--- Log opened Mon Jul 20 00:00:16 2015
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05:21 < kanzure> someone recommends this person for chemistry stuff http://sf.indiebio.co/mentor/j-william-efcavitch-ph-d/
05:32 < kanzure> http://blueturtlebio.com/ "a therapy for Gaucher's disease. Our product is an engineered gut microbe capable of secreting the required enzymes (Glucocerebrosidase)"
05:33 < CaptHindsight> "Bill is the co-founder and CSO of Molecular Assemblies, an early stage biotechnologies tool company dedicated to re-inventing the way that synthetic oligonucleotides are produced." so has anyone or not been able to synthesize synthetic nucleotides yet?
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05:33 < CaptHindsight> if they have, how long are they?
05:33 < kanzure> i don't understand your question
05:34 < CaptHindsight> heh, well if he's dedicated to "re-inventing the way that synthetic oligonucleotides are produced" does this mean that it's not been done successfully yet?
05:34 < kanzure> it's been done successfully, it just sucks
05:35 < CaptHindsight> what "sucks" about it?
05:35 < kanzure> what sucks about oligonucleotide synthesis? everything
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05:35 < kanzure> the no-water requirements, the low yield, etc.
05:35 < kanzure> gene assembly also sucks
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05:36 < kanzure> http://www.molecularassemblies.com/
05:36 < kanzure> .title http://www.google.com/patents/US8808989
05:36 < yoleaux> Patent US8808989 - Methods and apparatus for synthesizing nucleic acids - Google Patents
05:37 < CaptHindsight> so wouldn't it be a good idea to write up the current working synthesis methods and along side that the problems?
05:37 < kanzure> "The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using enzymes and specially designed nucleotide analogs. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template"
05:37 < kanzure> CaptHindsight: all of the phosphoramidite methods suck. and all of the phosphotriester methods.
05:37 < kanzure> "exposing a nucleic acid attached to a solid support to a nucleotide analog in the presence of a nucleotidyl transferase enzyme and in the absence of a nucleic acid template"
05:38 < kanzure> "wherein the nucleotide analog comprises an unmodified 3′ hydroxyl and a cleavable terminating group comprising an amino acid, wherein the cleavable terminating group blocks nucleotidyl transferase activity but results in a nucleotide substrate for nucleotidyl transferase upon cleavage"
05:38 < CaptHindsight> so who has the flowchart on all the working versions of synthesis and a list of problems?
05:39 < CaptHindsight> has anyone organized any of this info?
05:39 < kanzure> "In one aspect, the disclosed methods employ commercially-available nucleotidyl transferase enzymes, such as terminal deoxynucleotidyl transferase (TdT), to synthesize polynucleotides from nucleotide analogs in a step-by-step fashion. "
05:39 < kanzure> CaptHindsight: nobody has organized that, no
05:40 < CaptHindsight> seems like a good first step
05:40 < kanzure> i'm not sure which amino acid protecting groups they are using here
05:40 < kanzure> CaptHindsight: why? i already know it sucks :-)
05:41 < kanzure> "The linker can be any molecular moiety that links the inhibitor to the NTP and can be cleaved, e.g., chemically cleaved, electrochemically cleaved, enzymatically cleaved, or photolytically cleaved. For example, the linkers can be cleaved by adjusting the pH of the surrounding environment. The linkers may also be cleaved by an enzyme that is activated at a given temperature, but inactivated at another temperature. In some embodiments, ...
05:41 < kanzure> ... the linkers include disulfide bonds."
05:41 < CaptHindsight> since the people that seem to already work in this field don't really seem concerned about improvements
05:42 < CaptHindsight> it's been odd asking around, even the input from Cambrian
05:42 < kanzure> "As discussed above, the inhibitor coupled to the nucleotide analog will cause the transferase, e.g., TdT, to not release from the polynucleotide or prevent other analogs from being incorporated into the growing chain. A charged moiety results in better inhibition, however, research suggests that the specific chemical nature of the inhibitor is not particularly important. For example, both phosphates and acidic peptides can be used to ...
05:43 < kanzure> ... inhibit enzymatic activity. See, e.g., Bowers et al., Nature Methods, vol. 6, (2009) p. 593-95, and U.S. Pat. No. 8,071,755, both of which are incorporated herein by reference in their entireties. In some embodiments, the inhibitor will include single amino acids or dipeptides, like -(Asp)2, however the size and charge on the moiety can be adjusted, as needed, based upon experimentally determined rates of first nucleotide ...
05:43 < kanzure> ... incorporation and second nucleotide incorporation. That is, other embodiments may use more or different charged amino acids or other biocompatible charged molecule."
05:43 < kanzure> "In one embodiment, the polymerase/transferase enzymes can be modified so that they cease nucleotide addition when they encounter a modification to the phosphate of a 3′-unmodified dNTP analog. This scheme would require a deblocking reagent/reaction that modifies the phosphate end of the nucleotide analog, which frees up the nascent strand for subsequent nucleotide incorporation. Preferred embodiments of this approach would use ...
05:43 < kanzure> ... nucleotide analogs modified only at the phosphates (alpha, beta or gamma) although modifications of the purine/pyrimidine base of the nucleotide are allowed."
05:43 < kanzure> i'm not sure if this means they know how to do that.... or if they are just land grabbing.
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05:44 < kanzure> "Another embodiment for using non-template dependent polymerase/transferase enzymes would be to using protein engineering or protein evolution to modify the enzyme to remain tightly bound and inactive to the nascent strand after each single nucleotide incorporation, thus preventing any subsequent incorporation until such time as the polymerase/transferase is released from the strand by use of a releasing reagent/condition. Such ...
05:44 < kanzure> ... modifications would be selected to allow the use of natural unmodified dNTPs instead of reversible terminator dNTPs. Releasing reagents could be high salt buffers, denaturants, etc. Releasing conditions could be high temperature, agitation, etc. For instance, mutations to the Loop1 and SD1 regions of TdT have been shown to dramatically alter the activity from a template-independent activity to more of a template dependent activity. ...
05:44 < kanzure> ... Specific mutations of interest include but are not limited to Δ3384/391/392, del loop1 (386→398), D339A, F401A, and Q402K403C404→E402R403S404. Other means of accomplishing the goal of a post-incorporation tight binding TdT enzyme could include mutations to the residues responsible for binding the three phosphates of the initiator strand including but not limited to K261, R432, and R454."
05:44 < kanzure> okay so again...... this is just landgrabbing?
05:44 < kanzure> argh
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05:46 < kanzure> infuriating
05:46 < kanzure> "Specific mutations of interest include but are not limited to Δ3384/391/392, del loop1 (386→398), D339A, F401A, and Q402K403C404→E402R403S404."
05:47 < kanzure> ah yes, Q402K403C404→E402R403S404
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05:50 < kanzure> CaptHindsight: the closest comparison is going to be this document, http://diyhpl.us/~bryan/papers2/DNA/Large-scale%20de%20novo%20DNA%20synthesis:%20technologies%20and%20applications%20-%20Church%20-%202014.pdf
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05:58 < CaptHindsight> thank you, I've seen that one recently
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06:26 < kanzure> http://www.scientificamerican.com/article/stephen-hawking-and-yuri-milner-announce-100m-initiative-to-seek-extraterrestrial-intelligence/
06:27 < kanzure> "Milner's latest project is part of the Foundation's new Breakthrough Initiatives division and is called Breakthrough Listen. Providing $100 million in funding over the next decade to top SETI researchers, Breakthrough Listen will allow new state-of-the-art radio and optical surveys to take place using the world's premiere telescopes, creating the most ambitious and robust SETI program yet performed. The project is set to begin making ...
06:27 < kanzure> ... observations in 2016."
06:40 < kanzure> feynman explaining computers https://www.youtube.com/watch?v=EKWGGDXe5MA&t=5m
06:40 < kanzure> apparently filing cabinets used to be operated by file clerks
06:54 < archels> for some definitions of computing
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06:56 < kanzure> for some reason i really hope there were file clerks on pirate ships
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06:59 < kanzure> "if you could define exactly a definite procedure to tell someone how to think, then i wouldn't need you people, i would program a computer to do it" https://www.youtube.com/watch?v=EKWGGDXe5MA&t=44m20s
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07:01 < archels> yeah, but the whole bootstrapping process involves lots of people
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07:15 < kanzure> .title https://www.youtube.com/watch?v=d4QFNWBSZYg
07:15 < yoleaux> Building a liquid crystal display (LCD) - YouTube
07:18 < kanzure> "Light-driven motion of liquids on a photoresponsive surface" http://mipd.snu.ac.kr/upload/tep06_1_1/light_driven_liquid_motion_wetting(sci00_288_1624).pdf
07:23 < kanzure> why hasn't someone tried a "photoresponsive surface" with an LED array.
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08:02 < kanzure> davm_: hi
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09:21 < delinquentme> https://www.youtube.com/watch?v=lhjk5x54bsE
09:21 < delinquentme> super goo
09:21 < delinquentme> synth-EDM with a bit of funk
09:22 < kanzure> .title
09:22 < yoleaux> The Turntable Turnabout (Mystery Skulls - Money) - YouTube
09:27 < kanzure> fenn: what about using an inkjet just for dispensing, but you use macroscopic-sized tubes and vials. this way, you don't need a mechanical stage to move a micropipette a few microns to the next pore. you would use normal-sized pipetting.
09:29 < kanzure> microcentrifuge tubes have a height of 42 mm
09:29 < kanzure> and diameter of 11 mm
09:33 < kanzure> thus you would only need an 11 m^2 area :P
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09:33 < kanzure> (unless you stack or use space more efficiently...)
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10:26 < kanzure> http://blog.ycombinator.com/yc-fellowship
10:27 < kanzure> and https://news.ycombinator.com/item?id=9917334
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12:00 < kanzure> optoelectrowetting using a laser pointer https://www.youtube.com/watch?v=8PeYwGDnt7I
12:02 < kanzure> same person https://www.youtube.com/watch?v=FuhqoCV8YdM
12:03 < kanzure> https://www.youtube.com/watch?v=DVTU7OgWcHY
12:04 < kanzure> same thing but with better descriptions https://www.youtube.com/watch?v=UtH1-_r9TtY
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12:11 < kanzure> droplet seems to roll to the right at the end though.. so either it's following the path of the laser, or it's on an incline? https://www.youtube.com/watch?v=8PeYwGDnt7I&t=1m59s
12:12 < kanzure> fenn i'm almost completely sure that you have already built this system before
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12:23 < juri_> this is probably pretty far off of the wall, but i was recently reading an article in nature, "vapour mediated sensing and mobility in two component droplets", and was wondering if we could use similar techniques to 'move' the droplets that have a high number of successful encodings, to seperate them from the bad encoding droplets.
12:24 < juri_> we could print on X, move on Y, repeat, repeat, repeat.
12:25  * juri_ is not a biologist of any sort, sadly. :(
12:28 < jrayhawk> the dancing droplets paper also has some associated videos, fwiw
12:29 < jrayhawk> https://www.youtube.com/watch?v=K8Wx2PHIYGI
12:29 < jrayhawk> .title
12:29 < yoleaux> Droplet Dancing - YouTube
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12:52 < kanzure> juri_: so your idea is "move droplets"? and previously we were not thinking about moving droplets..?
12:53 < kanzure> vapor seems like a mechanism of contamination that should be avoided
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13:04 < juri_> my idea was using vapour. i said it wasn't a very good one. ;)
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14:09 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - george church
14:09 -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Wed May 20 12:46:25 2015]
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14:09 [ AmbulatoryCortex] [ crescendo    ] [ gnusha     ] [ marchtemp      ] [ Quashie_    ] [ the8thbit] 
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14:09 [ Betawolf        ] [ drewbot      ] [ jrayhawk   ] [ nsh            ] [ strages     ] [ yoleaux  ] 
14:09 [ bkero           ] [ dustinm      ] [ juri_      ] [ p4nd4          ] [ strangewarp ] [ yorick   ] 
14:09 -!- Irssi: ##hplusroadmap: Total of 90 nicks [0 ops, 0 halfops, 0 voices, 90 normal]
14:09 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010
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16:58 < kanzure> beep
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17:03 < streety> I thought moving droplets was being discussed. Or, was that for a later stage after synthesis?
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17:10 < kanzure> it was; it just seemed like someone claimed that movement was not being discussed
17:11 < kanzure> "and i was wondering if we could use techniques to 'move' the droplets"
17:26 < streety> now I follow
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17:50 < jrayhawk> https://www.youtube.com/watch?v=drD416THU7Y
17:50 < jrayhawk> .title
17:50 < yoleaux> CMR Demos Its Printed Polarity Magnets - YouTube
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18:08 < jrayhawk> https://www.youtube.com/watch?v=POc32aioLFE
18:08 < jrayhawk> .title
18:08 < yoleaux> Correlated Magnetics: Non-contact attachment - YouTube
18:19 < jrayhawk> i wonder how good that is for seismic isolation
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--- Log closed Tue Jul 21 00:00:17 2015