2009-04-19.log

--- Day changed Sun Apr 19 2009
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fenni take back my praise for the 'cleverness' of the arduino LCD+buttons shield03:22
fennthey actually did it wrong, so you can't press more than one button at once03:23
fennwhat were they thinking!03:23
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fennhttp://imagebin.org/46068  PCR idea07:14
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kanzurefenn: funny how there is more engineering on diybio in the last day than there has been on OM, ever10:02
kanzureor maybe that's sad. my meter is kind of messed up.10:02
kanzureheh in situ adaptive PCR control via adding SYBR green and detecting intensity every 0.5 s 10:50
kanzureincreased intensity -> increased number of strands10:50
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kanzurewhy not just find favorable thermozymes that let us do pcr without having to have a machine.11:15
kanzurejust sayin'11:15
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kanzureoh right. I was trying to find a cell life cycle phase that amplifies DNA, and then some mutant of that phase that can't stop doing that; then apply the photoporation technique, and you're good to go if you can bare to run some .. blah, what are those extractions of gel runs called? whatever it is you do to the gels to recover DNA.11:56
cis-actionhey11:57
cis-actionkanzure: http://jb.asm.org/cgi/content/full/182/13/367311:58
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kanzurecis-action: hey.15:02
cis-actionhi15:02
kanzure 15:02
kanzureComP, a Pilin-Like Protein Essential for Natural Competence in Acinetobacter sp. Strain BD413: Regulation, Modification, and Cellular Localization15:02
kanzureah, neat15:02
kanzurebut is this the only protein necessary?15:02
* cis-action read the last part of the abstract15:03
cis-actionor did you already?15:04
kanzure"dna binding and uptake" hr15:05
kanzurehrm15:05
kanzure"A deletion of comP completely abolished natural transformation but had no effect on piliation, as revealed by electron microscopy (33)."15:06
kanzurethis is pretty neat. :)15:06
kanzure"Expression of ComP in E. coli from plasmids pMP1 and pMP2 resulted in malE::comP fusion products of 58 and 53 kDa, respectively."15:08
cis-actionAhh!  I meant to say, read the last part of the discussion / conlusion.15:10
cis-actionconclusion*15:10
kanzure"Our data rather suggest that the comP promoter responds to nutrient limitations"15:10
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kanzureHey DrTread.15:11
kanzurecis-action: hrm. well. looks like ComP might not be our guy.15:12
kanzurebut that's why I suggested comB8, comB9, comB10 and maybe comB7.15:12
DrTreadhola15:14
DrTreadwhat's the sub-topic for today?15:16
kanzureI've been hunting down genes necessary to make an organism automagically take up DNA that happens to be floating by15:17
DrTreadah. a retrovirus sort if thingy. 15:18
kanzurenope15:18
kanzureholes in the membrane that DNA can go through15:18
DrTreadoh! ok. anthrax. creates lovely holes. 15:19
DrTreadusually fatal, tho. :(15:19
kanzurehm, the ComG genes look interesting too. (ComG-3, ComG-4, ComG-5)15:20
DrTreadtrouble is that you need a stable hole, not just a hole. 15:21
kanzureDrTread: there are specific organisms that have evolved these genes for the purpose of uptake of DNA15:22
kanzureor at least it seems to be for the purpose of uptake of DNA (because that's what they do)15:22
kanzureso it's a matter of importing the genes over, more or less, as long as the membrane composition is somewhat similar methinks15:22
kanzurehm. I like this one: "All seven comG ORFs are required for DNA binding during transformation of competent Bacillus subtilis"15:23
DrTreadthese things must be handled delicately. iirc, anthrax uses 4 genes, but many subunits. 15:24
DrTreadgenes are big things. 15:25
kanzureit would be ideal if I could find a single gene that encodes a single protein that enables this activity15:25
cis-actionThe DNA import machinery seems to be powered by the transmembrane proton gradient and seems to take dsDNA, chop one strand up, and suck the other strand through the cell as ssDNA15:26
kanzurein which case?15:26
kanzurethere are multiple systems I've been looking at. visP, comB, comP, comG, etc.15:27
kanzuresome papers are telling me that some ecoli has natural competence 15:31
kanzurewith some homologs of the com genes of H. influenzae15:31
DrTreadgoing to work (play) on my blinkey lights. 15:38
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kanzurethe paper called "Internalizing DNA" is good and includes a nice chart.16:16
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kanzuresonication leads to DNA fracture?16:50
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cis-actionok, signing off to get ready for the talk16:56
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kanzureyou get bonus points for speaking only in nucleotides16:57
kanzureblah16:57
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kanzureHey ericzhang.17:04
ericzhanghey kanzure17:04
kanzuremac just stepped out to give a presentation at codecon17:05
ericzhangi see.17:06
ericzhangfunny topic name here, haha.17:06
kanzure:)17:06
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kanzurewelcome back?17:09
ericzhangsorry...browser issues.17:09
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junglistric*name change17:10
kanzurehrm. this sucks. ADP1 uses 16 genes for the natural competence mechanism.17:11
kanzurewhy can't it be one gene. blah.17:11
junglistrichaha.17:12
fennhello eric17:12
kanzure"comE and comF mutants exhibit 10- and 1,000-fold reduced transformation frequencies"17:12
junglistrichi fenn17:13
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fenndiy-ish laptop: http://benheck.com/03-03-2009/darksiders-xbox-360-laptop-for-thq17:20
fennhis other mod is cooler though: http://benheck.com/04-05-2009/commodore-64-original-hardware-laptop#more-49617:20
fenner, scroll up17:21
junglistricthe first one is just a portable xbox...2nd one is pretty cool.17:23
junglistricwhat one does with a comm64 these days, i dunno.17:23
kanzurebrag17:23
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junglistricor play ThunderBlade and brag17:25
kanzurecompetence proteins of ADP1:17:26
kanzurehttp://heybryan.org/books/papers/competence_proteins_ADP1.jpg17:26
kanzurewhat the setup looks like in Heliobacter pylori: http://heybryan.org/books/papers/Natural%20transformation%20in%20Helicobacter%20pylori%20-%20DNA%20transport%20in%20an%20unexpected%20way.pdf.1.jpeg17:26
kanzureand what it looks like in a cousin of ADP1: http://heybryan.org/books/papers/Acquisition%20of%20foreign%20DNA%20by%20natural%20transformation%20in%20Acinetobacter%20baylyi%20-%20introgression%20process.pdf.1.jpg17:27
fennlooks about the same except they used letters instead of numbers17:30
fennof course colored blobs doesn't really tell you much17:31
kanzureSCIENCE!17:31
kanzurea blobby thingy works here by doing something like a blob17:31
fenni'm going to start doing technical diagrams with colored blobs in them for no particular reason17:32
kanzureactually I was surprised (and happy) to see that some people correctly guessed that there were various hydrophilic-domains of the amino acids that are specifically used in a "DNA sensor/grabber thingy"17:32
kanzureheh17:32
kanzurethis mechanism is fairly complicated17:32
kanzureI was expecting a single protein to make up the pore.17:32
kanzureall sorts of wild/funky regulation going on of each individual protein's expression too..17:33
kanzurefor instance, apparently only some species are naturally competent during log phase growth17:33
kanzurehowever gonororrhea is naturally competent all the time17:33
fennskyhook wireless maps wifi MAC addresses to geolocation.. eek17:35
kanzuregoing in the wrong direction.17:35
fennapparently they had 200 drivers go around with GPS and wifi antenna17:35
kanzurewasn't skyhook some sort of james bond movie military research study codename?17:35
kanzure"operation skyhook"17:35
fennmeh17:35
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fennskyhook is hans moravec's idea for an orbital space tether17:35
kanzureyou'd fire some sort of flair and a skyhook would come down and swing you away17:36
fennoh, was that called skyhook too?17:36
* kanzure nods17:36
kanzureI keep thinking of cows on hooks in slaughter houses though. that seems to be the result of trying to hitch a ride with a fast-moving "sky hook"17:36
junglistrichaha17:37
kanzurealso found some weird stuff on naturally competent ecoli in water17:39
kanzurehttp://heybryan.org/books/papers/Natural%20plasmid%20transformation%20in%20ecoli.pdf17:39
kanzureoh, B. subtilis competence proteins diagram: http://heybryan.org/books/papers/Internalizing_DNA.pdf.B_subtilis_competence_proteins.gif17:40
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kanzurewhat is supercoiled monomeric or linear concatemeric DNA? as opposed to linear monomeric DNA.17:41
kanzureis supercoiled monomeric == "plasmid" ?17:42
fennfancy words17:43
fennA concatemeric DNA is the product of multiple replication and recombination. The result of this multiple replication is a molecule which contains many copies of the same DNA connected end-to-end. 17:43
fennsupercoiled usually means plasmid17:44
junglistricplasmids have more than 1 type of 2ndary structure17:44
junglistricyeah17:44
fennchromatin keeps DNA in a supercoiled state but it's not in a loop17:44
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kanzureI want a gene pool rss feed.17:48
junglistricthanks for the ADP1 stuff Bryan.  doesn't seem so complex when you can just click and buy some competent cells.17:48
kanzurejunglistric: it's not diy if you get to buy your way to success :)17:49
junglistricthat's the new motto right there17:49
kanzurenew?17:49
genehackertalk going on today?17:49
kanzuregenehacker: in san francisco, codecon.17:49
genehackerhmmmmm...17:50
genehackercoordinates?17:50
kanzurecheck codecon.org for coords17:50
genehackerkanzure supercoiled is what you get when you twist a ruberband a lot and it starts to kink17:51
genehackerhaven't you ever played with deformed elastomer powered vehicles?17:52
kanzureI doubt the biologists are using proper terminology17:52
genehackeroops17:53
junglistrichttp://en.wikipedia.org/wiki/File:Circular_DNA_Supercoiling.png17:53
genehackerhttp://chemistry.umeche.maine.edu/CHY431/Supercoil3.gif17:53
genehackerthis is super coiling17:53
junglistricplectonemic rubber bands17:53
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genehackerhttp://chemistry.umeche.maine.edu/CHY431/Nucleic5.html17:54
junglistricdna might coil in different ways ex vivo17:55
junglistriclike in a gel17:55
junglistricsometimes when you run plasmids, you see these bands that don't migrate as they should17:56
kanzureright17:56
kanzureI've had gel streaking issues before17:56
junglistricor 2-3 distinct bands17:56
junglistricdifferent supercoils17:57
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junglistricstreaking tends to happen when your DNA is just obliterated17:57
junglistrica spectrum of lengths17:57
kanzureIIRC it was due to contamination and i.e. trusting invitrogen's DNA or something17:58
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junglistricit could be that the DNA is just degraded somehow17:58
junglistricsometimes you want to fragment DNA, when you're building a library17:59
junglistricfor diff. applications17:59
junglistricsequencing for example18:00
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junglistrichm dinner time.18:01
junglistriclater guys.18:01
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kanzurehm20:18
kanzure1.6 terabits/in^2 via an AFM in room temperature in air, 8 nm bits are written at a rate of 5 kbits/sec20:18
kanzureis it enough to shine a photodiode to detect some change in cantilever angle ?20:19
nshenough?20:25
nshi assume it's a pretty damn complicated instrument20:26
kanzurenot really20:27
kanzurepiezoelectric crystal with sample on it.20:27
kanzurea giant cantilever thingy with a sharp point20:27
kanzurelaser pointing at the cantilever20:27
kanzuresome way of reading the deflection 20:27
fennphotodiode will only give you a point signal20:27
fennyou need a camera sensor20:28
kanzurewikipedia suggests an array of photodiodes20:28
fennor photodiode strip20:28
kanzureyay20:28
fennwhy photodiode btw?20:28
kanzuredunno?20:28
fennok.. just remember there are megapixel camera sensors for $1020:28
kanzurewonder how much resolution that would give me.20:29
fenn1000 per axis20:29
kanzureerm, no, I mean in terms of .. nevermind.20:29
fennyou mean 'how much dynamic range would that give me'20:29
fennor something20:29
kanzureor something, yes.20:30
fennwhats the AFM writing on?20:31
fennand doesnt the tip get dull really quickly?20:31
kanzuretitanium20:31
kanzureit seems to be some sort of oxidization process20:31
fennoh20:32
kanzurewhat material should be used for the cantilever?20:33
kanzureit's basically a "spring" but I really don't know20:33
kanzureideally, running a silver-coated hair would be awesome, but it wouldn't necessarily stay put20:34
kanzureI guess I have to wonder about how much bend you get per nanoNewton of force or something on a metal bar?20:34
kanzure"the AFM can only imnage a maximum height on the order of micrometers and a maximum scanning area of around 150 by 150 micrometers"20:36
kanzurevideoAFM heh20:37
fennyou and your hair obsession20:40
fenndont you know hair varies by a factor of 10 in thickness20:41
genehackerhttp://blog.reprap.org/2009/04/first-reprapped-circuit.html20:58
genehackeryou talking about the millipede?20:59
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kanzurefenn: I can't help it, I grow so much of it21:04
kanzurehm.21:06
kanzurehttp://en.wikipedia.org/wiki/File:Atomic_Force_Microscope_Science_Museum_Lond.jpg21:06
kanzureerm21:06
kanzurehttp://en.wikipedia.org/wiki/File:Atomic_Force_Microscope_Science_Museum_London.jpg21:06
genehackerhttp://www.youtube.com/watch?v=Wnu4lmOnX00&feature=related21:10
kanzuregenehacker: that was linked in the comments on the last link you linked to..21:10
genehackeryeah21:11
genehackerit's cool nonetheless21:11
genehackerthat solder pump sounds a bit insidious21:11
kanzurehey, what are those alligator clip thingies that are made entirely out of metal? the ones that clip.21:13
fennalligator clips21:15
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kanzure-open flame + micropipette tip = bent AFM cantilever tip. then glue a sparkle-glitter-thingy on the bent part and shine the laser.21:48
kanzure-is there non-deflection AFM?21:49
fenni dont know anything about AFM21:55
fennbesides what you've dosed me with21:56
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fennwhy do they use lasers vs for example a capacitive probe?21:57
fennto detect bending of the cantilever21:57
kanzure-it's weird, I thought I knew what AFM was too22:02
kanzure-but I never heard of just watching for the bending angle or whatever22:03
kanzure-what do you mean a capacitive probe?22:03
kanzure-a capacitor?22:03
fennlike a touchpad22:05
fenncapacitor is two metal plates in close proximity22:05
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fennthe capacitance varies with the distance22:05
fennyou set up a resonant circuit and measure the frequency22:05
fennfrequency is proportional to capacitance is proportional to distance22:05
fennit's not linear though22:06
kanzure-good news, somebody already patented "scanning capacitance microscopy"22:06
kanzure-hand over a million dollars. or else.22:06
kanzure-198922:07
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fennseems people dont really go after patent infringers unless they've already made a lot of money on it22:08
genehackermicropippette tips are pretty big22:08
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kanzure-huh you must be in the clear then22:08
* kanzure- snickers22:08
fenni should infringe more patents22:08
genehackeryou can only infringe on patents if you make it and sell it22:09
genehackertrading it on the other hand...22:09
kanzure-genehacker: according to who22:09
fenngenehacker: not true22:09
genehackerthose fuckers22:09
fennif you build and use it you're infringing22:09
kanzure-it's a living hell22:09
genehackerLETS INFRINGE SOME PATENTS FOR THE LULZ22:10
fennkanzure i need you to apply your massive social networking skills towards getting me more money22:10
genehackerhttp://www.ifpi.org/22:10
genehackercheck it out22:10
kanzure-wait, wait, I have social networking skills?22:11
genehackeryeah22:11
fennsomething like that22:11
genehackeryou know a bunch of transhumanists22:11
kanzure-nobody that has any money.22:11
kanzure-fenn: I'll look into it.22:11
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kanzure-hrm, I'd like to capacitance scanning microscopy except my upload isn't all that good22:13
fennis that a book?22:13
kanzure-no. wireless just sucks here.22:13
kanzure-oh look, it jumped up to 8.2 kb/sec22:14
fennwowza22:14
fenntime to eat some pringles22:14
fenndon't buy a bunch of stuff from deal extreme if you expect to get it any time soon22:16
kanzure-fenn, how soon do you need monies?22:17
kanzure-scanning capacitance microscopy: http://heybryan.org/books/papers/Scanning%20capacitance%20microscopy%20on%20a%2025%20nm%20scale.pdf22:18
fennjust in general22:18
fennthere's a lot of things i could be working on right now if i had cash to throw around22:18
kanzure-andrew hessel suggested I needed a patron22:19
kanzure-do they make those any more?22:19
fenngood question. tell me if you find out22:19
fennit makes a lot more sense than paying for specific art objects as if they were products22:20
kanzure-I think that paper is exactly what you were thinking of22:21
fenndoes it measure capacitance between the tip and the surface of interest?22:22
fennbecause that's not what i meant22:22
kanzure-works for both insulators and conductors22:22
kanzure-so I would assume it's not tip-surface capacitance measurements22:22
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fennit measures capacitance between tip and surface22:31
kanzure-ouch.22:37
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fennanyway that's cool as it gives you another dimension to image22:42
fennyou could use the same tip for STM, AFM, and capacitance microscopy, right?22:42
kanzure-why do people and papers complain about having to switch out tips all the time then?22:42
katsmeowthey crash them? the tips oxidize?22:43
kanzure-ok, that's reasonable.22:43
fennafm wears out the tips doesn't it?22:43
fennit sounds like capacitance microscopy isnt used very much22:44
kanzure-you need a better name for your version of capacitance microscopy22:44
fennit's not 'my version of capacitance microscopy'22:44
kanzure-then what is it?22:45
fennit's just a bend sensor for a standard AFM cantilever22:45
kanzure-huh? I thought you said the distance between a sample-holding plate and the cantilever tip22:45
kanzure-oh well. I was wrong22:46
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kanzure-I can't seem to find piezo nanowires. am I missing out on some good search terms?23:05
katsmeowpiezo nanowires? never heard of it23:05
katsmeowpiezo implies crystal, which isn't a wire?23:06
kanzure-you can't have a crystal wire?23:06
fennThe International Federation of the Phonographic Industry (IFPI): introducing and improving copyright laws, anti-piracy enforcement, anti-piracy litigation, internet monitoring and closing of illegal sites (Censorship), marketing and public relations efforts, and working to create new forms of Digital Rights Management.23:06
katsmeowumm,, i think it would shatter easily23:06
kanzure-fenn: is that supposed to be funny, sad, or none of the above23:07
fennIn mid-October 2007, after the IFPI let the ifpi.com domain registration lapse, ownership of the ifpi.com domain was transferred to The Pirate Bay, under the backronym "International Federation of Pirates Interests,23:07
fennthen they tried to switch to ifpi.org but the DNS was hacked again23:08
fenner, hacked twice (first time was just stupidity by ifpi)23:08
katsmeowkanzure http://ltn.vbnlive.com/site/upload/document/Microsoft_PowerPoint_-_9._Paul_Beecher_Nokia.pdf 23:08
kanzure-katsmeow: what is it?23:09
katsmeowan url23:09
kanzure-..23:09
katsmeowto nanowire touch sensor23:09
kanzure-please don't make me click stuff23:09
katsmeowMicrosoft PowerPoint - 9. Paul Beecher Nokia.ppt23:09
katsmeowZnO Nanowires for flexible tactile arrays. Characteristics for sensor23:09
katsmeowapplications. • Uniaxial piezoelectric response. • Enabler of novel touch sensor23:09
katsmeow...23:09
katsmeowhttp://ltn.vbnlive.com/site/upload/document/Microsoft_PowerPoint_-_9._Paul_Beecher_Nokia.pdf23:09
kanzure-hm.23:09
kanzure-neat.23:09
katsmeowor23:09
katsmeowhttp://www-mcr.trinhall.cam.ac.uk/wiki/Aron_Rachamim23:10
katsmeow  Research23:10
katsmeowI am investigating the use of zinc oxide nanowires in touch sensor devices (e.g. displays on mobile phones). Zinc oxide nanowires are piezoelectric so compression of them generates a voltage. Conversely application of a voltage causes them to extend so there is also potential for touch feedback to the user (e.g. they could press on the screen to call someone and the screen could vibrate so they could feel that the call is taking p23:10
katsmeowThis research is being funded by Nokia.23:10
kanzure-so .. resolution anyone?23:10
kanzure-gah, wireless sucks here23:10
katsmeowsorry i mentioned it was for wireless devices23:11
kanzure-no, my wireless connection23:11
kanzure-because I can't download anything quickly, or upload23:11
katsmeowah23:11
fennwhere's "here"?23:12
kanzure-dorm23:12
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