--- Log opened Sat Feb 18 00:00:36 2017 00:15 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 00:55 -!- Urchin [~urchin@89.17.17.61] has joined ##hplusroadmap 01:12 -!- augur [~augur@2601:645:8300:2b03:1196:c94f:8905:f749] has joined ##hplusroadmap 01:41 -!- augur_ [~augur@2601:645:8300:2b03:3c88:1928:5d51:f4ab] has joined ##hplusroadmap 01:44 -!- augur [~augur@2601:645:8300:2b03:1196:c94f:8905:f749] has quit [Ping timeout: 255 seconds] 01:46 -!- augur_ [~augur@2601:645:8300:2b03:3c88:1928:5d51:f4ab] has quit [Read error: Connection reset by peer] 01:51 -!- augur [~augur@2601:645:8300:2b03:3c88:1928:5d51:f4ab] has joined ##hplusroadmap 02:02 -!- augur [~augur@2601:645:8300:2b03:3c88:1928:5d51:f4ab] has quit [Read error: Connection reset by peer] 02:03 -!- augur [~augur@2601:645:8300:2b03:3c88:1928:5d51:f4ab] has joined ##hplusroadmap 02:08 -!- augur [~augur@2601:645:8300:2b03:3c88:1928:5d51:f4ab] has quit [Read error: Connection reset by peer] 02:13 -!- augur [~augur@2601:645:8300:2b03:3c88:1928:5d51:f4ab] has joined ##hplusroadmap 02:16 -!- Gurkenglas [~Gurkengla@dslb-178-005-218-116.178.005.pools.vodafone-ip.de] has joined ##hplusroadmap 02:18 -!- augur [~augur@2601:645:8300:2b03:3c88:1928:5d51:f4ab] has quit [Ping timeout: 240 seconds] 02:24 -!- augur [~augur@c-98-210-157-162.hsd1.ca.comcast.net] has joined ##hplusroadmap 02:25 < streety> George Church also suggested that in situ sequencing would be the next big thing for the genome 02:25 < streety> although nanopore may get there first with in situ rising up in its wake 02:28 -!- augur [~augur@c-98-210-157-162.hsd1.ca.comcast.net] has quit [Ping timeout: 260 seconds] 02:35 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 02:47 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Read error: Connection reset by peer] 02:48 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 02:51 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Read error: Connection reset by peer] 02:54 -!- augur [~augur@c-98-210-157-162.hsd1.ca.comcast.net] has joined ##hplusroadmap 02:57 -!- augur_ [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 02:58 -!- augur_ [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Read error: Connection reset by peer] 02:58 -!- augur_ [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 02:59 -!- augur [~augur@c-98-210-157-162.hsd1.ca.comcast.net] has quit [Ping timeout: 260 seconds] 03:10 -!- augur_ [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Read error: Connection reset by peer] 03:10 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 03:23 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 03:24 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Read error: Connection reset by peer] 03:24 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 03:32 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Read error: Connection reset by peer] 03:35 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 03:46 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Read error: Connection reset by peer] 03:46 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 03:47 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Remote host closed the connection] 03:59 -!- eb3c90 [~kvirc@host81-147-141-244.range81-147.btcentralplus.com] has joined ##hplusroadmap 04:49 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 04:53 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Ping timeout: 240 seconds] 05:47 < kanzure> fisseq gets you things that nanopores can't do, they are unrelated 06:12 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-ohsitbtlqyjuplfk] has joined ##hplusroadmap 06:20 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 06:35 < streety> You get positional information with FISSEQ that you don't get with other approaches but you are still sequencing. You could pool all the data and get a dataset not unlike a nanopore or any other sequencning technology. 06:35 < streety> are there published reports of using FISSEQ for genomic sequencing? Rather than RNA? 06:37 < kanzure> http://gnusha.org/logs/2016-08-19.log 06:37 < kanzure> http://gnusha.org/logs/2016-07-14.log 06:37 < kanzure> http://gnusha.org/logs/2017-01-19.log 06:37 < kanzure> http://biorxiv.org/content/early/2016/05/27/055863 06:37 < kanzure> all i gots in my bookmarks 06:46 < streety> doesn't look like it has been reported then 06:51 < streety> 'The term "nucleic acid" refers to a polymer having multiple nucleotide monomers. A nucleic acid can be single- or double-stranded, and can be DNA (e.g., cDNA or genomic DNA), RNA, or hybrid polymers (e.g., DNA/RNA). ' There is this in paragraph 25 from https://www.google.com/patents/US20160304952 07:25 < kanzure> https://github.com/kanzure/esolid/issues/1 07:51 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 08:00 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 08:23 < chris_99> has anyone seen an idiots guide to creating an AFM, i've seen some very good STM ones 08:27 < kanzure> .title https://www.ncbi.nlm.nih.gov/pubmed/28203479 08:27 < yoleaux> Metformin Impairs Spatial Memory and Visual Acuity in Old Male Mice. - PubMed - NCBI 08:34 < justanotheruser> thoughts on this kit http://www.the-odin.com/diy-bacterial-gene-engineering-crispr-kit/ 08:39 < cluckj> it comes with a sticker, which is cool 08:39 -!- jtimon [~quassel@245.30.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 08:40 < kanzure> justanotheruser: yes a bunch of diybio people have been using that one 08:42 < justanotheruser> I accept appeals to popularity 08:43 < cluckj> but not appeals to cool stickers? :( :( :( 08:43 < justanotheruser> no 08:43 < justanotheruser> just the biohack the planet sticker? 08:43 < cluckj> ya 08:43 < justanotheruser> I'll probably throw that away, sorry 08:43 < cluckj> $150 is probably a good price for all that stuff, considering ordering all of it separately is going to cost you some time 08:48 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 08:52 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Ping timeout: 240 seconds] 09:12 -!- __mz_o_ [~drop_shot@68.232.180.123] has quit [Ping timeout: 252 seconds] 09:27 < kanzure> "Modeling allele-specific gene expression by single-cell RNA sequencing" http://biorxiv.org/content/early/2017/02/17/109629 09:40 < cluckj> https://medium.com/@lu_cyP/diy-science-policy-brussels-etc-58f8d663a916#.qonyd1ksh 09:40 < cluckj> .title 09:40 < yoleaux> DIY science, policy, Brussels etc - Lucy Patterson - Medium 10:07 -!- bsm117532 [~mcelrath@135.84.167.210] has joined ##hplusroadmap 10:17 < cluckj> tl;dr: put money where DIYers are doing work, not into professional science 10:18 < chris_99> did anyone get to the bottom of what that guy was saying about diy bio being hijacked 10:25 < chris_99> Has anyone looked into these kind of builds out of interest http://www.instructables.com/id/DIY-2k2560x1440-Beam-Projector/ if so, why do you need 2 fresnels, or even any? i assume theres a simple reason 10:35 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 10:36 < kanzure> amazing how responsive everyone is to reactionary emails 10:37 < chris_99> heh 10:38 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 260 seconds] 10:44 < cluckj> the spooky email, followed by "look at my video series" is kind of a giveaway :P 10:44 -!- eb3c90 [~kvirc@host81-147-141-244.range81-147.btcentralplus.com] has quit [Ping timeout: 255 seconds] 10:45 < chris_99> oh i must have missed some heh, i'll have another look 10:49 -!- eb3c90 [~kvirc@host81-147-141-244.range81-147.btcentralplus.com] has joined ##hplusroadmap 10:52 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 10:55 < chris_99> Am i right in thinking deliquentme (sp?) built an AFM based on some of the ideas of https://dberard.com/ ? i'm wondering, excluding an AFM tip, the BOM shouldn't be massive, like <$500? 11:02 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 11:20 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 11:21 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Remote host closed the connection] 11:31 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has joined ##hplusroadmap 11:44 < kanzure> .tw https://twitter.com/MikeTaylor/status/832973591847202816 11:44 < yoleaux> Here's the horrifying key table from the paper Siddhartha Roy co-authored on perverse incentives in academia. #AAASmtg https://pbs.twimg.com/media/C49RDmLWEAAA4If.jpg (@MikeTaylor, in reply to tw:832972050197278721) 11:45 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has quit [Ping timeout: 268 seconds] 11:46 < kanzure> too bad nobody has proposed an actual solution, like "braindumps instead of papers" 11:46 < kanzure> (or something) 12:00 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 12:00 < delinquentme> da! 12:00 < delinquentme> chris_99, kanzure 12:01 < chris_99> hey, delinquentme, i was just wondering about your AFMs they are based on that STM design right? if so, is the base cost exc. the tip, fairly cheap 12:01 < delinquentme> i think i spent just over 1000 all in for the materials from zero 12:02 < delinquentme> and yeah the designs were off berards stm 12:02 < delinquentme> both machines STM. 12:02 < chris_99> o wait, you mean they're not AFM? 12:02 < delinquentme> tips can be made cheap enough 12:02 < delinquentme> correct. 12:02 < chris_99> ahh 12:02 < delinquentme> they're STMs 12:02 < delinquentme> ( both machines ) 12:02 < delinquentme> what are you thinking chris_99 ? 12:03 < chris_99> i was curious about making an AFM, but i haven't found as much diy info as STMs, but i guess the sample could be placed on a piezo, cut into 4? 12:04 < chris_99> but i think for AFM you need to apply some kind of frequency to the cantelever if i'm understanding correctly 12:06 < delinquentme> i dont believe so? 12:06 < delinquentme> other than brownian maybe? but that shouldnt be needed? 12:06 < delinquentme> or.. it would already be present. 12:07 < delinquentme> why specifically an AFM? 12:07 < delinquentme> id assume optics are more complex ... laser focus etc. 12:07 < kanzure> chris_99: btw http://diyhpl.us/~bryan/papers2/AFM/ 12:07 < kanzure> http://diyhpl.us/~bryan/papers2/AFM/Print%20your%20atomic%20force%20microscope.pdf 12:08 < kanzure> http://diyhpl.us/~bryan/papers2/AFM/how-to-build-a-plastic-afm/ 12:08 < chris_99> to play with none conductive things delinquentme. Look at the fig on https://en.wikipedia.org/wiki/Atomic-force_microscopy they have a piezo attached to the cantelever 12:08 < chris_99> cheers kanzure 12:08 < chris_99> i'll have a look 12:08 < chris_99> ah with contact mode afm maybe you don't have a piezo 12:08 < chris_99> on the cantelever 12:14 < delinquentme> ohhh right tapping mode 12:18 < chris_99> so i could avoid that then i guess, and just drag it across 12:18 < delinquentme> i like the feedback available from tapping 12:18 < delinquentme> but yeah piezocrystals are fucking amazing 12:18 < chris_99> mmm it seems crazy how they can position stuff to me 12:18 < delinquentme> i had wanted to design a 3 axis stage which was powered by these and giving very precise actuations 12:19 < chris_99> interesting 12:20 < delinquentme> the fall out on that was 1) how to hold it together and 2) what surfaces would be sliding across other surfaces to give minimal friction ( and thus consistency in movement ) 12:20 < delinquentme> piezos also give off some kind of electrical signal when compressed right? 12:20 < chris_99> yes 12:21 < chris_99> theres a project whose name i forget atm 12:21 < chris_99> that weighs things 12:21 < chris_99> based on it 12:21 < delinquentme> yeap sure enough. Piezoelectric effect. 12:22 < delinquentme> so thats cool because if you position opposing crystals you could, perhaps, use the balance of electrical forces between the two 12:22 < chris_99> http://openqcm.com/ 12:22 < chris_99> .title 12:22 < yoleaux> Quartz Crystal Microbalance: the first scientific QCM entirely Open Source 12:22 < chris_99> oh that's a quartz crystal hmm, i thought it was a piezo thing 12:22 < delinquentme> as a method for placing the stage... not just moving it but verifying a given movement 12:23 < chris_99> ohh quartz crystals do use the piezo effect 12:23 < delinquentme> place the stage between each set of piezos and use one for interaction + the other for zeroing 12:23 < delinquentme> yeap! 12:24 < chris_99> i see what you mean wrt the optics, that does complicate stuff 12:25 < delinquentme> " the case is now water tight" 12:25 < delinquentme> ??? 12:25 < delinquentme> with magnets and 3d printed materials 12:26 < chris_99> is that from openQCM? 12:29 < chris_99> hmm dumb question, instead of using optics with afm, could you use a piezo on the cantelever, to measure the peaks and troughs? 12:37 -!- augur [~augur@2601:645:8300:2b03:6ddd:593c:21d5:d7d1] has quit [Remote host closed the connection] 12:48 < delinquentme> chris_99, yeap on the quote. 12:49 < chris_99> aha 12:49 < delinquentme> chris_99, thats possible 12:49 < delinquentme> I mean ... maybe ? 12:49 < delinquentme> given that compression gives feedback... 12:51 < chris_99> mmm 12:51 < chris_99> i wonder how accurate that'd be, as they seem to point the laser near the very end 12:52 < chris_99> oh one thing, have you seen places that sell probes in single quantities? 12:52 < chris_99> they often seem to be in packs of 10 13:00 < delinquentme> the tips are easily enough made :D 13:01 < delinquentme> how would you guys find out who the largest CRO on earth is? 13:01 < kanzure> largest by what dimension... 13:02 < chris_99> CRO? 13:07 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 260 seconds] 13:17 < chris_99> Apparently the principle behind AFM was invented in 1929 interestingly 13:25 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 13:29 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 13:31 < kanzure> chris_99: CROs are the places you send work to 13:31 < kanzure> you give them money and in return they give you magic biotech, like antibodies 13:32 < chris_99> oh heh, as in Contract Research Organization? 13:34 < yashgaroth> largest CRO is Quintiles...oh he's gone 13:36 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 13:49 < chris_99> https://www.nanosurf.com/en/applications thought those images were cool 14:13 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 14:16 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 240 seconds] 14:38 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 15:07 -!- TinKode [~TinKode@unaffiliated/tinkode] has joined ##hplusroadmap 15:15 < nmz787_> .tell chris_99 I'm pretty sure the fresnel is there to collect as much light, then redirect it from spreading outward, to spreading inward (and toward the film/LCD) (condenser lens), then after the inward-rays pass the film/LCD, then are again bent into an outward direction (projector lense) 15:15 < yoleaux> nmz787_: I'll pass your message to chris_99. 15:15 < nmz787_> .tell chris_99 http://www.freesciencefairproject.com/physics/Optical_Instruments/projector_1.jpg from the bottom of http://www.freesciencefairproject.com/physics/Optical_Instruments/index.html 15:15 < yoleaux> nmz787_: I'll pass your message to chris_99. 15:24 < nmz787_> .tell chris_99, specifically in that build, there is a first condenser lens on the LED itself, which seems to indicate the LED spread is very wide (i.e. maybe approaching 180 degrees) so that probably wrangles the beams to 90 degrees in spread or so (ideally just enough to illuminate the first fresnel completely/mostly) 15:24 < yoleaux> nmz787_: What kind of a name is "chris_99,"?! 15:24 < nmz787_> .tell chris_99 specifically in that build, there is a first condenser lens on the LED itself, which seems to indicate the LED spread is very wide (i.e. maybe approaching 180 degrees) so that probably wrangles the beams to 90 degrees in spread or so (ideally just enough to illuminate the first fresnel completely/mostly) 15:24 < yoleaux> nmz787_: I'll pass your message to chris_99. 15:26 < nmz787_> .tell chris_99 then the first fresnel probably takes that ~90 degree beam input and outputs what looks like potentially collimated (parallel) beam, to shoot directly through the LCD, perpendicular to the LCD... the second fresnel then condenses this closer-to-parallel so it will only illuminate the projector lens system, which looks like a stock zoom lens type thing 15:26 < yoleaux> nmz787_: I'll pass your message to chris_99. 15:37 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 15:38 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 15:40 < kanzure> "Prefrontal-hippocampal pathways underlying inhibitory control over memory" https://pdfs.semanticscholar.org/3e7f/006a778c91008f6d8c1c1318dfef37b0da86.pdf 15:47 < kanzure> "Prefrontal markers and cognitive performance are dissociated during progressive dopamine lesion" http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002576 15:47 < kanzure> "... inducing a very slow progressive dopaminergic lesion with the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)." 15:57 * eb3c90 is working on his manifesto 15:57 < kanzure> "Anterior cingulate implant for alcohol dependence: A case report" https://www.ncbi.nlm.nih.gov/pubmed/27077594 15:59 -!- Solgriffin [~Sol@c-69-141-24-242.hsd1.nj.comcast.net] has quit [Ping timeout: 245 seconds] 16:02 < eb3c90> I'd like to be writing code. But sometimes it is good to get stuff down. 16:04 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Read error: No route to host] 16:06 < eb3c90> kanzure: I'm interested in improving incentives for academics. It seems that for science, connecting researcher success somehow with practitoner success is needed. But I'm not sure how. And how to help researchers whose results aren't practical yet is another question. 16:07 < kanzure> "Acetaminophen attenuates error evaluation in cortex" http://www2.psych.ubc.ca/~heine/docs/2016%20Acetaminophen%20ERN.pdf 16:07 < kanzure> "acetaminophen reduces the magnitude of reactivity to social rejection, frustration, dissonance" 16:09 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 16:11 -!- delinquentme [~delinquen@2602:306:ceb7:990:5de:4bde:1643:65ce] has joined ##hplusroadmap 16:15 < kanzure> .wik rhodiola rosea 16:15 < yoleaux> "Rhodiola rosea (commonly golden root, rose root, roseroot,:138 western roseroot, Aaron's rod, Arctic root, king's crown, lignum rhodium, orpin rose) is a perennial flowering plant in the family Crassulaceae. It grows in cold regions of the world, including much of the Arctic, the mountains of Central Asia, scattered in eastern North ..." -- https://en.wikipedia.org/wiki/Rhodiola_rosea 16:15 < kanzure> reportedly effective against mental fatigue 16:16 < chris_99> delinquentme, http://www.electronics-eetimes.com/news/atomic-force-microscope-chip that seems to use the piezo effect for detection of the cantilever movement 16:16 < yoleaux> 18 Feb 2017 23:15Z chris_99: I'm pretty sure the fresnel is there to collect as much light, then redirect it from spreading outward, to spreading inward (and toward the film/LCD) (condenser lens), then after the inward-rays pass the film/LCD, then are again bent into an outward direction (projector lense) 16:16 < yoleaux> 18 Feb 2017 23:15Z chris_99: http://www.freesciencefairproject.com/physics/Optical_Instruments/projector_1.jpg from the bottom of http://www.freesciencefairproject.com/physics/Optical_Instruments/index.html 16:16 < yoleaux> 18 Feb 2017 23:24Z chris_99: specifically in that build, there is a first condenser lens on the LED itself, which seems to indicate the LED spread is very wide (i.e. maybe approaching 180 degrees) so that probably wrangles the beams to 90 degrees in spread or so (ideally just enough to illuminate the first fresnel completely/mostly) 16:16 < yoleaux> 18 Feb 2017 23:26Z chris_99: then the first fresnel probably takes that ~90 degree beam input and outputs what looks like potentially collimated (parallel) beam, to shoot directly through the LCD, perpendicular to the LCD... the second fresnel then condenses this closer-to-parallel so it will only illuminate the projector lens system, which looks like a stock zoom lens type thing 16:16 < chris_99> nmz787_, oh interesting! 16:18 < delinquentme> chris_99, "contract research org" and kanzure by headcount or net revenue 16:18 < delinquentme> chris_99, thats fucking SEXY 16:19 < chris_99> mmm heh 16:20 < kanzure> delinquentme: quintiles 16:20 -!- TinKode [~TinKode@unaffiliated/tinkode] has quit [Quit: Practicing escapism.] 16:26 < chris_99> delinquentme, with STM you get a current i think right from the tip?, but apparently with AFM, you can use a quadrant photodetector, so you can get an angle too along with intensity, so does that possibly mean theres kind of more information obtainable, from the sample you're scanning with AFM 16:39 -!- eb3c90 [~kvirc@host81-147-141-244.range81-147.btcentralplus.com] has quit [Ping timeout: 255 seconds] 16:44 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 16:48 < chris_99> i guess i'm wrong as reading some stuff saying stm seems to have a higher resolution than afm 16:58 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 17:29 -!- Gurkenglas [~Gurkengla@dslb-178-005-218-116.178.005.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 17:56 < nmz787_> kanzure: I feel like I took that rhodiola rosea years ago... I wonder if I still have some somewhere... 18:10 < nmz787_> well, looks like I can just buy this $10 luminescent plasmid that the-odin sells, comes packaged in E.coli... so I will have to purify the plasmid to test the experimental electroporator. I might have a sample plasmid prep kit, or I guess I have to buy some extra reagents to make some boiling lysis buffer (though I wonder if I'd get but usable efficiency with crude lysate) 18:11 < nmz787_> and I also will probably just get a plasmid free strain too, rather than trying to cure the plasmid-containing strain before re-transformation 18:11 < nmz787_> yashgaroth: ^ ? 18:11 < nmz787_> yashgaroth: re crude lysate transformation 18:12 < nmz787_> I read the LPS can prevent downstream restriction endonucleases... and to be sure to clean it all up, but since I don't want to tweak the plasmid, I wonder if this would substitute for EDTA in a sense 18:13 < nmz787_> I guess I can always just try a water-rinse to swell, then hit them with dish detergent, and finally just precip with alcohol and rinse that a few times 18:37 < yashgaroth> I guess you can use crude lysis, efficiency will be super low but commercial cells are about 1000x more efficient than they need to be if you just need one transformant 18:37 < yashgaroth> what restriction enzymes are you talking about, BL21 won't have any endogenous ones if you're trying to keep the plasmid stable 18:38 < yashgaroth> I don't think regular alkaline lysis reagents are super difficult to acquire 18:41 < yashgaroth> BL21s will have endonuclease I if that's what you mean 18:51 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 18:54 < yashgaroth> nmz787_: you can't just ask josiah nicely for the plasmid? he might even put it in DH5a cells; BL21s are a pain for getting good plasmid from 18:55 -!- c0rw1n [~c0rw1n@91.181.4.198] has quit [Remote host closed the connection] 19:03 < nmz787_> yashgaroth: the LPS/endonuclease mention is from Sambrook's protocol for boiling lysis, I assume they meant for downstream in-vitro reactions 19:04 < nmz787_> yashgaroth: $10 is not too expensive, I don't need any nickel and dime donations at this point 19:05 < yashgaroth> you will after banging your head against a desk because your prep from BL21s will be garbage without a column cleanup 19:07 < nmz787_> how so? I mean, junk is just clutter, right? unless the DNA is chewed up by nuclease as you mentioned... but I guess I thought the Sambrook cell-wall mention would save me from that 19:07 < nmz787_> or throw some EDTA in solutin 19:07 < nmz787_> honestly I could get away with simply transforming antibiotic resistance in 19:07 < nmz787_> I just want to test this electroporator 19:08 < nmz787_> he also has DH5a for sale 19:08 < nmz787_> which seems good for fidelity, but slower to grow I think 19:08 < nmz787_> been reading phenotype stuff on the genotype 19:08 < nmz787_> trying to compare 19:09 < yashgaroth> DH5a is infinitely better for plasmid preps, lacking enda1 and reca 19:09 < yashgaroth> it's not that much slower than BL21, you'll have plenty after an overnight 19:10 < nmz787_> seems like BL21 is preferred for protein expression because of knocked out protease? 19:10 < yashgaroth> yeah, but it has enda1/reca which help it grow better, but plasmids will be multimerized by reca and chewed up by enda1 19:11 < yashgaroth> which plasmid is it, pVIB? 19:11 < nmz787_> yea 19:11 < nmz787_> aka pJE202 19:11 < nmz787_> autoinducer 19:11 < nmz787_> based on some concentration dependent constitutive protein that is expressed 19:13 < nmz787_> the multimerization would happen in-vivo, right? but enda1 chewing only afer lysis? 19:14 < yashgaroth> yes, but if you get a transformant with a multimer plasmid...I guess it might still work; enda1 will chew after lysis and all the way through your purification, idk if it requires magnesium but I assume so 19:15 < kanzure> nmz787_: let me know if you want to buy some stuff 19:16 < yashgaroth> you could try transforming with a crude lysate and see if it works, then move on to more advanced purifications...still, I'd recommend doing the electroporation immediately afterward just in case your plasmid gets fucked 19:17 < nmz787_> yashgaroth: I did email the-odin directly... didn't use Josiah's direct email, though I could shoot him something quick now that I've refreshed my knowledge a bit 19:17 < nmz787_> yashgaroth: yeah, I would cram all the lab work together anyway 19:18 < yashgaroth> I'm sure he would be amenable, you being a regular poster on the mailing list and this being a test of DIYbio equipment etc 19:19 < nmz787_> yashgaroth: any idea if 5 year old, was already open back then, LB broth powder would still be good? 19:19 < yashgaroth> probably fine, but it's always cheap on ebay if not 19:20 < nmz787_> Josiah sells like 20L worth for $12 19:21 < yashgaroth> I don't like his face, but his LB is fine I'm sure 19:22 < kanzure> yes you should mention it's a test of open-electroporator hardware, give a link to the github repo etc 19:23 < kanzure> .wik receptor assay 19:23 < yoleaux> "Ligand binding assays (LBA) is an assay, or an analytic procedure, whose procedure or method relies on the binding of ligand molecules to receptors, antibodies or other macromolecules." -- https://en.wikipedia.org/wiki/Ligand_binding_assay 19:24 < kanzure> there should be a two-step chemistry system for targeting receptors only when other receptors are nearby, as a way of chemically specifying the location of some drug's action 19:24 < yashgaroth> plenty of off-brand plasmid cleanup kits on ebay as well, much more reproducible if you want to make a stock 19:24 < nmz787_> hmm, I think this was for sale last summer for same OBO https://portland.craigslist.org/wsc/hvo/6003471094.html 19:24 < nmz787_> I have a trailer... but idk if I'd use it enough to justify all the sweat and effort 19:25 < nmz787_> also, new filter(s) would have to be found likel 19:25 < nmz787_> likely 19:25 < nmz787_> yashgaroth: I feel like I have some 5-6 year old miniprep sample kits from mobio 19:26 < nmz787_> I'd guess the silica should be fine, and if any chems are sealed, I'd guess still fine too 19:27 < yashgaroth> yeah, one prep will get you enough plasmid for a thousand transformations 19:27 < nmz787_> kanzure: thanks, I will let you know 19:29 < kanzure> cc me on your josiah zayner emails yo 19:29 < nmz787_> I think the only equipment I might need would be some sterile microtubes and sterile petris, and maybe a 1-10 or 2-20uL micropipette... I have one or two but I need to pull them out and check 19:29 < nmz787_> k 19:30 < nmz787_> bbl 19:31 < kanzure> rhodiola rosea adaptogen stuff https://www.researchgate.net/profile/Laura_Mattioli/publication/235983909_Adaptogenic_and_Central_Nervous_System_Effects_of_Single_Doses_of_3_Rosavin_and_1_Salidroside_Rhodiola_rosea_L_Extract_in_Mice/links/00b49515307afc39c9000000.pdf 19:33 < kanzure> .wik salidroside 19:33 < yoleaux> "Salidroside (Rhodioloside) is a glucoside of tyrosol found in the plant Rhodiola rosea. It is thought to be one of the compounds responsible for the antidepressant and anxiolytic actions of this plant, along with rosavin." -- https://en.wikipedia.org/wiki/Salidroside 19:33 < kanzure> hm nevermind. 19:53 < kanzure> "Development of a short sleeper phenotype after third ventriculostomy in a patient with ependymal cysts" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899325/ 19:55 < kanzure> ".. Postoperative imaging revealed decreased pressure around the anterior third ventricle." 20:12 -!- drewbot [~cinch@ec2-54-146-160-224.compute-1.amazonaws.com] has quit [Remote host closed the connection] 20:12 -!- drewbot [~cinch@ec2-54-224-194-170.compute-1.amazonaws.com] has joined ##hplusroadmap 20:13 < kanzure> possible mutation caus of chronic fatigue syndrome, http://www.karger.com/Article/Abstract/326692 20:19 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 20:20 -!- c0rw1n [~c0rw1n@91.181.4.198] has joined ##hplusroadmap 20:31 < kanzure> "Is mental effort exertion contagious?" https://lirias.kuleuven.be/bitstream/123456789/504749/1/MS+Is+effort+exertion+contagious+-+Revision2.pdf 20:36 < kanzure> "Enhanced recognition memory following vagus nerve stimulation in human subjects" http://www.nature.com/neuro/journal/v2/n1/full/nn0199_94.html 20:39 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has joined ##hplusroadmap 20:43 -!- IRCFrEAK [~gk.1wm.su@2a03:4a80:2:2d3:2d3:9c14:a427:77be] has joined ##hplusroadmap 20:43 -!- IRCFrEAK [~gk.1wm.su@2a03:4a80:2:2d3:2d3:9c14:a427:77be] has left ##hplusroadmap [] 22:53 -!- jtimon [~quassel@245.30.134.37.dynamic.jazztel.es] has quit [Ping timeout: 268 seconds] 22:53 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:46 -!- eb3c90 [~kvirc@host81-147-141-244.range81-147.btcentralplus.com] has joined ##hplusroadmap --- Log closed Sun Feb 19 00:00:37 2017