--- Log opened Sun Dec 18 00:00:41 2016
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05:11 < kanzure> hrmph
05:47 < JayDugger> Pfui. Problem solved.
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06:43 < kanzure> magnetosome-based protein purification method http://2016.igem.org/Team:NEFU_China/Description
06:43 < kanzure> " Our team developed a novel protein purification approach that eliminates most weaknesses of other techniques. Our method is based on the highly specific recognition and covalent conjugation between Spytag (a peptide with 13 amino acids) and Spycatcher (a peptide with 116 amino acids). We also take the advantage of a magnetic bacterium AMB-1 that can produce magnet particles, also called Magn...
06:43 < kanzure> ...etosome, covered by a bilayer phospholipid membrane, in which Mms13 protein is anchored. We generate Spycatcher-Mms13 and express this fusion protein in AMB-1 bacteria to make Spycatcher linked to the Magnetosome. A protein of interest with a Spytag at its N- or C-terminus is expressed in E. coli and present in bacterial lysate. The Spycatcher-Mms13-linked Magnetosome can specifically and cova...
06:44 < kanzure> ...lently conjugate to the Spytag-tagged protein in the bacterial lysate and they can be simply co-purified by a magnet. Due to covalent linkage, stringent washing can be used to achieve high purity of the recombinant protein that is subsequently released by cleavage of a designated protease."
07:06 < kanzure> someone complains about formalin fixation of brain tissue https://www.reddit.com/r/Futurology/comments/5iqp84/the_human_brain_may_retain_latent_capacities_to/dbb0qy7/?context=3
07:09 < kanzure> hm this person seems useful https://www.reddit.com/user/4-fluoro-whatever
07:09 < kanzure> research chemical sourcing https://www.reddit.com/r/RCSources/
07:10 < kanzure> https://www.reddit.com/r/researchchemicals/
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08:29 < kanzure> directed evolution for improved sound sensing CHO cells http://2016.igem.org/Team:SUSTech_Shenzhen/Description
08:42 <@fenn> what did
08:42 <@fenn> what did "CHO" mean in the context of industrial algae production?
08:43 <@fenn> oh nevermind i re-read it
08:43 <@fenn> (chinese hamster ovary)
08:44 < cluckj> biotech is wild
08:44 < cluckj> using ovaries for industrial algae
08:45 <@fenn> using algae instead of ovaries
08:46 <@fenn> i see "algae biofuel production" and immediately stop thinking very hard
08:49 < cluckj> hah
08:49 <@fenn> i like how searching for "4-fluoro-whatever" returns something like a wildcard search
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09:01 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=b04cb3de Bryan Bishop: some igem 2016 projects >> http://diyhpl.us/diyhpluswiki/dna/projects/
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09:02 < kanzure> https://github.com/kanzure/diyhpluswiki/commit/b04cb3ded9b3ca6b5929363c9058c39e8bbabaf5
09:02 <@fenn> how long did it take to review those?
09:03 < kanzure> takes me maybe 1-2 minutes per page, depending on how terrible the page is
09:03 < kanzure> also i'm a highly distractable person, so most of my time is spent looking up awesome rap songs instead
09:03 < kanzure> (brb)
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09:05 <@fenn> "biodegradable chitosan nanoparticles to deliver glutathione reductase (GSR) and 25-hydroxylase (CH25H) to counteract the accumulation of crystallin proteins in the lens (cataracts)"
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09:06 <@fenn> sounds more pleasant than having 'em scooped out
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09:10 <@fenn> i'm surprised at the large number of entries from chinese universities
09:11 <@fenn> "two-phase bioreactor where cells only begin producing protein once signalling says they have reached a certain concentration level"
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09:48 < kanzure> well there's a lot of chinese universities
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11:11 < chris_99> Just wondering would a laser cutter generally be able to take 3D model format, to do both etching and cutting?
11:12 <@fenn> no
11:12 <@fenn> you usually do that with multiple dxf files for each power level
11:12 <@fenn> or coreldraw or whatever people use
11:13 < chris_99> ah hmm didn't realise that
11:13 <@fenn> there are laser cutters that can etch in 3D but it's pretty rare
11:13 <@fenn> also it looks like crap
11:14 < chris_99> gotcha, would there be tools to convert a 3D file to multiple ones like you mention
11:15 < kanzure> slicers
11:18 < chris_99> ah cheers
11:18 <@fenn> if you want to raster scan in x and y while varying Z you probably want a CAM program like for machining
11:19 <@fenn> a slicer will give you a series of contours that you could then stack to get a 3d shape
11:19 <@fenn> but honestly that's a dumb way to build things
11:20 <@fenn> it wastes a lot of sheet material and isn't very strong and looks bad
11:20 < chris_99> https://anfractuosity.com/files/lightguide.png is my very simple model, essentially i just need etching for the numbers, and cutting for the outside
11:20 <@fenn> yeah that's totally doable and standard laser cutter territory
11:21 <@fenn> might i suggest not using a serif font :P
11:21 < chris_99> oh yeah heh
11:21 < chris_99> i just picked the first font i found
11:22 < kanzure> fenn: here is an example of one that is taking me a few seconds to figure out .... http://2016.igem.org/Team:SZU-China
11:23 < kanzure> although they are non-rude for at least trying to explain what they are doing in the opening text
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11:48 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=d5cf2685 Bryan Bishop: igem 2016 china projects >> http://diyhpl.us/diyhpluswiki/dna/projects/
12:00 <@fenn> "hydrogen production in green algae Chlamydomonas reinhardtii switched on and off by blue-light induced microRNA"
12:00 <@fenn> i doubt i could have summarized that in under 2 minutes
12:01 < nmz787> kanzure: epiphany-V market competitiveness re: design and fab-prep: http://www.eetimes.com/document.asp?piddl_msgpage=2&doc_id=1330568&page_number=1
12:02 < nmz787> "One upside of the approach is "putting in support for a new instruction can be a day's work followed by one day of implementation," he said."
12:04 < nmz787> oh, that article is actually listed on the page you posted, cool
12:04  * nmz787 is now seeing the integration side of things at work... it is a whole lot more hellish than a day's worth of work
12:05 < kanzure> fenn: well my accuracy is low
12:06 < kanzure> the microRNA is not modified by blue light, IIRC it's blue light inducing the expression of microRNA somehow
12:07 < kanzure> oh you were proposing a summary
12:08 < kanzure> right, so the one i had come up with was 'something about regulating hydrogenase activity and photosynthesis/photosystem activity in green algae (Chlamydomonas reinhardtii)'
12:08 < kanzure> i'mma go with your version
12:09 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=5c7c9ab3 Bryan Bishop: fix SZU China 2016 igem project summary >> http://diyhpl.us/diyhpluswiki/dna/projects/
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12:40 < dpk> http://boingboing.net/2016/12/15/germany-wide-consortium-of-res.html
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12:40 < kanzure> .title
12:40 < yoleaux> Germany-wide consortium of research libraries announce boycott of Elsevier journals over open access / Boing Boing
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12:44 < kanzure> an all-girls catholic high school participating in igem http://2016.igem.org/Team:Alverno_CA
12:46 < kanzure> they are now going to be my go-to argument for "BUT YOU ARE PLAYING GOD"
12:48 < kanzure> juul: what is this about http://2016.igem.org/Team:BioBricks/Design
13:00 < kanzure> http://denverbiolabs.com/ a community lab in denver
13:02 < kanzure> https://github.com/denverbiolabs/OD-F
13:02 < nmz787> oh man, that would be a pretty fun facebook status: "all girls catholic high-school plays God in GMO biotech competition: http://2016.igem.org/Team:Alverno_CA"
13:03 < nmz787> maybe plays God should be in single-quotes
13:05 < kanzure> we'll keep that one behind a sign that reads "in case of emergency, break glass".
13:06 < kanzure> tardigrade proteins for bacterial resistance to desiccation http://2016.igem.org/Team:Genspace
13:11 < nmz787> maybe that's what that one futuristic sci-fi movie was talking about: https://plaintalkblog.files.wordpress.com/2015/12/1371978902434580.png?w=760
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13:16 < kanzure> "harvesting the cellular penetration capabilities of toxin B from the Clostridium difficile bacteria (TcdB), which is capable of entering epithelial cells, for the delivery of cas9" http://2016.igem.org/Team:Tufts
13:28 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=e0c82dda Bryan Bishop: more igem 2016 projects (latin america) >> http://diyhpl.us/diyhpluswiki/dna/projects/
13:28 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=d2e70dde Bryan Bishop: more igem 2016 projects >> http://diyhpl.us/diyhpluswiki/dna/projects/
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13:43 < kanzure> yashgaroth: https://twitter.com/kanzure/status/810255211168223232
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13:46 < yashgaroth> much easier on the eyes and brain
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13:48 < kanzure> yashgaroth: i think we should write down a list of igem project ideas for future teams, since a lot of these groups seem to have no idea what they should be doing
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13:49 < yashgaroth> idea: everyone just go nuts on TdT, see what they can come up with
13:50 < kanzure> yeah, 
13:50 < kanzure> and "go forth and multiply the number of good surface display techniques"
13:50 < kanzure> and "cell penetration and delivery stuff"
13:51 < kanzure> maybe a few projects about flagella, the protein nanoneedle injector proteins, adhesion patterning, etc.
13:51 < yashgaroth> the antifreeze projects might be worthwhile too
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13:59 < kanzure> yashgaroth: also, i was thinking "here is a list of fusion proteins you should make for me: ....."
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14:00 < yashgaroth> just don't put too much faith in them, undergrads are rather crap at wetwork
14:01 < kanzure> there's a surprising lack of software projects listed
14:01 < kanzure> i thought there would be lots more stuff going on in that category
14:02 < kanzure> turns out, biology is hard and software doesn't help
14:02 < yashgaroth> but big data
14:02 < yashgaroth> ...machine learning
14:02 < kanzure> machines learnin's
14:03 < yashgaroth> here's a nice project, reverse engineer foldit so I can put my own goddamn proteins in there and mess about with them
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14:05 < kanzure> you can complain on their irc server, if that would help
14:05 < nmz787> hey, I was damn good at wetwork when I was in undergrad!
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14:05 < nmz787> (but I came into it already self-taught at sterile technique)
14:05 < kanzure> if that was true, nmz787, then they would have never let you leave under any circumstances
14:05 < yashgaroth> supposedly there's a way that involves compiling rosetta and then doing a bunch of computer shit to get a much worse version of what foldit does, but that's far beyond me
14:05 < nmz787> (and noticed that most of my peers had shitloads more contamination probs)
14:06 < kanzure> yashgaroth: well if you investigate that sometime, feel free to ask questions about compilation problems to us. we are good at that.
14:06 < nmz787> kanzure: nah, I didn't gel with the biotech profs as much I did with the engineering and CS folks
14:06 < yashgaroth> I see plenty of phds that still have contamination problems, like "what do you mean I shouldn't need to put pen/strep in my 293 cells?"
14:06 < kanzure> wait isn't rosetta the one that you have to pledge your first born's life force to, in order to get a copy?
14:07 < yashgaroth> that's the other problem
14:07 < nmz787> I wonder if we could solve this with a few for-loops, a peptide synthesizer, and a cryo TEM to get 3D data
14:08 < nmz787> I feel like some peptides already have that stuff enumerated
14:08 < kanzure> which problem, contamination?
14:08  * nmz787 feels like kanzure linked to a database once of all combinations of peptides up to like 8-mer long
14:08 < nmz787> nah folding
14:09 < kanzure> dna origami is a much more solvable folding problem than protein folding
14:10 < kanzure> someone is going to find a subset of proteins that fold in a highly specific way, and then use sgRNA or something to force them to bind together in certain ways, and then protein folding will become a non-problem as long as you don't use natural shapes
14:12 < kanzure> it would be fun to do a selection project where you try to force all the bugs to use exclusively rod-shape proteins and nothing else
14:12 < kanzure> so you do crystallography on basically all the protein extract and do selection based on which cell cultures are producing mostly rod proteins
14:12 < kanzure> (because rod and cylindrical proteins seem to be slightly easier to analyze and predict)
14:12 < nmz787> I am supposed to be on vacation now to do CAD and fab things
14:13 < yashgaroth> I feel like as long as foldit isn't encrypting their files, there should be a way to feed it an arbitrary protein and get it to work, but I don't know how much extra data they layer on top server-side
14:13 < nmz787> I want to design and fab a microfluidic pump and hook it up
14:13 < kanzure> yashgaroth: i am also good at reverse engineering, i could run you through the steps to hax0r them completely if you would like to do that as a project
14:13 < kanzure> if they have some server-side steps, then we can do network capture to determine which information is getting transmitted to their server
14:14 < yashgaroth> intercept one of their project files when it downloads and see if it's actually just a rebranded PDB file
14:14 < kanzure> they might be using some encryption but that's also defeatable.
14:16 < kanzure> alright now i want to check
14:16 < yashgaroth> haha my plan worked
14:16 < kanzure> ./cmp-binary-00000000000000000000000000000000/game_library.so
14:16 < kanzure> ./cmp-binary-e38af73e8aff07f8763648db1f155c98/game_library.so
14:16 < kanzure> they use curl
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14:18 < yashgaroth> I feel like most of their security stuff is just to prevent people from cheating, rather than to prevent people from sticking random proteins in there
14:19 < kanzure> http://web.archive.org/web/*/http://foldit-dev.cs.washington.edu/*
14:24 < kanzure> https://fold.it/comm_cache/puzzle_user3_csv/995004_diff.txt
14:31 < kanzure> ./cmp-resources-91373e2e6560ddccd3827577bf0e0080/resources/levels/0000053530.ir_puzzle.pdb
14:31 < kanzure> yashgaroth: looks like they are using pdb files
14:31 < kanzure> in fact, you might be able to just replace their stupid pdb file with your own
14:31 < yashgaroth> fuckin' sickkk
14:31 < kanzure> ./cmp-resources-91373e2e6560ddccd3827577bf0e0080/resources/levels/0000000605.ir_puzzle.puzzle_setup
14:32 < kanzure> version: 1 {"can-design": "34||41||", "sidechain_locked": "1-31||44-83|", "backbone_locked": "1-31||44-83||"}
14:32 < kanzure> dunno what those values are
14:32 < nmz787> the .intro files are binary though
14:33 < kanzure> haha:
14:33 < kanzure> ./cmp-resources-00000000000000000000000000000000/resources/auth/server.crt
14:33 < kanzure> ./cmp-resources-00000000000000000000000000000000/resources/auth/cacert.pem
14:33 < yashgaroth> I think they place some restrictions on what parts can be changed between like helix and sheet, presumably we can just delete all the lock settings
14:34 < kanzure> hmm
14:41 < kanzure> in 2012, they did not have intro files
14:42 < kanzure> perhaps intro files are not required
14:46 < yashgaroth> at least not for our purposes
14:50 < kanzure> yeah so i would just try that randomly for starters and see what happens
14:50 < kanzure> they have a debug log enabled too, so that will give you a lot of useful information if it fails/crashes
14:50 < kanzure> C:\Foldit.dev\log.txt or something
14:50 < kanzure> C:\FolditLogs\
14:53 < yashgaroth> alright I'll give it a shot
14:57 < kanzure> yashgaroth: don't forget to play hacker music, https://www.youtube.com/watch?v=cyUrXe4q_-c
14:57 < yashgaroth> ha I love that song
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14:59 < kanzure> or https://www.youtube.com/watch?v=u556gwYhwnQ&t=1m
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15:11 < kanzure> construction of -80 C freezer http://2016.igem.org/Team:UMaryland/Hardware#construction
15:15 < chris_99> ooh that looks v. interesting
15:20 < kanzure> nmz787: continuous flow microfluidics design tool http://2016.igem.org/Team:BostonU_HW
15:25 < kanzure> "We will add ligation reactions containing small amounts of cut and pasted DNA to mid-log cultures of Acinetobacter baylyi ADP1" http://2016.igem.org/Team:Emory/Description
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15:40 < kanzure> bacterial microcompartments http://2016.igem.org/Team:CU-Boulder "requires minimal genes and can assemble and disassemble by the introducing a non-natural amino acid into the outer shell protein."
15:40 < kanzure> " Previous research has shown successful changes in chaperonin conformation by crosslinking cysteine residues with a light activated azobenzene - dimaleimide. At 450 nm azo-benzene will primarily be in its longer trans state but when exposed to 365 nm light, azo-benzene has a pinched cis conformation. This previous research demonstrated that taking advantage of these two conformations can be u...
15:40 < kanzure> ...sed to "close" and "open" a chaperonin. Towards the same end, we will be replacing amino acids within the EutS structure with azo-phenylalanine, a similar 'azobenzene' chemical structure linked to a phenylalanine amino acid, to create steric hindrance caused by cis to trans isomerization. If placed correctly in the EutS protein, this azobenzene containing residue could be used to prevent or al...
15:40 < kanzure> ...low the formation of EutS compartments."
15:54 < yashgaroth> looks like foldit uses a different notation to delineate secondary structure, should be able to convert to that from a normal file tho; I think there's a checksum in the IR_PUZZLE files in the main folder since any changes make it claim the file is corrupted
15:56 < yashgaroth> e.g. "file sums" : "{\n \".pdb\" : \"0cc3b75fb484cdd41f136d01000a2324\"\n}\n" and also ' verify: 26dd4b95d2276702b83c5e96b538075f '
16:06 < yashgaroth> nm if I change those values it just hangs a while and then loads anyway
16:07 < kanzure> what you got there is one heck of a magic checksum
16:07 < kanzure> btw that looks like crc32, sha1 or md5, if you actually need the checksum to work (you can check by running crc32/sha1/md5 against the original pdb file to see if it gives you the same value as you found in the file)
16:08 < kanzure> reversible gene editing system using Cas9 to target RNA and avoiding homology-directed repair, using APOBEC1 and ADAR1/2 to enable CRISPR-targeted C-to-U and A-to-I edits to RNA http://2016.igem.org/Team:WPI_Worcester
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16:19 < kanzure> cas9 delivery using outer membrane vesicles http://2016.igem.org/Team:Northwestern
16:26 < kanzure> radiation resistance for space exploration through a biotherapeutic transdermal patch to produce and deliver radioprotective peptide mBBI http://2016.igem.org/Team:UofC_Calgary/Design
16:29 < kanzure> MAGE and directed evolution of rhizobacterium for space exploration and legume agriculture on Mars http://2016.igem.org/Team:Yale/Description
16:29 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=d0a677a5 Bryan Bishop: finish igem 2016 projects >> http://diyhpl.us/diyhpluswiki/dna/projects/
16:31 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=760a198e Bryan Bishop: also include tweeter link >> http://diyhpl.us/diyhpluswiki/dna/projects/
16:32 < kanzure> there were about 50 less projects in 2016? that doesn't sound right.
16:32 < kanzure> maybe i just skipped lame stuff more
16:35 < kanzure> alright now for the arduous process of pretending to digest this material
16:41 < yashgaroth> it's md5 checksum but yeah it isn't needed; seems like the program loads the 1jj2.torsions file before erroring, which I guess is RNA torsion for this beast http://www.rcsb.org/pdb/explore/explore.do?structureId=1jj2 ... maybe using that as some convoluted key idk
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16:44 < kanzure> what is the actual error?
16:44 < yashgaroth> Exception: Puzzle file cmp-resources-ab3bbc6032c8a9370a11d4d559996aad\resources\levels/0000000013.ir_puzzle.pdb appears to be corrupted.
16:44 < kanzure> and it continues to load anyway?
16:45 < yashgaroth> nope that's the bad one, if it's okay it'll continue with "starting score : 3722.04" or w/e, and load up
16:45 < kanzure> torsion file might need to be placed next to the other files
16:46 < yashgaroth> it just reads that file regardless of which protein I'm opening
16:46 < yashgaroth> might be unrelated but idk why they'd load the torsion data for some ribosome just to view a file with three amino acids
16:48 < kanzure> hm.
16:48 < nmz787> the original file had 3 aminos?
16:49 < nmz787> or the one you replaced it with?
16:49 < yashgaroth> the original, I'm just mucking about with their intro puzzles
16:49 < yashgaroth> I can't modify the original at all, even to add a comment, or it gives the corruption error
16:49 < nmz787> did you try replacing the md5 hash too?
16:50 < yashgaroth> yeah it just takes longer but then loads, same with the verify string
16:50 < yashgaroth> I also deleted the verify string and it complained in the logfile but ignored it
16:51 < yashgaroth> also yeah if it opens the file correctly it corrects the md5 back to what it was
16:51 < kanzure> it's probably reading some values from the non-pdb files
16:51 < nmz787> i'd grep for 1jj2.torsions
16:51 < nmz787> and see if any files mention it, then try deleting the mention
16:52 < nmz787> or even grep for just 1jj2
16:53 < nmz787> btw you can get grep on Windows if you install GIT and choose the option to add GIT to your system path
16:53 < kanzure> to me it looks like each puzzle has the same set of files. deletion is a good guess but i doubt this software is robust.
16:53 < nmz787> hopefully they used "on error resume next" or whatever
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17:00 < yashgaroth> hrm ok
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17:20 < kanzure> i wonder if cells would survive if you forced all their organelles and proteins to be attached to their cytoskeleton.
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17:24 < kanzure> with optogenetics and recombinases, you can do long-term genetic memory insertion and readout, but it takes forever :(
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17:30 < kanzure> wel, with any signalling scheme, really. not optogenetics necessarily.
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17:44 < ebowden> http://adl.serveftp.org/papers/Role%20of%20layer%206%20of%20V2%20visual%20cortex%20in%20object-recognition%20memory.pdf
17:44 < ebowden> This link does not work.
17:45 < ebowden> Kanzure, do you have that paper?
17:45 < ebowden> sci-hub will not fetch it for me.
17:46 < kanzure> ebowden: http://diyhpl.us/~bryan/papers2/neuro/Role%20of%20layer%206%20of%20V2%20visual%20cortex%20in%20object-recognition%20memory.pdf
17:48 < ebowden> Thanks so much.
17:49 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=3575d9b2 Bryan Bishop: some igem project ideas >> http://diyhpl.us/diyhpluswiki/dna/projects/
17:50 < kanzure> Liu D R, Guilinger J P, Thompson D B. Cas9-recombinase fusion proteins and uses thereof: U.S. Patent Application 14/320,467[P]. 2014-6-30.
17:50 < kanzure> ( http://2015.igem.org/Team:Tsinghua/Description )
17:54 < kanzure> yashgaroth: http://diyhpl.us/wiki/dna/projects/#igem-project-ideas
17:58 < yashgaroth> genome sequencing is a bit outside iGEM's scope
18:03 < kanzure> i should put up an offer to buy igem team's discarded ideas with bitcoin, based on authentication of their igem wiki
18:03 < kanzure> and then i will buy up their unused ideas in exchange for contributing funds to their projects
18:03 < kanzure> ... hopefully they aren't an unimaginative cohort. bleh.
18:04 < yashgaroth> there's usually a few secondary ideas per team
18:04 < kanzure> there's probably some good stuff in thre "but we knew we wouldn't have time" etc
18:04 < kanzure> or "but we're lazy"
18:05 < yashgaroth> mhm
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18:56 < kanzure> urgh
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20:09 < kanzure> hrm
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20:54 < ebowden_> kanzure, I remember someone had a mechanism worked out for how RSG-14 over-expressed in layer 6 of area V2 enhanced object recognition memory.
20:54 < ebowden_> But I can't find the paper that had it.
20:56 < ebowden_> Well, I have the paper that showed it does that.
20:56 < ebowden_> But not the one that has what could be the mechanism by which it does that.
20:59 < ebowden_> *RGS-14
21:02 < ebowden_> I vaugely remember GTPase doing something or other to NMDA receptors.
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21:10 < ebowden_> OH.
21:12 < ebowden_> I wonder if it is expressed to cause certain populations of neurons to pass along information in a certain way by supressing LTP.
21:16 < ebowden_> Or maybe it just suppresses LTP in some regions and enhances it in others.
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