--- Log opened Mon Aug 17 00:00:51 2020 00:16 -!- darsie [~kvirc@84-113-55-200.cable.dynamic.surfer.at] has joined ##hplusroadmap 00:45 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 272 seconds] 03:08 -!- Livestradamus [~quassel@unaffiliated/livestradamus] has joined ##hplusroadmap 03:47 -!- CryptoDavid [uid14990@gateway/web/irccloud.com/x-ipegeywabrjowyby] has joined ##hplusroadmap 04:55 -!- Urchin[emacs] [~user@unaffiliated/urchin] has quit [Ping timeout: 256 seconds] 05:45 -!- fox2p [~fox2p@ec2-52-87-89-213.compute-1.amazonaws.com] has quit [Quit: hash] 06:29 < kanzure> ".. a collaborator with the lab in Argentina in which some of the rat studies for Harold Katcher's reprogramming work was done. I've been told that the plasma fraction is a bit of a misnomer, and that while it appeared to reset the epigenetic clock by a few months in the rats they did not actually undergo noticeable rejuvenation." 06:30 < kanzure> .wik H3K27me3 06:30 < saxo> "H3K27me3 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the tri-methylation at the 27th lysine residue of the histone H3 protein. / This tri-methylation is associated with the downregulation of nearby genes via the [...]" - https://en.wikipedia.org/wiki/H3K27me3 06:32 < kanzure> i don't really understand that, what is tri-methylation? is that demethylation or is it additive histone acetyltransfer? 06:33 < kanzure> "Lysine is able to be mono-, di-, or trimethylated with a methyl group replacing each hydrogen of its NH3+ group." 06:33 < kanzure> anyway i'm thinking maybe a reprogrammed histone methyltransferase targeting that "27th lysine residue of the histone H3 protein" 06:35 < kanzure> (possibly on a germinal basis) 06:36 < kanzure> we previously listed from the literature a few fusion proteins for programmable methyltransferases https://diyhpl.us/wiki/gene-editing 06:36 < kanzure> "Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389507/ 06:36 < kanzure> oh, DNA methylation, whoops 06:38 < kanzure> these guys tethered a dCas9 to a Ezh2 methyltransferase enzyme to induce targeted deposition of H3K27me3 https://academic.oup.com/nar/article/45/17/9901/3923391 06:42 < kanzure> "Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner" https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-019-0275-8 06:43 < kanzure> "Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner" https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-019-0275-8 06:43 < kanzure> ugh 06:44 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=fbf22d79 Bryan Bishop: programmable histone methyltransferase >> http://diyhpl.us/diyhpluswiki/gene-editing/ 06:45 < kanzure> anyway the downside is "Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested" so i'm not sure this is really practical 07:17 < kanzure> "Highly efficient knockout of a squid pigmentation gene" https://www.cell.com/current-biology/fulltext/S0960-9822(20)30985-4 08:48 -!- yashgaroth [~ffffffff@172.58.19.80] has joined ##hplusroadmap 08:55 -!- prometheus_035 [~root@88.230.137.28] has joined ##hplusroadmap 09:03 -!- prometheus_035 [~root@88.230.137.28] has quit [Quit: leaving] 09:05 -!- christianbundy [~christian@unaffiliated/christianbundy] has joined ##hplusroadmap 09:28 -!- CryptoDavid [uid14990@gateway/web/irccloud.com/x-ipegeywabrjowyby] has quit [Quit: Connection closed for inactivity] 09:41 -!- christianbundy [~christian@unaffiliated/christianbundy] has quit [Quit: WeeChat 2.9] 10:22 -!- strages [uid11297@gateway/web/irccloud.com/x-zirmjxepvddkubpc] has joined ##hplusroadmap 10:23 -!- justanotheruser 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[~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 16:54 < heath> gnusha = gnu + gnesha, fwiw 16:54 < heath> ganesha, rather 16:58 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 16:58 -!- darsie [~kvirc@84-113-55-200.cable.dynamic.surfer.at] has quit [Ping timeout: 265 seconds] 16:58 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 16:59 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 272 seconds] 17:08 < kanzure> nice backlog follow-up 17:12 < jrayhawk> does it actually take george church 8-10 weeks as claimed to return a 30x sequence and assembly? 17:13 < jrayhawk> i had assumed that was just a pessimistic customer service fiction 17:13 < jrayhawk> seems weird 17:13 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 17:14 < jrayhawk> as a followup question: if so, why would that be the case? 17:14 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 17:16 < jrayhawk> oh, maybe they're stockpiling samples and freight-shipping to a cheaper country for the reagents and labwork 17:24 -!- Human_G33k [~HumanG33k@62.147.242.8] has quit [Ping timeout: 256 seconds] 17:28 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 17:29 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 17:31 -!- strages [uid11297@gateway/web/irccloud.com/x-zirmjxepvddkubpc] has quit [Quit: Connection closed for inactivity] 17:43 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 17:44 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 17:58 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 17:59 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 18:12 -!- justanotheruser 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dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 19:30 < yashgaroth> took 12 weeks for me, the assumption is that they're shipping samples to China then running them as low-priority jobs on the sequencers...maybe add some time for manual review by a genetic counselor 19:34 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 19:35 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 19:49 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 19:50 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 20:05 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 20:06 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined ##hplusroadmap 20:22 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has quit [Read error: Connection reset by peer] 20:23 -!- dongcarl [~dongcarl@unaffiliated/dongcarl] has joined 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00:00:52 2020