--- Log opened Thu Sep 28 00:00:30 2017 00:04 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 240 seconds] 00:45 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-vxzfzdqejrpuenyw] has quit [Quit: Connection closed for inactivity] 00:59 -!- RebelCoder [~Yuriy@95.143.115.254] has joined ##hplusroadmap 01:08 -!- adlai [~adlai@unaffiliated/adlai] has quit [Ping timeout: 260 seconds] 01:17 -!- adlai [~adlai@unaffiliated/adlai] has joined ##hplusroadmap 01:30 -!- CRM114 [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 03:09 < pasky> doing anything without google must be incredible inconvenient 03:09 < pasky> *y 03:10 -!- adlai [~adlai@unaffiliated/adlai] has quit [Ping timeout: 240 seconds] 03:21 -!- adlai [~adlai@unaffiliated/adlai] has joined ##hplusroadmap 03:59 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 248 seconds] 04:22 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 04:39 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 04:44 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 248 seconds] 04:44 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 05:20 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 05:36 < kanzure> nmz787: can you deliver me a single electron to a nanopore? 05:38 -!- gene-hacker [~tetrapod@c-24-131-17-249.hsd1.pa.comcast.net] has quit [Ping timeout: 240 seconds] 05:38 < kanzure> or do i need to file a complaint with the bureau of dead worlds about this? 06:04 -!- delinquentme [~delinquen@173-132-28-117.pools.spcsdns.net] has joined ##hplusroadmap 06:27 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 260 seconds] 06:40 -!- gene-hacker [~tetrapod@CMU-943103.ANDREW.CMU.EDU] has joined ##hplusroadmap 06:48 < kanzure> "Whole-brain vasculature reconstruction at the single capillary level" https://www.biorxiv.org/content/early/2017/09/20/191502 https://twitter.com/biorxiv_neursci/status/910564656711966721 06:49 -!- delinquentme [~delinquen@173-132-28-117.pools.spcsdns.net] has quit [Ping timeout: 255 seconds] 06:53 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 07:02 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 258 seconds] 07:04 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 264 seconds] 07:10 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 246 seconds] 07:10 -!- delinquentme [~delinquen@c-76-126-145-167.hsd1.ca.comcast.net] has joined ##hplusroadmap 07:11 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap 07:18 -!- delinquentme [~delinquen@c-76-126-145-167.hsd1.ca.comcast.net] has quit [Ping timeout: 240 seconds] 07:20 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 07:44 -!- streety_ [~streety@156.40.252.2] has joined ##hplusroadmap 07:45 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 08:12 -!- delinquentme [~delinquen@h-67-102-118-110.snva.ca.globalcapacity.com] has joined ##hplusroadmap 08:17 -!- delinquentme [~delinquen@h-67-102-118-110.snva.ca.globalcapacity.com] has quit [Ping timeout: 248 seconds] 08:25 < heath> "split pool ligation transcriptome sequencing" 08:26 -!- streety_ [~streety@156.40.252.2] has quit [Remote host closed the connection] 08:33 < nmz787> kanzure: "1 fA equals 1^-15A, or 6240 electrons/sec" https://www.edn.com/design/analog/4368681/Design-femtoampere-circuits-with-low-leakage-part-one 08:34 < nmz787> kanzure: so... maybe (probably, I think, at least if that current was being produced as AC or some DC wave) 08:35 < nmz787> i.e. if 1 fA was modulated at 6240 Hz, you would get 1 electron flowing through at some point I think 08:37 < nmz787> "atto" is the next smallest unit after femto... it is 10^-18 08:37 < nmz787> so 1 attoAmp would be 6.24 electrons per second 08:45 < kanzure> "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage" http://evolve.harvard.edu/122-BaseEditing.pdf 08:47 < kanzure> http://pubmedcentralcanada.ca/pmcc/articles/PMC4873371/ 08:47 < kanzure> "Here we report the development of base editing, a new approach to genome editing that enables the direct, irreversible conversion of one target DNA base into another in a programmable manner, without requiring dsDNA backbone cleavage or a donor template. We engineered fusions of CRISPR/Cas9 and a cytidine deaminase enzyme that retain the ability to be programmed with a guide RNA, do not ... 08:47 < kanzure> ...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 point mutations relevant to human disease. In four transformed human and murine cell lines, second- and ... 08:48 < kanzure> ...third-generation base editors that fuse uracil glycosylase inhibitor (UGI), and that use a Cas9 nickase targeting the non-edited strand, manipulate the cellular DNA repair response to favor desired base-editing outcomes, resulting in permanent correction of ~15-75% of total cellular DNA with minimal (typically ≤ 1%) indel formation. Base editing expands the scope and efficiency of genome ... 08:48 < kanzure> ...editing of point mutations." 08:51 < kanzure> .wik cytidine deaminase 08:51 < yoleaux> "Cytidine deaminase is an enzyme that in humans is encoded by the CDA gene." — https://en.wikipedia.org/wiki/Cytidine_deaminase 08:51 < kanzure> "This gene encodes an enzyme involved in pyrimidine salvaging. The encoded protein forms a homotetramer that catalyzes the irreversible hydrolytic deamination of cytidine and deoxycytidine to uridine and deoxyuridine, respectively. It is one of several deaminases responsible for maintaining the cellular pyrimidine pool." 08:54 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=8c0b9a25 Bryan Bishop: fusion protein of cas9 and cytidine deaminase >> http://diyhpl.us/diyhpluswiki/gene-editing/ 09:00 < nmz787> one of the nanopore papers (maybe a theorhetical/model-based paper) was talking about translocating dsDNA... and how it was smoother than ssDNA, I guess due to charge equalization by the hybridization 09:00 < kanzure> "Uracil-DNA glycosylase excises uracil in both AU and GU pairs to prevent propagation of the base mismatch to downstream transcription and translation processes.[8] With high efficiency and specificity, this glycosylase repairs more than 10,000 bases damaged daily in the human cell.[9] Human cells express five to six types of DNA glycosylases, all of which share a common mechanism of base ... 09:00 < kanzure> ...eversion and excision as a means of DNA repair.[10]" 09:00 < nmz787> but then you need some weird pattern detection or something to detect which way you're sequencing, and I'm not sure if you get all messed up if the DNA molecule rotates during the translocation event 09:01 < nmz787> otherwise I am thinking maybe you have two pores adjacent, with some unzipping enzyme (or heater to melt?), then sequence each strand in parallel, then on the otherside get the two strands to zip back together so you prevent kinks/hairpins and such 09:02 < nmz787> and you also get some error-correction since they should be complementary 09:03 < nmz787> .wik glycosylase 09:03 < yoleaux> "Glycosylases (EC 3.2) are enzymes that hydrolyze glycosyl compounds. They are a type of hydrolase (EC 3). In turn, glycosylases are divided into two groups: glycosidases -- enzymes that hydrolyze O- and S-glycosyl compounds (EC 3.2.1) -- and enzymes that hydrolyze N-glycosyl compounds (EC 3.2.2)." — https://en.wikipedia.org/wiki/Glycosylase 09:04 < kanzure> i had not thought about hooking up deaminases to cas9 as a fusion protein, i think i have missed something about basic biochemistry. 09:05 -!- delinquentme [~delinquen@75.147.139.131] has joined ##hplusroadmap 09:05 < nmz787> I guess it makes sense, there is a lot of biochemistry that isn't organized as well as we might like 09:06 < nmz787> EE power electronics crossword puzzle: http://images.ic.maximintegrated.com/Web/MaximIntegratedProductsInc/%7B79634234-00c1-4208-8bcd-6e15954ac8d4%7D_Power_Design_Challenge_puzzle.pdf 09:06 < nmz787> "30 Australian rock band" I'm gonna guess AC/DC 09:13 < kanzure> we should do random fusion protein generation (from pdb or something) and then do machine learning to pull out the possibly-interesting fusions 09:23 -!- camcol [~camcol@109.181.76.45] has joined ##hplusroadmap 09:27 < kanzure> camcol: hi. 09:27 < camcol> hello 09:28 < kanzure> what brings you these ways 09:28 < camcol> Im just interested in learning new things 09:30 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 248 seconds] 09:48 < nmz787> camcol: lots of learning here, for sure 09:48 -!- camcol [~camcol@109.181.76.45] has quit [Ping timeout: 248 seconds] 09:50 -!- strages [uid11297@gateway/web/irccloud.com/x-plonjlhhnfkfcwnj] has quit [Quit: Connection closed for inactivity] 09:54 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 10:21 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 10:34 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 10:36 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 248 seconds] 10:45 < kanzure> nmz787: do you have the name of someone at microsoft doing dna data storage stuff? who is the one pushing for it? 11:50 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 11:57 -!- NikopolSohru [~NSohru@89.38.96.190] has joined ##hplusroadmap 12:01 < kanzure> .to 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..). 12:01 < yoleaux> kanzure: I'll pass your message to yashgaroth. 12:01 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-wjtsxjrplcgglghs] has joined ##hplusroadmap 12:02 < kanzure> nmz787: also, do you have any sense for feasibility of an addressable electrode array for a few thousand or million elements that can deliver those femtoamps you described earlier? 12:09 < kanzure> .title https://www.youtube.com/watch?v=Sx6FbYoFGmM 12:09 < yoleaux> Nanopore Technology - UIUC and Johns Hopkins Collaboration - YouTube 12:13 -!- delinquentme [~delinquen@75.147.139.131] has quit [Ping timeout: 258 seconds] 12:23 < nmz787> kanzure: not sure of any microsoft ppl, have you checked the "internet in a bottle" whitepaper they wrote? 12:23 < kanzure> no 12:24 < kanzure> we should find out who is pushing this inside microsoft 12:24 < nmz787> kanzure: my guess is an electrode array isn't impossible, they already make MEAs (micro electrode arrays) for neural studies.... I'm not sure why they haven't scaled up, probably because they're for life sciences market which apparently lacks funding for R&D of nanotech 12:25 < nmz787> fan-out of the control logic seems like it could be annoying, but that's what serial-to-parallel shift register and such are for, to help 12:25 < kanzure> yes but femtoamps? 12:25 < nmz787> so I only get 5 (uninteresting hits on Google for 'hackerproof born without birth certificate' 12:26 < nmz787> kanzure: um, probably not without being produced on non-research fab processes 12:26 < kanzure> but help me get a sense of how common this is. delivering ~6 electrons is extremely experimental? 12:26 < nmz787> i.e. FIB is a 'research' process, in the sense it doesn't scale to be included in high-volume production 12:27 < nmz787> umm, well 6 electrons is attoamps, not femto 12:27 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Quit: Leaving.] 12:27 < nmz787> I haven't really read an article on attoamp sensing (which would be required for controlled delivery/dosing of output-electrons) 12:27 < kanzure> oh femtoamps per millisecond is the target apparently. my ad. 12:27 < kanzure> *my bad. 12:29 < gene-hacker> what do you need such an electrode array for? 12:29 < kanzure> gene-hacker: knocking off a hydroxymethyl group from a dna molecule in a nanopore 12:29 < kanzure> and many nanopores per device 12:29 < gene-hacker> for synthesis? 12:29 < kanzure> for data storage 12:30 < gene-hacker> how do you index the DNA? 12:30 < gene-hacker> back and forth through the pore 12:30 < kanzure> each DNA molecule has custom barcode already attached 12:30 < nmz787> electrophoresis 12:30 < kanzure> you use PCR to pull out that DNA molecule 12:31 < kanzure> based on its barcode. etc. 12:31 < nmz787> IBM has done a bunch of work on electrophoresing for example 1bp at a time, using inter-nanopore electrodes (in addition to the sensing electrode) 12:31 < gene-hacker> so I take it you want to move dna through nanopores like tape storage? 12:31 < kanzure> yeah it's pretty common. dna nanopore sequencing works like that. 12:31 < gene-hacker> there are probably different polymer chains that you can read with nanopores 12:32 < nmz787> yep 12:32 < kanzure> yes that's true, but dna is easy to prepare and work with 12:32 < nmz787> anything based on electrons 12:32 < gene-hacker> it's harder to write 12:32 < kanzure> removing a hydroxymethyl group is not quite the same thing as writing 12:32 < gene-hacker> perhaps there's a molecule whose individual monomers can be oxidized and reduced 12:33 -!- emeraldgreen [~user@188.227.115.178] has joined ##hplusroadmap 12:34 < kanzure> yeah 12:34 < kanzure> https://www.nasa.gov/feature/experimental-demonstration-and-system-analysis-for-plasmonic-force-propulsion 12:36 < gene-hacker> well if you can selectively knock off a hydroxymethyl group on a single base pair then you could store data that way 12:36 < nmz787> methylation also removes an interesting avenue of search.... namely using primer hybridization 12:36 < kanzure> for data search? 12:36 < nmz787> if some other aspect of the architecture sucks, having really fast seek/search time might be valuable enough to be an overall interesting architecture 12:37 < gene-hacker> except using a chain of electrochromic molecules 12:37 < nmz787> otherwise we need to sequence the entire tape for search/seek 12:38 < nmz787> kanzure: some nanopores have done dsDNA... discrimination is harder/different... varying methyl in those scenarious might be a useful enough discriminator 12:40 < nmz787> using the two strands being simultaneously sequenced, either via separate adjacent pores, or by restricting their ability to twist in the channel could be seen as a sort of differential-signalling 12:40 < nmz787> which should help for error-correction/detection, and might help for distinguishing repeats (though maybe not) 12:41 < kanzure> yes i was worried about twisting but apparently separating the dsDNA fixes that 12:41 < kanzure> .title https://www.youtube.com/watch?v=Sx6FbYoFGmM 12:41 < yoleaux> Nanopore Technology - UIUC and Johns Hopkins Collaboration - YouTube 12:42 < emeraldgreen> Interesting drug https://en.wikipedia.org/wiki/Selank that was mentioned on slatestarcodex 12:42 < emeraldgreen> If I had a peptide synthesizer I could produce it 12:43 < emeraldgreen> I wonder if there are many more potential peptide drugs 12:43 < nmz787> kanzure: using research fab processes limits/eliminates the ability to process-in electronics... so we might have a great nano electrode array, and great nanopores... but if the power driver and sensing tech is off-chip connected by some big-honkin cable... then noise swamps the signal and a system cannot be realized effectively 12:44 < kanzure> perhaps wth other monomer units or another polymer chain you could get away with more amps 12:45 < kanzure> nucleotide sensing is already commonly done with nanopores 12:45 < kanzure> and that's capacitive i believe 12:47 < nmz787> kanzure: also just read a plasmon nanopore paper a night or two ago 12:49 < nmz787> there are two nanopore methods I know of, depending on the setup... through-pore like the oxford ppl, and across-pore (tunneling current) which the IBM paper I posted yesterday has electrodes setup for (though I imagine with the correct electronics they could do either, since their nanopore stack had 3 electrodes) 12:50 < nmz787> (though I am not sure if all 3, or only the middle, were atomic thickness) 12:59 -!- emeraldgreen [~user@188.227.115.178] has quit [Quit: Leaving.] 13:13 < kanzure> https://www.coindesk.com/two-bitcoin-futures-etfs-sec-approval/ 13:23 < kanzure> nmz787: need to deliver about 0.5 volts in that nanopore scheme. 13:28 < heath> "Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction." https://www.ncbi.nlm.nih.gov/pubmed/23651338 13:28 < kanzure> ~40 kbp 13:49 < fltrz> I was scanning my coursenotes yesterday, and noticed the question for delivering a single electron, but was too tired from scanning course notes to reply 13:50 < kanzure> "cell-free reprogrammable protein expression system using freeze-dried genetic circuits on filter paper" http://2016.igem.org/Team:BGIC_China/Description 13:50 < kanzure> (another) "cell-free transcription-translation system" http://2014.igem.org/Team:Caltech/TXTL 13:50 < fltrz> but just minutes before I read the question I actually scanned the instructions for the experimentation labs we did, one of which was millikan oil drop experiment, where we charged oil drops with high voltage 13:50 < fltrz> and levitated by high voltage electric fields as well 13:51 < kanzure> are you familiar with electrowetting and droplets 13:51 < fltrz> we could swap the polarity of the electric fields, and observe the oil drops through a microscope&webcam 13:51 < fltrz> kanzure: not really, only from reading, and that one millikan experiment we did 13:51 < fltrz> some of the oil drops were uncharged 13:51 < kanzure> oh it's the same mechanism? 13:52 < fltrz> some were charged 13:52 < fltrz> I think the charging mechanism for the oil drops was simple induction, i.e. the oil drop-still-connected to bulk oil being in a strong electric field 13:52 -!- emeraldgreen [~user@188.227.115.178] has joined ##hplusroadmap 13:53 < fltrz> so some ions or electrons in the hardly conducting oil preferentially go in the drop before it splits, and once split you have a charged drop 13:53 < fltrz> so some of the drops had no charge, or some had twice the charge 13:53 < fltrz> in the webcam you could see a bunch of drops, and how they reacted to changing the polarity of the HV electric field 13:54 < fltrz> many had a longitudinal velocity component or drift, so they went out of focus 13:54 < fltrz> the webcam stream was recorded of course 13:55 < fltrz> and there were 2 horizontal lines, one near top, one near bottom, if it reached bottom, you switch polarity, and now they move up, when they cross the upper switch again 13:55 < fltrz> back and aforth 13:56 < fltrz> then once you got the hang of it, and had multiple crossings of one good drop 13:56 < fltrz> you went through the recording and noted the times of crossing the line, from it you could deduce the elementary charge 13:57 < fltrz> I don't know how hard delivering a single electron to the nanopore is, but I do know it will be hard to separate a 'real' current from a capacitive one 13:58 < fltrz> I also estimate it to be highly probabilistic, but if you can asses the methylation or whatever you try to affect, then if this feedback tells you its still there you can just pulse again? 14:00 < fltrz> i.e. I think it would be hard to differentiate an electron leaving a conductor from a positive ion arriving to adhere at the electrode 14:02 * fltrz off to scan some more courses 14:07 -!- emeraldgreen [~user@188.227.115.178] has quit [Quit: Leaving.] 14:11 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 14:14 < nmz787> fltrz: I think you see a 'bottleneck' in the current-rate... i.e. you can start sending current, then if capacitance is happening/dominating you see the current decrease, requiring more voltage to break the dielectric insulation 14:20 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-wjtsxjrplcgglghs] has quit [Quit: Connection closed for inactivity] 14:24 -!- emeraldgreen [~user@188.227.115.178] has joined ##hplusroadmap 14:31 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 240 seconds] 14:32 -!- emeraldgreen [~user@188.227.115.178] has quit [Quit: Leaving.] 14:35 < kanzure> "You can generate long strands of poly CGAA ssDNA with a complementary single stranded circular template of repeating CGTT, doesn't even need to be that long. Get a primer and a strand displacing polymerase, and it'll keep spinning around the circle until it decides to fall off. This could generate a polymer of perhaps 100kbp, but it's gonna be an unknown-ish length depending on the pol and ... 14:35 < kanzure> ...random thermodynamics." 14:35 < kanzure> "Methylation you can probably incorporate during synthesis with methylated dCTP, hydroxy I assume an enzyme will do that reliably enough too." 14:35 < kanzure> "Remember that methylcytosine will deaminate into thymine spontaneously, probably faster at higher temps." 14:38 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 14:44 -!- atrus6 [~atrus6@72.241.82.247] has joined ##hplusroadmap 14:48 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-gsysuvdrwrvyagdf] has joined ##hplusroadmap 14:51 -!- augur [~augur@198-27-215-123.static.sonic.net] has joined ##hplusroadmap 14:51 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 14:51 -!- delinquentme [~delinquen@198.102.103.18] has joined ##hplusroadmap 14:58 < kanzure> fun deployment mechanism for gene therapy: deploy it, but also, it activates in everyone at roughly the same time, after some period of time for adoption to occur in a population. 15:00 < nmz787> quorum sensing 15:00 < nmz787> .wik 15:00 < yoleaux> Search for an article on Wikipedia 15:10 -!- delinquentme [~delinquen@198.102.103.18] has quit [Ping timeout: 240 seconds] 15:13 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Quit: Leaving.] 15:18 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 15:33 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Quit: Leaving.] 15:33 < nmz787> https://www.youtube.com/watch?v=LI_5ANmkVqo 15:33 < nmz787> .title 15:33 < yoleaux> EEVblog #1017 - Enter The World Of Atto Amps - YouTube 15:35 < nmz787> http://www.tek.com/sites/tek.com/files/media/document/resources/LowLevelHandbook_7Ed.pdf 15:47 -!- delinquentme [~delinquen@156.72.30.1] has joined ##hplusroadmap 15:48 -!- augur [~augur@198-27-215-123.static.sonic.net] has quit [Remote host closed the connection] 15:48 -!- augur [~augur@198-27-215-123.static.sonic.net] has joined ##hplusroadmap 15:52 -!- augur [~augur@198-27-215-123.static.sonic.net] has quit [Ping timeout: 240 seconds] 15:57 -!- delinquentme [~delinquen@156.72.30.1] has quit [Quit: Leaving] 15:58 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 240 seconds] 16:07 < kanzure> https://en.wikipedia.org/wiki/Asilomar_Conference_on_Recombinant_DNA 16:07 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap 16:09 < nmz787> wow, 32GHz o-scope dumpster dive that was throw away apparently due to a loose main power connector! https://youtu.be/d_S9YsD9Y0c 16:09 < nmz787> .title 16:09 < yoleaux> EEVblog #984 - World's Best Dumpster Find! ($300k!) - YouTube 16:09 < kanzure> "According to the conference, the proper response to new scientific knowledge was to develop guidelines that governed how to regulate it.[14]" 16:09 < kanzure> traitors 16:16 < nmz787> hrmm, people are crying that it was an april fools joke 16:21 < fltrz> when a scope doesn't work anymore an is out of support, and the owners are afraid of breaking the warranty/callibration stickers, they usually sell the scope 16:21 < fltrz> and a lot of this test equipment auction shops, don't really try to fix it either 16:22 < fltrz> they tend to sell at a fraction of the price, but still *something* 16:22 < fltrz> throwing it away wouldn't make sense in anyones mind 16:22 < fltrz> I got mine through ebay, was a broken TDS 5104 16:23 < fltrz> BSOD, so I knew it was either just a HDD/software issue, or the sellers had frankensteined a bunch of broken parts together and arranged BSOD... 16:23 < fltrz> turns out it was just a broken HDD 16:23 < fltrz> I could have lost 1700 euro in the gamble 16:24 < fltrz> now I got a pimped scope 16:24 < fltrz> since its SSD instead of HDD 16:26 < fltrz> * not in anyones mind except for widows, grandchildren, ex-gf's or whatever 16:26 < fltrz> i.e. people who don't know the value of the object 16:32 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 16:50 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-gsysuvdrwrvyagdf] has quit [Quit: Connection closed for inactivity] 17:06 -!- Gurkenglas_ [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 17:11 -!- mrdata- [~mrdata@unaffiliated/mrdata] has joined ##hplusroadmap 17:18 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 17:18 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 17:18 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 18:04 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 260 seconds] 18:08 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 18:30 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 260 seconds] 18:31 < kanzure> .title https://lists.linuxfoundation.org/pipermail/bitcoin-dev/2017-September/015093.html 18:31 < yoleaux> [bitcoin-dev] Rebatable fees & incentive-safe fee markets 18:32 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 18:32 < maaku> I got nerd-sniped 18:34 < kanzure> maaku: you got meta-nerdsniped https://www.reddit.com/r/Bitcoin/comments/72qi2r/redesigning_bitcoins_fee_market_a_new_paper_by/dnnk7kx/?context=2 18:45 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=582c71eb Bryan Bishop: include follow-up links for MAST stuff >> http://diyhpl.us/diyhpluswiki/transcripts/bitcoin-core-dev-tech/2017-09-07-merkleized-abstract-syntax-trees/ 18:49 < kanzure> http://diyhpl.us/~bryan/papers2/bio/protein-engineering/Advances%20in%20design%20of%20protein%20folds%20and%20assemblies%20-%202017.pdf 18:50 < kanzure> maaku: do you have a good overview/list of things that can be done if you had magical ability to make many different types of molecular shapes? e.g. not complete control over protein shape but some pretty good control like sheets, coils, rings, etc. 18:52 < kanzure> i think you might have a list like that for diamondoid molecular nanotechnology stuff... you mentioned "extremely low mass tools" (like even hammers etc) 18:52 < nmz787> omg southpark apparently has their latest episode about DNA ancestry testing services 19:20 < cluckj> did they at least make fun of racists? 19:28 -!- CRM114 [~urchin@unaffiliated/urchin] has quit [Ping timeout: 258 seconds] 19:35 -!- Pernille [~Pernille@55.92-220-69.customer.lyse.net] has joined ##hplusroadmap 19:41 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 20:00 -!- Pernille [~Pernille@55.92-220-69.customer.lyse.net] has quit [Quit: Leaving] 20:04 -!- jaboja [~jaboja@jaboja.pl] has quit [Remote host closed the connection] 20:09 -!- mrdata- [~mrdata@unaffiliated/mrdata] has quit [Read error: Connection reset by peer] 20:10 < kanzure> adlai: delinquentme has been helping out with joinmarket things? 20:12 -!- jtimon [~quassel@199.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 258 seconds] 20:13 -!- Darius [~quassel@66-215-89-229.dhcp.psdn.ca.charter.com] has joined ##hplusroadmap 20:13 -!- adlai [~adlai@unaffiliated/adlai] has quit [Ping timeout: 258 seconds] 20:16 < kanzure> "Correlated Light-Serial Scanning Electron Microscopy (CoLSSEM) for ultrastructural visualization of single neurons in vivo" https://www.biorxiv.org/content/early/2017/06/10/148585 20:16 < kanzure> ".. by adapting a genetically-encoded ascorbate peroxidase (APEX2) as a fusion protein to a membrane-targeted fluorescent reporter (CAAX-Venus), and introduce it in single pyramidal neurons in vivo using extremely sparse in utero cortical electroporation (IUCE). This approach allows to perform Correlated Light-SSEM (CoLSSEM) on individual neurons, reconstructing their dendritic and axonal ... 20:16 < kanzure> ...arborization in a targeted way via combination of high-resolution confocal microscopy, and subsequently imaging of its ultrastuctural features and synaptic connections with the ATUM-SEM (automated tape-collecting ultramicrotome - scanning electron microscopy) technology. Our method significantly improves the the feasibility of large-scale reconstructions of neurons within a circuit, and ... 20:16 < kanzure> ...bridges the description of ultrastructural features of genetically-identified neurons with their functional and/or structural connectivity, one of the main goal of connectomics." 20:18 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 20:23 < kanzure> some kinda fusion protein that can read histone-modified loci on DNA-protein chromatin bundles https://www.biorxiv.org/content/early/2017/06/03/145730 20:23 < kanzure> "... the enzyme EZH1/2 adds methyl groups to H3K27, and KDM6A (UTX) and KDM6B (JMJD3) remove these marks (reviewed in [37])." 20:23 < kanzure> [37] Swigut T, Wysocka J. H3K27 demethylases, at long last. Cell. 2007;131: 29–32. 20:25 < kanzure> .wik histone-modifying enzymes 20:25 < yoleaux> "The packaging of the eukaryotic genome into highly condensed chromatin makes it inaccessible to the factors required for gene transcription, DNA replication, recombination and repair. Eukaryotes have developed intricate mechanisms to overcome this repressive barrier imposed by the chromatin." — https://en.wikipedia.org/wiki/Histone-modifying_enzymes 20:25 < kanzure> "The nucleosome is composed of an octamer of the four core histones (H3, H4, H2A, H2B) around which 146 base pairs of DNA are wrapped. Several distinct classes of enzyme can modify histones at multiple sites.[1]" 20:25 < kanzure> "Enzymes have been identified for acetylation,[2] methylation,[3] demethylation,[4] phosphorylation,[5] ubiquitination,[6] sumoylation,[7] ADP-ribosylation,[8] deimination,[9][10] and proline isomerization.[11] For a detailed example of histone modifications in transcription regulation see RNA polymerase control by chromatin structure and table "Examples of histone modifications in ... 20:25 < kanzure> ...transcriptional regulation"." 20:26 < kanzure> https://en.wikipedia.org/wiki/Histone#Histone_modifications 20:27 < kanzure> so you could do a fusion protein to attach one of these histone-modifying enzymes with dCas9 (deactivated cas9) and just directly modify or write information on the histones 20:29 < kanzure> .wik histone code 20:29 < yoleaux> "The histone code is a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends." — https://en.wikipedia.org/wiki/Histone_code 20:29 -!- adlai [~adlai@unaffiliated/adlai] has joined ##hplusroadmap 20:33 < kanzure> ".. These results show promise for designing transcription factors that can read chromatin marks to rewire aberrant epigenetic programming. However, binding affinities observed in vitro for isolated polycomb chromodomain domains is poor, reported as 5 - 165 μM [12,13], compared to DNA-binding domains with target affinities in the pico- to nanomolar range such as TALEs (~3 - 220 nM), [14], ... 20:33 < kanzure> ...zinc fingers (~0.01 - 16 nM) [15,16], and CRISPR/Cas (~0.5 nM) [17]. In other work, we observed stronger gene upregulation when mCherry-VP64 was targeted to a promoter via a Gal4 DNA binding domain compared to the PCD histone binding domain [18]." 20:34 < kanzure> (PCD == polycomb chromodomain) 20:36 -!- gene-hacker [~tetrapod@CMU-943103.ANDREW.CMU.EDU] has quit [Ping timeout: 248 seconds] 20:39 < kanzure> 'cell cycle control Cas9 expression may be an effective strategy to bias DNA repair outcomes' https://www.biorxiv.org/content/early/2017/04/12/127068 (geminin fusion protein) 20:40 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 248 seconds] 20:40 -!- delinquentme [~delinquen@2602:306:ceb7:990:94e8:26b0:8ae1:a31e] has joined ##hplusroadmap 20:41 < kanzure> rna-binding protein (RBP) fusion protein with Adenosine deaminases acting on RNA (ADAR) https://www.biorxiv.org/content/early/2017/08/23/156828 20:41 < kanzure> "Adenosine deaminases acting on RNA (ADAR) are enzymes responsible for binding to double stranded RNA (dsRNA) and converting adenosine (A) to inosine (I) by deamination.[7] ADAR protein is a RNA-binding protein, which functions in RNA-editing through post-transcriptional modification of mRNA transcripts by changing the nucleotide content of the RNA.[8]" 20:44 < kanzure> "Impact of fluorescent protein fusions on the bacterial flagellar motor" https://www.biorxiv.org/content/early/2017/06/20/152595 20:45 -!- delinquentme [~delinquen@2602:306:ceb7:990:94e8:26b0:8ae1:a31e] has quit [Ping timeout: 246 seconds] 20:46 -!- delinquentme [~delinquen@2602:306:ceb7:990:94e8:26b0:8ae1:a31e] has joined ##hplusroadmap 20:46 < kanzure> "Chemical control of a CRISPR-Cas9 acetyltransferase" https://www.biorxiv.org/content/early/2017/08/16/176875 20:47 < kanzure> "Lysine acetyltransferases (KATs) play a critical role in the regulation of transcription and other genomic functions. However, a persistent challenge is the development of assays capable of defining KAT activity directly in living cells. Towards this goal, here we report the application of a previously reported dCas9-p300 fusion as a transcriptional reporter of KAT activity. First we ... 20:47 < kanzure> ...benchmark the activity of dCas9-p300 relative to other dCas9-based transcriptional activators, and demonstrate its compatibility with second generation short guide RNA architectures. Next, we repurpose this technology to rapidly identify small molecule inhibitors of acetylation-dependent gene expression. These studies validate a recently reported p300 inhibitor chemotype, and reveal a role ... 20:47 < kanzure> ...for p300s bromodomain in dCas9-p300-mediated transcriptional activation. Comparison with other CRISPR-Cas9 transcriptional activators highlights the inherent ligand tuneable nature of dCas9-p300 fusions, suggesting new opportunities for orthogonal gene expression control. " 20:49 < kanzure> "A rationally designed aminoacyl-tRNA synthetase for genetically encoded fluorescent amino acids" https://www.biorxiv.org/content/early/2017/05/14/065227 20:50 -!- delinquentme [~delinquen@2602:306:ceb7:990:94e8:26b0:8ae1:a31e] has quit [Ping timeout: 240 seconds] 20:52 < kanzure> "zinc finger-DNMT3A" 20:53 < kanzure> "Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation" https://www.biorxiv.org/content/early/2017/09/20/170506 20:53 < kanzure> "It is widely assumed that the addition of DNA methylation at CpG rich gene promoters silences gene transcription. However, this conclusion is largely drawn from the observation that promoter DNA methylation inversely correlates with gene expression in natural conditions. The effect of induced DNA methylation on endogenous promoters has yet to be comprehensively assessed. Here, we induced the ... 20:53 < kanzure> ...simultaneous methylation of thousands of promoters in the genome of human cells using an engineered zinc finger-DNMT3A fusion protein, enabling assessment of the effect of forced DNA methylation upon transcription, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that DNA methylation is frequently insufficient to transcriptionally repress ... 20:53 < kanzure> ...promoters. Furthermore, DNA methylation deposited at promoter regions associated with H3K4me3 is rapidly erased after removal of the zinc finger-DNMT3A fusion protein. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. These findings ... 20:54 < kanzure> ...suggest that promoter DNA methylation is not generally sufficient for transcriptional inactivation, with implications for the emerging field of epigenome engineering." 21:01 < kanzure> also there are cas9-DNMT3A fusion proteins 21:01 < kanzure> and the "methylcytosine dioxygenase (TET1)" stuff 21:06 -!- delinquentme [~delinquen@2602:306:ceb7:990:94e8:26b0:8ae1:a31e] has joined ##hplusroadmap 21:08 < kanzure> "Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions" https://www.nature.com/nbt/journal/v34/n10/abs/nbt.3658.html (ok but this is just dCas9-SunTag stuff.. see logs.) 21:11 -!- delinquentme [~delinquen@2602:306:ceb7:990:94e8:26b0:8ae1:a31e] has quit [Ping timeout: 255 seconds] 21:14 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 21:16 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Quit: Leaving.] 21:23 < kanzure> there should be a transcriptional repressor regulator thing that works with dcas9 and then just sticks on to the dna molecule to prevent expression completely. since apparently methylation is insufficient. 21:33 -!- gene-hacker [~tetrapod@c-24-131-17-249.hsd1.pa.comcast.net] has joined ##hplusroadmap 21:36 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 240 seconds] 21:36 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 21:36 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 21:38 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Read error: Connection reset by peer] 21:39 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 21:44 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 258 seconds] 21:46 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 21:57 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 22:02 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 22:02 -!- Darius [~quassel@66-215-89-229.dhcp.psdn.ca.charter.com] has quit [Remote host closed the connection] 22:22 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 22:26 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 248 seconds] 22:27 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has joined ##hplusroadmap 22:44 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 258 seconds] 22:44 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 260 seconds] 22:56 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 22:58 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 23:03 < mrdata> https://www.youtube.com/watch?v=QzaYnrrEKbU 23:14 < nmz787> .title 23:14 < yoleaux> Uplifting Animal & Aliens, Part 1 of 2 - YouTube 23:24 < nmz787> "My Ph.D. thesis is on characterizing the biophysical phenomena regarding LOV domains and apply that to make good photoswitchable proteins. Currently anyone can make two proteins colocalize or turn on a gene. I think what everyone wants or is trying to do is to make most "any" protein function activatable by light. Something cryptochromes and phytochromes will not be able to do this easily because 23:24 < nmz787> of their size and need to for exogenous chromophore. However, even in the context of LOV domains making something like the well characterized KcsA potassium channel light activated is no easy task." 23:24 < nmz787> "I can easily provide plasmids for engineered LOV domains if requested. 23:24 < nmz787> " 23:26 < nmz787> hmm, kanzure there's the market I posted on DIYbio about in 2013 "Lab-made DNA used to tackle copper cable theft" 23:27 < nmz787> not sure how much asset marking industry is worth 23:28 -!- mindsForge [~nak@174-26-0-148.phnx.qwest.net] has quit [Remote host closed the connection] 23:40 < maaku> kanzure: well there's everything Freitas has written about nanomedicine. but do you mean conventional things done better? there's drexler's rough estimates of the mechanical properties of macro-scale lightweight diamondoid materials. nanosystems ch. 2, and 11 23:40 < maaku> speaking of drexler he's up your alley as he's been pursuing DNA approaches to nanotech. I haven't kept up on that 23:41 < maaku> or do you mean things that can be done with protein molecules? 23:43 < nmz787> where is he? 23:44 < nmz787> K. Eric Drexler? 23:46 < maaku> Oxford I think? 23:46 < maaku> I don't know what he's done producitvely recently 23:48 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 248 seconds] 23:56 -!- CaptHindsight [~2020@unaffiliated/capthindsight] has joined ##hplusroadmap 23:56 < CaptHindsight> https://link.springer.com/article/10.1007/s13238-017-0475-6 23:57 < CaptHindsight> Correction of β-thalassemia mutant by base editor in human embryos ^^ 23:57 < CaptHindsight> brought to you by ChinaCo --- Log closed Fri Sep 29 00:00:31 2017