--- Log opened Mon Jul 06 00:00:02 2015
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02:46 < jrayhawk> https://www.flickr.com/photos/kylemcdonald/19266856649/sizes/o/
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03:27 < kanzure> .title https://news.ycombinator.com/item?id=9836336
03:27 < yoleaux> Hacking Team hacked, attackers claim 400GB in dumped data | Hacker News
03:44 < kanzure> "Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces" http://www.bakerlab.org/system/files/Gonen_2DArrays_Baker2015.pdf
03:44 < kanzure> "We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We used the method to design ...
03:45 < kanzure> ... proteins that self-assemble into layer groups P 3 2 1, P 4 2(1) 2, and P 6. Projection maps of micrometer-scale arrays, assembled both in vitro and in vivo, are consistent with the design models and display the target layer group symmetry. Such programmable 2D protein lattices should enable new approaches to structure determination, sensing, and nanomaterial engineering."
03:47 < kanzure> "Accurate design of co-assembling multi-component protein nanomaterials" http://www.bakerlab.org/system/files/King_Nature2014A.pdf
03:47 < kanzure> figure 4 "Electron micrographs of designed two-component protein
03:47 < kanzure> nanomaterials."
03:47 < kanzure> no wait, figure 5 is better
03:51 < kanzure> "Automating human intuition for protein design" http://www.bakerlab.org/system/files/Niv%C3%B3n_prot24463_13M.pdf
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03:54 < kanzure> a more general review of de novo protein design (open access) http://www.sciencedirect.com/science/article/pii/S0959440X1500069X
03:55 < kanzure> a grammar for protein backbone structure using "protein blocks" http://onlinelibrary.wiley.com/doi/10.1002/pro.2581/pdf
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05:52 < kanzure> eudoxia: same request goes for you (regarding listmaking of useful molecular machines)
05:54 < eudoxia> hmm
05:54 < eudoxia> MNT style machines or just anything useful?
05:59 < kanzure> anything useful
05:59 < kanzure> not necessarily molecular nanoprobe stuff
06:00 < eudoxia> right, also proteins and shit
06:02 < kanzure> well, protein-equivalent machines could count, but let's skip proteins themselves here
06:02 < kanzure> having a molecular differential gear is nice, but only if you have other components to make use of it. meanwhile there are probably simple molecular machines that are useful in isolation.
06:04 < eudoxia> sort of like what the parts library of NE was meant to become
06:05 < kanzure> huh?
06:06 < kanzure> the parts library was full of differential gears
06:06 < eudoxia> .title http://crnano.org/interview.freitas.htm
06:06 < yoleaux> Nanotechnology: Robert Freitas Interview
06:06 < eudoxia> >We’d expect the library of designed machine systems to rapidly expand from the current 1-2 dozen items (including mostly just a few bearings, gears, and joints) into the hundreds or thousands in just a few years.
06:06 < eudoxia> oh bobbie
06:07 < kanzure> so you're saying the only simple molecular machines you are aware of are the ones listed here? https://github.com/kanzure/nanoengineer/tree/874e4c9f8a9190f093625b267f9767e19f82e6c4/cad/partlib
06:08 < eudoxia> not really, there's also a nanotube linear motor and this rack and pinion system that's not there
06:09 < eudoxia> then there's all sorts of bespoke binding sites people have designed over the years
06:09 < eudoxia> wait a sec who did this https://github.com/kanzure/nanoengineer/tree/874e4c9f8a9190f093625b267f9767e19f82e6c4/cad/partlib/schafmeister
06:10 < justanotheruser> kanzure: do you have a list started?
06:10 < justanotheruser> All I know of are drexlers designs
06:11 < kanzure> well the files in nanoengineer.git are a list beyond just drexler's designs
06:11 < kanzure> here are some protein things that are interesting, if that's what you're asking about http://diyhpl.us/wiki/dna/projects/#proteins
06:12 < justanotheruser> yes, that is interesting
06:12 < justanotheruser> wasn't aware of all the designs that come with nanoengineer
06:13  * justanotheruser bookmarks
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06:26 < kanzure> i'm surprised at the lack of responses- i was expecting obvious things like antennae arrays, rod arrays (for sensors or even dna separation), polymerase clamps, springs, spheres or beads, machine tools...
06:27 < eudoxia> regarding springs
06:27 < eudoxia> drexler mentioned in the design of rod logic that you'd need springs to bring the rods back into place
06:27 < eudoxia> not knowing if there were small spring molecules like that, i imagined the way it would work would be something like
06:27 < eudoxia> a rotor with a cam would push the rods back into place, and travel perpendicular to a stack of identical rod-logical circuits
06:28 < eudoxia> but there are probably small linear spring molecules, no?
06:28 < kanzure> here is a more chemistry-oriented review of molecular machines http://www.researchgate.net/profile/Alberto_Credi/publication/12237218_Artificial_Molecular_Machines/links/0a85e531aec5618f45000000.pdf
06:30 < kanzure> i don't think that small-scale rod logic is likely to work for a while-- you need lots of other machinery to make use of it
06:30 < eudoxia> certainly, just asking cause it came to mind
06:32 < justanotheruser> http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002086
06:32 < justanotheruser> .title
06:33 < yoleaux> PLOS Biology: Open Labware: 3-D Printing Your Own Lab Equipment
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07:20 < kanzure> steganography framework https://github.com/bramcohen/DissidentX
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07:31 < CaptHindsight> kanzure: the Agilent inkjet may be used for more than oligo probe hybridization, they are just focusing on that with their NextGen
07:32 < CaptHindsight> HP makes lots of printheads that they don't resell
07:33 < kanzure> it's not the inkjet which limits it; it's the lack of sample recovery
07:33 < CaptHindsight> it looks like they have made some just for printing oligos
07:34 < CaptHindsight> what's stopping/preventing the sample recovery?
07:34 < CaptHindsight> it's a stack of oligos in wells
07:34 < kanzure> see pm
07:35 < kanzure> wells are problematic because the only way to recover dna from wells (in this scenario) is pipetting, and if you have 2 million pores/wells then uh.. well.. pipetting will take forever.
07:36 < CaptHindsight> drop the bottom out
07:36 < kanzure> to where? you need to keep the samples separated.
07:37 < CaptHindsight> you have to start connecting them somewhere
07:37 < kanzure> now would be an okay time for a phone call if you're up for it
07:44 < archels> hmm, these guys coded their spiking neural network in Julia. I wonder why
07:44 < archels> 447 SLOC, pretty tight
07:44 < archels> no parallelism though
07:46 < archels>                                 if spiked[cc] #spike occurred
07:46 < archels>                                         spiked[cc] = true;
07:46 < archels> # make **REALLY REALLY** sure that this variable is set to true
08:24 < kanzure> CaptHindsight: good talking with you capt'n
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08:39 < kanzure> win 5
08:39 < kanzure> eijroeqjrqi whoops
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09:06 < kanzure> https://np.reddit.com/r/IAmA/comments/38jawf/im_the_president_of_the_liberland_settlement/crw1d0f?context=10
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10:36 < nmz787_i1> kanzure: so what does CaptHindsight want to improve on specifically, just cost to manufacture a POSAM clone?
10:37 < nmz787_i1> if that's the case, then I think replicating the POSAM chemicals list would be the best idea
10:38 < nmz787_i1> and send me an email for the items that are no longer available with direct replacements... and we can search for a substitute
10:38 < nmz787_i1> kanzure: a more interesting question to me is, who here would want to help with a micro/nano device?
10:39 < kanzure> why bother with micro or nano if you can get enough scale without it? inkjet printing can do picoliter droplets.
10:39 < nmz787_i1> yeah but eww
10:39 < nmz787_i1> you want to do offsite sequencing
10:39 < kanzure> elaborate?
10:39 < nmz787_i1> how gross
10:39 < kanzure> yes, i want to do offsite sequencing for now
10:39 < kanzure> v2 can include other components
10:39 < nmz787_i1> you need sequencing after every 1 to 10 or 50 additions
10:40 < kanzure> putting all work upfront is not good.... likewise, putting everything off until later is also bad.
10:40 < nmz787_i1> tdt plus nanopore would be more interesting
10:40 < kanzure> i thought that required a mutated/not-yet-existing version of tdt
10:40 < nmz787_i1> na
10:41 < nmz787_i1> just some wires to sense the nanopore for when a nucleotide passes through
10:41 < nmz787_i1> impedanceometry or whatever
10:41 < kanzure> i'm not sure why you think that is easier than working with off-the-shelf inkjet heads?
10:42 < nmz787_i1> because I have access to a FIB and silicon and gas-injection... I don't have inkjets, know their interfaces aren't stable for offlabel use
10:45 < kanzure> fib is not the hard part when confining an enzyme in a nanopore
10:47 < nmz787_i1> you don't want the enzyme in the nanopore though
10:47 < nmz787_i1> the nanopore is just to limit diffusion and tunnel molecules past your molecule-counter electrodes
10:47 < nmz787_i1> so you can know when to turn off the nucleotide pump
10:48 < nmz787_i1> but anyway, yeah I'd say just replicate the POSAM chem list, and shoot me an email if there are items with questions or supply problems
10:49 < kanzure> one thing you might be able to convince me about is single-molecule emulsions
10:50 < nmz787_i1> the HO on water looks like the HO on the 2' site on the nucleotide rings, that's why it lowers efficiency... so anything with a similar HO can have that effect
10:50 < nmz787_i1> (just FYI)
10:50 < nmz787_i1> https://en.wikipedia.org/wiki/Directionality_(molecular_biology)
10:50 < nmz787_i1> err
10:50 < nmz787_i1> the 3'
10:51 < nmz787_i1> https://en.wikipedia.org/wiki/Nucleotide
10:51 < nmz787_i1> (the first link shows the hidden polymer form)
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10:55 < kanzure> .title http://www.sciencemag.org/content/333/6042/613.short
10:56 < kanzure> "A Single Molecule of Water Encapsulated in Fullerene C60"
10:56 < yoleaux> A Single Molecule of Water Encapsulated in Fullerene C60
10:57 < kanzure> https://scholar.google.com/scholar?hl=en&q=%22organic+cage%22+&btnG=&as_sdt=1%2C44&as_sdtp=
11:00 < kanzure> or nanopipette stuff.. hm.
11:07 < kanzure> huh i'm surprised that single-molecule emulsions are not a thing
11:08 < archels> superkuh: the website is down :(
11:17 < archels> this should be fun  https://www.youtube.com/watch?v=7u8mheM2Hrg
11:17 < archels> .title
11:17 < yoleaux> RESPONSE TO ROBOT DUEL CHALLENGE. - YouTube
11:17 < nmz787_i1> I think I'd basically just need some help with CAD models and idea putting-together... then I could convert them to FIB files or mask files, do the micro/nano work... then maybe send that off to someone with a machine shop to make the macro to micro manifold, hookup the pumps and chemicals. Before that the sensing board would need to be built or a good analog frontend (amplifier) would need purchased
11:18 < kanzure> which cad models?
11:19 < CaptHindsight> nmz787: what do you want to fabricate? the manifold?
11:20 < nmz787_i1> I'd do the actual micro and nano device (on-chip peristaltic pumps, some mixing areas, a nanopore for each nucleotide, a chamber for tdt, a nano-lattice/pore-matrix to retain tdt so waste can flow, some purification areas)
11:21 < superkuh> Uh oh. Something didn't come back up from the lightning strike.
11:21 < nmz787_i1> the manifold I'm guessing will look something like this http://www.ifitjams.com/images/f4-11.jpg
11:21 < superkuh> Oh, no, just another IP change.
11:22 < CaptHindsight> a zero insertion force socket
11:22 < nmz787_i1> the microchip just compresses onto the steel manifold, with some rubber or teflon between
11:22 < nmz787_i1> I think that is LGA
11:22 < nmz787_i1> so not quite ZIF
11:22 < CaptHindsight> nmz787: LGA PGA
11:22 < nmz787_i1> since there's no insertion
11:22 < CaptHindsight> yeah just the pores
11:23 < CaptHindsight> inlets
11:26 < CaptHindsight> CAD models are no problem
11:27 < CaptHindsight> kanzure: you have to decide which way you want to go
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11:28 < nmz787_i1> I would prefer BRL-CAD personally
11:28 < CaptHindsight> nmz787: heh, well you can spend the time converting from Step or Iges
11:29 < nmz787_i1> that seems like the only approach that is reliable
11:29 < nmz787_i1> nah i'd just use my python interface ;)
11:30 < nmz787_i1> To make the CAD automated for the FIB, I ultimated neem a .BMP type file
11:30 < nmz787_i1> need*
11:30 < nmz787_i1> but if the device is a one-off, I can do it by hand
11:31 < nmz787_i1> but we still need to layout the components, break/fan them out to the macro manifold, and design the manifold
11:33 < CaptHindsight> I have all the design tools. I just don't bother with all the open source almost CAD tools
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11:39 < CaptHindsight> heh, how does a single molecule qualify as in emulsion?
11:39 < CaptHindsight> in/an
11:39 < nmz787_i1> the cage would be the emulsifier
11:39 < CaptHindsight> kidding
11:39 < archels> superkuh: excellent
11:40 < CaptHindsight> low cost DIY FIB
11:41 < CaptHindsight> a handy tool of the nano machine shop
11:41 < nmz787_i1> yeah it would work as a mass-spec too, if reversed
11:42 < nmz787_i1> err, maybe the DIY SEM would be a better candidate
11:42 < CaptHindsight> what tools to build first? that was the discussion
11:42 < nmz787_i1> but the DIY DUAL-BEAM would definitely be reversible for mass-spec
11:42 < CaptHindsight> well both, but where do we start
11:42 < CaptHindsight> build tools to build tools
11:43 < CaptHindsight> 3-axis inkjet is pretty simple
11:44 < CaptHindsight> also DLP micro printer
11:44 < CaptHindsight> there are lots of old SEM's around
11:45 < CaptHindsight> the electronics could all be modular, motion control, imaging etc can all be done on a PC
11:45 < kanzure> there really is no substitute at the moment for solidworks, really
11:45 < kanzure> brlcad has iges/step support, so just do it in solidworks then export to step/iges
11:46 < CaptHindsight> there are not really any open analog boards for drivers and sensors
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11:46 < CaptHindsight> NX, Catia, Creo, SW we run em all
11:47 < CaptHindsight> brl is coming along
11:47 < nmz787_i1> BRL seemed to have better support for wide dynamic range in CAD models (they claim molecular to planetary scales)
11:48 < CaptHindsight> it's all the automated plug-ins and tools in the CAD package that save you so much time
11:49 < CaptHindsight> most on the surface act about the same
11:49 < nmz787_i1> BRL doesn't have great support for harder to define curves, at least in terms of defining them with math/equations
11:49 < CaptHindsight> extrude, cut, rotate, chamfer etc
11:50 < CaptHindsight> it's when you need to blend from one surface to another or hold some inner diameter on a contorted tube or similar is when the extra features come in handy
11:50 < CaptHindsight> or generate a pattern of holes etc
11:51 < CaptHindsight> but that's not holding us back
11:51 < CaptHindsight> that's just a preference for tools
11:52 < CaptHindsight> and how much time you have
11:52 < nmz787_i1> I just need a BMP file
11:52 < nmz787_i1> :P
11:52 < CaptHindsight> yeah
11:53 < nmz787_i1> 256-bit greyscale and single-layer per BMP
11:55 < kanzure> CaptHindsight: i'm a big fan of keeping it simple. nanopore stuff is fun, worth doing, but i still think keeping things simple can lead to good results.
11:55 < CaptHindsight> kanzure: we have to start somewhere
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11:56 < CaptHindsight> build a tool at a time, in a few years there will be a whole sub-micron CNC shop
11:58 < kanzure> oh regarding the emulsion question earlier: the idea was to use an emulsion where the contents of the emulsion is a single molecule
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11:58 < kanzure> the actual emulsifier could be many multiple molecules
12:00 < CaptHindsight> kanzure: whats the solvent or vehicle it's suspended in?
12:01 < nmz787_i1> CaptHindsight: IMO the nanopore stuff is immensely less complicated from a success standpoint... no one is going to care if you make POSAM cheaper, because the reagents are so relatively unavailable, short shelf life, low value output (it creates stuff that was available mail-order 30 years ago)
12:01 < kanzure> no idea, i was just looking around for papers to see if the emulsion idea exists elsewhere, doesn't matter
12:01 < CaptHindsight> I'm translating from Bio to coating, ink, paint chemistry terminology
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12:02 < kanzure> nmz787_i1: whether "no one is going to care if you make POSAM cheaper" does not modulate whether "the nanopore stuff is immensely less complicated from a success standpoint"...
12:02 < kanzure> short shelf life is probably because of contamination
12:02 < kanzure> being available by mail-order is irrelevant
12:02 < nmz787_i1> nope, that's why I included the chemistry point(s)
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12:03 < nmz787_i1> tdt is all water-based, can be achieved with a few home-brew enzymes and purified molecules
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12:12 < CaptHindsight> nmz787: https://en.wikipedia.org/wiki/Terminal_deoxynucleotidyl_transferase  making sure we are talking about this
12:12 < kanzure> yes
12:13 < kanzure> terrible diagram of tdt, it's essentially a donut
12:14 < kanzure> but the diagram fails to express this
12:17 < CaptHindsight> squished donut
12:18 < kanzure> a less delicious donut
12:25 < CaptHindsight> http://www.ebay.com/itm/Cambridge-Stereoscan-250-MK2-Scanning-Electron-Microscope-SEM-/400758845514  $800 as-is
12:25 < kanzure> working?
12:25 < CaptHindsight> looks like "untested" we have no clue how to either
12:28 < CaptHindsight> I usually spot one or two for a few $K that are in working condition
12:31 < nmz787_i1> e-ink remote control on Sony's home-grown crowdfunding site https://first-flight.sony.com/pj/2/HUIS%20REMOTE%20CONTROLLER
12:32 < CaptHindsight> http://www.ebay.com/itm/Zeiss-Electron-Microscope-EM-109-/181783812468  $3500 was working
12:32 < drethelin> nice
12:33 < CaptHindsight> and another: This instrument was pulled from service many years ago and its operational status is not known, thus we are listing it as "for parts or not working" because we cannot guarantee its proper operation.  http://www.ebay.com/itm/JEOL-JSM-35C-Scanning-Electron-Microscope-with-Spectrum-Analysis-/331482051373
12:33 < CaptHindsight> $2500
12:33 < CaptHindsight> with Spectrum Analysis
12:35 < CaptHindsight> http://www.ebay.com/itm/JEOL-T330A-Electron-Microscope-working/331599003517  $2500 working
12:35 < CaptHindsight> with video of it working  https://www.youtube.com/watch?v=FVpqDrAeKLU
12:36 < CaptHindsight> https://www.youtube.com/watch?v=gejSPGIcWPo
12:37 < nmz787_i1> the T330A looks pretty much like the scope I have (T200)... I think I might even have some schematics for the T330A too
12:40 < CaptHindsight> I should try to find surplus gun, chamber, detector assemblies
12:40 < nmz787_i1> https://www.tedpella.com/calibration_html/SEM_Calibration.htm
12:41 < nmz787_i1> I think that JSM-35C was on craigslist for a while
12:42 < nmz787_i1> oh, maybe not
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12:58 < kanzure> .tell eleitl http://www.metzdowd.com/pipermail/cryptography/2015-July/025971.html
12:58 < yoleaux> kanzure: I'll pass your message to eleitl.
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13:52 < kanzure> apparently firefly synchronization is a thing http://www.eecs.harvard.edu/ssr/projects/sync/
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13:59 < kanzure> "Some viruses that infect Archaea have complex structures that are unrelated to any other form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped structures, to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures.[80]"
13:59 < kanzure> [80]  Prangishvili D, Forterre P, Garrett RA. Viruses of the Archaea: a unifying view. Nature Reviews Microbiology. 2006;4(11):837–48. doi:10.1038/nrmicro1527. PMID 17041631.
13:59 < kanzure> http://www.nature.com/nrmicro/journal/v4/n11/full/nrmicro1527.html
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13:59 < kanzure> http://www.researchgate.net/profile/Patrick_Forterre/publication/6753226_Viruses_of_the_Archaea_a_unifying_view/links/53f5c8700cf2888a7491e75e.pdf
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15:20 < nmz787_i> .title http://hplusmagazine.com/2015/02/15/biology-technology-darpa-back-game-big-vision-h/
15:20 < yoleaux> Biology is Technology - DARPA is Back in the Game With A Big Vision and It Is H+ - h+ Mediah+ Media
15:26 < nmz787_i> 'Most lenses are, by definition, curved. After all, they are named for their resemblance to lentils, and a glass lens made flat is just a window with no special powers.'
15:26 < nmz787_i> /me had no idea of the relation to lentils
15:26 < nmz787_i> =-O
15:27 < kanzure> "Well known Silicon Valley venture capitalist, rocketeer, transhumanist, and super guy Steve Jurvetson was spotted “high fiving” a DARPA funded telepresence robot developed at Johns Hopkins APL at the reception."
15:27 < kanzure> (jurvetson is the J and draper is the D in DFJ)
15:28 < kanzure> (draper is the one with the kid that is desperate to fund someone building an iron man exoskeleton)
15:28 < kanzure> didn't know that these were the organ-on-a-chip people http://emulatebio.com/
15:36 < nmz787_i> .title http://keyssa.com/technology/
15:36 < yoleaux> Our Technology - Keyssa
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15:45 < nmz787_i> .title http://www.voxel8.co/
15:45 < yoleaux> Voxel8: 3D Electronics Printing
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18:08 < kanzure> .title https://news.ycombinator.com/item?id=9841209
18:08 < yoleaux> Antibody wipeout relieves symptoms of chronic fatigue syndrome | Hacker News
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18:22 < kanzure> .wik treponema pallidum
18:22 < yoleaux> "Treponema pallidum is a spirochaete bacterium with subspecies that cause treponemal diseases such as syphilis, bejel, pinta, and yaws. The treponemes have a cytoplasmic and an outer membrane. Using light microscopy, treponemes are only visible using dark field illumination. They are gram negative, but some regard them too thin to be gram stained." — https://en.wikipedia.org/wiki/Treponema_pallidum
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18:23 < kanzure> oh cool we have the genome of neurosyphilis
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18:29 < drethelin> great, now we can synthesize it!
18:30 < kanzure> there are easier ways to get neurosyphilis
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18:40 < kanzure> "The metalloprotease Mpr1 has been demonstrated to be critical in blood-brain barrier penetration.[16]"
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19:25 < ryankarason> nmz787: ha! @ lentils.. nor did i..
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20:09 < kanzure> hm
20:10 < kanzure> whatever happened to the brain preservation prize results. did that happen? or was it just a hit-and-run thing.
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21:06 < kanzure> hrm.
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--- Log closed Tue Jul 07 00:00:03 2015