--- Log opened Sat Aug 04 00:00:30 2018
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01:23  * fenn punts the decision to kanzure
01:27 < mrdata> once google gets around to punishing the spammed links, they could punish any pages that contain those links
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02:46 < archels> purging logs is falsifying history
02:47 < archels> what are you, an ex-Soviet?
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04:48 < kanzure> hmm
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06:25 < kanzure> "A processing protein chimera introduces mutations across defined DNA regions in vivo" https://pubs.acs.org/doi/abs/10.1021/jacs.8b04001
06:25 < kanzure> ".. MutaT7 chimera, a potent and highly targeted in vivo mutagenesis agent. MutaT7 utilizes a DNA-damaging cytidine deaminase fused to a processive RNA polymerase to continuously direct mutations to specific, well-defined DNA regions of any relevant length. MutaT7 thus provides a mechanism for in vivo targeted mutagenesis across multi-kb DNA sequences. MutaT7 should prove useful in diverse ...
06:25 < kanzure> ...organisms, opening the door to new types of in vivo evolution experiments."
06:28 < kanzure> ooh,
06:28 < kanzure> "Architecture of the mouse brain synaptome" https://www.cell.com/neuron/fulltext/S0896-6273(18)30581-6
06:28 < kanzure> .tw https://twitter.com/jaaanaru/status/1025037203980918784
06:28 < yoleaux> Whew! Single-synapse-resolution maps of postsynaptic proteins across the whole mouse brain. Areas controlling higher cognitive function contain the greatest synapse diversity, and mutations causing cognitive disorders reorganized synaptome maps. https://www.cell.com/neuron/fulltext/S0896-6273(18)30581-6 (@jaaanaru)
06:28 < kanzure> "Synapses are found in vast numbers in the brain and contain complex proteomes. We developed genetic labeling and imaging methods to examine synaptic proteins in individual excitatory synapses across all regions of the mouse brain. Synapse catalogs were generated from the molecular and morphological features of a billion synapses. Each synapse subtype showed a unique anatomical distribution, ...
06:29 < kanzure> ...and each brain region showed a distinct signature of synapse subtypes. Whole-brain synaptome cartography revealed spatial architecture from dendritic to global systems levels and previously unknown anatomical features. Synaptome mapping of circuits showed correspondence between synapse diversity and structural and functional connectomes. Behaviorally relevant patterns of neuronal activity ...
06:29 < kanzure> ...trigger spatiotemporal postsynaptic responses sensitive to the structure of synaptome maps. Areas controlling higher cognitive function contain the greatest synapse diversity, and mutations causing cognitive disorders reorganized synaptome maps."
06:29 < kanzure> some lore behind the monochromosome project https://bioengineeringcommunity.nature.com/users/172651-xiaoli-xue/posts/37239-creating-a-functional-single-chromosome-yeast
06:51 < kanzure> "Synthetic chromosome fusion: effects on genome structure and function" https://www.biorxiv.org/content/early/2018/08/01/381137 https://twitter.com/biorxivpreprint/status/1024716663990771712 https://twitter.com/DrTomEllis/status/1024781653170958337
06:52 < kanzure> "Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast" https://www.nature.com/articles/s41586-018-0374-x
06:52 < kanzure> "Creating a functional single-chromosome yeast" https://www.nature.com/articles/s41586-018-0382-x
06:52 < kanzure> "Yeast chromosome numbers minimized using genome editing" https://www.nature.com/articles/d41586-018-05309-4
06:52 < kanzure> "Entire yeast genome squeezed into one lone chromosome" https://www.nature.com/articles/d41586-018-05857-9
06:53 < kanzure> "Single-cell molecular connectomics of intracortically-projecting neurons" https://www.biorxiv.org/content/early/2018/07/27/378760 https://twitter.com/denisjabaudon/status/1023885594278199296 https://twitter.com/TonyZador/status/1024653561479815174
06:54 < kanzure> "To address this question, we developed a high-throughput approach, "ConnectID", to link connectome and transcriptome in single neurons. ConnectID combines MAPseq projection mapping (to identify single-neuron multiplex projections) with single-cell RNA sequencing (to identify corresponding gene expression). Using primary somatosensory cortex (S1) ICPN as proof-of-principle neurons, we ...
06:54 < kanzure> ...identify three cardinal targets: (1) the primary motor cortex (M1), (2) the secondary somatosensory cortex (S2) and (3) subcortical targets (Sub). Using ConnectID, we identify transcriptional modules whose combined activities reflect multiplex projections to these cardinal targets. Based on these findings, we propose that the combinatorial activity of connectivity-defined transcriptional ...
06:54 < kanzure> ...modules serves as a generic molecular mechanism to create diverse axonal projection patterns within and across neuronal cell types."
06:56 < kanzure> .tw https://twitter.com/SynBioCU/status/1024663336359784449
06:56 < yoleaux> Fellow Canadian scientists if are you interested in editing or writing DNA at genome scale you need to join us the the GP-write Canada meeting in Montreal https://bit.ly/2Oy7V69. Registration is free! @GP_write @GenomeQuebec @ontariogenomics @GenomeCanada @FRQ_NT @FRQS1 @FRQSC https://pbs.twimg.com/media/DjhVAWFXcAI52yq.jpg (@SynBioCU)
06:57 < kanzure> .tw https://twitter.com/4LOVofScience/status/1024323598348050432
06:57 < yoleaux> Biohack The Planet 2018 is a conference we started 3 years ago and will happen Aug 31 & Sept 1 in Oakland. This year we have one of the best line-ups yet! The conference is smaller(on purpose) which allows you to directly interact with speakers. Be there! http://biohacktheplanet.com (@4LOVofScience)
06:59 < kanzure> why is "mammoth biosciences" not church's mammoth resurrection project? -_- https://techcrunch.com/2018/07/31/mammoth-biosciences-funding-crispr-doudna/
07:00 < kanzure> completely irresponsible
07:00 < kanzure> .tw https://twitter.com/castelli_jmp/status/1024116641192398848
07:00 < yoleaux> @BoredSynBio Uber pool, but instead of sharing rides you share lanes on an e-gel. #SharingEconomy (@castelli_jmp)
07:02 < kanzure> "Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling" https://www.biorxiv.org/content/early/2018/07/28/374058 https://twitter.com/HiroshiSasak1/status/1023590832526569472
07:12 < kanzure> http://sequencemedianews.com/the-lbn-blog/2015/7/31/how-much-is-a-womans-egg-worth-federal-lawsuit-will-look-for-an-answer
07:22 < kanzure> .wik surrogate medical expense liability insurance
07:22 < yoleaux> "" — https://en.wikipedia.org/wiki/Healthcare_in_Kosovo
07:24 < kanzure> some background on surrogacy http://woodllp.com/Media/Press/pdf/When_Your.pdf
07:24 < kanzure> https://en.wikipedia.org/wiki/Surrogacy
07:29 < kanzure> i wonder if you could get statistically-significant embryo transfer  using testicle-ovaries. there's probably no use for this but at least on the delivery side it seems to be possible.  the incubation side would be much more difficult of course.
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11:42 < fenn> could monochromosomal yeast sexually reproduce with other monochromosomal yeast?
11:42 < fenn> did they do that experiment?
12:05 < kanzure> yashgaroth: would it be possible to extract many human eggs from recently deceased human ovaries?
12:06 < yashgaroth> ...very recently, maybe, but unless they were already on an IVF cycle you aren't gonna get many mature ones
12:07 < kanzure> how many could you get (including immature)?
12:07 < kanzure> same as a regular IVF cycle?
12:07 < kanzure> assume you had total access to the entire ovary
12:11 < yashgaroth> uhm I believe they mature passing out of the ovaries into the fallopian tubes, so it depends on if we can replicate that process in vitro
12:12 < yashgaroth> all the surrounding support cells, polar body, various signalling factors
12:12 < kanzure> ehh nevermind then.
12:12 < kanzure> maybe there's a drug that causes spontaneous maturation of 1000s of human oocytes and nobody has noticed yet
12:12 < kanzure> (in vivo)
12:13 < yashgaroth> .wik in vitro maturation
12:13 < yashgaroth> oh no where's yoleaux
12:13 < kanzure> yoleaux is kill
12:14 < fenn> there are different levels of "deceased" - most organ transplants come from bodies on life support that are still very much alive
12:14 < yashgaroth> so it may be possible...seems like more of a pain than getting them from live donors, all things considered
12:15 < fenn> good luck getting permission to dink around with that in preference to, you know, dying people who need the organs
12:15 < kanzure> well it could be something like, you pay some of the medical bills for keeping someone alive, we get some regular eggs from the coma patients.   their families would consent because medical expenses. but probably this is paid for by insurance anyway so not an option.
12:16 < fenn> you'd need consent from the patient
12:17 < kanzure> i think you just need power of attorney, which is often with the family, not the coma patient.
12:17 < fenn> that's fucked up
12:17 < kanzure> anyway, i agree with yashgaroth, this doesn't seem to have any particular benefit over live donors
12:20 < nmz787> could life support patients be surrogates?
12:20 < nmz787> ugh, now I'm getting private-message spam :(\
12:21 < nmz787> in some sense, they could be perfect
12:21 < nmz787> unless the brain has some developmental influence
12:21 < nmz787> otherwise they're immobile, fed precisely, able to tolerate indefinite periods in controlled environ
12:22 < nmz787> hmm, this feels like a real potential winner
12:27 < yashgaroth> I suppose they don't need to push or w/e if it's a c-section birth
12:28 < fenn> https://en.wikipedia.org/wiki/Maternal_somatic_support_after_brain_death
12:31 < nmz787> even pushing might happen automagically
12:32 < nmz787> contractions are involuntary.... my wife says she did assist in the end, and maybe it would've taken way longer, and maybe the kid would've suffocated
12:33 < fenn> "the average cost of medical ventilation for adults in the ICU to be $1,500 per day and long-term ICU care to be approximately $5,000 per day"
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12:34 < fenn> i bet you could pay someone less than that to behave according to some consistent rules
12:34 < fenn> and hire someone else to watch them
12:42 < fenn> weird phenomenon of the day: https://en.wikipedia.org/wiki/Lithopedion
13:03 < nmz787> prisoners?
13:04 < fenn> don't be evil
13:04 < nmz787> fenn: people are really inconsistent and prone to bias and witholding info
13:04 < nmz787> I don't think paying someone would work well for scientific stuff, unless you were properly randomizing the trial
13:04 < nmz787> but then you need more N
13:37 < archels> https://www.eevblog.com/forum/projects/rfc-low-leakage-uvlo-(under-voltage-lockout)-for-magsafe/
13:39 < archels> my alter ego posted this
13:43 < fenn> i really just want a connector that won't break when you trip over the cord
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13:49 < archels> exactly
13:50 < archels> magsafe 1 is almost perfect
13:53 < archels> it would be even better if it had a built-in thermometer to protect against overheating, which would be pretty simple as there's already a 1-wire GPIO chip inside
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14:04 < nmz787> archels: pic of the lenovo+port?
14:04 < nmz787> archels: ports available for cheap en-masse?
14:07 < archels> haha, my laptop was already falling apart, I stopped caring and so it's all rather more ugly than it needs to be
14:07 < archels> this was a photo of the installation --> https://imgur.com/a/HozzVt6
14:08 < archels> in the next iteration, I would like to move it outwards so that it's inbetween the plastic and the metal strips
14:08 < archels> yeah, connectors are cheap, for adapters you just way what you want to pay (Apple genuine or cheap Chinese ripoff)
14:24 < Jenda`> archels: reminds me of my phone. I found it in a thrash bin a few years ago (a scratched, complete functioning Nokia 6230i), no battery -> https://jenda.hrach.eu/f/mobil.jpg
14:25 < Jenda`> just random 18650s from laptop battery (also from trash)
14:28 < nmz787> Jenda`: are you still using it?
14:30 < nmz787> archels: cool
14:32 < nmz787> archels: hmm, ebay only seems to have used connectors for $25 each! have you found a source for less than say $5 each? no leads/wires required
14:33 < Jenda`> nmz787: yes
14:33 < nmz787> hmm, here's magsafe for 110V AC: https://ilovehandles.com/shop/tug/
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14:37 < kanzure> it's because of +r
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15:50 < kanzure> hm
15:58 < nmz787> blah
15:58 < nmz787> soo distracted
16:07 < fenn> Jenda`: what's the battery life like?
16:26 < fenn> ok so apparently people like adopting kids, here's some evidence: http://imgur.com/gallery/FHZswg3
16:48 < Jenda`> fenn: one to two months, I don't know, I charge it occasionally before it's empty and the cells aren't new
16:48 < Jenda`> new 18650s have 3000 mAh one, so it should last ~4 times more than with the original battery
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--- Log closed Sun Aug 05 00:00:31 2018