--- Log opened Fri Mar 23 00:00:26 2018
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04:44 < superkuh> https://zeptobars.com/en/read/HP-DeskJet-840c-thermal-inkjet-printing-head "weekend die-shot"
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05:00 < MrHindsight> those holes are enormous for ion beam drilling, laser can easily make those cleanly
05:02 < MrHindsight> plus that is 90's tech
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06:13 < superkuh> Wow. https://onlinelibrary.wiley.com/ has blocked all 5 of my IPs I use for proxies.
06:14 < superkuh> The 'net is getting more and more segmented.
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06:25 < kanzure> "Quantifying expansion microscopy with DNA origami expansion rulers" https://www.biorxiv.org/content/early/2018/02/14/265405 https://twitter.com/eboyden3/status/976886574771208200
06:25 < kanzure> "Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859009/ https://twitter.com/eboyden3/status/976405932413538305
06:27 < kanzure> "Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses" https://www.biorxiv.org/content/early/2018/03/20/281121 https://twitter.com/eboyden3/status/974045521928212481
06:29 < kanzure> "Expansion stimulated emission depletion microscopy (ExSTED)" https://www.biorxiv.org/content/early/2018/03/08/278937 https://twitter.com/eboyden3/status/973521208355577859
06:30 < kanzure> .tw https://twitter.com/eboyden3/status/973504244799197184
06:30 < yoleaux> Boston Museum of Science, Mar 28, 7PM: I will discuss "Cyborgs, Futurists & Transhumanism" with writer Mark O'Connell. Hosted by the Institute for Cross-Disciplinary Engagement at Dartmouth College, and its director, Marcelo Gleiser. https://www.mos.org/public-events/cyborgs-futurists-and-transhumanism?platform=hootsuite (@eboyden3)
06:34 < kanzure> "Temporally-precise single-cell resolution optogenetics" http://syntheticneurobiology.org/PDFs/17.11.shemesh.FULL.pdf
06:36 < kanzure> well that's fun.
06:37 < kanzure> "A hybridization-chain-reaction-based method for amplifying immunosignals" https://www.nature.com/articles/nmeth.4611
06:46 < kanzure> let's put 12 year olds in charge of the NIH budget. i am starting to really like the idea.
06:47 < kanzure> also the NASA budget
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07:09 < kanzure> optical model of anti-aging: tissue culture microscopy and scoring of aging indicators, get tissue cultures that are naturally aged (i'm not convinced all the "aging-simulating" protocols are legitimately useful for aging studies), do optimization of virus payload for mutated proteins that seem to clear out optically-identifiable problems. do iteration loop things by mutating the virus ...
07:09 < kanzure> ...payloads. etc. you don't necessarily need to throw out a tissue culture once you run one batch of virus too.
07:10 < kanzure> orient yourself https://www.iers.org/IERS/EN/DataProducts/EarthOrientationData/eop.html
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07:19 < kanzure> "Functional germ cells from non-testicular adult stem cells: A dream or reality?" http://www.eurekaselect.com/156876/article
07:21 < CaptHindsight> life would be easier for nero
07:21 < CaptHindsight> oops
07:22 < CaptHindsight> life would be easier for neuroscientists if they could find some flat brains to study (2d)
07:28 < kanzure> agree
07:29 < kanzure> "Full-term development of mice from enucleated oocytes injected with cumulus cell nuclei" https://www.nature.com/articles/28615
07:30 < kanzure> "assisted oocyte activation" http://www.rbmojournal.com/article/S1472-6483(10)60313-6/abstract
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07:31 < kanzure> "Piezo-actuated mouse intracytoplasmic sperm injection" https://www.researchgate.net/profile/Tony_Perry2/publication/6414539_Piezo-actuated_mouse_intracytoplasmic_sperm_injection_ICSI/links/547d9d2b0cf2cfe203c21f24/Piezo-actuated-mouse-intracytoplasmic-sperm-injection-ICSI.pdf
07:32 < kanzure> hmm.
07:33 < kanzure> "Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line" https://genome.cshlp.org/content/24/12/2059.short
07:37 < CaptHindsight> http://www.machinedesign.com/motion-control/nano-and-micromotors-new-medical-delivery-systems
07:37 < CaptHindsight> has a bad link to the actual paper
07:38 < CaptHindsight> easy to make
07:41 < kanzure> why are these people doing it manually tho? wtf?
07:42 < CaptHindsight> http://mmbr.asm.org/content/80/1/161.full
07:42 < CaptHindsight> Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism
07:42 < kanzure> "Overexpression of STRA8, BOULE, and DAZL genes promotes goat bone marrow-derived mesenchymal stem cells in vitro transdifferentiation toward putative male germ cells" http://journals.sagepub.com/doi/abs/10.1177/1933719116654990
07:42 < kanzure> "Taken together, these results demonstrate that the overexpression of STRA8, BOULE, and DAZL was able to promote the transdifferentiation of gBMSCs to early goat germ cell–like cells in vitro, which probably enhanced maturation and progression through meiosis. This approach would be important to generating gametes for future basic science as well as for potential clinical applications."
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07:43 < kanzure> i'm a little confused about that "Functional germ cells" paper. it mentions that they aren't "fertile". but what the hell does that mean? did they even try intracytoplasmic injection, or were they just doing co-culturing fertilization attempts?
07:44 < CaptHindsight> https://pubs.acs.org/doi/ipdf/10.1021/nn507097k
07:44 < kanzure> why are they putting motors in a mouse stomach
07:45 < JayDugger> Jokes are too easy to make for that, must be a serious question.
07:46 < JayDugger> At a guess, easy animal model for tissue reactions?
07:47 < JayDugger> Yeah, in the abstract. Tests toxicity, with the additional effect that the motors get digested.
07:47 < kanzure> spermatid-like cells injected into oocytes seem to work, but spermatids aren't really that surprising, why not try something higher up the pipeline, http://www.cell.com/cell-stem-cell/abstract/S1934-5909(16)00018-7
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07:50 < CaptHindsight> edible motors, using the term loosely
07:51 < CaptHindsight> like a vinegar and baking soda "rocket"
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08:11 < kanzure> "Fertilization of mouse oocytes using somatic cells as male germ cells" http://www.rbmojournal.com/article/S1472-6483(10)62037-8/fulltext
08:11 < kanzure> "Ooplasmic transfer" http://www.nejm.org/doi/pdf/10.1056/NEJM200203073461013
08:11 < kanzure> "To restore oocyte viability, ooplasm from a normal donor is removed with a micropipette and injected into an oocyte from the infertile woman. The resulting oocyte, which is fertilized by intracytoplasmic sperm injection, contains mitochondrial DNA from both women."
08:11 < kanzure> cool.
08:14 < kanzure> "Inability of mature oocytes to create functional haploid genomes from somatic cell nuclei" http://www.fertstert.org/article/S0015-0282(02)04537-5/fulltext
08:20 < kanzure> "Blastocysts derivation from somatic cell fusion with premature oocytes (prematuration somatic cell fusion)" https://onlinelibrary.wiley.com/doi/full/10.1111/dgd.12264
08:21 < kanzure> ^good paper. uses fluorescence to track the physical movements of genetic material after induced cell fusion.
08:26 < kanzure> they should have tried the overexpression of STRA8, BOULE, and DAZL in the somatic cells they were fusing to the oocytes.
08:44 < kanzure> reliability and efficiency of this stuff is way too low
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12:05 < CaptHindsight> https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201309629?sharing_unavailable=unsupported_browser&sharing_referrer=http%3A%2F%2Fwww.iflscience.com%2Ftechnology%2Fnanomotors-steered-inside-living-human-cells-first-time%2F
12:06 < CaptHindsight> some yotubes of the above in action  http://www.iflscience.com/technology/nanomotors-steered-inside-living-human-cells-first-time/
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14:49 < CaptHindsight> want one  https://www.youtube.com/watch?time_continue=16&v=QixTsqn7RBE
14:49 < CaptHindsight> New wearable brain scanner
14:56 < kanzure> .title
14:56 < yoleaux> New wearable brain scanner - YouTube
14:56 < kanzure> "an antibody specific for mouse germ cell nuclear antigen has recently been described [8]."
14:57 < kanzure> (mid 90s)
14:59 < kanzure> "Germ cell transplantation from large domestic animals into mouse testes" https://onlinelibrary.wiley.com/doi/full/10.1002/1098-2795%28200011%2957%3A3%3C270%3A%3AAID-MRD9%3E3.0.CO%3B2-Z
14:59 < kanzure> works but doesn't generate spermatozoa. hrm.
15:01 < kanzure> "Long-term survival of human spermatogonial stem cells in mouse testes" http://www.fertstert.org/article/S0015-0282(02)04345-5/abstract
15:10 < kanzure> testicular tissue xenotransplantation http://digital.csic.es/bitstream/10261/128746/6/RepFerDevelopment%2026(8)%20817-826%20(2014)%20POSTPRINT.pdf
15:13 < kanzure> human fetal testicular tissue xenotransplantation into mice http://www.jurology.com/article/S0022-5347(15)00209-8/abstract
15:14 < kanzure> .. and of course bioethicists are already worried about testicular xenotransplantation: https://link.springer.com/article/10.1007/s40592-015-0031-1
15:14 < kanzure>     ("Ethical aspects of creating human–nonhuman chimeras capable of human gamete production and human pregnancy")
15:17 < kanzure> "Germ cell transplantation and neospermatogenesis" https://link.springer.com/chapter/10.1007/978-3-319-42396-8_20
15:18 < kanzure> "Testicular tissue xenografting [... is where] grafted testicular tissue grows and produces xenogenic sperm in a mouse host"
15:18 < kanzure> "Transplanted SSCs move towards the basal compartment of the seminiferous tubule to colonize, and subsequently undergo mitosis and meiosis to generate sperm"
15:45 < kanzure> huh, testicular tissue xenografting seems to work pretty well.
15:51 < kanzure> is there a way to do positive/negative selections on human cell cultures? other than cell sorting ideally.
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20:04 < kanzure> "Extremely scalable spiking neuronal network simulation code: From laptops to exascale computers" https://www.frontiersin.org/articles/10.3389/fninf.2018.00002/full
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20:11 < kanzure> "Each MPI process receives the global ids (GIDs) of all neurons that emitted a spike since the last MPI communication took place, and each thread needs to determine the thread-local neurons to which it needs to deliver the events."
20:11 < kanzure> blargh what
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20:36 < kanzure> hmm
20:37 < nmz787> so how bout that nucleus direct-injection?
20:37 < nmz787> ever search that?
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20:37 < kanzure> hm?
20:38 < kanzure> intracytoplasmonic injection?
20:38 < nmz787> ha, sci-bay.org is already down
20:38 < nmz787> :(
20:38 < nmz787> no, injecting DNA solution into the nucleus
20:38 < kanzure> what dna?
20:39 < nmz787> .title https://www.ncbi.nlm.nih.gov/pubmed/18243328
20:39 < yoleaux> An automated system for intracellular and intranuclear injection. - PubMed - NCBI
20:39 < nmz787> kanzure: that synDNA yo
20:41 < nmz787> "automated system capable of injecting up to 600 oocytes per hour" "intranuclear injection of cDNA gave a rate of expression >50%"
20:41 < kanzure> how does this work, again? you flood the cell with dna or just a single molecule of dna..?
20:43 < nmz787> "Oocytes were injected 2 ng of cDNA per oocyte in 10 nl of water"
20:46 < nmz787> they used a fine syringe pump with a glass syringe having a stainless steel piston, backfilled with mineral oil, which was connected to a pipette tip they pulled from glass capillary
20:46 < nmz787> the pipette tips were apparently only 40 microns OD
20:46 < nmz787> which seems way too big for nucleus
20:46 < nmz787> but maybe xenopus nuclei are huge?
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20:47 < nmz787> I'd be uploaded to a squid
20:47 < nmz787> that seems legit
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20:50 < nmz787> .title https://pubs.acs.org/doi/abs/10.1021/nl901384x
20:50 < yoleaux> nmz787: Sorry, that doesn't appear to be an HTML page.
20:50 < nmz787> FluidFM: Combining Atomic Force Microscopy and Nanofluidics in a Universal Liquid Delivery System for Single Cell Applications and Beyond
20:50 < nmz787> hmm
20:50 < nmz787> fenn ^
20:50 < nmz787> that's dip-pen litho + whack-a-mole
20:51 < nmz787> "a game for the whole family"
20:51 < nmz787> "something the littlest to the oldest will enjoy playing"
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21:02 < kanzure> someone tried dna + sperm injected into an oocyte and that seemed to sorta work http://science.sciencemag.org/content/284/5417/1180
21:02 < kanzure> not sure why they didn't try that during blastomere stage. maybe it's too difficult to catch.
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21:16 < kanzure> good review of testis-mediated gene transfer stuff https://onlinelibrary.wiley.com/doi/full/10.1111/j.1447-0578.2006.00117.x
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21:21 < kanzure> "... our preliminary trial of repeated injections (up to six injections) of plasmid/liposome (FuGENE6) complex failed to improve the TMGT system.23 The choice of reagents used for gene transfer may be important in improving TMGT: in particular, the use of DMRIE‐C and TransFect appears promising.20"
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21:25 < kanzure> .wik pronuclear injection
21:25 < yoleaux> "Microinjection is the use of a glass micropipette to inject a liquid substance at a microscopic or borderline macroscopic level." — https://en.wikipedia.org/wiki/Pronuclear_injection
21:25 < kanzure> erm..
21:29 < kanzure> direct delivery of mammalian artificial chromosomes into mouse oocyte ...
21:29 < kanzure> ...https://www.researchgate.net/profile/Carl_Perez3/publication/5819227_Pronuclear_microinjection_of_purified_artificial_chromosomes_for_generation_of_transgenic_mice_pick-and-inject_technique/links/591a1cdba6fdccb149f3821f/Pronuclear-microinjection-of-purified-artificial-chromosomes-for-generation-of-transgenic-mice-pick-and-inject-technique.pdf
21:30 < kanzure> oh, it's their protocol. that's nice of them to write that down.
21:32 < kanzure> yeah efficiency of all this stuff is too low to be useful
21:35 < kanzure> it's not clear to me how much engineering has really gone into intracytoplasmic sperm injection.. for example, there's many, many stains available. are they using all those stains for visualizing current state of oocyte? spindle formation? meiosis lifecycle status? chromosome labeling and tracking? oocyte maturity measurement?
21:36 < kanzure> and are they delivering any co-factors (such as proteins or mRNA or whatever) to improve outcomes..
21:37 < kanzure> you should also be able to do the same with sperm of course.. or even spermatids.. e.g. why don't i see lots of fluorescent sperm or fluorescently-labeled chromosomes in sperms in any of the diagrams from these papers? how does the operator know that the sperm cell they picked is a good choice...?
21:39 < kanzure> also it sounds like these people are manully doing intracytoplasmic injection.. so that means they probably only do it on one or two cells total because people get tired, right? but really if it has low efficiency then you want to be doing this hundreds of times on all the available cells.
21:40 < kanzure> robotic intracytoplasmic injection system thingy https://www.ncbi.nlm.nih.gov/pubmed/21521663
21:42 < kanzure> and here's a patent from "the inventor of intracytoplasmic injection" for microfluidic automation of the procedure? not sure why this isn't picked up by a company yet: https://flintbox.com/public/project/24702/
21:42 < kanzure> .title https://patents.google.com/patent/WO2013158658A1
21:42 < yoleaux> WO2013158658A1 - Automated intracytoplasmic sperm injection assisted fertilization system - Google Patents
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--- Log closed Sat Mar 24 00:00:27 2018