--- Log opened Wed Oct 04 00:00:36 2017
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00:30 < kanzure> bloarf
00:30 < kanzure> that is all. bloarf.
00:31 < nmz787> hmm, are there any prior art on micro/nanofluidic DNA assembly, possibly involving nucleosomes?
00:34 < nmz787> I seem to be finding nothing much immediately
00:34 < kanzure> there was the pico whoeverwhatthefuck LC Sciences thing from houston
00:34 < kanzure> not nucleosome tho
00:35 < kanzure> isn't it going to be like 7am for you? for the meeting?
00:35 < nmz787> basically thinking of a way to start coiling DNA as it is synthesized (or soon after)
00:36 < nmz787> yeah
00:36 < nmz787> :(
00:36 < kanzure> ok it's only midnight for you that's not so bad
00:37 < nmz787> I should go to bed now, I hate being tired
00:37 < nmz787> ttyl
00:37 < kanzure> i've been thinking about a chemistry-only approach where the ssDNA oligonucleotide has many "caps" in between each "nucleotide" and each "nucleotide" is a molecular group that self-catalyzes in response to four different wavelengths of life
00:37 < kanzure> wavelengths of light, rather.
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00:38 < nmz787> mmm
00:39 < nmz787> hrmm, I wonder if retrosynthesis can take into account not only desired starting and end products... but also energy level requirements (i.e. in line with the energy of a single photon of those wavelengths)
00:39 < kanzure> there's probably a way to do it without optical gating too.... like, different de-capping agents. if you decap with one chemical then it's an adenosine (etc.). and then you decap the next cap (not choosing a nucleotide). then you do the nucleotide reaction step again (maybe another adenosine). etc.
00:40 < kanzure> mm optical goating
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00:40 < nmz787> I guess we can at least get a rough idea, find the reaction kinetics of some common polymerizations, and also the energy range of say 300nm to 3000nm
00:40 < kanzure> in this scheme the general idea is that the polymer is already "there" you just chisel away at it like a sculpture
00:41 < kanzure> probably will have the same yield rates/issues as other chemistry schemes though...... so it might ultimately be pointless in that department.
00:42 < nmz787> in reading about atomic layer deposition, where they grow monolayers... it sounds like maybe we could look into that... but it's really just pulsing gases onto a surface (which don't self-react, they only react with the starting layer), then swapping gasses (to re-activate the last deposited layer), and repeating such a cycle
00:42 < nmz787> ah, hmm, the sculpting idea sounds interesting
00:43  * nmz787 actually shuts laptop
00:45 < kanzure> "Human and nonhuman primate meninges harbor lymphatic vessels that can be visualized noninvasively by MRI" https://elifesciences.org/articles/29738
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01:33 < archels> kanzure: that was cool when it was revealed, couple years ago
01:33 < archels> now it's more like a confirmation study
02:10 < kanzure> yes it's just MRI stuff
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02:12 < kanzure> https://en.wikipedia.org/wiki/Gene_doping
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03:56 < kanzure> 2017 nobel prize in chemistry https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2017/press.html    is for cryo-EM stuff.
03:57 < kanzure> seems kinda timely since i was looking at that cryo-EM playlist the other day https://www.youtube.com/playlist?list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8-
03:57 < kanzure> .title https://www.youtube.com/playlist?list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8-
03:57 < yoleaux> Getting Started in Cryo-EM - YouTube
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06:22 < kanzure> pasky: so..... jrayhawk points out that grognor was an hplusroadmap user O_O. i missed this.
06:26 < kanzure> http://gnusha.org/logs/2013-02-23.log
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06:32 < kanzure> win 3
06:33 < kanzure> je8qr09821 blah
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07:03 < redlegion> kanzure, was grognor famous for something? All I'm getting is the usual social footprint of a prolific net user.
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07:24 < nmz787> http://advances.sciencemag.org/content/3/9/e1700555
07:24 < nmz787> .title
07:24 < yoleaux> Laser streaming: Turning a laser beam into a flow of liquid | Science Advances
07:29 < nmz787> hrmm, I am a bit skeptical of that "A flow will emerge from the focused laser spot on the window after the laser is turned on for a few to tens of minutes; the flow remains after the colloidal solution is completely replaced by pure water. Microscopically, this transformation is made possible by an underlying plasmonic nanoparticle-decorated cavity, which is self-fabricated on the glass by
07:29 < nmz787> nanoparticle-assisted laser etching and exhibits size and shape uniquely tailored to the incident beam profile."
07:29 < nmz787> (specifically the self-etched part)
07:46 < kanzure> nmz787: so was that worth waking up at 7am for
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08:02 < kanzure> redlegion: just some guy who assumed the identity of his parrot and then he died (i dunno, i don't have the story, ask jrayhawk)
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08:34 < CaptHindsight> didn't the other parrots notice?
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09:20 < kanzure> as far as i can tell, there are no parrots trained to recite particle physics equations or carl sagan
09:22 < mrdata> who died?
10:04 < nmz787> kanzure: meh, I was tired so wasn't terribly happy
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11:11 < kanzure> titanium oxide phthalocyanine is a photoconductor right?
11:26 < kanzure> http://web.stanford.edu/class/cs379c/archive/2013/class_messages_listing/figures/marblestone.stanford.cs379c.04-29-13.pdf
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16:09 < kanzure> .tw https://twitter.com/Gassensmith/status/915518592346677248
16:09 < yoleaux> If you’ve never seen a proper cryo TEM, here is the one we have @UTSWNews. These things are MASSIVE and awesome. #chemNobel https://pbs.twimg.com/media/DLSTTXJVoAE5dPS.jpg (@Gassensmith)
16:10 < kanzure> .tw https://twitter.com/EricTopol/status/915245833133494273
16:10 < yoleaux> Whoa. Fecal transplants for diabetes http://www.cell.com/cell-metabolism/fulltext/S1550-4131(17)30559-4 @Cell_Metabolism @CellCellPress instructive on #microbiome #OA https://pbs.twimg.com/media/DLObJG4VAAAGuog.jpg https://pbs.twimg.com/media/DLObKvJVwAAvy76.jpg https://pbs.twimg.com/media/DLObMh_VwAAxrw5.jpg (@EricTopol)
16:12 < kanzure> "Intercellular mRNA trafficking via membrane nanotubes in mammalian cells" https://www.biorxiv.org/content/early/2017/05/14/137836 https://twitter.com/biorxivpreprint/status/863831367649554433
16:12 < kanzure> "RNAs have been shown to undergo transfer between mammalian cells, though the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g. exosomes). However, in contrast to a diffusion-based transfer mechanism, we find ...
16:12 < kanzure> ...that full-length mRNAs undergo direct cell-cell transfer via cytoplasmic extensions, called membrane nanotubes (mNTs), which connect donor and acceptor cells. By employing a simple co-culture experimental model and using single-molecule imaging, we provide quantitative data showing that mRNAs are transferred between cells in contact. Examples of mRNAs that undergo transfer include those ...
16:12 < kanzure> ...encoding GFP, mouse β-actin, and human Cyclin D1, BRCA1, MT2A, and HER2. We show that intercellular mRNA transfer occurs in all co-culture models tested (e.g. between primary cells, immortalized cells, and in co-cultures of immortalized human and murine cells). Rapid mRNA transfer is dependent upon actin, but independent of de novo protein synthesis, and is modulated by stress conditions and ...
16:12 < kanzure> ...gene expression levels. Hence, this work supports the hypothesis that full-length mRNAs undergo transfer between cells through a refined structural connection. Importantly, unlike the transfer of miRNA or RNA fragments, this process of communication transfers genetic information that could potentially alter the acceptor cell proteome. This phenomenon may prove important for the proper ...
16:12 < kanzure> ...development and functioning of tissues, as well as host-parasite or symbiotic interactions."
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18:06 < kanzure> blortula
18:17 < kanzure> "DNA amplification by electric field cycling" https://techtransfer.universityofcalifornia.edu/NCD/27267.html
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--- Log closed Thu Oct 05 00:00:37 2017