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/9GKF26MT/7630402.html:text/html}
},

@article{liu_graded_2009,
	title = {Graded synaptic transmission at the Caenorhabditis elegans neuromuscular junction},
	issn = {0027-8424},
	url = {http://www.pnas.org.ezp-prod1.hul.harvard.edu/content/early/2009/06/15/0903570106.full.pdf+html?frame=sidebar},
	doi = {10.1073/pnas.0903570106},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Liu, Q. and Hollopeter, G. and Jorgensen, E. M.},
	month = jun,
	year = {2009}
},

@article{zimmer_structure_2008,
	title = {Structure of a complex of the {ATPase} {SecA} and the protein-translocation channel},
	volume = {455},
	issn = {0028-0836},
	url = {http://dx.doi.org/10.1038/nature07335},
	doi = {10.1038/nature07335},
	number = {7215},
	journal = {Nature},
	author = {Zimmer, Jochen and Nam, Yunsun and Rapoport, Tom A.},
	month = oct,
	year = {2008},
	pages = {936--943}
},

@incollection{buehler_stanley:_2007,
	address = {Berlin, Heidelberg},
	title = {Stanley: The Robot That Won the {DARPA} Grand Challenge},
	volume = {36},
	isbn = {978-3-540-73428-4, 978-3-540-73429-1},
	shorttitle = {Stanley},
	url = {http://www.springerlink.com/content/r01240114858137n/},
	booktitle = {The 2005 {DARPA} Grand Challenge},
	publisher = {Springer Berlin Heidelberg},
	author = {Thrun, Sebastian and Montemerlo, Mike and Dahlkamp, Hendrik and Stavens, David and Aron, Andrei and Diebel, James and Fong, Philip and Gale, John and Halpenny, Morgan and Hoffmann, Gabriel and Lau, Kenny and Oakley, Celia and Palatucci, Mark and Pratt, Vaughan and Stang, Pascal and Strohband, Sven and Dupont, Cedric and Jendrossek, {Lars-Erik} and Koelen, Christian and Markey, Charles and Rummel, Carlo and Niekerk, Joe and Jensen, Eric and Alessandrini, Philippe and Bradski, Gary and Davies, Bob and Ettinger, Scott and Kaehler, Adrian and Nefian, Ara and Mahoney, Pamela},
	editor = {Buehler, Martin and Iagnemma, Karl and Singh, Sanjiv},
	year = {2007},
	pages = {1--43},
	file = {SpringerLink - Abstract:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/8X77D7V4/r01240114858137n.html:text/html}
},

@article{lazard_muco-ciliary_2009,
	title = {Muco-ciliary differentiation of nasal epithelial cells is decreased after wound healing in vitro},
	volume = {64},
	issn = {0105-4538},
	doi = {10.1111/j.1398-9995.2009.02003.x},
	abstract = {Epithelial damage and modifications of cell differentiation are frequent in airway diseases with chronic inflammation, in which Transforming Growth Factor-β1 {(TGF-β1)} plays an important role. The aim of this study was to evaluate the differentiation of human nasal epithelial cells {(HNEC)} after wound healing and the potential effects of {TGF-β1.}

Basal, mucous and ciliated cells were characterized by cytokeratin-14, {MUC5AC} and {βIVtubulin} immunodetection, respectively. Their expression was evaluated in situ in nasal polyps and in an in vitro model of wound healing in primary cultures of {HNEC} after wound closure, under basal conditions and after {TGF-β1} supplementation. Using {RT-PCR}, the effects of {TGF-β1} on {MUC5AC} and {DNAI1} genes, specifically transcribed in mucous and ciliated cells, were evaluated.

In situ, high {TGF-β1} expression was associated with low {MUC5AC} and {βIVtubulin} expression. In vitro, under basal conditions, {MUC5AC} expression remained stable, cytokeratin-14 expression was strong and decreased with time, while {βIV} tubulin expression increased. {TGF-β1} supplementation down-regulated {MUC5AC} and {βIV} tubulin expression as well as {MUC5AC} and {DNAI1} transcripts.

After a wound, differentiation into mucous and ciliated cells was possible and partially inhibited in vitro by {TGF-β1}, a cytokine that may be involved in epithelial remodeling observed in chronic airway diseases.},
	number = {8},
	author = {Lazard, Diane S. and Moore, Anne and Hupertan, Vincent and Martin, Clémence and Escabasse, Virginie and Dreyfus, Patrick and Burgel, {Pierre-Régis} and Amselem, Serge and Escudier, Estelle and Coste, André},
	month = aug,
	year = {2009},
	note = {{PMID:} 19245428
{PMCID:} 2846321},
	pages = {1136--1143}
},

@article{franco_molecular_????,
	title = {Molecular vibration-sensing component in Drosophila melanogaster olfaction},
	url = {http://www.pnas.org.ezp-prod1.hul.harvard.edu/content/early/2011/02/08/1012293108.abstract},
	doi = {10.1073/pnas.1012293108},
	abstract = {A common explanation of molecular recognition by the olfactory system posits that receptors recognize the structure or shape of the odorant molecule. We performed a rigorous test of shape recognition by replacing hydrogen with deuterium in odorants and asking whether Drosophila melanogaster can distinguish these identically shaped isotopes. We report that flies not only differentiate between isotopic odorants, but can be conditioned to selectively avoid the common or the deuterated isotope. Furthermore, flies trained to discriminate against the normal or deuterated isotopes of a compound, selectively avoid the corresponding isotope of a different odorant. Finally, flies trained to avoid a deuterated compound exhibit selective aversion to an unrelated molecule with a vibrational mode in the energy range of the carbon–deuterium stretch. These findings are inconsistent with a shape-only model for smell, and instead support the existence of a molecular vibration-sensing component to olfactory reception.},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Franco, Maria Isabel and Turin, Luca and Mershin, Andreas and Skoulakis, Efthimios M. C.}
},

@article{bargmann_chemosensation_2006,
	title = {Chemosensation in C. elegans},
	issn = {15518507},
	url = {http://www.wormbook.org/chapters/www_chemosensation/chemosensation.html},
	doi = {10.1895/wormbook.1.123.1},
	journal = {{WormBook}},
	author = {Bargmann, Cornelia},
	year = {2006}
},

@article{bargmann_laser_1995,
	title = {Laser killing of cells in Caenorhabditis elegans},
	volume = {48},
	issn = {{0091-679X}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8531727},
	journal = {Methods in Cell Biology},
	author = {Bargmann, C I and Avery, L},
	year = {1995},
	note = {{PMID:} 8531727},
	keywords = {Ablation, Animals, Caenorhabditis elegans, Cell Death, Lasers, Print Me!},
	pages = {225--250},
	file = {paper.pdf:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/8N7QWBTM/paper.pdf:application/pdf;PubMed Snapshot:/Users/andy/Library/Application Support/Firefox/Profiles/x5qrcnjz.default/zotero/storage/9VBK522B/8531727.html:text/html}
},

@article{rankin_context_2000,
	title = {Context conditioning in habituation in the nematode Caenorhabditis elegans},
	volume = {114},
	issn = {0735-7044},
	url = {http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed/10883800},
	abstract = {Habituation has traditionally been considered a nonassociative form of learning. However, recent research suggests that retention of this nonassociative form of learning may be aided by associations formed during training. An example of this is context conditioning, in which animals that are trained and tested in the presence of a contextual cue show greater retention than animals trained and tested in different environments. This article reports context conditioning in habituation in the nematode Caenorhabditis elegans. The results showed that retention of habituation to tap at both 10- and 60-s interstimulus intervals was significantly greater if training and testing occurred in the presence of the same chemosensory cue {(NaCH3COO).} This context conditioning showed both extinction and latent inhibition, demonstrating that these simple worms with only 302 neurons are capable of associative context conditioning.},
	number = {3},
	journal = {Behavioral Neuroscience},
	author = {Rankin, C H},
	month = jun,
	year = {2000},
	note = {{PMID:} 10883800},
	keywords = {Animals, Association Learning, Caenorhabditis elegans, Conditioning, Classical, Cues, Extinction, Psychological, Habituation, Psychophysiologic, Retention {(Psychology)}},
	pages = {496--505}
},

@article{_genome_1998,
	title = {Genome sequence of the nematode C. elegans: a platform for investigating biology},
	volume = {282},
	issn = {0036-8075},
	shorttitle = {Genome sequence of the nematode C. elegans},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9851916},
	abstract = {The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms. There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly conserved genes provides evidence for a regional organization of the chromosomes.},
	number = {5396},
	journal = {Science {(New} York, {N.Y.)}},
	month = dec,
	year = {1998},
	note = {{PMID:} 9851916},
	keywords = {Animals, Caenorhabditis elegans, Chromosomes, {DNA}, Helminth, Evolution, Molecular, Genes, Helminth, Genome, Helminth Proteins, Molecular Sequence Data, Physical Chromosome Mapping, Repetitive Sequences, Nucleic Acid, {RNA}, Helminth, Sequence Analysis, {DNA}},
	pages = {2012--2018}
},

@article{torring_dna_2011,
	title = {{DNA} origami: a quantum leap for self-assembly of complex structures},
	issn = {1460-4744},
	shorttitle = {{DNA} origami},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21594298},
	doi = {10.1039/c1cs15057j},
	abstract = {The spatially controlled positioning of functional materials by self-assembly is one of the fundamental visions of nanotechnology. Major steps towards this goal have been achieved using {DNA} as a programmable building block. This tutorial review will focus on one of the most promising methods: {DNA} origami. The basic design principles, organization of a variety of functional materials and recent implementation of {DNA} robotics are discussed together with future challenges and opportunities.},
	journal = {Chemical Society Reviews},
	author = {Tørring, Thomas and Voigt, Niels V and Nangreave, Jeanette and Yan, Hao and Gothelf, Kurt V},
	month = may,
	year = {2011},
	note = {{PMID:} 21594298}
}