--- Log opened Sat Mar 11 00:00:55 2017
00:03 < fenn> " We had a CRISPR workshop in our lab, and 25 people went through the procedure of the ODIN's CRISPR kit. During the experiment
00:03 < fenn> we told everyone that we would actually need a permit for completing the experiment, but if they wanted too they could just go ahead and do it anyway. To my surprise no one wanted to finish the
00:03 < fenn> experiment."
00:21 < fenn> "since 1990 organic food sales exploded, and so did autism" lool
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03:53 < jrayhawk> that limpet thing is cool
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04:28 < cluckj> fenn, where is that CRISPR quote from?
04:30 < streety> I think Pieter Waag made the comment on one of his posts to the DIYbio mailing list
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04:31 < streety> I wonder how that event was marketed. If I attended a 'CRISPR workshop' I think I would expect to actually perform a CRISPR experiment
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05:58 < kanzure> "Erythroxylum coca cocaine synthase mRNA, complete cds" https://www.ncbi.nlm.nih.gov/nuccore/KC140149
05:58 < kanzure> "The last step in cocaine biosynthesis is catalyzed by a BAHD acyltransferase" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281001/
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08:21 < kanzure> hmph i still haven't found a good brain neuroanatomy visualization tool
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08:27 < kanzure> "Understanding understanding source code with fMRI" http://www.infosun.fim.uni-passau.de/cl/publications/docs/SKA+14.pdf (2014)
08:32 < kanzure> i wonder if they looked at non-programmers trying to decode syntax, like in the style of searle's chinese room.  supposedly it should cause similar activation, i think, just less efficient.
08:33 < kanzure> next up "microneuroanatomy of brain inflammation caused by prolonged exposure to gdb"
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09:00 < kanzure> daylight savings time shifts and myocardial infarctions and fatal car crashes http://www.nejm.org/doi/full/10.1056/NEJMc0807104 https://www.aeaweb.org/articles?id=10.1257/app.20140100
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10:30 < maaku> entity8421[m]: GTD works just fine as-is. just also surround yourself with super productive people as kanzure says
10:38 < c0rw1n> wow wait we can now check if people understand things? or is that specifically for source code only?
10:40 < c0rw1n> mm this one only checked for comprehension of code
10:44 < kanzure> https://snarky.ca/how-the-heck-does-async-await-work-in-python-3-5/
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11:38 < nmz787_> fenn: my love of the movie "Mr. Limpet" has renewed meaning now :)
11:43 < nmz787_> heh, USPS somehow glitched and my package went from downtown Portland, last night, to Phoenix AZ this morning...
11:43 < nmz787_> frigging computotrons and their messed up programs
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18:32 < kanzure> "Precise base editing in rice, wheat and maize with a Cas9- cytidine deaminase fusion" http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3811.html https://twitter.com/NatureBiotech/status/836271198355009536
18:33 < kanzure> "Multiplexed confocal and super-resolution fluorescence imaging of cytoskeletal and neuronal synapse proteins" http://www.biorxiv.org/content/early/2017/02/25/111625 https://twitter.com/eboyden3/status/836175796117065728
18:34 < kanzure> "Neuronal synapses contain dozens of protein species whose expression levels and localizations are key determinants of synaptic transmission and plasticity. The spectral properties of fluorophores used in conventional microscopy limit the number of measured proteins to four species within a given sample. The ability to perform high-throughput confocal or super-resolution imaging of many protei...
18:34 < kanzure> ...ns simultaneously without limitation in target number imposed by this spectral limit would enable large-scale characterization of synaptic protein networks in situ. Here, we introduce PRISM: Probe-based Imaging for Sequential Multiplexing, a method that sequentially utilizes either high affinity Locked Nucleic Acid (LNA) or low affinity DNA probes to enable diffraction-limited confocal and PAI...
18:34 < kanzure> ...NT-based super-resolution imaging. High-affinity LNA probes offer high-throughput, confocal-based imaging compared with PAINT, which uses low affinity probes to realize localization-based super-resolution imaging. Simultaneous immunostaining of all targets is performed prior to imaging, followed by sequential LNA/DNA probe exchange that requires only minutes under mild wash conditions. We appl...
18:34 < kanzure> ...y PRISM to quantify the co-expression levels and nanometer-scale organization of one dozen cytoskeletal and synaptic proteins within individual neuronal synapses. Our approach is scalable to dozens of target proteins and is compatible with high-content screening platforms commonly used to interrogate phenotypic changes associated with genetic and drug perturbations in a variety of cell types."
18:34 < kanzure> oops i mean http://biorxiv.org/content/early/2017/03/01/111625
18:34 < kanzure> hm is that FISSEQ?
18:36 < kanzure> technique diagram on page 17 figure 1
18:36 < nmz787_> I just got introduced to someone at ReadCoor (FISSEQ company) a few days ago
18:37 < kanzure> "Nucleic acid imaging probes specific to each [antibody] marker (e.g., p1-p10) are applied and imaged sequentially, with each imaging strand washed out after image acquisition at each step."
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19:14 < kanzure> " Array Tomography (AT) has been applied to volumetric imaging of synapses within intact brain tissue by sequentially staining and stripping the same ultrathin tissue sections with different antibodies[8,12,13]. More recently, gel embedding and expansion of whole intact organs has been used with sequential antibody loading and stripping to generate 13-channel fluorescence imaging datasets[14]....
19:14 < kanzure> ... In addition, Cyclic Immunofluorescence (CycIF) has been applied to cancer cell lines to generate 9-channel diffraction-limited imaging using repetitive antibody loading-bleaching cycles."
19:15 < kanzure> 'imaging mass cytometry'
19:16 < kanzure> "Protein-fragment-based probes have alternatively been used to generate multiplexed cytoskeletal and focal adhesion super-resolution images with higher labeling density compared with antibody-based approaches[21]."
19:17 < kanzure> .wik photoactivated localized microscopy
19:17 < yoleaux> "Photo-activated localization microscopy (PALM or FPALM) and stochastic optical reconstruction microscopy (STORM) are widefield (as opposed to point scanning techniques such as laser scanning confocal microscopy) fluorescence microscopy imaging methods that allow obtaining images with a resolution beyond the diffraction limit." -- https://en.wikipedia.org/wiki/Photoactivated_localization_microscopy
19:22 < kanzure> so why didn't they go for receptor types as their targets instead of cortactin, synapsin, etc.
19:22 < kanzure> oh it looks like they did an NMDA receptor (NR2B)
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19:36 < kanzure> 'site-specific chemoenzymatic labeling'
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21:11 < nmz787_> :( bricked two micropython boards
21:12 < kanzure> someone attempts to explain soft-fork backwards compatible upgrades https://www.reddit.com/r/Bitcoin/comments/5ywghq/a_soft_fork_is_just_a_reversed_hard_fork/detjc2d/
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21:55 < kanzure> "Neural episodic control" https://arxiv.org/pdf/1703.01988.pdf
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21:57 < nmz787_> got them back up :)
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22:00 < kanzure> bricking was unsuccessful, please try again
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--- Log closed Sun Mar 12 00:00:56 2017