--- Log opened Mon Mar 06 00:00:50 2017
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01:32 < kanzure> freenode spam banning sucks
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04:34 < kanzure> O_o "Here's an idea for creating new GMO that may appeal to staunch organic-food consumers/farmers: don't insert a foreign gene in today's domestic plants --- delete already existing genes in semi-domesticated or even wild plants to make those plants more domestic."
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05:20 < kanzure> FourFire: welcome back.
05:20 < FourFire> Thanks, I was just checking another channel
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06:50 < kanzure> badusb protection stuff https://github.com/robertfisk/USG
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07:49 < kanzure> https://chrome.google.com/webstore/detail/sci-hub-links/olcgjijbclchlliaffaghajlbfppkbkl
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09:38 < kanzure> "Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli
09:38 < kanzure> "Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli" http://biorxiv.org/content/early/2017/02/21/110254
09:39 < kanzure> "Serine integrases are bacteriophage proteins responsible for integrating the phage genome into that of the host. Synthetic biologists have co-opted these proteins into useful tools for permanent DNA logic, utilizing their specific DNA recombination abilities to build synthetic cell differentiation and genetic memory systems. Each integrase has a specific pair of DNA sequences (attP/attB sites...
09:39 < kanzure> ...) that it recombines, but multiple identical sites can result in unpredictable recombination. We have developed a way to control integrase activity on identical attP/attB sites by using catalytically dead Cas9 (dCas9) as a programmable binding protein that can compete with integrase for binding to specific attachment sites. Utilizing a plasmid that contains two identical Bxb1 attP sites, integ...
09:39 < kanzure> ...ration can be repressed up to 8 fold at either one of the two attP sites when guide RNA and dCas9 are present. Guide RNA sequences that bind specifically to attB, or either of two attP sites, have been developed. Future goals are to utilize this technology to construct larger and more complex integrase logic circuits."
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10:10 < nmz787_i1> sup
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11:34 < andytoshi> does anyone know of research into removal of lead contamination from soil, e.g. with fungal agents?
11:35 < kanzure> ecoli lead sequestration http://2014.igem.org/Team:BUGSS_Baltimore/Project
11:35 < kanzure> lead remediation using metallothioneins http://2014.igem.org/Team:Cornell/project
11:35 < andytoshi> how did you do that? i spent several minutes googling and got mostly noise
11:36 < andytoshi> and thanx
11:36 < kanzure> i read all igem projects and summarized them http://diyhpl.us/wiki/dna/projects/
11:36 < andytoshi> oh nice, bookmarked
11:40 < bluebear_> kanzure: wow, impressive!
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13:01 < rk[ghost]> removal of heavy metals with mushrooms is quite interesting:)
13:02 < rk[ghost]> i have some blue oysters i planted a back yard mulch pile today.. we'll see how it goes. i have heard of oyster's ability to consume petroleum.. which is interesting.
13:02 < nmz787_i1> andytoshi: check out "Mycelium Running" by Stamets
13:03 < chris_99> but then you can't eat the mushrooms i assume?
13:04 < rk[ghost]> chris_99: that would be the idea, the mycelium often pushes all of the heavy metals to its fruiting bodies, and then you need tofind a way to extract the metals from the mushrooms
13:04 < rk[ghost]> which i haven't done much research in to that step.. though i am interested..
13:04 < rk[ghost]> i think collecting Lithium in this way would be.. neat
13:05 < chris_99> ah interesting
13:11 < andytoshi> nice nmz787_i1, i'll chase down a copy
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14:14 < heath> .title https://twitter.com/da5ch0/status/838785216143638530
14:14 < yoleaux> o??s?p ? auf Twitter: "Look, I'm not saying ATMs are trivial to hack, just that lots of them seem to run Doom okay. Infer what you will ? https://t.co/PNPPj4L4Tp"
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15:11 < rk[ghost]> oh and there is a copy of Mycelium Running on libgen.io btw
15:17 < nmz787_i1> andytoshi: there's a TED talk that is loosely based on Mycelium Running: https://www.ted.com/talks/paul_stamets_on_6_ways_mushrooms_can_save_the_world
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19:02 < kanzure> a chart showing off "class 1 crispr-cas systems" http://www.cell.com/cell/pdf/S0092-8674(17)30196-4.pdf
19:04 < kanzure> lots of other charts and diagrams http://www.cell.com/snapshots
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19:05 < kanzure> and class 2 http://www.cell.com/cell/pdf/S0092-8674(16)31754-8.pdf
19:06 < nmz787_i> do they tell us the diff?
19:13 < kanzure> some stuff about bacterial shape http://curiosidadesdelamicrobiologia.blogspot.co.uk/2017/02/tomando-forma.html
19:13 < kanzure> and http://schaechter.asmblog.org/schaechter/2017/03/on-shape.html
19:23 < nmz787_i> that is tending toward 'politics' (phylogenetics)
19:23 < kanzure> hmm okay, agreed.
19:25 < nmz787_i> I guess it would be a nice public-radio style announcements for students and people-not-yet-scientists
19:28 < kanzure> i was expecting more focus on the genetics of shape. there are proteins that influence more pointy and less pointy shapes.
19:39 < fenn> yves brun was studying caulobacter crescentus morphology at IU when i was a student, and i messed around in his lab
19:43 < fenn> apparently the curvature helps daughter cells attach to a surface
19:44 < fenn> the more divisions a cell has undergone, the longer its stalk
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23:34 < superkuh> Last time I tried to find out why red blood cells are the shape they are (what mechanism, not what it's good for) I couldn't find anyone who wrote that they believed they knew. There was some bits about maintaining asymmetric lipid ratios in the inner and outer layers of the bilayer but that wasn't sufficient.
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23:57 < nmz787_> superkuh: it isn't surface area?
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23:58 < nmz787_> oh, mechanism
--- Log closed Tue Mar 07 00:00:06 2017