NOTES;
Synthetic chromosomes end game: human
what is life? the definition of life is the capacity to be infected by viruses.
what are genes necessary for life? what tasks must the cell do in order to live? tasks: ie. the cell must have lysine. can synthesize out of metabolic pathway or use a transporter.
most chosen genes are for expression and preservation of genome genes, but there were 149/450 genes function was undetermined.
over the years 49 of the unknown were characterized by wet science. (takes a phd students thesis to solve one gene)
for hw: try to come up with what the other tasks could be.
genomic redundancy: 2 things that are not alike but does the same thing.
phix174, 11genes- bacteria phage. (like the basic hydrogen atom physicists used to study physics.) less genomic redundancies, easier to study.
early question: can we build a minimal synthetic bacterial cell?
minimal cell: genome only encodes for independent grow under ideal lab conditions. to make computational model of cell behavior to predict effects of environmental variations.
Mycoplasma mycoides- first target for minimizing. produces no amino acids. live in fbs. produces colonies in 2-3days.
yeast are the perfect vehicle, can put dna molecules with 50 base pair overlap in and they’ll assemble.
top down ecoli: dropped genome size by sequential deletions.
bottom up ecoli: design genome based on essential genes, synthesize, boot it up. transposon, can integrate into a genome.
Hail mary genome (hypothetical minimal genome): “hail mary pass” fling caution to the wind. 1/8 synthetic to 7/8 wild type genome. need better transposon. tn5 mutagenesis analysis< product is genome thats 50% designed.
in calcium chloride and peg treatment the isolated genome is transported into cell. treat with tetracycline(tet) to eliminate cells with old genome. mytocycin C to create zombie cells to eliminate false parses.
only 1/8 synthesized genome cells grew well.
synthetic lethal: “left and right engines both are not essential for flight” transposon bombardment found 26 genes that were quasi essential, added back.
2016 JCVI-syn3.0: listed all components, to determines what genes are in and what genes are out. the challenges in 3 previous versions.
bsl 2 should be a functional definition. micro plasma as analogous to the hydrogen atom has to be accessible to everyone.
how to change definition to lower it to bsl 1.
synthetic human chromosomes, take existing ie. 21, y put in microcells and build these chromosomes to build new genes into synthetic cells.
build fully functional human artificial chromosomes on yeast with some necessary genes. used cell cycle arrest, at the process of cell degradation. from 1/1000 to 1/800.
if you expose cells to double stranded dna they are not used to seeing double stranded in cytoplasm.
