--- Log opened Fri Sep 29 00:00:31 2017 00:08 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 00:10 -!- MrHindsight [~2020@162.221.206.203] has joined ##hplusroadmap 00:10 -!- MrHindsight [~2020@162.221.206.203] has quit [Changing host] 00:10 -!- MrHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 00:10 < nmz787> https://academic.oup.com/nar/article/36/17/e107/2410200 00:11 < nmz787> .title 00:11 < yoleaux> De novo DNA synthesis using single molecule PCR | Nucleic Acids Research | Oxford Academic 00:11 < nmz787> not the best title to describe what it actually is... 00:12 < MrHindsight> well biologists have to constantly use different words to describe the same things.. 00:12 < MrHindsight> otherwise biology is just boring 00:13 < nmz787> it is actually more like: sythesize a bunch of semi-errorneous sequences, then PCR them with stringent intolerance of mismatch so only correct overlaps are amplified, then use exonuclease to chew back the non-overlapped sections, then feed back into PCR reaction, assuming the correct matched segments now all join up 00:13 -!- MrHindsight [~2020@unaffiliated/capthindsight] has quit [Read error: error:1408F10B:SSL routines:SSL3_GET_RECORD:wrong version number] 00:13 -!- MrHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 00:14 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has quit [Ping timeout: 255 seconds] 00:15 < MrHindsight> how many molecules make up DNA? 00:15 < nmz787> at least 1 00:15 < nmz787> do you mean atoms? 00:15 < MrHindsight> a) 1, b) 2, c) 3 or more, d) none of the above 00:15 < nmz787> hehe, from the paper you posted "Notably, the gene correction efficiency was over 23.0% in these embryos by base editor." -- aka failure rate was 77% 00:15 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 00:16 < MrHindsight> single molecule PCR 00:16 < nmz787> hmm? 00:17 < MrHindsight> please define molecule as used by the people in the paper 00:18 < MrHindsight> DNA or DNA fragment? 00:18 < nmz787> oh, I'm not sure... probably something about only needing 1 perfect molecule, given enough PCR reactions and ratio of # of enzyme molecules to # of DNA molecules and the volume of the reaction chamber (diffusion space) 00:19 < nmz787> i.e one molecule with a correct sequence 00:19 < MrHindsight> someone needs an eye poke 00:19 < nmz787> I just look at the methods section really, aside from the intro 00:21 < MrHindsight> How to obfuscate the writing of your Biology paper has moved to room #304 00:22 * nmz787 sleeps 00:22 < MrHindsight> good idea 00:49 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-iwylomvhowuheryz] has joined ##hplusroadmap 01:05 < fenn> does "base editor" have a less vague name? 01:07 < fenn> "fusions of CRISPR/Cas9 and a cytidine deaminase enzyme that retain the ability to be programmed with a guide RNA, do not induce dsDNA breaks, and mediate the direct conversion of cytidine to uridine, thereby effecting a C→T (or G→A) substitution. The resulting “base editors” convert cytidines within a window of approximately five nucleotides (nt), and can efficiently correct a variety of 01:07 < fenn> point mutations relevant to human disease." 01:07 < fenn> .title https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873371/ 01:07 < yoleaux> Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage 01:07 < fenn> i guess they call it BE1 01:28 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 01:45 -!- CRM114 [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 02:14 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 02:20 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has joined ##hplusroadmap 03:05 -!- Nikopol_ [~NSohru@89.38.96.190] has joined ##hplusroadmap 03:06 -!- NikopolSohru [~NSohru@89.38.96.190] has quit [Ping timeout: 248 seconds] 03:28 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-iwylomvhowuheryz] has quit [Quit: Connection closed for inactivity] 04:15 < kanzure> are the LOV domains the ones that are photoswitchable within a few microseconds/milliseconds? there's some slow switching stuff and it's not as helpful. need big conformational changes that happen very quickly. 04:16 < kanzure> maaku: oh strange i was just flipping through nanosystems yesterday and i was remarking "wtf he didn't consider business opportunities in this book". however, i hadn't thought to check chapter 2. 04:17 < kanzure> CaptHindsight: yes the base editor thing is what led me to some of the histone-modifying enzymes, http://gnusha.org/logs/2017-09-28.log 04:31 < kanzure> read yer backlogs, folks 05:44 -!- Nikopol_ [~NSohru@89.38.96.190] has quit [Quit: Leaving] 05:46 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 05:47 -!- gene-hacker [~tetrapod@c-24-131-17-249.hsd1.pa.comcast.net] has quit [Ping timeout: 240 seconds] 06:53 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 258 seconds] 06:57 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-nbknvyouejibubml] has joined ##hplusroadmap 07:03 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 246 seconds] 07:04 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap 07:09 -!- cluckj [~cluckj@static-173-59-27-112.phlapa.ftas.verizon.net] has quit [Quit: Leaving] 07:16 -!- cluckj [~cluckj@static-173-59-27-112.phlapa.ftas.verizon.net] has joined ##hplusroadmap 07:23 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 260 seconds] 07:48 < kanzure> .title https://www.youtube.com/watch?v=iVWQfFAyhZ0 07:48 < yoleaux> A Valve that controls your internet bandwidth developed by Near East University - YouTube 08:11 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap 08:21 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 08:24 -!- MrHindsight [~2020@unaffiliated/capthindsight] has quit [Ping timeout: 240 seconds] 08:40 -!- MrHindsight [~2020@c-73-247-91-143.hsd1.il.comcast.net] has joined ##hplusroadmap 08:40 -!- MrHindsight [~2020@c-73-247-91-143.hsd1.il.comcast.net] has quit [Changing host] 08:40 -!- MrHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 09:06 -!- pepesza [~pepesza@185.83.218.228] has quit [Ping timeout: 240 seconds] 09:07 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 260 seconds] 09:07 -!- JayDugger [~jwdugger@47.185.237.246] has joined ##hplusroadmap 09:10 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 09:11 -!- pepesza [~pepesza@185.83.218.228] has joined ##hplusroadmap 09:20 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 09:31 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-nbknvyouejibubml] has quit [Quit: Connection closed for inactivity] 09:39 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 09:40 < JayDugger> The world as SF novel, co-written by Stanislaw Lem and possibly Julian Jaynes (though that depends on what the voices tell me). 09:49 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 09:50 < fltrz> nmz787: not sure why it was the first thing that came to my mind when I woke up: 'no way a 300k oscilloscope will no longer be serviced by manufacturers' 09:59 < kanzure> MrHindsight: you alive? 10:09 < kanzure> https://arstechnica.com/science/2017/09/musk-revises-his-mars-ambitions-and-they-seem-a-little-bit-more-real/ 10:15 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 10:16 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 11:04 < fltrz> he's going to store gold on the moon for the banks? 11:05 < MrHindsight> the story about "sonic" attacks on uhmerican diplomats in Cube is interesting 11:05 < MrHindsight> I wonder what is really up and by whom 11:06 < nmz787> maybe it was that air force satellite that they just opened up to amateurs 11:07 < nmz787> someone hacked the MIL stuff to turn back on 11:07 < MrHindsight> shouldn't the story be ultrasonic? 11:08 < MrHindsight> if that is even it 11:13 < kanzure> MrHindsight: see pm 11:13 < MrHindsight> have to read it later 11:13 < MrHindsight> busy day 11:31 -!- fltrz [4d6d6154@gateway/web/freenode/ip.77.109.97.84] has quit [Quit: Page closed] 11:43 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 11:56 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 11:56 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 12:01 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 12:10 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 12:32 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-ypxknimzldhwmdkj] has joined ##hplusroadmap 12:51 < maaku> MrHindsight: (b) 2, right? the double strands are only hydrogen bonded 12:52 < maaku> kanzure: ch2 is also available on his website for easier HTML reading 12:54 < maaku> drexler seems to have no business sense whatsoever. neither do freitas and merkle, or anyone else I know working in that field. 12:59 < nmz787> maaku: DNA is usually synthesized as ssDNA though 13:01 < nmz787> according to some wiki article, it said nanotech wasn't even a word before that drexler guy... which is weird to me, since I've always assumed any nano-engineered thing is nanotech (I guess drexler would call the semiconductor processes at that time something something "thin films" instead) 13:15 < maaku> nmz787: Drexler coined the term in the mid 80's at the latest, maybe as early as '79. Other than biology there was nothing at the nano scale at that time, nor the ability to make measurements (AFM etc was all invented later) 13:19 < kanzure> so without drexler we'd be talking about dna technology instead? sounds okay to me. 13:39 < nmz787> hmm, around 1980 accroding to this graph we were still around 1100nm process-node http://www.iue.tuwien.ac.at/phd/filipovic/img34.png 13:39 < nmz787> so I guess they were calling it microtech if anything 13:40 < nmz787> although "By the late 1930s electron microscopes with theoretical resolutions of 10 nm were being designed and produced, and by 1944 this was further reduced to 2 nm." 13:41 < nmz787> so I guess viewing nano isn't/wasn't considered tech 13:41 < nmz787> :/ 13:41 < nmz787> or the word/phrase just wasn't popularized 13:41 < nmz787> kanzure: nucleotech 13:42 < kanzure> protein tech. 14:40 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-ypxknimzldhwmdkj] has quit [Quit: Connection closed for inactivity] 14:58 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-nzbxpcsvckvjiwre] has joined ##hplusroadmap 15:13 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 248 seconds] 15:31 -!- aeiousomething [~aeiousome@117.195.143.206] has joined ##hplusroadmap 15:53 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Quit: Leaving.] 15:54 < kanzure> nmz787: so why were they worried about archival tape supply evaporating, precisely? 15:54 < kanzure> they said silicon but surely they meant archival tape? 15:56 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 248 seconds] 16:09 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 246 seconds] 16:10 -!- andytoshi-web [ac3a6075@gateway/web/freenode/ip.172.58.96.117] has joined ##hplusroadmap 16:20 -!- CRM114 [~urchin@unaffiliated/urchin] has quit [Remote host closed the connection] 16:30 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 16:31 < kanzure> "a collection of soviet control rooms" http://blog.presentandcorrect.com/27986-2 16:40 < MrHindsight> http://blog.presentandcorrect.com/wp-content/uploads/2017/09/68426c45c8b5.jpg what is the lunchroom staff doing in the control room? 16:45 < kanzure> they are sweeping for pastries and fingerprints 16:48 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 255 seconds] 16:50 < kanzure> "Deep forest: Towards an alternative to deep neural networks" https://arxiv.org/abs/1702.08835 https://twitter.com/moorejh/status/912682675575468033 16:51 < kanzure> "Kinetics of dCas9 target search in Escherichia coli" http://science.sciencemag.org/content/357/6358/1420 https://twitter.com/jijzarco/status/913511511238352897 16:51 < kanzure> "... used single-molecule fluorescence methods and bulk biochemistry to show that Cas9 takes 6 hours to find its target sequence, with each potential target bound for less than 30 ms" 16:52 < kanzure> bryan johnson challenges dalai lama to implant an electrode to regulate negative emotions https://twitter.com/bryan_johnson/status/913194287667453952 16:54 < kanzure> i wonder if an enzyme that does a linear scan over a long dna molecule would be faster than cas9 16:58 < MrHindsight> how long is Cas9? 16:58 < MrHindsight> how many are active at a time? 16:59 < MrHindsight> how many areas of the DNA can be reached at any given time? 17:00 -!- andytoshi-web [ac3a6075@gateway/web/freenode/ip.172.58.96.117] has quit [Ping timeout: 260 seconds] 17:00 < MrHindsight> how long a segment are you replacing? 17:01 < kanzure> well in the dCas9 fusion protein (with cytidine deaminase) they deactivated the ability to do double strand breaks of dsDNA. instead it's just a point-mutator. 17:10 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-nzbxpcsvckvjiwre] has quit [Quit: Connection closed for inactivity] 17:14 -!- mrdata- [~mrdata@unaffiliated/mrdata] has joined ##hplusroadmap 17:19 < MrHindsight> kanzure: now explain that using sets of different words a few more times and you are a biologist! 17:20 < MrHindsight> or a rather a published one 17:20 < MrHindsight> is there some reason why they refuse to just keep it simple? 17:21 < kanzure> it's culture. 17:22 < kanzure> actually i don't know what it is. it might even be brain damage. 17:23 < kanzure> we need a general library of "string manipulation" methods to modify dna molecules. i thought it would have to be proteins that iteratively scan a molecule and update it, but now i'm not so sure. 17:24 < kanzure> how about modifying a terminal deoxytidyl transferase (TdT) enzyme, or any other enyme that has a ring shape, to function as a nanopore, and copy-paste the cytidine deaminase protein domain of interest into the ring 17:25 < kanzure> and then you need to construct a chimeric protein (a ring nanopore thing + the protein domain that modifies dna molecules) to either (1) operate very slowly at a known rate, or (2) selectively operate in the presence of an electric signal 17:26 < kanzure> in the case of (1) slow operation at a known rate, you would move a dna molecule through the nanopore. the molecule would have a known sequence. and you would play/rewind the dna molecular tape through the nanopore before the next write operation is expected to occur, based on the known sequence. 17:26 < kanzure> in the case of (2) you would have direct write capability 17:27 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap 17:27 < kanzure> but only for conversion of one nucleotide type into another...... which is not useful for biological applications really :-(. 17:28 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 248 seconds] 17:29 < kanzure> i guess you could have four different nanopore types that each modify nucleotides in different ways. i think you only need two actually. so you have four nucleotides, but you only need to flip 2 types. 17:29 -!- eb3c90 [~kvirc@host109-155-47-183.range109-155.btcentralplus.com] has joined ##hplusroadmap 17:30 < kanzure> what's the current status on electrical control of protein conformational shape anyway. 17:34 < kanzure> "Organic bioelectronics probing conformational changes in surface confined proteins" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911579/ 17:35 < kanzure> "Organic electrochemical transistor immuno-sensor operating at the femto-molar limit of detection" http://ieeexplore.ieee.org/abstract/document/7974217/ 17:36 < kanzure> i guess the "organic transistor" people might have a few choice words to say? 17:38 < MrHindsight> edible organic? :) 17:39 < kanzure> "Recent trends in field-effect transistors-based immunosensors" http://www.mdpi.com/2227-9040/4/4/20/html 17:39 < kanzure> "..The electrical signal of FET-based immunosensors is generated as a result of the antigen-antibody conjugation. FET biosensors present real-time and rapid response, require small sample volume, and exhibit higher sensitivity and selectivity" 17:39 < kanzure> 'electrochemical immunosensors' 17:49 < kanzure> sub-picomolar sensitive ion channel http://pubs.rsc.org/-/content/articlelanding/2016/cc/c6cc04899d/unauth#!divAbstract ("A conformation and charge co-modulated ultrasensitive biomimetic ion channel") 17:50 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 17:55 < kanzure> "Interprotein electron transfer between FeS‐protein nanowires and oxygen‐tolerant NiFe hydrogenase" http://onlinelibrary.wiley.com/doi/10.1002/ange.201702042/full 17:55 < kanzure> no.. 17:56 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 246 seconds] 17:57 < kanzure> although it makes sense that hydrogenase would be used. really i just want to see something simple like green fluorescent protein hooked up to an electrode and it can turn on/off. 17:58 < kanzure> there needs to be a science search engine that takes your hand-drawn diagram and then finds the same thing in the scientific literature 18:00 < kanzure> "Direct electrical control of IgG conformation and functional activity at surfaces" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121884/ 18:01 < kanzure> "We have devised a supramolecular edifice involving His-tagged protein A and antibodies to yield surface immobilized, uniformly oriented, IgG-type, antibody layers with Fab fragments exposed off an electrode surface. We demonstrate here that we can affect the conformation of IgGs, likely pushing/pulling electrostatically Fab fragments towards/from the electrode surface. A potential difference ... 18:01 < kanzure> ...between electrode and solution acts on IgGs’ charged aminoacids modulating the accessibility of the specific recognition regions of Fab fragments by antigens in solution. Consequently, antibody-antigen affinity is affected by the sign of the applied potential: a positive potential enables an effective capture of antigens; a negative one pulls the fragments towards the electrode, where ... 18:01 < kanzure> ...steric hindrance caused by neighboring molecules largely hampers the capture of antigens. Different experimental techniques (electrochemical quartz crystal microbalance, electrochemical impedance spectroscopy, fluorescence confocal microscopy and electrochemical atomic force spectroscopy) were used to evaluate binding kinetics, surface coverage, effect of the applied electric field on IgGs, ... 18:01 < kanzure> ...and role of charged residues on the phenomenon described. These findings expand the concept of electrical control of biological reactions and can be used to gate electrically specific recognition reactions with impact in biosensors, bioactuators, smart biodevices, nanomedicine, and fundamental studies related to chemical reaction kinetics." 18:05 -!- RebelCoder [~Yuriy@95.143.115.254] has quit [Ping timeout: 248 seconds] 18:10 < kanzure> "Our idea was trying to influence IgG’s conformation by direct electrochemistry, i.e. by changing the potential of the substrate hosting IgGs with respect to the solution with the help of an external potentiostat. By adjusting the ionic strength of the solution to a proper value (typically 5 mM) it is possible to achieve a diffuse layer thickness of the order of the thickness of our ... 18:10 < kanzure> ...molecular layer (10 nm, for a 1:1 electrolyte)24, enabling thus the action of the electric field on the antibody." 18:10 < kanzure> ".. It is plausible that the different behavior of the IgG layer subjected to electric fields of different sign could be traced back to the different molecular conformation, hence to the different exposure that Fab fragments achieve in the two different configurations. A positive substrate potential tends to push Fabs off the substrate towards the solution, enabling a more efficient antigen ... 18:10 < kanzure> ...capture due to a more efficient Fab exposure." 18:11 < kanzure> well pushing something away from a surface is not necessarily a conformational change.... 18:11 < kanzure> dunno why this is not elaborated 18:19 -!- mrdata-- [~mrdata@unaffiliated/mrdata] has joined ##hplusroadmap 18:21 -!- mrdata- [~mrdata@unaffiliated/mrdata] has quit [Ping timeout: 240 seconds] 18:26 < kanzure> "Conformational control of human transferrin covalently anchored to carbon-coated iron nanoparticles in presence of a magnetic field" http://www.sciencedirect.com/science/article/pii/S1742706116304433 18:28 < kanzure> 'electroswitchable' 18:32 < kanzure> hm nevermind. 18:35 < kanzure> "Protein bioelectronics: a review of what we do and do not know" https://arxiv.org/abs/1702.05028 18:36 < kanzure> "We review the status of protein-based molecular electronics. First we discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic ... 18:36 < kanzure> ...properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their link to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronics devices, and how ... 18:36 < kanzure> ...conductance measurements can shed light on protein properties." 18:36 < kanzure> hey this is a good review. this is good. 18:37 -!- axlshear [~axlshear@172.93.51.50] has quit [Quit: axlshear] 18:42 < kanzure> "... Cofactors with delocalized electronic states can be viewed as a “dopant” of the peptide skeleton." 18:43 < kanzure> hey aren't there small molecules that are known to slow down polymerase? like basic antibiotics? or do they completely disrupt RNA polymerase activity. 18:49 -!- mrdata-- [~mrdata@unaffiliated/mrdata] has quit [Read error: Connection reset by peer] 18:50 -!- Darius [~quassel@66-215-89-229.dhcp.psdn.ca.charter.com] has joined ##hplusroadmap 18:59 < kanzure> "Reading the primary structure of a protein with 0.07 nm^3 resolution using a subnanometre-diameter pore" https://www3.nd.edu/~gtimp/images/Reading.pdf 19:05 -!- aeiousomething [~aeiousome@117.195.143.206] has quit [Ping timeout: 240 seconds] 19:13 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 19:21 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Remote host closed the connection] 19:23 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap 19:37 < kanzure> plasmonic detection of cytochrome c conformational changes http://pubs.acs.org/doi/abs/10.1021/jacs.7b00839 19:41 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 19:46 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 240 seconds] 19:51 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 19:51 < kanzure> maybe the optogenetic method of a azobenzene photoswitchable tethered ligand could be enough to selectively block and de-block arbitrary protein activity, e.g. by physically blocking the active site, which get you switching times of a few milliseconds. 19:56 < kanzure> "Controlled inhibition of methyltransferases using photoswitchable peptidomimetics" http://pubs.rsc.org/-/content/articlehtml/2017/sc/c7sc00137a ... in this paper, they use a free-floating photoswitchable inhibitor, although i would imagine it could be tethered to be very nearby, to modulate the activity of a histone methyltransferase. 19:56 < kanzure> (figure 1 is particularly revealing) 19:58 < kanzure> so that would be a.. tethered photoswitchable peptide inhibitor of polymerase (or some other dna-modifying enzyme). 20:00 < kanzure> millisecond switching time is also pretty good, i think that matches the dna transport rate through a nanopore 20:01 < kanzure> s/matches/is compatible with 20:10 -!- Storyteller [~Storytell@unaffiliated/storyteller] has joined ##hplusroadmap 20:13 < kanzure> "Protein methyl transferases (PMTs) catalyze the transfer of the sulfonium methyl group of SAM to the side chain amino groups of lysine and arginine residues of specific protein substrates. There are more than 60 genes in the human genome that encode for protein methyl transferases. These include nine protein arginine methyltransferases (PRMTs) and more than 50 protein lysine ... 20:13 < kanzure> ...methyltransferases (PKMTs). With the exemption of DOT1L and several METTL (methyltransferase like) homologues all PKMTs contain a characteristic, catalytic SET domain (about 130 aa; named for the founding enzymes SuVar(3-9), Ezh, Trithorax)." 20:13 < kanzure> "Probing chromatin-modifying enzymes with chemical tools" http://repository.kaust.edu.sa/kaust/bitstream/10754/600475/1/Fischle+ACS+Chem+Biol+2016.pdf 20:13 -!- Darius [~quassel@66-215-89-229.dhcp.psdn.ca.charter.com] has quit [Remote host closed the connection] 20:14 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has quit [Ping timeout: 260 seconds] 20:18 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap 20:22 < nmz787> kanzure: silicon because SSDs because datacenters that read it often for processing 20:24 < kanzure> so the assumption is huge multiplex dna read...? even then, you still aren't going to reach ssd speed. 20:25 < kanzure> archival tape is still abundant 20:25 < kanzure> you can dig it right out of the ground! er... hmm. 20:25 < nmz787> kanzure: chemspider sort of tried/tries to take drawings and find info (maybe just what chem it is, idk) 20:26 < kanzure> ah maybe their diagram search is more than molecular diagram search. 20:28 < nmz787> kanzure: re: pushing off substrate... I think there point might be 'modulate with negative potential, so the shit doesn't pop off' 20:31 -!- Storyteller [~Storytell@unaffiliated/storyteller] has quit [Quit: Leaving] 20:31 < nmz787> kanzure: I think I was reading something recently about some metal ion messing up polymerase, manganese "error-prone PCR" 20:32 < nmz787> 0-10nM 20:32 < nmz787> sorry, mM 20:32 < nmz787> (millimolar) 20:32 < nmz787> brb 20:33 < kanzure> ya lots of things can screw with polymerase activity 20:35 < kanzure> not explicitly stated above: could use protein methyltransferases to store data on long filament proteins floating through a nanopore.. but hard to align everything, probably less good for data storage, probably less research done on reading methylation sites off of filamentous proteins floating through a nanopore. 20:49 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Quit: Leaving.] 20:50 < kanzure> "Slowing DNA translocation through a nanopore using a functionalized electrode" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875158/ 20:50 < kanzure> "Nanopores were fabricated with an integrated microscale Pd electrode coated with either a hydrogen-bonding, or hydrophobic monolayer. Bare pores, or those coated with octane thiol, translocated single-stranded DNA with times of a few microseconds per base. Pores functionalized with 4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide slowed average translocation times, calculated as the ... 20:50 < kanzure> ...duration of the event divided by the number of bases translocated, to about 100 microseconds per base at biases in the range of 50 to 80 mV." 20:53 < nmz787> back 20:53 < nmz787> sorry I was reading and didn't see your responses til now 20:53 < nmz787> kanzure: we can reach SSD speed today with minION tech, highly parallelized, and still be under 1 mm sq 20:54 < nmz787> remember "some number from nathan" 20:54 < kanzure> add agarose gel to other side of nanopore to slow it down http://onlinelibrary.wiley.com/doi/10.1002/elps.201400488/full 20:55 < nmz787> hrmm, idk about that, from what I remember it might be super hard to get it in there 20:55 < nmz787> we should check that last nanopore paper i posted 20:55 < nmz787> for newer hits from the authors 20:56 < nmz787> the one where they used reactive ion etch (RIE) and atomic layer deposition (ALD) 20:58 < kanzure> slow nanopore is necessary for initial version of write. as long as you take less than 1 minute/nucleotide it's still competitive with almost everything. 21:00 < nmz787> https://imgur.com/a/p9sKa 21:00 < nmz787> .title 21:00 < yoleaux> error-prone PCR using manganese chloride tetrahydrate - Album on Imgur 21:01 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 21:03 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 260 seconds] 21:12 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap 21:14 < abetusk> https://github.com/Microsoft/LightGBM/issues/331 <-- deep forest overhyped? Also, the only FOSS implementation I could find: https://github.com/pylablanche/gcForest 21:18 -!- CaptHindsight [~2020@192.171.29.66] has joined ##hplusroadmap 21:18 -!- CaptHindsight [~2020@192.171.29.66] has quit [Changing host] 21:18 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 21:19 < abetusk> specifically: https://github.com/Microsoft/LightGBM/issues/331#issuecomment-305957740 21:19 < kanzure> .title 21:19 < yoleaux> Support gcForest · Issue #331 · Microsoft/LightGBM · GitHub 21:21 -!- MrHindsight [~2020@unaffiliated/capthindsight] has quit [Ping timeout: 248 seconds] 21:21 < abetusk> .title https://arxiv.org/pdf/1702.08835v2.pdf 21:21 < yoleaux> abetusk: Sorry, that doesn't appear to be an HTML page. 21:23 < abetusk> anyway, that's the same Zhou and Feng paper but with a supplement added to it at the end (link followed from https://github.com/tkchris93/ForwardThinking/issues/4) that talks about only getting 69% to RseNet's ~93% and AlexNet's ~83% on CIFAR-10 21:29 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 21:33 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 21:47 < kanzure> well that's unfortunate. 21:55 < kanzure> "Nanopore sensing of individual transcription factors bound to DNA" https://www.nature.com/articles/srep11643?WT 21:56 < kanzure> hmph, looks like alpha-hemolysin + exonuclease is the only fusion protein constructed so far for the nanopores 21:58 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 21:59 < kanzure> "Genome editing with targeted deaminases" https://www.biorxiv.org/content/early/2016/07/28/066597 22:01 < kanzure> "Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions" http://pubmedcentralcanada.ca/pmcc/articles/PMC5388574/ 22:02 < kanzure> "Here we report the development of five new C→T (or G→A) base editors that use natural and engineered Cas9 variants with different protospacer-adjacent motif (PAM) specificities to expand the number of sites that can be targeted by base editing by 2.5-fold. Additionally, we engineered new base editors containing mutated cytidine deaminase domains that narrow the width of the apparent ... 22:02 < kanzure> ...editing window from approximately 5 nucleotides to as little as 1 to 2 nucleotides, enabling the discrimination of neighboring C nucleotides that would previously be edited with comparable efficiency, thereby doubling the number of disease-associated target Cs that can be corrected preferentially over nearby non-target Cs." 22:11 < kanzure> "Beyond editing to writing large genomes" http://diyhpl.us/~bryan/papers2/bio/Beyond%20editing%20to%20writing%20large%20genomes%20-%20Church%20-%202017.pdf (2017) (church stuff) 22:11 < kanzure> this one has a lot of good overview tables and figures. 22:11 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-cnliafhqrovfiafg] has joined ##hplusroadmap 22:13 < kanzure> wtf "However, this difference in cost is much smaller than it once was, as we have observed a million-fold reduction in cost in a decade for genome sequencing[85] and solid-phase DNA synthesis86, to the point where the cost for sequencing is about US$1,000, whereas synthesis runs about US$6,000 (REF. 9) per human genome." 22:16 < kanzure> i want to see the numbes on $6k for de novo synthesis and assembly of a human genome. 22:16 < yashgaroth> I'll let NASA know we can build a ladder to the moon for half a billion dollars 22:16 < yoleaux> 27 Sep 2017 06:34Z yashgaroth: is there an enzyme that will take a primer and search a soup of dsDNA, then lock on to all 3 (easily reversible, but stays on long enough to filter/electrophorese away, etc, then remove after that...) 22:16 < yoleaux> 28 Sep 2017 19:01Z yashgaroth: could we produce a ssDNA molecule that is repeats of GCAA pretty easily? some repeating pattern. for up to like... 50k bp or 100k bp. some length where the dna molecule will still stay in tact but still pretty long (millons of bp would be nice too..). 22:16 < yashgaroth> gah ah 22:16 < kanzure> well you already answered the second one 22:17 < yashgaroth> yeah nmz787 the RecA recombinases I mentioned in my talk are probably the closest you'll get to that 22:17 < yashgaroth> RecA-like, I should say 22:20 < kanzure> i know genome synthesis can get cheap but claiming a million fold cost reduction in genome synthesis in the last 10 years.... wat? 22:20 < kanzure> does this work outside of church's lab? 22:21 < kanzure> is there a parallel dimension that a harvard professor is stealing technology from? 22:22 < yashgaroth> anything is possible when you believe in yourself and fudge numbers 22:22 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 22:22 < kanzure> ( https://www.youtube.com/watch?v=sn5tQ0WjsdE ) 22:26 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 258 seconds] 22:26 < nmz787> yashgaroth: cool 22:27 < nmz787> I am thinking about whether or not I should buy a minION once I get my SEM working 22:27 < nmz787> and see if I couldn't mate it with some sort of prototype handling system 22:28 < nmz787> or at least see what they're doing 22:29 < yashgaroth> also it won't necessarily lock onto the third strand, but all three stay associated due to the surrounding basepair interactions 22:29 < kanzure> yashgaroth did you know about cytidine deaminases 22:30 < yashgaroth> vaguely, in the sense that cytosine methylation is a big driver of mutations wrt induced pluripotent stem cells 22:31 < yashgaroth> don't know much about deaminase enzymes, I figured it was mostly spontaneous 22:31 < kanzure> they made a fusion protein out of cytidine deaminase and dCas9 and removed/deactivated the nuclease activity, so it only flips a nucleotide. 22:32 < yashgaroth> ah I see that in the log 22:35 < nmz787> yashgaroth: any papers on protein longevity/life-span/time-to-break 22:35 < nmz787> ? 22:35 < nmz787> or any feeling of it? 22:36 < yashgaroth> can be years at 37C for some enzymes, hard to predict in silico 22:37 < kanzure> cool 22:37 < nmz787> I am thinking to have on-chip closed-system drying of DNA (maybe only for archival, but maybe as an optimization for power or something, retention-time, etc) would probably need to have some sort of peltier type device, with a hot and cold side, so you can evap from one chamber to another via condensation 22:37 < nmz787> idk, haven't thought too much into that yet 22:38 < yashgaroth> there's a few rules, like asn-gly deamidation, and thermostability correlates with stability but only somewhat/in some cases 22:38 < kanzure> what was the LOV domain stuff about, nmz787? 22:38 < nmz787> oh, just something from years ago on DIYbio 22:38 < kanzure> let's check if that person is still alive 22:39 < nmz787> it was josiah zayner 22:39 < kanzure> so yes 22:40 < yashgaroth> baker lab has some designed proteins that are stable in 6.7M guanidine which is pretty nuts, but scaffold proteins are more durable vs. enzymes, which need a little flex in them to catalyze reactions 22:41 < nmz787> minION 'ligation kit' (the other kit has a transposase to fragment the DNA into <30kb frags) protocol "high-molecular-weight DNA; optional fragmentation; end-prep; ligation of sequencing adapters; tether attachmentl; loading" 22:41 < nmz787> yashgaroth: mostly just thinking about something like tdt, polymerase for high-fidelity copy, and that recA-like 3-grabber 22:41 < nmz787> I guess nucleotide kinase 22:42 < nmz787> and for far-future the ATP synthase stuff 22:42 < nmz787> also, what do you think about feasibility to feed that electrons directly, instead of using the ionic water-wheel? 22:43 < yashgaroth> TdT I have no idea, polymerases there's some pretty stable ones but they're quite large which is a minus for stability, recA-likes I've found are good for a few months 22:43 < yashgaroth> I have dreamt of running metabolism off electricity but I've no idea how to approach it 22:44 < nmz787> let 22:44 < nmz787> let's grow them big trees off hydro yo 22:44 < yashgaroth> hell yee 22:44 < nmz787> or nuk-ya-ler 22:46 < nmz787> kanzure: we should include yashgaroth's proposal into the technical document in some 'other approaches not mentioned here' section 22:46 < nmz787> or rather, should we? 22:47 < yashgaroth> :3 22:49 < nmz787> yashgaroth: if you had much better DNA synthesis, how much better would it have to be (order of magnitude, based on price I guess) to have good chance of making it better/more-stable within 6 months? 22:50 < nmz787> or another way: if the protein was 4000bp... how many times would you have to try different sequences and test them for stability before probably finding someting better? 22:50 < nmz787> my assumption here is that engineering for stability is easier than engineering new function 22:51 < nmz787> since we really don't know how to do the latter 22:51 < yashgaroth> what, like directed evolution for stability? might be easier, though the general opinion is that proteins tend to be pretty stable for their environment due to evolution, minus some short-lived signalling proteins or w/e 22:52 < yashgaroth> you'd still have to continually test that they retain activity, unless you're ok with a 100x lower reaction rate as a trade-off 22:53 < yashgaroth> it's not necessarily a DNA synthesis cost if you have an error-prone polymerase and a whole lot of wells 22:53 < nmz787> good point.... might be tolerable, but it is a good idea for that idea's test-plan 22:54 < nmz787> I was kind of thinking well if we can prove a first-gen system of any approach... how long before that could self-accelerate gen-2 22:54 < yashgaroth> hey robots are cool even if they can't make better robots, anyway enzymes are cheap 23:04 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has quit [Quit: sleep] 23:13 < nmz787> kanzure: I guess I was reading this and saw the LOV mention and then searched my inbox for that and saw josiah's comments https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926219/ 23:13 < nmz787> .title 23:13 < yoleaux> Recent advances in the photochemical control of protein function 23:23 -!- Douhet [~Douhet@unaffiliated/douhet] has quit [Ping timeout: 246 seconds] 23:36 -!- Douhet [~Douhet@unaffiliated/douhet] has joined ##hplusroadmap 23:47 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 23:51 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Quit: Leaving.] --- Log closed Sat Sep 30 00:00:32 2017