--- Log opened Wed Sep 27 00:00:29 2017
00:06 < nmz787_> huh, so there aren't any top-hits for "make baby crib out of TVs" or "make baby crib LCD panel"...
00:06 < nmz787_> (or good hits for that matter)
00:08 < nmz787_> I see some more on-topic for "baby crib tablet" but that is so entry-level...
00:19 < nmz787_> http://harald.ist.org/self-pc/tricks/linux/howto/molecule-screensaver.html
00:19 < nmz787_> way to get PDB files to display as a screensaver... for my baby training crib overhead/ceiling display
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03:13 < fenn> "The product [Calysta FeedKind fish feed] is formed during the formation of methanotrophic microorganisms (Methylococcus capsulatus (Bath), with small amounts of scavenger microorganisms to assist in culture stability (Alca ligenes acidovorans, Bacillus brevis and Bacillus firmus), with methane, ammonia, and mineral salts. Natural gas or other methane source is pumped through a specialized
03:13 < fenn> fermenter, and the microorganisms metabolise the gas as their sole source of energy, producing a high-protein biomass. Wet product is extracted from the fermenter and dried, before being pelletized and packaged for shipping. ... Commercial production is expected to begin in 2018, with an expected production rate of 20,000 tonnes per annum."
03:14 < archels> nmz787_: hah, cool idea
03:15 < archels> GeodesicGears also looks cool (from XScreenSavers)
03:16 < archels> or some dynamical systems... boids come to mind
03:20 < fenn> how about nature scenes
03:44 < fltrz> I was working on software to visualize metamath proofs as graphs
03:44 < fltrz> DAG's
03:46 < fltrz> if the software was in working condition it could be made to randomly browse the DAG structures
04:03 < kanzure> merkle dags for life
04:05 < kanzure> regarding nate's concern for ssDNA stability... we should make nanotube proteins that store DNA. they need to actively load up any ssDNA or dsDNA. and they need to have a flush function. so basically a virus capsid that gets coated in some material i suppose.
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04:12 < kanzure> .tw https://twitter.com/eboyden3/status/907248282019225605
04:12 < yoleaux> If you can imagine a molecule-based biotechnology, there's a chance it exists in an organism somewhere. The trick is, how do you find it? (@eboyden3)
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04:16 < kanzure> "it's like tinder for preprints/papers" http://www.sciencemag.org/news/2017/06/great-paper-swipe-right-new-tinder-preprints-app
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04:16 < kanzure> ( https://twitter.com/scicurious/status/879784021227692033 )
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04:51 < kanzure> .tw https://twitter.com/Numenta/status/910922871454695426
04:51 < yoleaux> Two neurons forming a synapse. The electron microscopy on the left and the 3D reconstruction on the right. By Seung Lab- @SebastianSeung https://pbs.twimg.com/media/DKQ_hZyVwAAw3DM.jpg (@Numenta)
04:53 < kanzure> "A deep structured learning approach towards automating connectome reconstruction from 3d electron micrographs" https://arxiv.org/abs/1709.02974 https://twitter.com/herrsaalfeld/status/907991034474356742
04:54 < kanzure> "Simulating extracted connectomes" https://www.biorxiv.org/content/early/2017/08/16/177113 https://twitter.com/biorxiv_neursci/status/897926211858567169
04:55 < kanzure> "Connectomes derived from volume EM imaging of the brain can generate detailed physical models of every neuron, and simulators such as NEURON or GENESIS are designed to work with such models. In principal, combining these technologies, plus transmitter and channel models, should allow detailed and accurate simulation of real neural circuits. Here we experiment with this combination, using a ...
04:55 < kanzure> ...well-studied system (motion detection in Drosophila. Since simulation requires both the physical geometry (which we have) and the models of the synapses (which are not currently available), we built approximate synapses corresponding to their known and estimated function. Once we did so, we reproduced direction selectivity in T4 cells, one of the main functions of this neural circuit. This ...
04:55 < kanzure> ...verified the basic functionality of both extraction and simulations, and provided a biologically relevant computation we could use in further experiments."
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05:26 < fltrz> assumption 1: consumers don't want to insert reagent cartridges in their phones/laptops/... assumption 2: alternative mass storage may use reagents proportional to device usage => consumers still consume silicon for storage => still 'run out' of silicon
05:26 < fltrz> assumption 2 may be hard to relax by having to design for bistable biopolymer, but assumption 1 could be much harder to change
05:29 < fltrz> part of me is still skeptical about running out of silicon, sure abundance does not mean purity, but perhaps 'prohibitively expensive' purification becomes less expensive with experience (which may be avoided as long as pure enough silicon is still around)
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07:16 < kanzure> yes i have not looked into whether there are any methods to purify beach sand into usable silicon
07:33 < fltrz> I do know that during the Czochralski process, impurities get introduced into the grown single crystal boule, and that after the boule is formed, and ciricular heater is put around the cylindrical boule, locally heating the boule redhot
07:33 < fltrz> and this redhot heating zone is slowly traversed along the length of the boule
07:33 < fltrz> multiple passes (in the same direction IIRC) and that it drags the impurities with it
07:34 < fltrz> as we visited Umicore in material physics class at uni
07:34 < fltrz> and saw these processes
07:36 < fltrz> I think some steps of the purification methods rely on (re)crystallisation, but not with large boules, just like crystallization purification of other chemicals?
07:40 < fltrz> " However, even greater purity is needed for semiconductor applications, and this is produced from the reduction of tetrachlorosilane or trichlorosilane. The former is made by chlorinating scrap silicon and the latter is a byproduct of silicone production. "
07:40 < fltrz> "These compounds are volatile and hence can be purified by repeated fractional distillation, followed by reduction to elemental silicon with very pure zinc metal as the reeducing agent."
07:40 < fltrz> distillation!
07:41 < fltrz> but now you need very pure zinc as well
07:42 < fltrz> "The spongy pieces of silicon thus produced are melted and then grown to form cylindrical single crystals, before being purified by zone refining."
07:42 < fltrz> zone refining was the process I described
07:44 < kanzure> scrap silicon ain't the same thing as beach sand
07:44 < fltrz> of course! the purity requirements increase with decreasing device feature size!
07:45 < fltrz> that will ultimately perhaps form the biggest economic pressure to switch to exact atomic design of devices
07:46 < fltrz> how do we dope an N or P region which consists of 100 atoms from the bulk perspective? where exactly do we place the single dopant?
07:47 < fltrz> I'm pretty sure silicon purity was less demanding with bigger feature sizes
07:59 < fltrz> perhaps Diatoms can purify silicon for us?
07:59 < fltrz> https://en.wikipedia.org/wiki/Diatom#Silica_uptake_mechanism
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08:13 < fltrz> from metallurgical scrap silicon, iron is used as impurity getter
08:14 < fltrz> no wonder China is by far the leading exporter of silicon, with all their steel manufacture
08:15 < fltrz> oh it seems like just an experimental technique from 2011
08:17 < kanzure> all of the main quartz/silicon mines are owned by chinese interests anyway
08:24 < kanzure> (according to a friend of mine who checked recently.)
08:27 < kanzure> philip lubin stuff: "A roadmap to interstellar flight" https://arxiv.org/abs/1604.01356 (2016)
08:28 < kanzure> ".. Spacecraft from gram level complete spacecraft on a wafer ("wafersats") that reach more than 1/4 c and reach the nearest star in 20 years ..."
08:28 < kanzure> https://scholar.google.com/scholar?cites=16067310815226662343&as_sdt=5,44&sciodt=0,44&hl=en
08:30 < kanzure> "Centimeter-scale suspended photonic crystal mirrors" https://arxiv.org/abs/1707.08128
08:31 < kanzure> "photonic crystal membranes (PhC)"
08:31 < kanzure> "Advances in nanofabrication have shown that photonic crystal (PhC) membranes are an ideal alternative to conventional mirrors, as they provide high reflectivity with only a single layer of dielectric material. In particular, devices made of silicon nitride constitute the state-of-the-art in PhC mirrors with low optical absorption and mechanical loss. However, fabrication technology has ...
08:31 < kanzure> ...constrained their effective area to a few square-micrometers. Here we experimentally demonstrate the first example of suspended PhC mirrors spanning areas up to 10×10 mm. We overcome the limitations imposed by the finite size of the PhC, which allows us to measure reflectivities greater than 99% on 210 nm thin devices at 1550 nm wavelength and beyond 90% on 56 nm thick mirrors -- an ...
08:31 < kanzure> ...unrivaled performance compared to PhC mirrors with micro scale diameters. We also consider their use as mirrors in gravitational wave detectors where they could potentially reduce mirror coating noise at cryogenic temperatures."
08:33 < kanzure> "Here we study a PhC consisting of a periodic lattice of holes in a membrane, whose hole radius and lattice constant can be tuned to reflect light at a wavelength of choice. When fabricated from materials with low optical absorption such as low-pressure chemically vapor-deposited silicon nitride (LPCVD SiN), one can realize mirrors with subwavelength thicknesses and reflectivities > 99%, ...
08:33 < kanzure> ...onlylimited by scattering losses [8]."
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08:53 < kanzure> .tw https://twitter.com/kanzure/status/913068895887609856
08:53 < yoleaux> I'm reviewing 235 pages of #bitcoin research papers & proposals for @scalingbitcoin 2017. There's a lot of great work here. (@kanzure)
08:56 < kanzure> for each in `ls *.pdf`; do pdftk $each dump_data|grep NumberOfPages| awk '{print $2}'; done > numbers.txt; awk '{s+=$1} END {print s}' numbers.txt;
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09:17 < kanzure> "Visualization and characterization of individual type III protein secretion machines in live bacteria" http://diyhpl.us/~bryan/papers2/bio/Visualization%20and%20characterization%20of%20individual%20type%20III%20protein%20secretion%20machines%20in%20live%20bacteria%20-%202017.pdf
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09:22 < kanzure> "Incorporation of native antibodies and Fc-fusion proteins on DNA nanostructures via a modular conjugation strategy" http://pubs.rsc.org/en/content/articlepdf/2017/cc/c7cc04178k
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09:27 < kanzure> "Efficient in situ barcode sequencing using padlock probe-based BaristaSeq" https://www.biorxiv.org/content/early/2017/08/24/180323
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09:49 < pasky> BTW chido started PhD this month at MPI-CBG Dresden on getting CRISPR work in Planaria (at a lab studying regeneration), in case that'd be a useful information for anyone
09:57 < kanzure> there's a lot of cas9 alternatives these days, like cpf1
09:57 < kanzure> and cas1 and cas2
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10:53 < kanzure> "Design and synthesis of digitally encoded polymers that can be decoded and erased" https://www.nature.com/articles/ncomms8237 (lutz stuff)
10:53 < kanzure> "Biopolymers such as DNA store information in their chains using controlled sequences of monomers. Here we describe a non-natural information-containing macromolecule that can store and retrieve digital information. Monodisperse sequence-encoded poly(alkoxyamine amide)s were synthesized using an iterative strategy employing two chemoselective steps: the reaction of a primary amine with an ...
10:53 < kanzure> ...acid anhydride and the radical coupling of a carbon-centred radical with a nitroxide. A binary code was implemented in the polymer chains using three monomers: one nitroxide spacer and two interchangeable anhydrides defined as 0-bit and 1-bit. This methodology allows encryption of any desired sequence in the chains. Moreover, the formed sequences are easy to decode using tandem mass ...
10:54 < kanzure> ...spectrometry. Indeed, these polymers follow predictable fragmentation pathways that can be easily deciphered. Moreover, poly(alkoxyamine amide)s are thermolabile. Thus, the digital information encrypted in the chains can be erased by heating the polymers in the solid state or in solution."
10:55 < pasky> kanzure: I'm not sure which gene targetting variant she'll choose in the end (or maybe she already has her sights on some...), the goal is to gain the ability to effectively edit the planarian genome by whatever means i guess
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11:37 < nmz787_> fltrz: why not assume a closed-system? I am...
11:38 < nmz787_> fltrz: other than, to start, something like ATP being pumped in a bit... but eventually we can just engineer a better ATP synthase that runs directly on electrons supplied by wires
11:39 < nmz787_> fltrz: there are also folks using nuclear refineries to get isotopically pur silicon for performance reasons
11:41 < fltrz> nmz787_: yes if it's a closed system it would be good, but then it's not really consuming reagents
11:42 < nmz787_> correct ;)
11:42 < nmz787_> most storage systems are closed
11:42 < fltrz> nmz787_: I can imagine it would be a lot harder to get complex chemical pathways running in a device
11:42 < nmz787_> and don't consume more than electrons
11:43 < nmz787_> fltrz: idk, do you consider cells devices? (I do )
11:44 < fltrz> sure, what I mean was devices that can be easily interfaced with electronics, for practical usage
11:45 < fltrz> I think we all agree cells are devices, and in the long term cellular devices may even be the best answer for certain niches, like huge DNA storage of information within the brain or whatever, but right now thats too far out
11:49 < fltrz> I just bought a second hand printer for its scanner with automatic document feeder
11:50 < fltrz> so i can finally start scanning my 4 crates of university courses, so I can browse them digitally, and have less stuff whenever I have to move...
11:51 < nmz787_> "Moreover, these polymers are thermolabile and therefore dynamic at temperatures above 60 °C. Thus, the molecular information encrypted in the chains can be erased by heating the polymers in the solid state or in solution."   --- aka they won't work in datacenters or embedded devices
11:51 < nmz787_> but nice starting point
11:52 < kanzure> data centers don't maintain those temperatures because they don't have to, not because they can't be engineered to do so
11:54 < nmz787_> well you have to think about failure modes
11:54 < nmz787_> also more air conditioning means more power, more $
11:54 < fltrz> which polymers are they talking about, where are you quoting from?
11:55 < nmz787_> kanzur's 10:53 post
11:55 < fltrz> I don't really like when people use the word "encryption" for encoding
11:56 < kanzure> biologists are not computer people, forgive them
11:57 < kanzure> biologists are a completely different subspecies
11:57 < kanzure> oh actually that was a chemist damn
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12:02 < nmz787_> HAHA
12:02 < nmz787_> sorry didn't mean to laugh so loud
12:09 < kanzure> "Genetics has been shown to account for 40–60% of a person’s likelihood to develop an addiction.[2][3]" https://en.wikipedia.org/wiki/Addiction_vulnerability
12:09 < kanzure> is there any genetic immunity to physiological addiction?
12:11 < kanzure> the genetics section of this article really sucks. nevermind.
12:17 < nmz787_> seems associated with short-term reward seeking... or maybe the less-likelihood of waiting for long-term rewards
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12:21 < kanzure> sounds like ΔFosB inhibitors should be enough
12:22 < kanzure> you can have a genetic circuit that downregulates delta FoSB this should be pretty simple
12:23 < kanzure> https://en.wikipedia.org/wiki/FOSB
12:23 < kanzure> thankfully this is an exceptionally well-researched subject >:-)
12:24 < kanzure> https://en.wikipedia.org/wiki/Epigenetics_of_cocaine_addiction
12:37 < nmz787_> with all the wonky interdependencies in regulation networks, I'd expect you'd find clusters of genes in certain motifs/sets that would indicate troubles... and these could change through lifetime, epigenetics, other life events that got those networks in some weird oscillation
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16:01 < fltrz> just scanned a whole course and course notes
16:01 < fltrz> 30 ish more to go...
16:13 < nmz787> wow this paper is pretty great: dx.doi.org/10.1039/c3nr06723h
16:13 < nmz787> .title
16:13 < yoleaux> Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales - Nanoscale (RSC Publishing)
16:15 < kanzure> how many pores per surface?
16:17 < nmz787> I see a pic of a grid where the 18 nm +- 2nm pores are ~66nm center to center
16:18 < nmz787> I can't tell yet if the electrodes are all connected, or if they fanned out the control to each pore separately
16:19 < nmz787> parallel on/off for at least groups of pores seems like it could be incorporated potentially into some architecture
16:24 < kanzure> hm parallel activation of pores/electrodes    yeah that wouldn't be the worst thing i guess.  except each one is processing dna molecules that are moving at different rates :-(.
16:24 < nmz787> unless the molecules are all the same size
16:25 < kanzure> heath wants to talk about business ideas for dna synthesizers that aren't "sell dna synthesizers" and aren't "sell custom dna molecules as a service"
16:25 < nmz787> if they were different, then you'd need to have variable-speed readout converters (i.e. they'd need clocked separately or something)
16:26 < nmz787> kanzure: heath: like sell bioengineering as a service?
16:26 < nmz787> I am interested in that
16:26 < kanzure> andytoshi: "Adenosine triphosphate blocks opiate withdrawal symptoms in rats and mice" https://www.ncbi.nlm.nih.gov/pubmed/2755901
16:27 < kanzure> nmz787: hmm i dunno.
16:28 < nmz787> did they inject the ATP into their brain or spinal cord or something?
16:28 < nmz787> or was it into blood, or stomach?
16:28 < heath> i have to do a lot more research before i have much of anything to say
16:28 < kanzure> yeah i don't know why adenosine triphosphate was effective. seems pretty simple. i'm a little confused about that.
16:30 < nmz787> I wonder how much a RIE (reactive ion etch) system costs... I really don't know much about them other than they are very selective and very precise (or at least they /can/ be)
16:31 < nmz787> ebay shows $7500 to $117k
16:32 < nmz787> I guess that is only for etching though, ALD is also needed (atomic layer deposition) to put down the atomic-thick layer for the electrode(s)
16:33 < nmz787> hmm, only seems like 1 hit on ebay for that, not sure it's complete either... $10k tho http://www.ebay.com/itm/Atomic-Layer-Deposition-Machine-ASM-ALCVD-Reactor-F120-SAT-/252915655100?epid=836030116&hash=item3ae2f2a1bc:g:cT8AAOSwONBZCM3k
16:35 < kanzure> it's interesting that custom dna has sort of an information creation barrier for now
16:35 < kanzure> copies are easy so it's bad for DRM (sort of)
16:35 < kanzure> but the creation of new information in dna molecules currently violates "[new] information wants to be free"
16:35 < kanzure> in a way that other mediums don't
16:36 < nmz787> violates and tears  it open
16:37 < nmz787> in the sense that the majority of DNA currently being copied/accessed worldwide is basically happening for free (minus billions of years of evolutionary investment cost)
16:38 < kanzure> except that the encoding of information isn't.
16:38 < nmz787> "Compared to previously reported nanopore fabrication protocols by FIB or TEM, where nanopores are drilled after the membrane formation (pore-last process) on individual, small chips, the pore-first RIE strategy used here avoids processing of a membrane-containing wafer. This allows for the use of a wide range of semiconductor processing and integration steps, in conjunction with and following the
16:39 < nmz787> nanopore etching process, as well as the use of full-size wafer substrates (200 and 300 mm diameter) throughout the entire fabrication process. This enhances both process reproducibility and safety. Therefore, the pore-first strategy is compatible with VLSI integration allowing for integration options such as on-chip circuits or the integration of nanopores with existing FET devices on the Si
16:39 < nmz787> substrate."
16:40 < nmz787> kanzure: well presumably once we get semiconductor based read/write pretty good, we'll get much better at bioengineering, then we can just engineer some cellular mechanism to read/write/convert to some other format... optical i/o or something
16:41 < nmz787> no one actually has a totally open-source computer that can interface with any current electronic storage media... so  :/
16:41 < kanzure> no doubt. but there is not really a good business reason for cheap dna synthsizers or cheap dna synthesis. we know there are good reasons but they are several steps removed.
16:41 < nmz787> I mean, if you include any/all factories are not open
16:42 < nmz787> the only thing we can push/market is density and maybe energy requirements (it seems better, but we still need to run through an architecture to really get a better idea of end-to-end/overall)
16:43 < kanzure> it's currently not better :-)
16:43 < nmz787> I mean, I'd love to also push that this tech will inevitably make bioengineering much easier/faster... but that is more steps removed (but potentially massively more pay-off)
16:43 < nmz787> SRC estimates were like 6 orders less energy per operation
16:44 < nmz787> anyway, more numbers are in the works
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16:49 < kanzure> it will make bioengineering easier. but that's not an argument that anyone seems to want to finance.
16:49 < nmz787> damnit, I want a cinderella pumpkin carriage
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17:02 < kanzure> the estimates are better yes but that doesn't count for much
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17:33 < kanzure> if you had an argument for engineered proteins of any desired shape then does that have a sufficient motivation for dna synthesis?
17:33 < kanzure> well, almost any desired shape at least.
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17:47 < fltrz> second course digitized
17:47 < fltrz> the biggest hell will be all the random notes though
17:53 < kanzure> huh?
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18:57 < kanzure> https://www.ncbi.nlm.nih.gov/pubmed/27677507
18:57 < kanzure> .title
18:57 < yoleaux> Designed Protein Origami. - PubMed - NCBI
19:00 < kanzure> i should send heath to thr virusfab
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19:44 < kanzure> what exactly do you get if you have arbitrary protein shape engineering
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19:52 < kanzure> you could get some kind of semiconductor manufacturing masks out of them i guess (similar to dna origami tiles)
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20:47 < heath> btw, re: protein folding, check out protein origami: 10.1016/j.cbpa.2017.06.020
20:48 < heath> oh, you did find ljubetic's work
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20:51 < kanzure> hm
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21:33 < kanzure> nmz787: heath wants jurassic park. just do giant crocodiles that are 10x bigger (people don't know what dinosaurs are, it doesn't matter).
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23:06 < nmz787> kanzure: heath: works for me
23:06 < nmz787> I like off-grid living ideas anyway...
23:08 < nmz787> actually a daydream I had in my first year of biotech was something like parachuting into a jungle and starting a gmo lab from scratch
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23:21 < nmz787> "Also for single-component materials, the properties may be dramatically altered when they are deposited as thin films as compared to the bulk state. This may be due to the limited size of the material in one dimension, e.g., the thickness of the film is less than the mean free path length of the electrons in the material."
23:46 < nmz787> "it can take environmental dna, scramble it with DnaseI, ligate with T4, and express any inframe sequence with a his tag. a random protein generator. Each colony can be, in theory, a novel protein never before studied. The heart of the construct is a type 2 S restriction cutter that cuts blunt right after the ATG and another one that cuts right before the stop codon TAA. Allows for seamless ligation
23:46 < nmz787> of coding sequences that have been statistically randomly inserted. Can be modified to add random nucleotide sequences to specific protein domains for directed evolution, has binding sites for all sequencing variants, and will have origin for both plant (agrobacterium) and bacterial replication so the result will be transferable to plants." -- Sebastian S. Cocioba
23:46 < nmz787> 1775 bp
23:49 < nmz787> "Simple Protocol: cheeck swab, isolate dna, cut dna with DnaseI overnight, ligate for 2hrs with T4, cut IDM plasmid with MlyI, ligate vector and insert overnight. screen colonies using M13. 200bp is negative. anything larger is positive for insert. miniprep colonies, send for sequencing with M13 primers. if in frame, do a his tag miniprep, run protein gel, send sequence to RaptorX for structural and
23:49 < nmz787> functional analysis, spend the rest of your life screening every colony for new proteins to isolate and characterize. enjoy infinite discovery" -- Sebastian S. Cocioba
--- Log closed Thu Sep 28 00:00:30 2017