The human transcription factor repertoire is a complex collection of paralogous proteins that represent the major portion of lineage commitment and differentiation.
Estimates of mitochondrial DNA content in wastewater are on the order of 105 copies per mL, substantially higher than other accessible sources (~104 copies per 100mL in river water, for instance), and thus wastewater will be used for this initial study \cite{Caldwell_2009,20208426}. As the copy number in direct fecal samples is 109 per gram, and wastewater is approximately 99.5% water; thus in 1L of wastewater we expect 5g of feces, which corresponds to ~5e9 mtDNA and 5e6 nuclear DNA copies per liter. This is comparable to the estimates obtained from direct wastewater samples and will be used going forward.
Aim 1: A sensitive and specific method for isolation of human DNA sequences from wastewater.
Goal: derive accurate, rare allele frequency estimates.
Simulation of allele frequencies
Show off pretty figures.
DNA purification
Get some gallons of wastewater. Isopropanol extraction, followed by ethanol precipitation, maybe followed by beads?
Library preparation and sequencing
#figure
Comparison to ExAC
So much better, so much cheaper, beat that.
Aim 2: Population modeling of functional diversification in the homeobox transcription factor HOXC6.
Prime & go home. Basically we have a class case of subfunctionalization going on
Aim 3: Downstream functional characterization of constrained HOXC6 variants with a high throughput sequencing assay.
Clone library of plasmids using the essential gene protocol or technique from AB2.2 cells. Sequence that shit.
Conclusions
There is also the possibility of detecting disease in samples \cite{Putaporntip_2011}.