--- Log opened Mon Dec 25 00:00:53 2017
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00:36 < juul> the building where Counter Culture Labs is located is crowdfunding to renovate our shared commercial kitchen :) https://www.generosity.com/community-fundraising/open-a-kitchen-at-the-omni-commons-in-oakland--2/
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00:56 < juul> kanzure: my irc client line-broke that in an unfortunate way and for a moment i thought it was a new celebrity sexual harassment scandal talking about "the rapy crispr interview"
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10:23 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=d902a953 Bryan Bishop: ZFHX2 pain insensitivity mutation >> http://diyhpl.us/diyhpluswiki/genetic-modifications/
10:56 <@kanzure> "Label-free luminescent oligonucleotide-based probes" http://repository.umac.mo/bitstream/10692/2225/1/10116_0_14-Chem_Soc_Rev%20%20Label-free%20luminescent%20oligonucleotide-based%20probes.pdf
10:56 <@kanzure> "Molecular imaging with nucleic acid aptamers" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205285/
10:59 <@kanzure> "Fabrication of DNA polymer brush arrays by destructive micropatterning and rolling circle amplification" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092525/
11:15 <@kanzure> "Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces" https://www.nature.com/articles/srep12066
11:15 <@kanzure> "... oligonucleotide probes which are assembled at a very low density on gold microelectrodes. By applying alternating electrical potentials these probes are set in motion and perform an oscillatory orientation switching from which two types of measurement variables are obtained in real-time: The switching speed depends on the hydrodynamic friction of the probes and thus indicates the ...
11:15 <@kanzure> ...presence of a bound polymerase, its position along the DNA, and its conformation. At the same time, the extension of electrically aligned “standing” DNA molecules is measured, revealing how many base-pairs have formed in the course of polymerization activity. From these two complementary signals a number of parameters characteristic for the interaction (affinities, kinetics, thermodynamic ...
11:15 <@kanzure> ...energies) and the enzymatic activity (elongation rate, Michaelis-constant, changes in the polymerase conformation) can be analyzed with unprecedented sensitivity. This is demonstrated for the Taq DNA polymerase from T. Aquaticus and the Klenow fragment of Pol I from E. coli. The described assay is applicable to DNA and RNA polymerases and is performed using commercially available chips and ...
11:15 <@kanzure> ...instruments."
11:17 <@kanzure> "Polymerase detection by dynamic DNA switching in alternating electric fields: the binding of a polymerase slows the electrically driven DNA orientation-switching due to an increase in hydrodynamic drag"
11:17 <@kanzure> "Polymerase activity measurement at static DNA orientation: when holding the DNA in an upright orientation by applying a constant repulsive potential, the incorporation of dNMPs results in a fluorescence enhancement proportional to the length of the DNA extension"
11:18 <@kanzure> "The first measurement principle, the dynamic measurement mode, involves an electrical actuation of the DNA by applying alternating voltages of typically ±0.4 V to the gold microelectrodes (Fig. 2A). The negatively charged DNA is repelled from the negatively charged surface and then attracted to the positively charged surface39, and oscillates (switches) between lying and standing ...
11:19 <@kanzure> ...orientations at typically 10 kHz frequency. This movement is monitored in real-time by time-correlated single photon counting, which generates a fluorescence histogram every second to resolve the upward and downward motions as well as the steady state fluorescence levels of lying and standing DNA, respectively (switchSENSE technique)40"
11:19 <@kanzure> "Upon addition of dNTPs to complexes of Taq bound to ss-dsDNA, the fluorescence increases significantly. As the polymerase converts the upper DNA part from a floppy single- to a rigid double-strand, the dye effectively moves away from the fluorescence-quenching surface. This is a consequence of the short-ranged electric field that decays rapidly above the surface due to Debye screening39,41. ...
11:20 <@kanzure> ...It does not significantly affect flexible single-stranded DNA segments which are more than a few nanometers away from the surface and thus they can move about freely. By contrast, for a fully double-stranded helix the repulsion of its surface-proximal segment is effectively transduced to the upper DNA end, because the molecule is rod-like. The fluorescence after removing the Taq by urea from ...
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11:20 <@kanzure> ...the polymerized strand is comparable to the fluorescence of the same layer after removing the polymerized strand and re-hybridizing it with a full length 54 nt cDNA."
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11:23 <@kanzure> i think i am going to propose a concept called a "co-aptamer"... aptamers can sense on their own but you can also develop an aptamer in combination with (1) a template, (2) polymerase, (3) rolling circle amplification, (4) your targets..... and it's a combination of the "aptamer template" and the polymerase that produces a molecular signal in the nascent molecule. in some cases it will ...
11:23 <@kanzure> ...entirely be a function of the template strand and the nascent molecule in which case it's a regular aptamer; however, the total function is defined as an interaction between the polymerase, template, nascent molecule, and the target of interest.
11:24 <@kanzure> advantage of this type of biosensor is that it's much more programmable, and it's basically a molecular recordamer or molecular recorder
11:34 <@kanzure> "The discovery of rolling circle amplification and rolling circle transcription" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568012/
11:41 < nmz787> basically that electro-switchable paper sounds like it's doing impedance spectroscopy, and sees a shift in one of the peaks
11:41 < nmz787> peaks/troughs
11:41 <@kanzure> "... RCA is particularly useful for signal amplification of padlock probes, i.e. linear DNA probes that become circularized upon recognition of a specific nucleic acid sequence (10), since only reacted probes are amplified. Padlock probes have been used to genotype samples of genomic DNA or RNA in solution (5,11–13), or for in situ genotyping of metaphase chromosomes and interphase nuclei ...
11:41 <@kanzure> ...(12,14,15). The combination of padlock probe circularization and amplification through RCA has proven useful for genetic analysis (5,16)."
11:42 < nmz787> hmm
11:42 <@kanzure> yeah...
11:48 < nmz787> hmm, so self-checks for embryos would be good DNA programs
11:49 < nmz787> like for whatever reason embryos don't self-abort for things like trisomies
11:49 < nmz787> or other recessive conditions we know and dislike (cystic fibrosis)
11:51 < nmz787> I guess for recessive conditions, you'd need something like two dCAS9 proteins fused together, each with a primer for the recessive SNP, then somehow engineer them to elicit an AND signal, upon which they re-activate into woking CAS9 and snip the SNP
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11:52 <@kanzure> i think any delivery system for that sort of self-abort will basically involve enough equipment that you might as well directly do the screening using conventional techniques anyway
11:53 < nmz787> sperm-mediated gene transfer is already a thing though
11:53 < nmz787> you just add DNA under the right ionic conditions or something
11:53 < nmz787> then you don't have to extract eggs, do IVF, etc
11:56 < nmz787> http://pubs.acs.org/doi/abs/10.1021/ed4007698
11:57 < nmz787> .title
11:57 < yoleaux> nmz787: Sorry, that doesn't appear to be an HTML page.
11:58 < nmz787> Cost-Effective Systems for Atomic Layer Deposition
11:58 < nmz787> "Each system cost less than $10,000, and they were used to deposit aluminum oxide thin films using trimethylaluminum and water/isopropyl alcohol as coreactants. Whereas the horizontal hot-walled system was able to deposit alumina thin films at a growth rate of 1.2–1.4 Å/cycle, the more sophisticated vertically aligned reactor deposited films at 0.95–1.1 Å/cycle, which is comparable to
11:58 < nmz787> commercial systems costing $100,000 or more. Most importantly, both systems were fabricated entirely by M.S. and undergraduate students"
11:59 <@kanzure> OK, so you want to deliver basic sanity checks through sperm, and do self-abort on failure conditions
12:01 < nmz787> yeah
12:02 < nmz787> then you could expand it to self-abort when intelligence markers aren't found
12:05 <@kanzure> this ain't gonna work unless you have a large number of eggs to sample against...
12:05 <@kanzure> because otherwise you're going to hit a failure each time
12:05 <@kanzure> due to the low probability of finding a high quality match that meets all the conditions
12:06 < nmz787> hmm, well you could self-select for sperm that have recessive conditions at least
12:06 < nmz787> but still, self-abortion means you get at least one chance a month
12:06 < nmz787> otherwise you're waiting many months to get tests on the mother, which aren't 100% diagnostic
12:07 < nmz787> and aborting a big baby is more difficult in any case, regardless of the mental/emotional component
12:09 <@kanzure> it's interesting how resilient these eggs are; you can freeze them, thaw them, inject stuff, and even after all of this they can generally turn into healthy humans
12:13 <@kanzure> "human ovum measures approximately 0.1 mm in diameter"
12:15 <@kanzure> .wik humster
12:15 < yoleaux> "A humster is a hybrid cell line made from hamster oocyte fertilized with human sperm. It always consists of single cells, and cannot form a multi-cellular being." — https://en.wikipedia.org/wiki/Humster
12:16 <@kanzure> ".. male fruit flies have sperm measuring 6 centimeters (2.4 inches) in length, 20 times the size of the flies themselves. ... smaller organisms tend to have the largest sperm."
12:16 <@kanzure> i mean, essentially the booting up of another genome in the wrong species chasis was done by jcvi, just not in the context of oocytes
12:18 < nmz787> wtf
12:18 < nmz787> I have never heard of humsters before today
12:18 <@kanzure> unfortunately the target oocytes have genomic material already. otherwise you could just deliver everything you want in the sperm....
12:19 < nmz787> humsters are my new favorite pet
12:20 < nmz787> only found in the creepy kid on the block's bedroom... and in upstanding university labs
12:20 <@kanzure> "When the sperm enters the egg, the egg's nucleus goes through its final nuclear division and the chromatids separate from one another. One set of chromatids becomes a so-called polar body and is ejected from the cell, while the other set combines with the sperm's half-complement of chromosomes to form a complete genome."
12:20 <@kanzure> "Earlier experiments with mouse and human cells had revealed that immature sperm that still contain two copies of each chromosome could fertilize an egg and produce live births--the egg is evidently able to expel two extra sets of chromosomes before proceeding with normal development."
12:20 <@kanzure> might be possible to deliver everything with sperm *shrug*
12:22 < nmz787> "sperm are transcriptionally silent. So they won't read the introduced DNA."
12:22 <@kanzure> i wonder if it expels any extra chromosome
12:22 < nmz787> re: my comment about sperm self-selection
12:23 <@kanzure> so if you deliver like 100x chromosomes, the chances that it expels the stuff you want would be super low and it will just expel the egg's programming and the extras
12:23 <@kanzure> (not sure if this is true. requires study. and it probably would only work probabilistically-- e.g., not useful if you only have a single oocyte to work with )
12:23 < nmz787> "You'd have to introduce guide rna and protein, even then sperm genomes are packed pretty tight might not get good access."
12:24 <@kanzure> yes but fruit fly sperm are enormous and you can put anything in there
12:28 <@kanzure> too bad, looks like chromosome number regulation is the primary problem "The most common cause of miscarriage is egg aneuploidy—the oocyte contains too many or too few chromosomes"
12:29 <@kanzure> so you're out of luck on that front
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12:53 <@kanzure> "Puzzle imaging: Using large-scale dimensionality reduction algorithms for localization" http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131593
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13:05 < shamir-kh917> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ HAPPY NIGGER MAS!! IF YOU WANT JOIN A CELEBRATION THAT IS NIGGER FREE PLEASE JOIN #/JOIN RIGHT HERE ON THIS NETWORK!! eqygjwjon: potatope jrayhawk ybit Mrkva nsh mrdata- Gurkenglas vikraman abetusk Taek berndj bkero ebowden TMA maaku Burn_ pasky_ y0no dustinm- Cory Hooloovo0 sachy FourFire mrdata jur
13:05 < shamir-kh917> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ HAPPY NIGGER MAS!! IF YOU WANT JOIN A CELEBRATION THAT IS NIGGER FREE PLEASE JOIN #/JOIN RIGHT HERE ON THIS NETWORK!! rgsuze: Hooloovo0 nanotube catern DataPacRat gwillen Malvolio ebowden superkuh FourFire nmz787 thundara_ traumschule balrog Joshchamp juri_ mrdata- saurik Taek Mrk
13:05 < shamir-kh917> ▄▄▄▄▄▄▄▄▄▄▄▄ HAPPY NIGGER MAS!! IF YOU WANT JOIN A CELEBRATION THAT IS NIGGER FREE PLEASE JOIN #/JOIN RIGHT HERE ON THIS NETWORK!! ngoasyhy: mrdata- Gurkenglas justan0theruser redlegion Burn_ catern spurserh berndj maaku saurik darsie jrayhawk DataPacRat yoleaux y0no andytoshi vikraman superkuh drewbot Aurelius Hooloovo0 juri_ HEx1 dustinm- balrog traumschule abetusk ybit
13:05 < shamir-kh917> ▄▄▄▄▄▄▄▄▄▄▄ HAPPY NIGGER MAS!! IF YOU WANT JOIN A CELEBRATION THAT IS NIGGER FREE PLEASE JOIN #/JOIN RIGHT HERE ON THIS NETWORK!! gnopk: Hooloovo0 Cory y0no catern Burn_ thundara_ sachy Aurelius mrdata- TMA Taek nanotube Joshchamp s0ph1a darsie gwillen dustinm- potatope justan0theruser abetusk Gurkenglas kanzure maaku augur redlegion balrog ebowden kuldeep DataPacRat nmz787 nsh sa
13:05 < balrog> kanzure: help
13:05 < shamir-kh917> ▄▄▄▄▄▄▄▄▄▄▄ HAPPY NIGGER MAS!! IF YOU WANT JOIN A CELEBRATION THAT IS NIGGER FREE PLEASE JOIN #/JOIN RIGHT HERE ON THIS NETWORK!! rnwflnydqb: spurserh pasky_ EnabrinTain nanotube ebowden Burn_ potatope kuldeep hehelleshin y0no justan0theruser Cory juri_ andytoshi streety nmz787 berndj Gurkenglas bkero Taek TMA darsie Hooloovo0 drewbot redlegion gwillen Mrkva Aurelius superkuh Data
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13:11 < redlegion> The hell?
13:15 <@kanzure> it's just spam. ignore.
13:15 < redlegion> the frequency and diversity of freenode spam seems to be increasing in the most unlikely places
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14:09  * EnabrinTain stirs in the darkness
14:09  * EnabrinTain extinguishes another spammer
14:36 < nmz787> kanzure: the weird thing is, trisomies are not that uncommon in live births
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20:25  * nmz787 reads http://diyhpl.us/~nmz787/pdf/Cost-Effective_Systems_for_Atomic_Layer_Deposition.pdf
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21:46 <@kanzure> hrm
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--- Log closed Tue Dec 26 00:00:54 2017