# HG changeset patch # User Steve Losh # Date 1694013030 14400 # Node ID 0e785a0371e14744545e7268e37c04618680ca36 # Parent 87004230f40dcb1cfafd326c7206a8e845e48756 Update diff -r 87004230f40d -r 0e785a0371e1 README.markdown --- a/README.markdown Tue Sep 05 16:12:10 2023 -0400 +++ b/README.markdown Wed Sep 06 11:10:30 2023 -0400 @@ -1010,3 +1010,33 @@ " --short2 {input[1]}" " --out assemblies/{wildcards.sample}/" ) + +Puttered around changing my StumpWM and terminal colors/borders/etc a bit to +make them a little easier on my eyes. We'll see if it sticks. + +## 2023-09-06 + +HG545 in the morning. Mostly understood things. + +Asked the professor after about a question I had while reading the paper. One +of the things the paper did to confirm the region of interest was to use a PAC +(P1-derived artificial chromosome) to "rescue" the golden embryos. The +resulting fish showed mosaic rescue, confirming that the wild-type gene was +likely on that PAC, i.e. in the region of interest. + +What I didn't understand is how injecting the plasmid into the embryos resulted +in the expression of the genes farther down the developmental line, e.g. does it +somehow get incorporated into the cells' genomes? It turns out to be messy. + +First: you don't inject "a PAC" into the embryos, you inject "a shitload of +copies of the PAC" into the embryo. So all of the embryo's cells will have +copies of the PAC floating around inside. As the cell divides, those will get +diluted in daughter cells over time. Some of these copies will, by chance, make +it into the nucleus of their cells. And some of those (rarely) will get +randomly incorporated into the cell's genome, and from then on mitosis takes +over and the gene gets propagated normally. So the mosaic region from that +point forward will have the gene (and if the region happens to contain some +melanophores, also the rescued wild-type phenotype). + +Got my Armis access at some point during class, so it's time to figure out how +to log into the various HPC clusters today.