--- Log opened Fri Oct 06 00:00:38 2017 00:06 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 00:07 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 00:07 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 00:13 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 01:03 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 01:37 -!- CRM114 [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 03:16 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 04:20 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 05:41 < JayDugger> Yes, nmz787, I did. 05:57 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has joined ##hplusroadmap 06:01 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has quit [Ping timeout: 248 seconds] 06:05 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has joined ##hplusroadmap 06:17 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 240 seconds] 06:32 -!- strages [uid11297@gateway/web/irccloud.com/x-pcrtamcnkoqbzugx] has joined ##hplusroadmap 06:37 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has joined ##hplusroadmap 07:19 < kanzure> i'm not sure a "90 day free trial" is scalable way of selling software and source code https://writing.kemitchell.com/2017/09/12/The-License-Zero-Manifesto.html 07:19 < kanzure> .tw https://twitter.com/feross/status/916131603927097344 07:19 < yoleaux> @wycats A CLI tool automates figuring out how much to pay / who to pay it to / produces a signed file as proof (in case of dispute later). (@feross, in reply to tw:916131408514473984) 07:20 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 255 seconds] 07:38 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 07:53 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Remote host closed the connection] 07:57 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-wnucvyolnwnepkpg] has joined ##hplusroadmap 07:57 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 08:20 < JayDugger> kanzure, do you know of anyone in the "crypto community" using Ada? 08:21 < kanzure> that is a good question for maaku 08:21 < JayDugger> I'll ask. 08:21 < JayDugger> @maaku, do you know of anyone in the "crypto community" using Ada? 08:27 < kanzure> http://www.the-odin.com/products.php?product=Open-Human-Plasmid 08:27 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 08:27 < kanzure> http://www.the-odin.com/blog/a-new-era-of-humans/ 08:29 < kanzure> "I wanted to make this post because one of my projects just reached a significant milestone, the Open Source Human Cell Engineering Project. I designed what I and Scientific literature thought might be the best plasmid DNA vector to introduce genes and express genes inside Human cells. " 08:29 < kanzure> "I want to say that I have successfully had the OpenHuman DNA synthesized, turned that DNA into a plasmid vector and sequenced it. I will begin distributing it soon with a protocol on how to add whatever gene you wish or pay someone else a few hundred dollars to add it for you." 08:30 < kanzure> http://www.the-odin.com/blog/our-statement-about-beer-brewing-using-our-yeast-kits/ 08:41 -!- augur [~augur@2601:645:c100:1132:195f:1aeb:90d9:cf7c] has joined ##hplusroadmap 08:43 < mindsForge> awesome @ the-odin 09:00 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Quit: Leaving.] 09:04 < kanzure> .tw https://twitter.com/elonmusk/status/915831795446190085 09:05 < yoleaux> @RickandMorty Final episode was disgustingly good (@elonmusk, in reply to tw:915359755438141440) 09:05 < kanzure> .tw https://twitter.com/RickandMorty/status/915948791907311616 09:05 < yoleaux> @elonmusk Thanks, E. Just riding this out until the singularity hits, you know? (@RickandMorty, in reply to tw:915831795446190085) 09:18 < aeiousomething> yeah the final episode was pretty good 09:22 -!- sachy [~sachy@nat.brmlab.cz] has joined ##hplusroadmap 09:54 < heath> speaking of conferences, did anyone grab day 1 or day 3 of synbiobeta? 09:54 < heath> i have the talks from the day 2, but missed day 1 and became so busy yesterday that i forgot to grab day 3 in time 09:59 -!- augur [~augur@2601:645:c100:1132:195f:1aeb:90d9:cf7c] has quit [Remote host closed the connection] 10:00 < adlai> JayDugger: what's the "crypto community"? 10:12 < kanzure> heath: you should look at my conference talk video aggregator proposal from yesterday. 10:38 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 10:48 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 10:49 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 255 seconds] 11:12 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has quit [Quit: Leaving.] 11:20 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 258 seconds] 11:41 -!- gene-hacker [~gene@c-24-131-17-249.hsd1.pa.comcast.net] has joined ##hplusroadmap 11:41 < gene-hacker> kanzure, does the current version of nanoengineer have a GUI? 11:42 < gene-hacker> as in the one you have on github? 11:43 < kanzure> yea 11:43 < kanzure> it's solidworks-like 11:43 < kanzure> extrude carbon atoms 11:43 < kanzure> do whatever 11:44 < kanzure> https://www.youtube.com/watch?v=nqfXzTrwI3c&t=2m 11:44 -!- WeirdTolkienishF [~Weird@unaffiliated/weirdtolkienishf] has quit [Quit: Leaving] 11:45 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 248 seconds] 11:47 < gene-hacker> yeah, but do you have the source code for the GUI? 11:48 < kanzure> it's in there 11:48 < kanzure> https://github.com/kanzure/nanoengineer#3-installing-from-source 11:48 < kanzure> http://diyhpl.us/~bryan/irc/nanoengineer/ 11:49 < kanzure> here are the executables with GUIs, 11:49 < kanzure> http://diyhpl.us/~bryan/irc/nanoengineer/snapshots/ 11:50 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 11:51 < kanzure> http://diyhpl.us/~bryan/irc/nanoengineer/snapshots/NanoEngineer-1_Suite_v1.1.1.14.exe 12:03 < gene-hacker> ok good 12:16 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-wnucvyolnwnepkpg] has quit [Quit: Connection closed for inactivity] 12:17 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has joined ##hplusroadmap 12:22 -!- gene-hacker [~gene@c-24-131-17-249.hsd1.pa.comcast.net] has quit [Ping timeout: 240 seconds] 12:25 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 240 seconds] 12:37 < nmz787> idk, the last rick and morty episode was a bit underwhelming to me, actually 12:37 < nmz787> that was the one with the president, right? 12:37 -!- gene-hacker [~gene@c-24-131-17-249.hsd1.pa.comcast.net] has joined ##hplusroadmap 12:43 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 260 seconds] 12:47 -!- WeirdTolkienishF [~Weird@204.48.46.11] has joined ##hplusroadmap 12:47 -!- WeirdTolkienishF [~Weird@204.48.46.11] has quit [Changing host] 12:47 -!- WeirdTolkienishF [~Weird@unaffiliated/weirdtolkienishf] has joined ##hplusroadmap 12:51 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 12:59 < kanzure> .tw https://twitter.com/gwern/status/916335124895162368 12:59 < yoleaux> Another oddity: inventor of the Stroop test, most replicated effect, died in obscurity as professor of bible studies http://garfield.library.upenn.edu/classics1981/A1981MF70500001.pdf (@gwern, in reply to tw:916068799513747456) 13:01 < kanzure> .title https://www.youtube.com/watch?v=o6A9bbDI6fo 13:01 < yoleaux> DIY Human CRISPR Myostatin Knock-Out - YouTube 13:03 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has quit [Quit: Leaving.] 13:05 -!- drewbot [~cinch@54.197.168.176] has joined ##hplusroadmap 13:07 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 260 seconds] 13:13 < WeirdTolkienishF> diy CRISPR 13:13 < WeirdTolkienishF> isn't that gene injection? 13:14 < kanzure> cas9 cuts dna 13:14 < kanzure> and then you hope that the repair machinery inserts any other dna floating around into that open space as part of the repair process 13:15 < kanzure> from an immune perspective, i wonder what the evolutionary conditions were that forced bacteria to prefer self-reprogramming 13:15 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 13:28 < nmz787> isn't it the same reason we have V(D)J mutation? 13:29 < nmz787> to be able to respond to a dynamic environment that changes faster than the organism replication/death time 13:29 < kanzure> the reason is simple but that ddoesn't explain how a programmable mechanism was evolved 13:45 -!- WeirdTolkienishF [~Weird@unaffiliated/weirdtolkienishf] has quit [Quit: Leaving] 14:01 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 14:21 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 14:21 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has joined ##hplusroadmap 14:21 < kanzure> the reason why i ask is because if adaptive immunity evolution/selection experiments can create and find cas9 analogs, then it would be interesting to see what other programmability you can select for 14:24 < kanzure> e.g. directed evolution of additional (and programmable) adaptive immunity mechanisms, maybe by spraying in random chimeric protein motifs into all sorts of dna binding molecules (polymerases, methyltransferases, deaminases, whatever) 14:26 < kanzure> casposons http://www.sciencedirect.com/science/article/pii/S1369527416301710 14:26 < kanzure> "A casposon, a member of a distinct superfamily of archaeal and bacterial self-synthesizing transposons that employ a recombinase (casposase) homologous to the Cas1 endonuclease, appears to have given rise to the adaptation module of CRISPR-Cas systems as well as the CRISPR repeats themselves. Comparison of the mechanistic features of the reactions catalyzed by the casposase and the ... 14:26 < kanzure> ...Cas1–Cas2 heterohexamer, the CRISPR integrase, reveals close similarity but also important differences that explain the requirement of Cas2 for integration of short DNA fragments, the CRISPR spacers." 14:28 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 14:29 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 14:30 < kanzure> "Although most transposases belong to the DDE superfamily (named after two aspartate and one glutamate residues that form the catalytic triad of these enzymes) [10, 13, 16], some transposons encode transposases homologous to the rolling-circle replication initiation endonucleases found in numerous viruses and plasmids [17, 18, 19], to phage integrase-like tyrosine recombinases [20, 21] or to ... 14:30 < kanzure> ...the serine integrases/invertases [22]. ." https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-12-36 14:31 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 14:32 < kanzure> ".. features resembling the eukaryotic self-synthesizing DNA transposons" 14:35 < kanzure> "Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems" http://www.sciencedirect.com/science/article/pii/S1369527416000084 14:35 < kanzure> "Self-synthesizing transposons are the largest known transposable elements that encode their own DNA polymerases (DNAP). The Polinton/Maverick family of self-synthesizing transposons is widespread in eukaryotes and abundant in the genomes of some protists. In addition to the DNAP and a retrovirus-like integrase, most of the polintons encode homologs of the major and minor jelly-roll capsid ... 14:35 < kanzure> ...proteins, DNA-packaging ATPase and capsid maturation protease. Therefore, polintons are predicted to alternate between the transposon and viral lifestyles although virion formation remains to be demonstrated." 14:36 < kanzure> "... Recently, a group of predicted self-synthesizing transposons was discovered also in prokaryotes. These elements, denoted casposons, encode a DNAP and a homolog of the CRISPR-associated Cas1 endonuclease that has an integrase activity but no capsid proteins. Thus, unlike polintons, casposons appear to be limited to the transposon life style although they could have evolved from viruses." 14:36 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 14:39 < kanzure> how does this thing not spam copies of itself everywhere in the host genome? 14:40 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 14:41 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 14:43 < kanzure> this doesn't really explain why the endonuclease acquired gRNA activity. 14:46 < kanzure> "Directed evolution of Cas9 to reduce identified off-target cleavage" http://www.editasmedicine.com/data/documents/bigsky_2017_pd1_final_1497379395_1497468459.pdf 14:50 < kanzure> ah, 14:50 < kanzure> "Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems" https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-6-38 14:52 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 240 seconds] 14:54 < kanzure> "The Repeat-Associated Mysterious Proteins (RAMPs) containing a distinct form of the RNA Recognition Motif (RRM) domain, which are major components of the CRISPR-Cas systems, were classified into three large groups, Cas5, Cas6 and Cas7 ... Evidence is presented that large subunits contained in most of the CRISPR-Cas systems could be homologous to Cas10 proteins which contain a polymerase-like ... 14:54 < kanzure> ...Palm domain and are predicted to be enzymatically active in Type III CRISPR-Cas systems but inactivated in Type I systems. These findings, the fact that the CRISPR polymerases, RAMPs and Cas2 all contain core RRM domains, and distinct gene arrangements in the three types of CRISPR-Cas systems together provide for a simple scenario for origin and evolution of the CRISPR-Cas machinery. Under ... 14:54 < kanzure> ...this scenario, the CRISPR-Cas system originated in thermophilic Archaea and subsequently spread horizontally among prokaryotes." 14:54 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 15:03 < kanzure> "Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains" https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-5-43 15:06 < kanzure> "Many structures of Palm domain-containing polymerases from all domains of life and numerous viruses have been solved and compared [32]." 15:06 < kanzure> [32] Steitz TA, Yin YW: Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases. Philos Trans R Soc Lond B Biol Sci. 2004, 359 (1441): 17-23. 10.1098/rstb.2003.1374. 15:13 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 16:12 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 255 seconds] 16:22 -!- sivoais [~zaki@unaffiliated/sivoais] has quit [Ping timeout: 252 seconds] 16:22 -!- sivoais [~zaki@unaffiliated/sivoais] has joined ##hplusroadmap 16:32 -!- slicedbread [~slicedtoa@47-34-161-131.dhcp.mtpk.ca.charter.com] has joined ##hplusroadmap 16:35 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 16:36 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has quit [Quit: Leaving.] 16:36 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has joined ##hplusroadmap 16:38 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 240 seconds] 16:43 < kanzure> we need a plasmid + polymerase heterodimer thing that is permanently attached. no "falling off" nonsense (unless the polymerase has been degraded). 16:45 -!- slicedbread [~slicedtoa@47-34-161-131.dhcp.mtpk.ca.charter.com] has left ##hplusroadmap ["Leaving"] 16:51 < kanzure> use a really enormous circular dna molecule, divided into four quadrants of homopolymer nucleotide sequence (all A, all T, etc.), use a polymerase that can be inhibited from polymerizing but can still move anyway, then you wait for the polymerase to move to the "A" quadrant and you remove the inhibitor so that it can incoporate "A"s. 16:52 < kanzure> needs two pieces of magic that we don't have: (1) a polymerase that scans a DNA molecule at a constant rate without polymerizing (e.g. when inhibited), and (2) a polymerase that only incorporates one nucleotide per ~second (needs to be super slow.. but we also need to be sure incorporation has happened). 16:54 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 16:54 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has quit [Client Quit] 16:55 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 16:55 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 248 seconds] 17:03 -!- bkero [~bkero@osuosl/staff/bkero] has quit [Remote host closed the connection] 17:03 -!- bkero [~bkero@osuosl/staff/bkero] has joined ##hplusroadmap 17:06 -!- Darius [~quassel@66-215-89-229.dhcp.psdn.ca.charter.com] has joined ##hplusroadmap 17:06 < nmz787> hmm, that's an interesting idea 17:06 < nmz787> maybe instead of being slow, it could be gated otherwise 17:06 < nmz787> like the error-prone PCR via manganese 17:06 -!- mrdata- [~mrdata@unaffiliated/mrdata] has joined ##hplusroadmap 17:07 < nmz787> something to gate polymerization, and another thing to gate movement around (ATP??) 17:10 -!- alt_nod [5ad4f050@gateway/web/freenode/ip.90.212.240.80] has joined ##hplusroadmap 17:16 < kanzure> you don't need to gate movement, only incorporation 17:16 < kanzure> movement can be timed/averaged 17:22 < alt_nod> kanzure, check pm 17:23 < kanzure> you didn't send anything 17:30 -!- alt_nod [5ad4f050@gateway/web/freenode/ip.90.212.240.80] has quit [Quit: Page closed] 17:31 -!- alt_nod [5ad4f050@gateway/web/freenode/ip.90.212.240.80] has joined ##hplusroadmap 17:33 -!- Darius [~quassel@66-215-89-229.dhcp.psdn.ca.charter.com] has quit [Ping timeout: 248 seconds] 17:35 -!- alt_nod [5ad4f050@gateway/web/freenode/ip.90.212.240.80] has quit [Client Quit] 17:37 -!- eudoxia [ba348ed3@gateway/web/freenode/ip.186.52.142.211] has joined ##hplusroadmap 17:37 < eudoxia> hello kanzure-sama 17:38 < kanzure> eudoxia: welcome back. 17:38 < eudoxia> haha yeah long time no see :) 17:40 < eudoxia> i directed a friend who had a cryptocurrency question here but he's having trouble with his IRC client, what he wanted to ask is: do you know of https://github.com/metacurrency/holochain and if you do is it bullshit? 17:40 < eudoxia> I figure you might know since from your twitter I figure you're still working with ledgerx 17:44 -!- Darius [~quassel@66-215-89-229.dhcp.psdn.ca.charter.com] has joined ##hplusroadmap 17:49 < kanzure> eudoxia: they talk about data integrity, but then they say "run facebook on our system" (e.g. data storage). pass. 17:50 < kanzure> er, i mean, skip 'em. 17:51 < eudoxia> you mean the claims of data integrity are incompatible with running an app like facebook? 17:51 < eudoxia> a service, rather 17:51 < kanzure> i mean they are obfuscating their purpose (data storage). they should just say "data storage" not integrity/validation. 17:52 < eudoxia> hmm, so it's a company with an object store trying to cash in on the blockchain craze 17:53 < kanzure> i'm not really sure you need decentralization for data storage-- since you want to communicate with the hosts that have your data (eventually). maybe for finding peers that are willing to accept your contract/payment for data storage... 17:54 < eudoxia> ah, alright, thanks kanz, I will pass this along :) 17:54 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 248 seconds] 17:55 < kanzure> eudoxia: take a look at siacoin's underlying contracts stuff. not sure it really requires a blockchain either, but it's clser. 17:55 < kanzure> *closer 17:57 < eudoxia> huh, it's like a bidding market for on-chain storage 17:57 < eudoxia> by the way, did counterparty go anywhere? 17:58 < kanzure> dunno 17:59 < kanzure> nmz787 is bugging me, responses will be delayed 17:59 < eudoxia> it's ok, thanks! i hope you're doing well c: 18:05 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has quit [Quit: Leaving.] 18:07 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Quit: Leaving.] 18:08 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 18:11 -!- eudoxia [ba348ed3@gateway/web/freenode/ip.186.52.142.211] has quit [Ping timeout: 260 seconds] 18:21 < kanzure> thread a polymerase with a plasmid, put the plasmid through a nanopore.. the polymerase can't fit, the plasmid can, might be useful for controlled synthesis. 18:22 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 18:30 < kanzure> "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage" https://www.nature.com/nature/journal/v533/n7603/abs/nature17946.html 18:31 < kanzure> "uracil glycosylase inhibitor" 18:31 < kanzure> "cytidine deaminase" 18:32 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 18:36 -!- mrdata- [~mrdata@unaffiliated/mrdata] has quit [Read error: Connection reset by peer] 18:46 < kanzure> 'Synthesis of single-stranded DNAzymes' seems to exist according to google 19:04 < kanzure> yashgaroth: do you have a paper that contains a lot of polymerase comparisons/benchmarks? having trouble finding this. 19:07 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 19:11 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 19:12 < kanzure> .wik nucleotide salvage 19:12 < yoleaux> "A salvage pathway is a pathway in which nucleotides (purine and pyrimidine) are synthesized from intermediates in the degradative pathway for nucleotides." — https://en.wikipedia.org/wiki/Nucleotide_salvage 19:16 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Ping timeout: 240 seconds] 19:24 < kanzure> other helpful enzymatic magic: delete single nucleotide in presence of metal/ions (and re-combine strand), then 1s recharge period before it can act again, and wait for metal/ions to come back. move dna through nanopore in forward and reverse directions, to check that the edit was correct. keep repeating until you have the desired dna molecule. probably need to start from a known dna ... 19:24 < kanzure> ...molecule. 19:25 < kanzure> i'm not sure how to be sure which nucleotide will be deleted. maybe it will always be like +4 bp up the strand from whatever the nanopore is reading at the moment. 19:26 < kanzure> and it might take a few thousand deletes for 1 bp to be written.. and you'll run out of tape/input dna.. but at least you'd have a good output molecule eventually. 19:27 < kanzure> .wik https://en.wikipedia.org/wiki/Base_excision_repair 19:27 < yoleaux> kanzure: Sorry, that command (.wik) crashed. 19:27 < kanzure> .wik base excision repair 19:27 < yoleaux> "In biochemistry and genetics, base excision repair (BER) is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from the genome. The related nucleotide excision repair pathway repairs bulky helix-distorting lesions." — https://en.wikipedia.org/wiki/Base_excision_repair 19:27 < kanzure> Other examples of base lesions repaired by BER include: 19:27 < kanzure> Oxidized bases: 8-oxoguanine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG, FapyA) 19:27 < kanzure> Alkylated bases: 3-methyladenine, 7-methylguanosine 19:27 < kanzure> Deaminated bases: hypoxanthine formed from deamination of adenine. Xanthine formed from deamination of guanine. (Thymidine products following deamination of 5-methylcytosine are more difficult to recognize, but can be repaired by mismatch-specific glycosylases) 19:27 < kanzure> Uracil inappropriately incorporated in DNA or formed by deamination of cytosine[2] 19:27 < kanzure> (aka cytidine deaminase) 19:28 < kanzure> yashgaroth: is there a nicking enzyme that can excise a single nucleotide from dna? like prolly has been used with a zinc finger or TALENs or something before? 19:33 < kanzure> or do you just digest the nucleotide on the dna molecule, and then use a repair enzyme to delete the gap? 19:41 < kanzure> "ADAR deaminases" (adenosine deaminase) "L.Y. and G.M.C filed patents for targeted deaminases including US20110104787 A1, 2009" 19:58 < yashgaroth> there's restriction enzymes that leave a single base overhang on both strands that you could chew back and re-ligate, but they're sequence-specific 19:58 < yashgaroth> you mean from both strands, or just one? 20:01 -!- CRM114 [~urchin@unaffiliated/urchin] has quit [Ping timeout: 258 seconds] 20:03 < kanzure> uhh i don't know 20:04 < kanzure> single bp deletion is much better than having two different deaminase enzymes 20:05 < kanzure> (according to a memo from "the department of impossible shit") 20:06 < yashgaroth> "DNA fragments that have a single-base 5´ extension are more difficult to ligate than blunt-ended fragments" didn't know that, interesting 20:08 < yashgaroth> is that stuff about pushing DNA back and forth through a nanopore possible with single-nanopore control? 20:09 < yashgaroth> rather, is single-nanopore control possible 20:09 < kanzure> uhh well it's usually some sort of electric field, i'll check for a ref 20:10 < kanzure> it's basically electrophoresis as far as i know 20:10 < kanzure> "Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision" http://www.nature.com/nbt/journal/v30/n4/full/nbt.2147.html 20:11 < kanzure> 'controlled by phi29 DNA polymerase without the need for active voltage control' 20:11 < kanzure> hrmm. 20:11 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 255 seconds] 20:11 < kanzure> well anyway, one way to get around that problem is a plasmid... if you need to change a mistake, just wait until it loops around again 20:15 < yashgaroth> ahh so one direction is via electric current, the other is from the polymerase polymerizing on the strand 20:23 -!- rpifan [~rpifan@73.106.74.213] has joined ##hplusroadmap 20:27 < kanzure> http://lab.loman.net/2017/03/09/ultrareads-for-nanopore/ 20:28 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 20:34 < yashgaroth> "in MinKNOW 1.4 luckily it has been dispensed with entirely in favour of a much smarter system that dynamically unblocks individual pores on demand" instead of "periodic ‘global voltage flicks’ - meaning that the voltage is reversed across the flow cell every 10 minutes" 20:34 < yashgaroth> so are they reversing voltage in individual pores? 20:39 -!- Darius [~quassel@66-215-89-229.dhcp.psdn.ca.charter.com] has quit [Remote host closed the connection] 20:40 < yashgaroth> "Each nanopore channel is controlled and measured individually by the bespoke ASIC" alright seems like it 21:27 -!- rpifan [~rpifan@73.106.74.213] has quit [Remote host closed the connection] 21:49 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has joined ##hplusroadmap 22:14 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap 22:44 -!- mindsForge [~nak@75-171-117-42.phnx.qwest.net] has quit [Quit: Leaving.] 22:54 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 22:54 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 22:56 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 248 seconds] 23:47 -!- preview [~quassel@2407:7000:842d:4000::3] has joined ##hplusroadmap 23:56 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap --- Log closed Sat Oct 07 00:00:39 2017