--- Log opened Fri Sep 15 00:00:18 2017
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00:13 < kanzure> hrmph
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05:58 < fltrz> suppose you have a long ssDNA string of repeating [ACGT]* where ACGT was an arbitrary string, but the same string was repeated, does the repetition unit have a name in polymer chemistry? can it be considered a monomer?
05:59 < fltrz> i.e. a homopolymer of ACGT
05:59 < fltrz> I guess I'm looking for the word "repetition chemical", perhaps monomer encompasses this concept as well?
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06:08 < kanzure> repeats are a problem in sequencing fure sho
06:15 < fltrz> the sequencing would not measure the confusing repeating base calls but the bistable state, say the secondary structure of folding
06:15 < fltrz> to avoid chemical reactions
06:16 < fltrz> (during writing)
06:16 < fltrz> nanopore just measures the geometric obstruction of the pore, which lowers its conductivity
06:19 < fltrz> if the repeating segment of the molecular tape can fold in 2 or more ways, and they obstruct the pore differently, you can measure that as a different conductivity of the pore, so instead of sequencing the individual nucleotides you sequence the secondary structure
06:19 < fltrz> if the repeating segment has just 2 secondary folding states it would be bistable, and the alphabet would be binary
06:21 < fltrz> historically we wrote additively (adding ink and solvent to paper, the solvent evaporates, the ink is added to the paper locally) and erased subtractively (a pencil eraser for examples abrades and erodes paper away, so you cant indefinitely erase, at some point you get through the paper)
06:23 < fltrz> but at some point we realized bistable stated (flip flop in SRAM, charge across an open circuit capacitor [if leaky refresh], spin up or spin down in the crystal of the magnetic material on HDD platter/magnetic tape,
06:25 < fltrz> different phase state of the optical medium in DVD-RW (crystalline/amorphous)
06:25 < fltrz> once you have bistable state you don't need reagents for reading and writing
06:26 < fltrz> the HDD does not need ink and eraser refills
06:29 < fltrz> how is DNA initially threaded through a pore? a bead does not fit through the pore
06:30 < fltrz> or is the DNA on a beadd on one side of the pore, then that side temperature lowered, and other side temperature increased in order for some entropic effect to pull the dna through the pore?
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07:10 < fltrz> suppose you find (using DNA origami software) a sequency of (ss)DNA/RNA/... so that the secondary structure has 2 states, say a disklike structure which is either parallel or orthogonal to the DNA strand, if its orthogonal the pore blockade will be high, if its parallel it will be low
07:11 < fltrz> then you just need a means of changing the state for writing
07:12 < fltrz> from https://en.wikipedia.org/wiki/DNA_origami
07:12 < fltrz> "In a study conducted by a group of scientists from iNANO center and CDNA Center at Aarhus university, researchers were able to construct a small multi-switchable 3D DNA Box Origami."
07:13 < fltrz> "The proposed nanoparticle was characterized by AFM, TEM and FRET. The constructed box was shown to have a unique reclosing mechanism, which enabled it to repeatedly open and close in response to a unique set of DNA or RNA keys."
07:13 < fltrz> "The authors proposed that this "DNA device can potentially be used for a broad range of applications such as controlling the function of single molecules, controlled drug delivery, and molecular computing.""
07:14 < fltrz> seems these guys would know how to switch bistable DNA states since they dunnit
07:14 < fltrz> screw reagents
07:14 < nmz787> no beads with nanopore
07:15 < fltrz> nmz787: so its the electrical current that drags the DNA?
07:15 < nmz787> threaded with electrophoresis i believe
07:15 < nmz787> elctric field
07:16 < fltrz> nmz787: but how does the first end to enter find its way?
07:16 < fltrz> isn't the DNA thermodynamically coiled?
07:17 < fltrz> electrophoresis somehow guides the loose end of DNA into the pore?
07:19 < fltrz> "Given the fact that the sugar-phosphate backbone in DNA molecules is negatively charged, this electric force can drag any DNA molecule which comes close to the nanopore."
07:19 < fltrz> but what if the middle of a long strand of DNA came close to the pore first?
07:22 < fltrz> or at that point the DNA strand is glued to the pore like a steel wire to a magnet, and brownian motion drags the DNA strand back and forth until eventually a terminating end is pulled over the pore and gets sucked in?
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07:26 < fltrz> the wikipedia page on nanopore sequencing shows the dna and biological nanopore initially connected with an oligomer
07:28 < fltrz> https://www.researchgate.net/post/Good_software_for_DNA_RNA_3D_structure_prediction for DNA origami?
07:29 < fltrz> http://physicstoday.scitation.org/doi/abs/10.1063/PT.3.1909?journalCode=pto
07:29 < fltrz> .title
07:30 < fltrz> "Threading DNA through a nanopore"
07:37 < nmz787> fltrz: most likely you can find a video of soeone threading some long DNA through nanopore/nanochannel... people must have had the same idea
07:38 < nmz787> they might do something with alternating electric fields, idk
07:38 < fltrz> nmz787: hm not sure how to find such a video?
07:38 < nmz787> the halyon folks were linearizing DNA using an air/water interface... but i don't think I've heard any indication that oxford nanopore has done that
07:39 < nmz787> fltrz: google scholar, I guess
07:39 < nmz787> halcyon*
07:40 < fltrz> hmm aparently threading refers to the translocation itself, not the initial putting the thread through the eye of the needle
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07:43 < nmz787> this paper reviews some different nanopore fab methods
07:43 < nmz787> http://www.sciencedirect.com/science/article/pii/S1672022915000133
07:43  * nmz787 read the solid state section
07:43  * nmz787 reads*
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08:40 < fltrz> nmz787: interesting
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09:43 < kanzure> "Complete genes may pass from food to human blood" http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0069805
10:00 < nmz787> hmm, you are what you eat, eh?
10:03 < nmz787> the wifi at the airport seems MUCH better than that of the hotel :/
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10:26 < kanzure> streety: streety_: check PMs
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11:18 < nmz787> fltrz: just confirmed you need to ligate adapters before using the oxford nanopore... I guess that guides the end to the pore, then they must melt with heat and start the voltage
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11:44 < streety> thanks, will read this evening
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12:20 < kanzure> twist mentioned they are using a "deposition system" but it's not inkjets
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14:06 < kanzure> forrest says do a knockdown MTCH2
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14:15 < kanzure> "I think one RNAi payload could knock down mtch2, myostatin, ccr5, and a few other things that'd be best gone [for sperm-mediated]"
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16:30 < nmz787> kanzure: I think they were just rebranding/renaming inkjets because they aren't dispensing ink
16:31 < kanzure> hmm. maybe.
16:32  * nmz787 checks out mtch2
16:50 < nmz787> diyhpl.us doesn't have any info on mtch2  :/
16:50 < nmz787> gotta get my infoz elsewherez
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16:54 < kanzure> "Loss of muscle MTCH2 increases whole-body energy utilization and protects from diet-induced obesity" http://www.cell.com/cell-reports/fulltext/S2211-1247(16)30024-9
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17:29 < delinquentme> Obesity genes [ FTO, MC4R, KCTD15, MTCH2, NEGR1, and BDNF ] identified in genome-wide association studies are associated with adiposity measures and potentially with nutrient-specific food preference http://ajcn.nutrition.org/content/90/4/951
17:32 < delinquentme> "For the SH2B1, KCTD15, MTCH2, and NEGR1 loci, the obesity-risk alleles were associated with dietary intake of saturated fat, carbohydrates, mono- and disaccharides, and polysaccharides. "
17:37 < kanzure> .wik geopolymer cement
17:37 < yoleaux> "From a terminological point of view, geopolymer cement is a binding system that hardens at room temperature, like regular Portland cement. If a geopolymer compound requires heat setting it may not be called geopolymer cement but rather geopolymer binder." — https://en.wikipedia.org/wiki/Geopolymer_cement
17:37 < kanzure> sodium silicate + fly ash
17:38 < nmz787>  www.23andMesettlement.com
17:38 < nmz787> I might get a few multiples of $12.50
17:39 < cluckj> hah
17:39 < cluckj> that could be tens of dollars
17:39 < delinquentme> what exactly was the claim over?
17:41 < nmz787> "Personal Genome Service (“PGS”)... PGS was sold to consumers based on inaccurate or misleading information regarding the PGS specifications and capabilities"
17:41 < nmz787> idk, I felt pretty satisfied
17:42 < nmz787> but then I guess I 'm a semi-power-user
17:43 < kanzure> it's not about satisfaction. the compalint is that it was not in compliance with the laws.
17:45 < nmz787> kanzure: is that geopolymer thing just what the Romans used? https://www.nature.com/news/seawater-is-the-secret-to-long-lasting-roman-concrete-1.22231
17:45 < kanzure> yea basically
17:45 < kanzure> sand + lye
17:50 < kanzure> "Doesn't a storm slightly above the sub send waves of pressure that are about as dangerous?"
17:57 < nmz787> submarine?
17:58 < kanzure> yes this is re: subs
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17:59 < nmz787> ok, not grinders/hoagies/footlongs/big-long-sandwiches
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23:22 < fltrz> https://www.azonano.com/news.aspx?newsID=35656
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--- Log closed Sat Sep 16 00:00:19 2017