--- Log opened Sun Mar 26 00:00:08 2017 01:16 -!- Alpha703 [~Alpha703@2602:306:3021:6a40:7c20:3e5f:faa:f3e5] has quit [Ping timeout: 240 seconds] 01:16 -!- Alpha703 [~Alpha703@99-2-22-164.lightspeed.snantx.sbcglobal.net] has joined ##hplusroadmap 01:27 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 01:38 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:d042:e9ec:a978:ccc0] has quit [Quit: Leaving] 02:08 < archels> .title https://techxplore.com/news/2017-03-filters-tetrachromatic-vision-humans.html 02:08 < yoleaux> archels: Sorry, that doesn't appear to be an HTML page. 02:17 < darsie> looks like HTML to me. 02:17 < darsie> not sure about 02:18 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has quit [Read error: Connection reset by peer] 02:58 -!- drewbot [~cinch@ec2-54-196-97-224.compute-1.amazonaws.com] has quit [Remote host closed the connection] 02:59 -!- drewbot [~cinch@ec2-54-211-243-20.compute-1.amazonaws.com] has joined ##hplusroadmap 03:50 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has joined ##hplusroadmap 04:09 < archels> .tr :fr :en Je crois aussi que le corps naturel sera toujours plus performant qu'un corps robotis?. 04:09 < yoleaux> archels: Sorry, that command (.tr) crashed. 04:09 < archels> sigh 04:09 < archels> (St?phan Beauregard) 04:14 -!- Gurkenglas_ [~Gurkengla@dslb-188-103-066-228.188.103.pools.vodafone-ip.de] has joined ##hplusroadmap 04:18 < archels> further down he states that if cryo procedures are imperfect and we lose some memory fidelity (akin to Alzheimer's), we can fix that by somehow "downloading" digital memories into our brains 04:19 < archels> no further explanation offered. think he goes a little off-track there 04:20 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has quit [Ping timeout: 258 seconds] 04:32 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 04:38 < kanzure> even with 100% memory loss, it's still worth pursuing 05:52 -!- c0rw1n [~c0rw1n@18.153-201-80.adsl-dyn.isp.belgacom.be] has quit [Quit: Leaving] 05:54 -!- c0rw1n [~c0rw1n@18.153-201-80.adsl-dyn.isp.belgacom.be] has joined ##hplusroadmap 06:32 < archels> well, yes, for a slew of reasons, but still I think that for many who are interested in cryopreservation/uploading that would be a little beside the point 06:59 -!- urchin__ [~urchin@dsl-89-17-19-6.dsl.h-1.hr] has joined ##hplusroadmap 07:02 -!- urchin_ [~urchin@dsl-89-17-5-73.dsl.h-1.hr] has quit [Ping timeout: 240 seconds] 07:20 -!- Gurkenglas_ [~Gurkengla@dslb-188-103-066-228.188.103.pools.vodafone-ip.de] has quit [Ping timeout: 258 seconds] 07:31 -!- augur [~augur@84.207.252.45] has joined ##hplusroadmap 07:32 -!- augur [~augur@84.207.252.45] has quit [Read error: Connection reset by peer] 07:36 -!- augur [~augur@84.207.252.45] has joined ##hplusroadmap 07:36 -!- augur [~augur@84.207.252.45] has quit [Read error: Connection reset by peer] 07:44 -!- JayDugger [~jwdugger@47.185.237.246] has joined ##hplusroadmap 07:46 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has quit [Ping timeout: 268 seconds] 08:01 -!- augur [~augur@94.117.22.230] has joined ##hplusroadmap 09:00 -!- aedla [~quassel@c21-76.uvn.zone.eu] has quit [Quit: ["hip","hip"] array!] 09:07 < kanzure> bloop 09:19 < JayDugger> splat 09:20 -!- augur [~augur@94.117.22.230] has quit [Remote host closed the connection] 09:27 -!- sachy [~sachy@nat.brmlab.cz] has quit [Quit: Leaving.] 09:47 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 09:47 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 246 seconds] 10:15 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 10:16 -!- TC [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 10:17 -!- TC is now known as Guest35260 10:20 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 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[~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 12:27 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 264 seconds] 12:31 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:bc34:2d81:9442:409a] has joined ##hplusroadmap 12:54 -!- augur [~augur@94.118.203.235] has joined ##hplusroadmap 12:59 -!- augur [~augur@94.118.203.235] has quit [Ping timeout: 240 seconds] 13:08 -!- m4l3z [~m4l3z@2a01cb040226f20030d16c1d6e6ef030.ipv6.abo.wanadoo.fr] has joined ##hplusroadmap 13:14 -!- m4l3z [~m4l3z@2a01cb040226f20030d16c1d6e6ef030.ipv6.abo.wanadoo.fr] has quit [Quit: Leaving] 13:20 < nmz787_> sup yashgaroth 13:20 < yashgaroth> yo 13:20 < nmz787_> just added EtOH and RNase to the plasmid prep kit 13:22 < yashgaroth> coo' 13:22 < nmz787_> was thinking I would make up some TAE for storage solution 13:22 < nmz787_> but I guess it includes elution buffer 13:22 < nmz787_> I have been hand-swirling my liquid cultures 13:23 < nmz787_> since the shaker I bought is /just/ a shaker... kinda forgot I needed it to be warm when I grabbed it from a e-junk store 13:24 < yashgaroth> should be okay at room temp, they'll just take longer to grow 13:24 < nmz787_> for electroporation recovery I was thinking of using a 15mL tube for the 1.4 or whatever mL of transformant solution, and maybe a small buzzer motor if I can find 13:25 < nmz787_> throw an old android phone under it, on vibe mode somehow 13:25 < nmz787_> heh 13:25 < nmz787_> yashgaroth: do you think shaking or heat is more important in general? 13:26 < nmz787_> yashgaroth: do you think I need to liquid subculture the un-transformed cells before electroporating, or will I do OK with just a agar colony scraping? 13:27 < yashgaroth> shaking; solid cultures are also an option, I like spreading them all over a plate and growing that overnight, you get a lot of biomass 13:27 < yashgaroth> just pick a single colony first, then dilute into some PBS and dump that onto a plate 13:27 < nmz787_> i always used ~6 hour shaking culture for my competent cell prep 13:28 < nmz787_> well I have overnight agar culture that is fresh 13:28 < yashgaroth> they're happier on solid media tbh, it just doesn't scale too well so most people use liquid 13:28 < nmz787_> i was thinking of trying to scrape some, resuspend in water, pellet, resuspend in water, add DNA, electroporate, add LB, shake/buzz incubate, then plate on LB agar+amp 13:29 < nmz787_> oh, if they're happier then I think I can just get away with scraping the plate 13:29 < nmz787_> how much sq mm of goo should I target? 13:29 < nmz787_> (for transforming with DNA) 13:29 < yashgaroth> you can plate immediately with ampicillin right? you don't need to pre-culture like with kanamycin since it's not -cidal, just -static 13:29 < nmz787_> (I have liquid GFP and agar from yesterday, too... for plasmid prep) 13:29 < nmz787_> hmm 13:30 < nmz787_> I thought it might be cause electroporation makes holes, so best to give them no drugs at first 13:30 < nmz787_> all electroporation guides say recover with plain/excellent media first for 30-60 mins 13:30 < nmz787_> I think Sambrook recommends SOC broth 13:31 < yashgaroth> ah the electroporation itself might be a shock yeah, no pun intended 13:31 < nmz787_> but I've got better-than-CaCl results with just LB 13:31 < yashgaroth> put a little magnesium in if you have it, but yeah unless you need maximum efficiency LB is fine 13:32 < nmz787_> so how much plate goo to start with? 13:32 < nmz787_> normally I'd use 1mL culture 13:32 < nmz787_> liquid 13:32 < nmz787_> then pellet 13:32 < yashgaroth> I wouldn't worry too much about shaking them in the media for that hour, just invert the tube every 15 minutes or w/e 13:32 < nmz787_> ok 13:32 < nmz787_> I guess I will need to pellet 1mL of GFP for plasmid prep 13:32 < nmz787_> so I can just try to match the pellet size with goo 13:33 < yashgaroth> was just typing that out, but yeah go from that and eyeball it 13:33 < nmz787_> ok, well that pretty much means I can go do all this pretty much now, instead of needing to wait 6 hours for liquid to come up 13:33 < yashgaroth> indeed, good luck 13:34 -!- augur [~augur@94.117.150.228] has joined ##hplusroadmap 13:34 < nmz787_> hmm, I was actually planning to debug the electroporation scheme a bit more over that 6 hours 13:34 < nmz787_> I guess I'll just do it now 13:34 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 13:35 < nmz787_> how many uL of liquid culture for a not-too-wet agar lawn? 13:37 < yashgaroth> you got glass beads? if yes, 100uL should be ok, if not then maybe 250uL and tilt the plate around; do a quick flip and it shouldn't drip too much 13:38 < yashgaroth> I'd still leave it facing up for like an hour beforehand just to make sure they have a chance to stick 13:38 -!- augur [~augur@94.117.150.228] has quit [Ping timeout: 240 seconds] 13:39 < nmz787_> hmm, no, I never used beads either, I always used a wire triangle thing 13:40 < nmz787_> which I don't know if I have now, or if I do, where it is 13:40 < nmz787_> got some plastic innoc loops, that I could probably make due with somehow 13:40 < nmz787_> was thinking of maybe using a coathanger that I torch with a propane torch to get any plastic off, etc 13:41 < nmz787_> make my own spreader 13:41 < nmz787_> was thinking copper electric AC wire could work, but copper might rub off and toxify 13:41 < cluckj> glass stirring rod? we used to heat them up and bend them 13:43 < cluckj> even clear plastic rods you could heat and bend? 13:44 < yashgaroth> yeah I'd avoid copper, if you've got a paperclip that'd work 13:45 -!- wrldpcmbl [sid145438@gateway/web/irccloud.com/x-zfxnubxwhqqyrnsz] has quit [Ping timeout: 252 seconds] 13:45 -!- wrldpcmbl [sid145438@gateway/web/irccloud.com/x-zlqrduuidwooiozc] has joined ##hplusroadmap 13:46 < nmz787_> hmm, I don't think I've got any glass stirrers 13:46 < nmz787_> maybe some old burets 13:47 < nmz787_> I can probably scrounge up a paperclip... then again, I don't really need a good spread other than for quantification 13:47 < cluckj> that might be more difficult 13:47 < cluckj> lol, I bet you could bend the end of the inoculation rod to make it a spreader :) 13:47 < nmz787_> oh, hmm, I do have a steel/metal innoc loop with handle 13:48 < nmz787_> like a camping spoon/fork or spork/knife 13:48 < cluckj> I meant the plastic ones you bought 13:48 < nmz787_> oh 13:53 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 14:20 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 15:11 -!- Gurkenglas_ [~Gurkengla@dslb-188-103-066-228.188.103.pools.vodafone-ip.de] has joined ##hplusroadmap 15:11 -!- augur [~augur@94.117.117.69] has joined ##hplusroadmap 15:16 -!- augur [~augur@94.117.117.69] has quit [Ping timeout: 258 seconds] 15:39 -!- augur [~augur@94.117.207.204] has joined ##hplusroadmap 15:44 -!- augur [~augur@94.117.207.204] has quit [Ping timeout: 260 seconds] 15:47 < yashgaroth> apparently I am confirmed to present at GP-write 15:53 < kanzure> congrats! 15:53 < kanzure> let's blow this shit up 15:57 < yashgaroth> hell yee 15:57 < yashgaroth> also they posted the agenda, which is how I found out 15:58 < kanzure> haha 15:58 < kanzure> link? 15:58 < yashgaroth> http://engineeringbiologycenter.org/2017-agenda/ 15:58 < yashgaroth> idk who wrote the titles since "to Extend Genetic Gene Sequence" is garbage, but whatever 16:01 < kanzure> weird, your talk looks the most relevant to me 16:01 < kanzure> you're the only one speaking about actual synthesis and assembly technology? wtf? 16:01 < yashgaroth> ikr 16:01 < kanzure> ah, day two 16:01 < kanzure> Duhee Bang, Yonsei University | DNA Synthesis Technologies (10 minutes) 16:01 < kanzure> J William Efcavitch | Molecular Assemblies (10 minutes) (Confirmed) 16:02 < kanzure> Emily Leproust | Twist Bioscience (10 minutes) 16:02 < kanzure> and then some "foundries" 16:04 < yashgaroth> why do they have a moderator 16:04 -!- augur [~augur@94.117.207.204] has joined ##hplusroadmap 16:06 < kanzure> it's someone responsible for the set of presentations, and/or they put all the people on the stage at the end to talk together 16:08 < kanzure> in this agenda my guess would be, they are just a person-wrangler 16:08 < kanzure> and timelimit keeper 16:08 < cluckj> ^ 16:08 < yashgaroth> ah. well there's only seven "pilot projects" including mine, and two of those are ethics bullshit, so that's...good? 16:09 -!- augur [~augur@94.117.207.204] has quit [Ping timeout: 256 seconds] 16:09 < kanzure> ranger things have happened https://www.youtube.com/watch?v=hx6aRVL8wfc 16:09 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has joined ##hplusroadmap 16:11 < kanzure> yashgaroth: 10 minutes isn't much... maybe stuff everything into the slides and hope people look later. 16:12 < yashgaroth> I'm just hoping everyone's familiar enough with how shitty pamidite synthesis is, that I can just note it real quick...still gonna be tight though 16:15 < kanzure> hmm "2-3 minute "elevator pitch" speaking opportunities for scientists to present new ideas for GP-write pilot projects selected from Abstracts submitted prior to the meeting" 16:15 < kanzure> perfect time to propose my human-pig hybrids 16:18 < kanzure> "Dana Carroll, The University of Utah | Protein Based Target Recognition Systems (Tyr/Ser SSRs, Meganucleases, SFNs, TALENs) (10 minutes)" 16:18 < kanzure> which ones are the meganucleases? 16:20 < yashgaroth> dunno really, there's all kinds of arbitrary classifications 16:24 -!- augur [~augur@94.117.207.204] has joined ##hplusroadmap 16:27 < kanzure> lemme know if you need assistance on slides 16:28 -!- augur [~augur@94.117.207.204] has quit [Ping timeout: 240 seconds] 16:31 < yashgaroth> probably will, it's been a long time since I've had to make anything remotely presentable in powerpoint 16:36 < kanzure> mannn why aren't there talks planned like "where's our $1 genomes?" grr 17:38 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Remote host closed the connection] 17:38 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 17:43 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 240 seconds] 17:55 -!- jtimon [~quassel@70.30.134.37.dynamic.jazztel.es] has quit [Ping timeout: 256 seconds] 18:14 -!- SolGriffin [~Sol@c-69-141-24-242.hsd1.nj.comcast.net] has joined ##hplusroadmap 18:17 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:f8bf:3ea3:9d7d:5ce7] has joined ##hplusroadmap 18:20 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 18:39 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 260 seconds] 18:48 -!- JayDugger1 [~jwdugger@47.185.237.246] has joined ##hplusroadmap 18:50 -!- JayDugger [~jwdugger@47.185.237.246] has quit [Ping timeout: 260 seconds] 18:54 < kanzure> "An immortalized adult human erythroid line facilitates sustainable and scalable generation of functional red cells" http://www.nature.com/articles/ncomms14750 18:59 < superkuh> Wow. That one sounds like it could be clinically useful soon and on a massive scale. 20:03 < kanzure> .tw https://twitter.com/hackaday/status/846007839189585921 20:03 < yoleaux> 3D Printed Rick is not impressed with the @MidwestRRfest https://pbs.twimg.com/media/C71Iu_dXwAAkapE.jpg (@hackaday) 20:06 < kanzure> http://cen.acs.org/articles/95/i13/Biosensors-enable-imaging-localized-cell.html https://twitter.com/LightUpScience/status/845616633875976193 20:06 < kanzure> "SOFI (stochastic optical fluctuation imaging)" 20:07 < kanzure> "Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution" http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4221.html 20:08 < kanzure> "FLINC (fluorescent fluctuation increase by contact)" 20:08 < kanzure> "... FRET (fluorescence resonance energy transfer) and BiFC (bimolecular fluorescence complementation) have mechanisms reminiscent of FLINC. But FRET is not easily compatible with superresolution imaging, and BiFC is a one-time, irreversible fluorescence-generation process that can't track dynamic bioactivity" 20:09 < kanzure> "Zhang and coworkers discovered serendipitously that a fluorescent protein, Dronpa, significantly increases the rate of fluorescence fluctuations of another protein, TagRFP-T, when the two are in close proximity. The team created biosensors in which these proteins are placed at either end of a peptide sequence that an enzyme or signaling molecule can recognize and modify. Normally, the biosens... 20:09 < kanzure> ...ors have extended conformations in which the two proteins remain far apart. But when an enzyme modifies the peptide sequence--for example, by phosphorylation--the biosensor changes to a compact shape. This brings the proteins into close proximity and turns on a FLINC signal that can be imaged. Zhang and coworkers used the biosensors with SOFI to visualize kinase activity in cell microdomains... 20:09 < kanzure> ... at superresolution." 20:10 -!- sbodin [~sbodin@91.226.141.245] has joined ##hplusroadmap 20:12 < kanzure> why is everyone using fluorescence instead of xray 20:30 -!- sbodin [~sbodin@91.226.141.245] has quit [Ping timeout: 264 seconds] 20:37 -!- midnightmagic [~midnightm@unaffiliated/midnightmagic] has quit [Ping timeout: 264 seconds] 20:55 < kanzure> .tw https://twitter.com/mcnees/status/845720570067140608 20:55 < yoleaux> It's my duty to occasionally remind u that John Berkey's painting "The Mechanical Planet" was George Lucas's inspiration for the Death Star. https://pbs.twimg.com/media/C7yaDNGW4AEQmhP.jpg (@mcnees, in reply to tw:845719428859867136) 20:55 < kanzure> .tw https://twitter.com/mcnees/status/845719428859867136 20:55 < yoleaux> Cleaning out the ol' downloads folder. Enjoy this John Berkey painting of a spaceship. https://pbs.twimg.com/media/C7yZU_JWkAE6o8n.jpg (@mcnees) 21:01 < kanzure> "Canonical Wnt signaling ameliorates aging of intestinal stem cells" http://www.cell.com/cell-reports/fulltext/S2211-1247(17)30254-1 https://twitter.com/CellReports/status/845757209074110466 21:01 < kanzure> "... reactivating canonical Wnt signaling enhances the function of both murine and human ISCs and, thus, ameliorates aging-associated phenotypes of ISCs in an organoid assay. Our data demonstrate a role for impaired Wnt signaling in physiological aging of ISCs and further identify potential therapeutic avenues to improve ISC regenerative potential upon aging." 21:01 -!- midnightmagic [~midnightm@unaffiliated/midnightmagic] has joined ##hplusroadmap 21:05 < kanzure> "Decoding directional genetic dependencies through orthogonal CRISPR/Cas screens" http://biorxiv.org/content/early/2017/03/25/120170 21:05 < kanzure> in which they do combinatorial screening using crispr-cas9 knockouts 21:08 < kanzure> more art things http://johnberkey.com/gallery/space/ 21:34 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Quit: Leaving.] 21:37 -!- augur [~augur@94.116.67.42] has joined ##hplusroadmap 22:17 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:bc34:2d81:9442:409a] has quit [Quit: Leaving] 22:34 -!- augur [~augur@94.116.67.42] has quit [Remote host closed the connection] --- Log closed Mon Mar 27 00:00:09 2017