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07:07 < kanzure> http://www.businessinsider.com/kallyope-raises-66-million-for-gut-brain-axis-drug-and-platform-development-2018-2
07:08 < kanzure> "We show by real-time movies that a single condensin protein complex extrudes loops of DNA" https://twitter.com/cees_dekker/status/966750529266348032
07:08 < kanzure> "Real-time imaging of DNA loop extrusion by condensin" http://science.sciencemag.org/content/early/2018/02/21/science.aar7831
07:08 < kanzure> "We find that a single condensin complex is able to extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1,500 base pairs per second, using the energy of ATP hydrolysis. Condensin-induced loop extrusion is strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it in from only one side."
07:12 < kanzure> https://www.bioverlay.org/post/welcome/ "our process directly mirrors academic peer review other than the stage of submission"
07:12 < kanzure> https://maliciousaireport.com/
07:13 < kanzure> https://img1.wsimg.com/blobby/go/3d82daa4-97fe-4096-9c6b-376b92c619de/downloads/1c6q2kc4v_50335.pdf
07:30 < kanzure> i think catalog (the "dna data storage" company) is not using dna. i think they are using some other polymer system and a library/ligation approach. i think someone said 60 inks?
07:31 < kanzure> their reaction time per ligation could be somewhat fast (actually i'm not sure, do they have the same cycle time porblem as phosphoramidite chemistry here?)
07:31 < kanzure> and multiplexing 60 inks is sort ofannoying and probably limits the number of simultaneous reactions you could be doing
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08:23 < kanzure> .tw https://twitter.com/GATTAquant/status/964059678727720961
08:23 < yoleaux> Quantifying Expansion Microscopy with DNA Origami Expansion Nanorulers https://doi.org/10.1101/265405 #ExM #nanoruler https://pbs.twimg.com/media/DWEHADGX0AA_H40.png (@GATTAquant)
08:23 < kanzure> https://medium.com/@ktemme/revolutionary-self-fertilizing-corn-enables-better-agriculture-productivity-2be5b0045e03
08:32 < superkuh> Too bad medium jumped the shark.
08:50 < JayDugger1> Does the shark-jump really surprise you?
08:53 < superkuh> Centralized platform begins censoring? No, I suppose not.
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08:53 < JayDugger1> Sad, but so.
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09:19 < kanzure> man why does multiplexing suck so much
09:24 < kanzure> .g IARPA-BAA-18-03
09:24 < yoleaux> https://www.iarpa.gov/index.php/research-programs/mist
09:28 < kanzure> i think catalog is going to get diluted if they try to do fast reactions. they will have lots of incomplete molecules that are missing segments. but on average it might not matter, since you can do error correction. but not if the average molecule is so damaged that you lose all of the benefits of a quick reaction time (e.g. you have to redundantly encode information 100x or something).
09:30 < kanzure> something about chalk or polymers
09:32 < kanzure> it would be nice to make a polymerase that can separately use adenosine triphosphate for energy, unrelated to the polymer monomers that get incorporated into the nascent molecule
09:32 < kanzure> or from electrodes i guess.
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10:13 < kanzure> "Bricks and blueprints: Methods and standards for DNA assembly" http://scienseed.com/clients/tomellis/wp-content/uploads/2015/08/BricksReview.pdf
10:16 < kanzure> "Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4110908/
10:16 < kanzure> "Design of synthetic epigenetic circuits featuring memory effects and reversible switching based on DNA methylation" https://www.nature.com/articles/ncomms15336
10:17 < kanzure> "Designer diatom episomes delivered by bacterial conjugation" https://www.nature.com/articles/ncomms7925
10:17 < kanzure> "Direct transfer of whole genomes from bacteria to yeast" https://www.nature.com/articles/nmeth.2433
10:18 < kanzure> "Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast–embryonic stem cell fusion" https://www.nature.com/articles/nprot.2013.093
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10:33 < nmz787> wtf that pivot bio article said nothing about self fertilizing corn
10:39 < kanzure> perhaps the nitrogen teleports into the ground
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11:14 < fenn> "microbes"
11:14 < fenn> it's got what plants crave
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11:56 < kanzure> hanselt: hi.
11:57 < hanselt> hi c:
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13:39 < razzy> fenn: right soil microbiome should take care of anything plants need, and yeah, they put nitrogen to ground as well :]
13:40 < razzy> kanzure: ^^
13:40 < fenn> i was poking fun at the total lack of detail provided
13:41 < fenn> apparently there are non-rhizobium nitrogen fixers that don't require an anaerobic microenvironment
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13:42 < fenn> this is a relatively recent discovery, like 5 years ago
13:43 < razzy> fenn: wow did not know :]. but any microbiome is VERY complex system and we did not scratch the surface of any human-important microbiome
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13:43 < fenn> growing crops is human-important
13:43 < fenn> so are tons of simple systems
13:45 < fenn> i remember cuba doing something like this, inoculating seeds with bacteria to improve fertilization
13:46 < fenn> .title https://books.google.com/books?id=JKF0l88jqqYC&pg=PA297&lpg=PA297&dq=cuba+inoculating+seeds&source=bl&ots=nibXbc0yvY&sig=G6tOqm31zTArpPE7Z_bdY7nCblM&hl=en&sa=X&ved=0ahUKEwjF_tmTw7_ZAhUI1GMKHcUfCVcQ6AEIJDAF
13:46 < yoleaux> Microbial Strategies for Crop Improvement - Google Books
13:46 < razzy> fenn:  i am saying, there could be many organisms in the world we do not know nothing about and they could be beneficial or decremental in unforeseen way :]
13:48 < fenn> yeah it's a war out there
13:49 < fenn> if you believe in panspermia they are not just "in the world" but everywhere else too
13:49 < razzy> i am not suprised there are not-anaerobical nitrogen fixers. I would not know if it is possible to manage them as farmer :]
13:49 < fenn> i am surprised
13:50 < razzy> fenn: live is build to fill any available niche
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13:51 < razzy> and viruses transport genes horizontally between species. so any capability is propably in more than one species :]
13:52 < razzy> fenn: it is society out there. some parts are in war, some in symbiosis :].
13:53 < razzy> fenn: life steal code from one another :]
13:54 < fenn> the problem is the nitrogen reducing enzymes are poisoned by oxygen
13:54 < fenn> they have special purpose compartments just to house them and keep out oxygen and other poisons
13:55 < fenn> then in addition, the bacteria induce plants to make little anaerobic rooms for them to live in
13:55 < fenn> so it's surprising that none of that is actually necessary
13:56 < razzy> fenn: some life still use historic and suboptimal code :].
13:57 < razzy> fenn: so how they do it? aerobically?
13:57 < fenn> i don't recall
13:58 < razzy> hmm :]
13:58 < razzy> i remember anaerobic way :]
13:59 < razzy> it seems reasonable :]
14:01 < razzy> anaerobic way of fixing nitrogen looks like build in security measure :] for not letting plants go wild :]
14:01 < razzy> and to make them dependent on rest of the ecosystem :]
14:02 < fenn> hmm this is related but not what i'm remembering: http://gnusha.org/logs/2013-04-12.log
14:02 < fenn> http://diyhpl.us/~bryan/papers2/paperbot/N2%20Fixation%20by%20Streptomyces%20thermoautotrophicus%20Involves%20a%20Molybdenum-Dinitrogenase%20and%20a%20Manganese-Superoxide%20Oxidoreductase%20That%20Couple%20N2Reduction%20to%20the%20Oxidation%20of%20Superoxide%20Produced%20from%20O2by%20a%20Molybdenum-CO%20Dehydrogenase.pdf
14:02 < razzy> maybe i am paranoid asshole :]
14:03 < fenn> life doesn't have any forethought
14:04 < razzy> oh, use of molybden in biology :] nice :]
14:04 < fenn> if something could have happened it would have happened
14:04 < fenn> not to an infinte limit of course
14:05 < razzy> fenn: evolution makes natural safeguards :] for making ecosystem interdependent :] it is more efficient that way :]
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14:06 < fenn> http://wiki.biohackers.la/Aerobic_Nitrogenase
14:07 < fenn> moved to https://www.thel4b.com/Aerobic_Nitrogenase/
14:07 < fenn> oops
14:07 < fenn> oh fuck everything is broken
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14:10 < razzy> people invest too much time in poitless shifting of data
14:12 < fenn> this one works http://web.archive.org/web/20131218200545/http://wiki.biohackers.la/Aerobic_Nitrogenase
14:13 < razzy> cool research :]
14:14 < razzy> i was thinking i have to sing up at that page :]
14:14 < fenn> are you in LA?
14:16 < razzy> fenn: what i should look for in gnushka.org?
14:16 < razzy> fenn: no :] why?
14:17 < fenn> oh i thought you wanted to join LA biohackers
14:17 < fenn> or whatever they're called now
14:17 < razzy> fenn: and could i?
14:17 < fenn> gnusha.org is just channel logs and our wiki and various project repositories and books and papers and stuff
14:18 < fenn> looks like thel4b.com is only $100/mo for lab access
14:19 < razzy> cool :] i am fine with data simulations and low tech experiments :]
14:19 < razzy> like plants in pots :]
14:20 < razzy> fow now :] thank you for informations :]
14:20 < fenn> you can do a lot with just a pressure cooker and a desk
14:21 < fenn> and a shell corporation for keeping up appearances for ordering reagents and stuff
14:21 < fenn> razzy biotechnology LLC incorporated
14:21 < razzy> yop :] standard kitchen and alchemy mindset is enough for my real-world experiments :]
14:22 < razzy> alchemy-mindset "look it, smell it, lick it, write data :] "
14:22 < razzy> :D :D :D :D :D
14:23 < fenn> eh, stay out of my lab
14:23 < fenn> no licking allowed
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14:24 < razzy> :D
14:24 < razzy> you need to know, what biology you are allowed to lick :]
14:24 < razzy> fenn: i had lab at the university, but it was too much of hassle :]
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14:30 < razzy> fenn: i liked talking to you :]
14:35 < fenn> thel4b published a paper called "Streptomyces Thermoautotrophicus Does Not Fix Nitrogen"
14:36 < fenn> .title https://www.nature.com/articles/srep20086
14:36 < yoleaux> Streptomyces thermoautotrophicus does not fix nitrogen | Scientific Reports
14:37 < fenn> "conclude that the existence of the previously proposed oxygen-tolerant nitrogenase is extremely unlikely"
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15:02 < kanzure> huh. didn't know they published or came to any conclusions like that. cool.
15:04 < razzy> fenn: i like the idea of directed evolution to enhancing microbiomes :]
15:05 < razzy> in soil, or in gut :]
15:05 < razzy> (for start in domestic animals :])
15:12 < razzy> fenn: thank you for article :]
15:15 < razzy> fenn: I am predicting, that there would be more than one way get around anaerobic nitrogen fixing :]. (one way would be to use plants root cooperation, and there should be many more version of coperation :]  )
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17:28 < kanzure> i wonder if a polymerase fusion protein (fused to other polymerases) would retain polymerase activity in each of the fused members.
17:29 < fenn> depends where you fuse them
17:29 < fenn> but most of the time it should work
17:30 < kanzure> i was thinking of a large circular ring of polymerases maybe. the advantage of this is that they are all localized to each other and can do concentration gradient sensor things in uniform way.
17:31 < kanzure> actually, doesn't need to be circular ring. just long linear array would also be capable of doing such a thing.
17:38 < kanzure> polymerases are too slow :-/
17:39 < kanzure> you need a dna molecule flying through a nanopore at 100kbp/sec
17:40 < kanzure> i'm not sure why polymerases are slow.  presumably something about concentration of dNTPs and also it would be suboptimal to have hyper-fast dna replication in a cell since you can't provision all of the necessary resources that quickly, so it would be a useless optimization?
17:40 < kanzure> (and it seems that cells just use 10,000 replication forks anyway during mitosis to speed things up)
17:56 < kanzure> "Exploring alternative leaving groups for enzyme catalyzed DNA synthesis" https://lirias.kuleuven.be/handle/123456789/357148
17:58 < kanzure> "Polymerase capable of producing non-dna nucleotide polymers" https://patents.google.com/patent/US20150275192A1/en
17:59 < kanzure> "Reading, writing, and modulating genetic information with boranophosphate mimics of nucleotides, DNA, and RNA" http://onlinelibrary.wiley.com/doi/10.1196/annals.1281.004/full
18:05 < kanzure> "CyDNA: synthesis and replication of highly Cy-dye substituted DNA by an evolved polymerase" https://pubs.acs.org/doi/abs/10.1021/ja909180c
18:05 < kanzure> "short-patch compartmentalized self-replication (spCSR)"
18:05 < kanzure> " In just two rounds of spCSR selection, we have isolated a polymerase that allows the PCR amplification of double stranded DNA fragments up to 1kb, in which all dC bases are substituted by its fluorescent dye-labeled equivalent Cy3- or Cy5-dC. The resulting “CyDNA” displays hundreds of aromatic heterocycles on the outside of the DNA helix and is brightly colored and highly fluorescent. "
18:13 < kanzure> these are good reviews about adding chromophores into the dna backbone or as monomers https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3387364/ http://pubs.rsc.org/en/Content/ArticleLanding/2010/CS/B910030J#!divAbstract
18:15 < kanzure> "This study showed that neither hydrogen bonding nor canonical purine-pyrimidine shapes is necessary for enzymatic synthesis of a base pair by this enzyme, but that steric complementarity was an important factor.[85]"
18:15 < kanzure> [85] Selective and stable DNA base pairing without hydrogen bonds
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