Genetic Engineering (starts at around IV)

[swagXDragonSlayer46YT]

Sterilizization

Sterilization filter blocks would be made of HEPA filters and ultraviolet emitters.

Used glassware is washed with bleach and autoclaved to be sterilized. Plastic wares and other not-so-heat-resistant objects are just washed with bleach.

New Multiblocks/Machines

Bacteria Incubators

• Uses air with certain conditions including heat, moisture, composition, etc (Similar to green house)
• Takes in petri dish containing organisms, and a growth medium (there will be multiple types of growth mediums)
• Can duplicate bacteria or irradiate bacteria if a radiation source is provided
• Creates depleted growth medium anytime a growth medium is used
• May also require a light source for organisms that need light

Biosafety cabinets

• This would be a higher tier of bacteria incubator, used for dealing with viruses and extraterrestrial organisms.

UV Box

• For sterilization

EV stuff:

Begin with isolating bacteria from the natural environment. Collect natural materials that contain the bacteria of interest. For example, dirt, which contains E. coil. The organisms in the natural material are cultivated in a petri dish.

Different species can also be separated by diluting a solution containing bacteria via serial dilution. This reduces the amount of colony forming units to the point that there will only be a few sparse colonies growing after the diluted solution is cultured. This makes it possible to select a single species of cell.

These species can then be used to ferment new things.

IV genetic engineering:

Begin with isolating bacteria from the natural environment. Collect natural materials that contain the bacteria of interest. For example, dirt, which contains E. coil. The organisms in the natural material are cultivated in a petri dish.

Different method will be used to sort the different organisms, based on the situation.

Different species in the petri dish can be sorted using a flow cytometry machine. The machine would requires some laser, sensors, and computers to build. Fluorescent dyes will also be needed in this process.

List of fluorescent dyes (chains will be needed for them)

• coumarin
• rhodamine
• fluorescin
• DAPI
• cyanine

Different species can also be separated by diluting a solution containing bacteria via serial dilution.

Organisms of the same species can be sorted by strength of certain genes, using a blue-white screen, which is explained here: https://en.wikipedia.org/wiki/Blue%E2%80%93white_screen

This will require a derivative of galactose that is blue (5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside), some plasmids, and the gene that is desired.

Bacteria can be cultivated in incubator. Depending on what is being grown, a different growth medium will be used.

• Nutrient agar is used to cultivate easy bacteria. Even school kids use it.
• Lysogeny broth is the main medium used for bacteria with medium requirements. Used for cultivating E. Coil.
• Potato dextrose agar culture (or YPD media) is used for cultivating fungi and mold
• Blood cell agar culture used for virus and bacteria with advanced nutrient requirements
• Cultures made of cells are used to cultivate virus in general due to their need to infect other cells
• Brain heart infusion is used to cultivate the most challenging bacteria
• Add more from here if needed: https://en.wikipedia.org/wiki/Agar_plate#General_bacterial_media

Note: Casein for lysogeny broth comes in the form of milk

Methods for making all of these are on wikipedia.

Similarly to what is seen in GTNH's bacterial vat multiblock, bacteria may be irradiated to get random genes. Rods of radioactive material may be provided to reach certain Sievert levels required to mutate certain organisms.

Mutated bacteria with certain new genes can then be sorted, and cultivated to make more. Mutated bacteria may be used to ferment stuff for more products or new products.

LuV genetic engineering:

These processes will need certain proteins and enzymes isolated from cells. Cells with the desired proteins or enzymes are broken down using detergents and surfactants, releasing its contained proteins and DNA. Ice-cold chloroform is added to precipitate purified DNA, which is centrifuged from the rest of the proteins and enzymes.

"Any DNA extracted will have to undergo quantification and quality control. This can be done using a nanodrop. This basically uses a very small quantity of DNA solution and a spectrophotometer in order to quantify DNA concentration. A qubit is even better than a nanodrop insofar as to be able to measure the purity of the DNA using some funny reagents." - planetme

The purified DNA can be stored in ultra-pure water.

The individual proteins and enzymes from this step can be sorted using a variety of techniques mentioned here: https://en.wikipedia.org/wiki/Protein_purification

The general process is: Ultracentrifugation -> Purification Step -> Concentration (via Ultrafiltration)

Several techniques used in the purification step include various chromatrography techniques and immunoprecipitation.

"Immunoprecipitation basically uses antibodies to bind to certain proteins. You can make the monoclonal antibodies used by fusing a cancer cell nucleus with an immune cell nucleus that produces the antibody to form a heterokaryon that absolutely churns the immune cell out. So that basically produces a cell line that produces the specific antibody" - planetme

Purification of Cas9:

"you will also need western blots/SDS-PAGE for separation of useful proteins such as Cas9 or restriction enzymes such as HindIII. For this, you will need sodium dodecylsulfate, polyacrylamide gel, buffers, chelators, etc. Most importantly you will need beta-mercaptoethanol for the denaturation of the enzymes synergistically with SDS" - planetme

Here are some things that are obtained:

• Ultracentrifuged debris (List of stuff: https://en.wikipedia.org/wiki/Differential_centrifugation#Procedure)
• Restriction enzymes, which will be needed later
• Cas9 proteins from streoptococcus bacteria
• Taq polymerase from thermophilus aquaticus

To move traits from isolated DNA into new DNA, the isolated DNA is cut into genes using restriction enzymes. The genes are then sorted using gel electrophoresis, where DNA is sorted in a gel based on length. The gel is prepared by dissolving agar in tris(hydroxymethyl)aminomethane, acetic acid, and EDTA, which is cast into a block. The DNA is prepared by mixing with fluorescent intercalating dyes (ethidium bromide or SYBR green). Voltage is then applied to separate the different DNA fragments. The gel is then pressed onto a nitrocellulose paper or nylon sheet to get the DNA out, allowing analysis or extraction of certain genes.

The isolated genes are inserted into Cas9 proteins. The gene-holding Cas9 proteins are then sent into cells to edit their genes.
Genes may also be added to heavy metal particles, which are shot into cells. This is used mainly for plants.

Both of these would be done in a gene insertion machine.

Bacteria and crops can be genetically modified this way to make new products or more products.

ZPM genetic engineering

Cellular growth medium

Growth mediums to cultivate cells rather than bacteria generally need:

• fatty acids
• vitamins
• minerals
• amino acids
• carbohydrates
• ultrapure water
• sugar
• salt
• sodium dodeceyl sulfate

Normal Cells

First, cells will have to be isolated from living animals or humans. Isolated cells are first immersed in a cellular growth medium to keep them alive for the following processes.

The isolated cells can be turned into immortalized cell lines. Viral proteins/genes such as SV40 Large T antigen, 5E1 gene, or the Epstein-Barr virus are introduced to disturb the cell cycle, making it impossible to die. When these immortalized cells are immersed in a cellular growth medium, they will divide infinitely. This will create depleted growth medium, and will mass produce meat, fat, blood cells, and any other cell that is able to divide itself. It can also be used to grow organs and animal parts to be harvested.

These cells can be grown into 3D shapes using 3D cell culturing, which needs magnetic nanoparticles, gold nanoparticles, and poly-L-lysine, which are used to make cells magnetic. A shaped magnetic field, made by a neodymium magnet, is used to pull on the cells to create shapes. This can be used for growing organs or animal parts to be harvested.
Source: https://en.wikipedia.org/wiki/3D_cell_culturing_by_magnetic_levitation

Stem Cells

Stem cells will be used to create grown brain cells, to be used in wetware. Brain cells can't divide, but stem cells can divide and can be cultivated into brain cells.

Pluripotent stem cell article: https://pubmed.ncbi.nlm.nih.gov/16904174/

Pluripotent stem cells may be sourced from various sources. Besides needing a cellular growth medium, the stem cells require a culture of living tissue to support the stem cells. Without growth factors, the stem cells won't differentiate and will multiply indefinitely as long as there's still culture.

To develop the stem cells into specific cells, it must be cut off and put in a new serum with growth factors to begin cell specialization. For brain cells, this requires:

• Fibroblast growth factors
• Psilocybin
• N,N-Dimethyltryptamine

The brain cells can be shaped into artificial brains for wetware using the 3D cell culturing mentioned earlier.

Source: https://en.wikipedia.org/wiki/Neurogenesis#Substance-induced_neurogenesis

UV genetic engineering

First, Oligonucleotide synthesis is used to create custom DNA molecules about 20 bases long. The whole process is detailed here and doesn't need to be copied into github: https://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Synthesis_by_the_phosphoramidite_method

These DNA fragments are then conjoined to create genes using the Gibson assembly. The whole process is detailed here and doesn't need to be copied into github: https://en.wikipedia.org/wiki/Gibson_assembly

Next, DNA is mass produced using chemistry. The polymerase chain reaction is used to mass produce DNA itself, from pre-existing DNA (includes custom made DNA). The whole process is detailed here and doesn't need to be copied into github: https://en.wikipedia.org/wiki/Polymerase_chain_reaction#Procedure. CRISPR/Cas9 is then used to transfer this DNA into stem cells to create any organism you wish.

After that, the player can design whatever bacteria, mobs, or organism for industrial purposes or funny purposes. Take inspiration from here if needed: https://www.youtube.com/c/thethoughtemporium