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03:26 < fenn> the indiebio live streams seem to have vanished into the aether from whence they came
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06:33 < kanzure> there will be articles written about whatever it was showing. nothing of value lost etc.
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06:48 < chris_99> is tritium obtainable for a random person out of interest, since you can get those tube light things, i was wondering if you can obtain the gas somewhere
07:05 < archels> probably, what for?
07:06 < chris_99> was just curious about betavoltaics, i recall reading something that the technology to make them, uses something very similar/identical to a PV cell
07:07 < chris_99> saw https://www.youtube.com/watch?v=UzV_kzrcSXA on reddit which seems rather suspect to me
07:08 < chris_99> (i meant using PV with just the gas, not a phosphor coated light)
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07:38 < fenn> there are other sources of beta particles besides tritium
07:38 < chris_99> indeed
07:40 < chris_99> maybe a solid would be more suitable, although the commercial chip i saw used tritium
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07:53 < mz_o_> http://www.sciencedirect.com/science/article/pii/S0092867415015056
07:53 < mz_o_> woops putty copied and pasted
07:54 < mz_o_> interesting abstract
07:54 < mz_o_> im gonna visit genspace next week
07:55 < mz_o_> is there anything else i should check out in nyc?
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08:57 < kanzure> "Rapidly evolving homing CRISPR barcodes" http://biorxiv.org/content/early/2016/05/27/055863 (church etc)
08:58 < kanzure> "We present here an approach for engineering evolving DNA barcodes in living cells. The methodology entails use of a homing guide RNA (hgRNA) scaffold that directs the Cas9-hgRNA complex to target the DNA locus of the hgRNA itself. We show this homing CRISPR-Cas9 system acts as an expressed evolving genetic barcode, and corresponding small RNAs can be assayed as single molecules in situ. This integrated approach will have wide ranging ...
08:58 < kanzure> ... applications, such as in deep lineage tracing, cellular barcoding, molecular recording, dissecting cancer biology, and connectome mapping."
08:59 < ebowden_> God, it's always church.
09:00 < ebowden_> That guy's a juggernaut.
09:04 < kanzure> "Massively parallel whole-organism lineage tracing using CRISPR/Cas9 induced genetic scars" http://biorxiv.org/content/early/2016/06/01/056499.abstract
09:14 < kanzure> "Nucleic acid memory" https://news.boisestate.edu/update/files/2016/04/nmat4594Commentary.pdf
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09:53 < nmz787_i> why did hessel say we only have 6 gigabytes worth of DNA?
09:54 < nmz787_i> can a bit have more than a single radix?
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09:54 < nmz787_i> i.e. more than two states?
09:54 < nmz787_i> I thought more states means it is no longer a bit (i.e. that's why there are qubits)
09:57 < kanzure> are you expecting it to be more data or less data?
09:57 < nmz787_i> more
09:58 < kanzure> 3 billion bp * ~3.5 bits per bp (i don't know, you need to include more than 2 bits because maybe methylation data)
09:58 < kanzure> plus or minus all the conserved stuff that is repeated between everyone.  you should really only store the differences against some reference genome.
10:01 < kanzure> i dunno what our longest single-run reads are at the moment, or what the accuracy is, so perhaps you could argue that you would want to store all of the reads from each of the 80x rounds
10:02 < nmz787_i> nah
10:02 < nmz787_i> he was talking about inside cells
10:02 < kanzure> "We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb rRNA operon was covered by a single read."
10:02 < kanzure> from http://www.sciencedirect.com/science/article/pii/S2214753515000224
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10:39 < kanzure> one way to increase the reliability of biology would be to use a selection experiment where you select for cells that are able to survive for long periods with their genome removed from the cell body, followed by reintroduction of the dna at a later time. for the intervening period the cell must survive with whatever it has already manufactured. also gene expression programs wont work.
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11:05 < kanzure> also: if an enzymatic system could be developed to copy a DNA barcode and then copy a pre-existing template message from the genome (like, say, 1 of 20 different hardcoded options) then with dna secretion you could have a simple way to do cell-specific debugging. this is simpler than the ticker tape concept because you don't need custom messages in every cell. you would only be receiving messages regarding 10-30 different distinct states.
11:06 < kanzure> re: "use a nanopore dna sequencer array in the human heart to receive dna memory device messages from the bloodstream", i wonder what the maximum dna content of blood could be before you start clogging up the circulatory system....
11:09 < kanzure> if that was reliably working for the whole brain then you could do animal selection experiments where you try to force all the neurons to use fewer different states (while still preserving behavior) (well, really you would want the cells to prefer the specified states, rather than trying to cheat by using all the unmeasured states)
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13:41 < kanzure> "Flash memory: photochemical imprinting of neuronal action potentials onto a microbial rhodopsin" http://cohenweb.rc.fas.harvard.edu/Publications/Venkatachalam_Cohen_Flash%20Memory_JACS.pdf (2014)
13:41 < kanzure> "We developed a technique, “flash memory”, to record a photochemical imprint of the activity state—firing or not firing—of a neuron at a user-selected moment in time. The key element is an engineered microbial rhodopsin protein with three states. Two nonfluorescent states, D1 and D2, exist in a voltage-dependent equilibrium. A stable fluorescent state, F, is reached by a photochemical conversion from D2. When exposed to light of ...
13:41 < kanzure> ... a wavelength λwrite, population transfers from D2 to F, at a rate determined by the D1 ⇌ D2 equilibrium. The population of F maintains a record of membrane voltage which persists in the dark. Illumination at a later time at a wavelength λread excites fluorescence of F, probing this record. An optional third flash at a wavelength λreset converts F back to D2, for a subsequent write–read cycle. The flash memory method offers the ...
13:41 < kanzure> ... promise to decouple the recording of neural activity from its readout. In principle, the technique may enable one to generate snapshots of neural activity in a large volume of neural tissue, e.g., a complete mouse brain, by circumventing the challenge of imaging a large volume with simultaneous high spatial and high temporal resolution. The proof-of-principle flash memory sensors presented here will need improvements in sensitivity, ...
13:41 < kanzure> ... speed, brightness, and membrane trafficking before this goal can be realized."
13:44 < kanzure> "The evolving capabilities of rhodopsin-based genetically encoded voltage indicators" http://dukespace.lib.duke.edu/dspace/bitstream/handle/10161/10439/2015_GongGEVIreview_0.pdf?sequence=1 (2015)
13:44 < kanzure> "Rational design and large-scale screening efforts have steadily improved the dynamic range and kinetics of the rhodopsin voltage-sensing domain, and coupling these rhodopsins to bright fluorescent proteins has supported bright fluorescence readout of the large and rapid rhodopsin voltage response. The rhodopsin-fluorescent protein fusions have the highest achieved signal-to-noise ratios for detecting action potentials in neuronal ...
13:44 < kanzure> ... cultures to date, and have successfully reported single spike events in vivo."
13:45 < kanzure> "Imaging GFP-based reporters in neurons with multiwavelength optogenetic control" http://cohenweb.rc.fas.harvard.edu/Publications/Venkatachalam_GFPreporters_BiophysJ.pdf (2014)
13:46 < kanzure> "Light-gated ion channels, e.g., Channelrhodopsin-2, enable precise control of firing patterns; green fluorescent protein-based reporters, e.g., the GCaMP6f Ca2+ reporter, enable highly sensitive probing of cellular physiology. However, for most actuator-reporter combinations, spectral overlap prevents straightforward combination within a single cell. Here we explore multiwavelength control of channelrhodopsins to circumvent this ...
13:46 < kanzure> ... limitation. The “stoplight” technique described in this article uses channelrhodopsin variants that are opened by blue light and closed by orange light. Cells are illuminated with constant blue light to excite fluorescence of a green fluorescent protein-based reporter. Modulated illumination with orange light negatively regulates activation of the channelrhodopsin."
13:47 < kanzure> this seems to be a thing to do protein-based imprint lithography? http://pubs.rsc.org/is/content/articlelanding/2015/ra/c5ra08246c#!divAbstract
13:49 < kanzure> "proteorhodopsin optical proton sensor (PROPS)"
13:49 < kanzure> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559597/
13:49 < kanzure> "Until recently, the best results were obtained using voltage-sensitive dyes, in particular a class of organic dyes called the amino-naphthyl-ethenyl-pyridinium (ANEP) dyes, such as di-4-ANEPPS and di-8-ANEPPS (Fluhler et al., 1985)."
13:51 < kanzure> "The general approach to creating a genetically encoded voltage sensor is to fuse a fluorescent reporter, usually from the family of green fluorescent protein (GFP), with a voltage-sensing domain (VSD) in such a way that the conformational changes of the sensor with voltage result in a change in the fluorescence of the reporter.  [....] An entirely new alternative approach emerged in 2011 based upon microbial opsins rather than the GFP ...
13:51 < kanzure> ... family. These proteins transduce light into cellular signals, including changes in membrane potential; the concept behind engineering them into voltage sensors was to reverse this relationship, transducing changes in membrane potential into changes in fluorescence emission."
14:00 < kanzure> "Comparative performance of a genetically-encoded voltage indicator and a blue voltage sensitive dye for large scale cortical voltage imaging" http://journal.frontiersin.org/article/10.3389/fncel.2015.00147/full
14:00 < kanzure> "In this study, we directly compared the performance of a prototypic GEVI, VSFP2.3, with that of a widely used small molecule voltage sensitive dye (VSD), RH1691, in terms of their ability to resolve mesoscopic scale cortical population responses. We used three synchronized CCD cameras to simultaneously record the dual emission ratiometric fluorescence signal from VSFP2.3 and RH1691 fluorescence. The results show that VSFP2.3 offers more ...
14:00 < kanzure> ... stable and less invasive recording conditions, while the signal-to-noise level and the response dynamics to sensory inputs are comparable to RH1691 recordings."
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14:02 < kanzure> "Micro- and nanotechnologies for optical neural interfaces" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781845/
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14:02 < kanzure> ^is good review
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14:09 < kanzure> "A family of photoswitchable NMDA receptors" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786437/ (2016)
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14:14 < kanzure> oh this is a weird one,
14:15 < kanzure> "Optical magnetic detection of single-neuron action potentials using quantum defects in diamond" http://arxiv.org/pdf/1602.01056
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14:53 < kanzure> i only see stuff scheduled up to the 15th but the header says the 17th? http://scipy2016.scipy.org/ehome/146062/332965/
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15:32 < kanzure> "Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864854/ ("crispr imaging")
15:40 < kanzure> "Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666381/ (2015)
15:40 < kanzure> "We describe a modular approach to image RNA in living cells using an RNA aptamer that binds to dinitroaniline, an efficient general contact quencher. Dinitroaniline quenches the fluorescence of different fluorophores when directly conjugated to them via ethylene glycol linkers by forming a non-fluorescent intramolecular complex. Since the binding of the RNA aptamer to the quencher destroys the fluorophore-quencher complex, fluorescence ...
15:40 < kanzure> ... increases dramatically upon binding. Using this principle, a series of fluorophores were turned into fluorescent turn-on probes by conjugating them to dinitroaniline. These probes ranged from fluorescein-dinitroaniline (green) to TexasRed-dinitroaniline (red) spanning across the visible spectrum. The dinitroaniline-binding aptamer (DNB) was generated by in vitro selection, and was found to bind all probes, leading to fluorescence ...
15:40 < kanzure> ... increase in vitro and in living cells. When expressed in E. coli, the DNB aptamer could be labelled and visualized with different-coloured fluorophores and therefore it can be used as a genetically encoded tag to image target RNAs."
15:40 < kanzure> "DNB (the quencher-binding RNA aptamer) and SRB-2 aptamers (a fluorophore-binding RNA aptamer)"
15:42 < kanzure> i wonder if their fluorophore-binding aptamer can be extended to bind to a second aptamer-binding object as well.
15:43 < kanzure> "GFP-tagged RNA binding proteins (RBP) that recognize specific RNA motifs" huh.. okay.
15:43 < kanzure> "Previous attempts using systematic evolution of ligands by exponential enrichment (SELEX) (8) have been made to identify small RNA sequences (aptamers) that bind to fluorogenic dyes (with low or no intrinsic fluorescence) which light up upon binding (9–15). Additionally, aptamers that bind to various fluorophores such as fluorescein (16), sulforhodamine B (16), and tetramethyl­rhodamine (17), have been developed. They could, however, ...
15:43 < kanzure> ... not be used for in vivo applications, primarily due to high background fluorescence. Recently, an aptamer (Spinach) that binds to 3,5-difluoro-4-hydroxybenzylidine imidazoli­none (DFHBI), a derivative of the GFP chromophore, has been developed and used for in vivo RNA imaging, which was the first successful attempt to image RNA with small molecules in live cells (18–20)."
15:45 < kanzure> wasn't there a paper a long time ago about aptamers and positron emission tomography things...
15:54 < kanzure> "Molecular imaging with nucleic acid aptamers" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205285/
15:55 < kanzure> "In one early study, in vivo imaging of inflammation in a rat model was achieved using 99mTc-labeled aptamers [81]. The enzyme elastase, which binds to the surface of activated neutrophils [82], was chosen as the target. An aptamer inhibitor of elastase, isolated in a previous report [83], was tested for imaging applications. Higher target-to-background ratio than antibody-based agents was observed."
15:56 < kanzure> [81] In vivo imaging of inflammation using an aptamer inhibitor of human neutrophil elastase.
15:57 < kanzure> oh PET has ~1 mm resolution so i guess it doesn't matter here
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16:03 < kanzure> hrm there are aptamers that bind to microbubbles to act as ultrasound imaging contrast agents
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16:15 < kanzure> for controlled polymerase projects i think we should be considering modifications of a polymerase ribozyme instead of a protein-based polymerase
16:19 < kanzure> there's a deoxyribozyme ligase
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16:22 < kanzure> "Turning the 10–23 DNAzyme On and Off with Light" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2908382/
16:23 < kanzure> "pH-triggered switchable Mg2+-dependent DNAzymes"
16:23 < kanzure> "DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates"
16:24 < kanzure> there does not seem to be a dna polymerase dnazyme
16:31 < kanzure> here's someone who has made a deoxyribozyme for synthesis of branched RNA molecules? http://www.ncbi.nlm.nih.gov/pubmed/12783536
16:32 < kanzure> "In vitro selection was used to obtain deoxyribozymes that selectively join an internal RNA 2'-hydroxyl with a 5'-terminal triphosphate in a convenient "binding arms" format. At least 85% yield of 2',5'-branched RNA is obtained at 37 degrees C and 20 mM Mn2+, pH 7.5 in </=30 min, and for some DNA enzymes in as little as 2 min (kobs approximately 0.1-2 min-1). This represents a rate enhancement of up to 5 million-fold over the background ...
16:32 < kanzure> ... reaction. Lariat RNA is also synthesized by the new deoxyribozymes."
16:41 < kanzure> "Engineering a selective small-molecule substrate binding site into a deoxyribozyme" https://www.researchgate.net/profile/Claudia_Hoebartner/publication/6144114_Engineering_a_selective_small-molecule_substrate_binding_site_into_a_deoxyribozyme/links/0fcfd5094e6cc81a2a000000.pdf
16:45 < kanzure> "DNA oligonucleotide 3′-phosphorylation by a DNA enzyme" http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00151 (2016)
16:51 < kanzure> "Convergent and general one-step DNA-catalyzed synthesis of multiply branched DNA" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628329/ (2008)
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17:18 < Th3_Prince> hello
17:18 < Th3_Prince> would anyone like to give a 18year entering uni some advice
17:18 < Th3_Prince> deciding a major
17:33 < kanzure> don't go
17:33 < kanzure> "Supercooling enables long-term transplantation survival following 4 days of liver preservation" http://www.nature.com/nm/journal/v20/n7/full/nm.3588.html (2014)
17:33 < kanzure> only lasts 4 days on a perfusion machine? that's dumb.
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17:47 < kanzure> this guy seems to be doing graph rewriting rules for simulation of dnazymes http://repository.dl.itc.u-tokyo.ac.jp/dspace/bitstream/2261/58373/1/A30773.pdf   although i'm not sure why this wouldn't involve molecular dynamics simulation stuff...
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17:56 < kanzure> "Highly-efficient self-replicating RNA enzymes" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943892/ (2014)
17:57 < kanzure> "In-ice evolution of RNA polymerase ribozyme activity" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920166/ (2013)
18:05 < kanzure> "Generation of Oligonucleotides Under Hydrothermal Conditions by Non-enzymatic Polymerization" http://link.springer.com/article/10.1007/s00239-014-9623-2 (2014) early rna world stuff
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18:12 < kanzure> "Self-sustained replication of an RNA enzyme" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652413/ (2009)
18:15 < kanzure> "RNA synthesis by in vitro selected ribozymes for recreating an RNA world" http://www.mdpi.com/2075-1729/5/1/247/htm
18:15 < kanzure> "The most successful polymerase ribozyme to date was developed in three stages: First, a ligase ribozyme was developed by in vitro selection from a random sequence library containing ~1015 different sequences with 220 randomized nucleotides [15]. This ribozyme, termed the “Class I Ligase” (Figure 6A) catalyzes the nucleophilic attack of 3'-hydroxyl groups on RNA 5'-triphosphates, generating 3'-5'-phosphodiester bonds at a rate about ...
18:15 < kanzure> ... 107-fold above that of the uncatalyzed reaction. Second, variants of this ligase ribozyme were designed to extend an RNA primer by six nucleotides, using nucleoside triphosphates [41]. Importantly, the fidelity of these nucleotide additions was 92%, on average. This is much higher than the fidelity estimated from the stability of Watson-Crick pairing (~40%) [41], implying that the ribozyme recognizes to some extent the geometry of a ...
18:15 < kanzure> ... Watson-Crick base pair between the template strand and the incoming nucleoside triphosphate at the catalytic site [82]."
18:15 < kanzure> "Third, an accessory domain was developed for the polymerase ribozyme by in vitro selection [42]. To do this, a 76-nucleotide long randomized sequence was appended to the 3'-terminus of the ligase domain. After 18 rounds of in vitro selection this library gave rise to the R18 (round 18) polymerase ribozyme, which facilitates the templated primer extension of 14 nucleotides, with an average fidelity of 97%. The R18 ribozyme has been the ...
18:15 < kanzure> ... starting point for reselections which have generated the closely related R18 family: notable members include the B6.61 [16] (Figure 6B) and tC19z RNA polymerase ribozymes [17] (Figure 6C)."
18:16 < kanzure> er, 10^15 and not 1015, obviously
18:16 < kanzure> and 10^7 not 107.. bleh. we should really just take over the world and force everyone to use actual notation.
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18:20 < kanzure> the low performance of these polymerase ribozymes is somewhat concerning, i'm sure they could be optimized through some rounds of selection but it seems that protein polymerase will have significantly higher performance for now
18:22 < kanzure> certain aspects of ribozyme catalytic activity can be arrested and switched thanks to lots of research on rna photo(in)activation, and maybe it would be possible to select for photosensitive-selection of nucleotide incorporation... which would be much faster and much easier than directed evolution of a protein.
18:23 < kanzure> actually i take that back. protein chromophores are probably the easier thing because they are specified by amino acids, whereas in oligos you need to apply weird chemicals and it's not often a genetically-encoded photosensitive component (but maybe someone has solved that already, it seems like a thing that people would try to do)
18:24 < kanzure> oh.... "Only one specific 10-nucleotide long template sequence is known to give efficient polymerization (Figure 6B), repeats of which have been demonstrated to yield polymerization of 95 nucleotides (10 repeats, [17]) and 206 nt (19 repeats [87]) when repeats of this sequence were used as template and tethered to the 5'-terminus of the polymerase by direct hybridization (Figure 6C). These reactions demonstrate that there are no steric ...
18:24 < kanzure> ... factors preventing the polymerization of long RNA polymers, consistent with earlier findings with the R18 polymerase [42]."
18:24 < kanzure> well that's not very useful.
18:26 < CaptHindsight> I just logged back in, what is the goal here?
18:27 < kanzure> CaptHindsight: instead of an electronically-controlled protein polymerase, i have proposed using a catalytic RNA ribozyme polymerase mutant
18:28 < kanzure> .wik ribozyme
18:28 < yoleaux> "Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes." — https://en.wikipedia.org/wiki/Ribozyme
18:28 < kanzure> ribozymes can be evolved much more quickly than protein enzymes
18:29 < kanzure> unfortunately it seems that a synthetic polymerase ribozyme had absolutely terrible performance and was only polymerizing incredibly short strands of RNA
18:30 < CaptHindsight> early generation and who knows what their goal was for first pass
18:30 < kanzure> their goal was related to "origins of life" and "RNA world hypothesis" stuff
18:32 < kanzure> "Mutagenesis and selection has been performed resulting in isolation of improved variants of the "Round-18" polymerase ribozyme from 2001. "B6.61" is able to add up to 20 nucleotides to a primer template in 24 hours, until it decomposes by cleavage of its phosphodiester bonds.[3] The "tC19Z" ribozyme can add up to 95 nucleotides with a fidelity of 0.0083 mutations/nucleotide.[4]"
18:32 < kanzure> (from wikipedia)
18:33 < CaptHindsight> I'm going with QC as you synthesize for my work
18:34 < CaptHindsight> it should be programmable
18:35 < kanzure> .wik Spiegelman's Monster
18:35 < yoleaux> "Spiegelman's Monster is the name given to an RNA chain of only 218 nucleotides that is able to be reproduced by an RNA replication enzyme. It is named after its creator, Sol Spiegelman, of the University of Illinois at Urbana-Champaign." — https://en.wikipedia.org/wiki/Spiegelman%27s_Monster
18:35 < CaptHindsight> and the QC part should be usable as a sequencer
18:36 < CaptHindsight> and be under 1um in dia for the whole synthesizer
18:38 < kanzure> 1 micron diameter is your target for v1 ?
18:38 < CaptHindsight> gen3
18:38 < kanzure> :)
18:39 < CaptHindsight> gen1 is tabletop
18:41 < CaptHindsight> whats the name of the co in Germany trying to make synthetic blood?
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18:42 < CaptHindsight> I can't believe that it 2016 and we are still using the real stuff from meat sacks
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18:44 < kanzure> CaptHindsight: liquidia? i think they do synthetic blood stuff.
18:46 < CaptHindsight> was thinking about the best way to do it in the short term
18:46 < kanzure> well then not freitas's respirocyte
18:47 < CaptHindsight> stem cells vs synthetic bone marrow
18:47 < kanzure> megakaryon?
18:48 < CaptHindsight> I just got back from a short stay talking to the hematologists
18:48 < CaptHindsight> be back after I get some sleep
18:49 < CaptHindsight> hospitals suck for sleep
18:49 < kanzure> https://en.wikipedia.org/wiki/Blood_substitute#Current_therapeutics
18:49 < CaptHindsight> it's the stone age
18:49 < kanzure> also some weird stuff about hollowing out red blood cells and inserting other junk http://www.darpa.mil/news-events/2013-11-12
18:50 < kanzure> "In 2010, Hard to Treat Diseases, Inc. (HTD) merged with an anonymous Canadian biotechnology company in hopes to enhance donated blood or hemoglobin based blood substitutes to have a shelf life of 42 days and higher levels of Nitric Oxide when packaged.[6]"
18:51 < kanzure> "In 2013, IIT Madras was approved to mass-produce artificial blood.[8]"
18:51 < kanzure> also pretty sure you don't mean polyheme
18:52 < kanzure> john schloendorn was doing something related to this but it escapes me
18:52 < CaptHindsight> kanzure: what countries tend to be more open to new med tech and clinical trials?
18:52 < kanzure> anything that advertises "medical tourism"
18:53 < CaptHindsight> was looking at those earlier in the week
18:53 < kanzure> you dying?
18:53 < CaptHindsight> was, not anymore
18:53 < kanzure> hmm.
18:54 < CaptHindsight> back later
18:54 < kanzure> seeya
18:55 < kanzure> ".... More recently, engineered polymerases [208] that enable the replication of xeno-nucleic acids XNAs with sugar-altered structures were used in selection experiments to generate XNAzymes [209,210]. Four types of XNA chemistries, including FANAs (5) and HNAs (6), were used to fabricate all-RNA cleaving XNAzymes [210]."
18:56 < kanzure> "A large variety of dN*TPs, equipped with amino acid-like residues as well as non-natural functional groups, have been developed for their use in in vitro selection experiments to generate DNAzymes with an expanded catalytic repertoire [135,136,198,211,212,213,214,215,216]. However, no further modified DNAzymes have been reported so far."
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19:18 < kanzure> "Ribozyme-catalyzed transcription of an active ribozyme" http://bioinfo2.ugr.es/PDFsClase/EvolMol/Ribozyme-Catalyzed%20Transcription_2011.pdf
19:19 < kanzure> it is not clear to me whether they were attempting to optimize for length at all
19:20 < kanzure> if you select for length of polymerized RNA molecules in lieu of anything to do with the template strands, then perhaps you could get some SELEX results that give you polymerase ribozymes that produce really really long RNA strands
19:22 < kanzure> and they probably weren't working towards a templateless polymerase ribozyme because they were investigating early-world self-replication stuff
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19:23 < kanzure> plus i think the branching RNA ribozyme synthesis stuff is evidence that big RNA molecules could be polymerized by ribozymes
19:24 < kanzure> yashgaroth: context is that i'm considering a controlled polymerase made out of RNA instead of protein
19:26 < yashgaroth> it's worth investigating
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19:29 < yashgaroth> also, I just read that technology review article about the glowing plant kickstarter bullshit, and then they just drop in "btw austen hanged himself in the lab" like what the fuck
19:31 < kanzure> :\ his family was asking really nicely that people not mention the circumstances of his demise
19:31 < yashgaroth> well technology review are pricks anyway so I guess I'm not surprised
19:32 < kanzure> it's more likely that they heard it from glowing plant, who have been nothing but annoying
19:32 < kanzure> i think they were being incubated by cambrian or something
19:33 < kanzure> iirc at least some sort of vaginal yeast people were being incubated, if not glowing plant
19:33 < yashgaroth> yeah they said he was found in the lab where they were growing their plants, so I doubt he'd head over to their space just to do it there if they were separate
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19:56 < kanzure> "Photoswitch nucleic acid catalytic activity by regulating topological structure with a universal supraphotoswitch" http://pubs.acs.org/doi/abs/10.1021/sb300120n
19:56 < kanzure> using azobenzene for ribozymes and DNAzymes
19:58 < kanzure> "Light-driven DNA nanomachine with a photoresponsive molecular engine" http://pubs.acs.org/doi/abs/10.1021/ar400308f
19:58 < kanzure> "There are several photoresponsive molecules that convert light energy to mechanical motion through the change of geometry of the molecules; these include spiropyran, diarylethene, stilbene, and azobenzene. Although each molecule has both advantages and drawbacks, azobenzene derivatives are widely used as “molecular photon engines”. In this Account, we review light-driven DNA nanomachines mainly focusing on the photoresponsive DNAs ...
19:58 < kanzure> ... that we have developed for the past decade. The basis of our method is installation of an azobenzene into a DNA sequence through a d-threoninol scaffold. Reversible hybridization of the DNA duplex, triggered by trans–cis isomerization of azobenzene in the DNA sequences by irradiation with light, induces mechanical motion of the DNA nanomachine. Moreover we have successfully developed azobenzene derivatives that improve its ...
19:59 < kanzure> ... photoisomerizaition properties."
20:03 < kanzure> huh cool, dna origami is electrically conductive https://www.researchgate.net/profile/Jinglin_Kong/publication/271525802_Ionic_Conductivity_Structural_Deformation_and_Programmable_Anisotropy_of_DNA_Origami_in_Electric_Field/links/5610fffe08ae0fc513f1a33e.pdf
20:31 < kanzure> i jotted down some notes re: engineering a controlled polymerase ribozyme, https://groups.google.com/d/msg/enzymaticsynthesis/RihLymYxz_E/_gzGuIt6BwAJ
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21:01 < nmz787> I saw some paper recently going around on facebook about DNA being conductive... and the title was more interesting than I felt the paper actually was... like, we've known DNA is conductive/semi-conductive for years
21:02 < nmz787> (or maybe I am lucky to have heard an almost-100-year-old woman give a lecture at my school on her work on it)
21:10 < nmz787> ugh, I can't remember the name for the stronger type of chemical bond.... oh there it is, covalent... took me like 20 seconds of searching/trying hard
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22:18 < kanzure> nmz787_i: welp, sounds like the solution is going to be "use three or more electrodes around the dna origami or dnazyme object, then switch between different electric field shapes to cause different conformational changes".   (probably requires SELEX stuff to select for a dnazyme that has useful conformational changes in the first place, etc.)
22:30 < kanzure> "GaN-based micro-LED arrays on flexible substrates for optical cochlear implants" https://www.researchgate.net/profile/Christian_Gossler/publication/261956236_GaN-based_micro-LED_arrays_on_flexible_substrates_for_optical_cochlear_implants/links/55b23f1808aed621ddfda6e2.pdf
22:30 < kanzure> cc archels
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22:42 < nmz787_i> ok then
22:42 < nmz787_i> looking forward to the results
22:42 < kanzure> :\
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