2009-04-29.log

--- Day changed Wed Apr 29 2009
kanzurecis-action: hey00:17
kanzuresorry, I had a meeting with someone00:17
kanzure-I}ruid: hey.00:23
kanzure-_so, the first protein worth expressing would be GFP, which could be done with a kit00:41
kanzure-_but beyond that I'm not quite sure00:41
kanzure-_hey Splicer_. talking about agrobacterium.00:41
kanzure-_http://pubs.caes.uga.edu/caespubs/pubcd/images/B1286-17.jpg02:02
kanzure-_crown gall02:02
kanzure-_http://www.ag.ndsu.edu/pubs/plantsci/crops/a1219-3.jpg02:03
kanzure-_http://forestpests.org/rootbutt.html02:08
cis-actionfinally back02:19
kanzure-_hi02:20
cis-actionuh oh gotta leave again02:29
kanzure-_hahah02:51
kanzure-_"the mammary gland: bioreactor for the production of recombinant proteins"02:51
kanzure-_YES02:51
kanzure-_Using a 3.6-kb promoter of mouse uroplakin II gene, we have generated transgenic mice that express human growth hormone (hGH) in their bladder epithelium, resulting in its secretion into the urine at 100−500 ng/ml.02:52
kanzure-_is there a plant that has a ridiculously convenient way to express proteins in plants? for harvesting purposes. other than latex (which you will have to centrifuge for)02:57
kanzure-_http://en.wikipedia.org/wiki/Lemna03:22
kanzure-_search for "secrete"03:22
kanzure-_Lemna has been transformed by molecular biologists to express proteins of pharmaceutical interest. Expression constructs were engineered to cause Lemna to secrete the transformed proteins into the growth medium at high yield. Since the Lemna is grown on a simple medium, this substantially reduces the burden of protein purification in preparing such proteins for medical use, promising substantial reductions in manufacturing costs.[3][4]03:23
kanzure-_genehacker: transgenic protein expression in mammary glands03:47
kanzure-_fenn: are you going to show up tomorrow?03:58
genehackerhahahahhahahahaha04:01
genehackeris that the llama one?04:01
kanzure-_no04:01
genehackerlink?04:01
kanzure-_one moment04:02
genehackerllamas  actual produce microantibodies which are great for a lot of things04:04
kanzure-_http://heybryan.org/books/papers/The%20mammary%20gland%20-%20bioreactor%20for%20the%20production%20of%20recombinant%20proteins.pdf04:04
kanzure-_but actually I've been thinking of using dandelions for protein expression04:04
kanzure-_because of the specific composition of the latex/plastic from the plant04:04
kanzure-_and transfectability by agrobacterium04:05
kanzure-_the bladder as a bioreactor: http://heybryan.org/books/papers/The%20bladder%20as%20a%20bioreactor%20-%20urothelium%20production%20and%20secretion%20of%20growth%20hormone%20into%20urine.pdf04:05
genehackerdandelions?04:06
genehackerwhat do we want to produce first off?04:07
genehackerillegal neuroenhancers perhaps?04:07
genehackerhttp://craphound.com/overclocked/Cory_Doctorow_-_Overclocked_-_Printcrime.html04:08
kanzure-_what illegal neuroenhancers?04:08
genehackerthere are none as of yet...04:09
kanzure-_so ...04:09
genehackerwhat?04:10
genehackerwhy  dandelions?04:10
kanzure-_because it's easy.04:10
kanzure-_you can eat them.04:10
kanzure-_you can extract the latex04:10
genehackerlatex for what?04:11
kanzure-_do you not know where plastic comes from?04:12
genehackeryes I do04:13
genehackerit comes from04:13
genehackeroil04:13
genehackerare you talking about making stuff like PE?04:13
genehackerin dandelions?04:13
kanzure-_"Latex refers generically to a stable dispersion (emulsion) of polymer microparticles in an aqueous medium. Latexes may be natural or synthetic. Latex as found in nature is the milky sap of many plants that coagulates on exposure to air"04:13
kanzure-_PE?04:13
kanzure-_I don't care about polyester really- although that would be neat04:14
kanzure-_more interested in other proteins more than anything04:14
kanzure-_the thing is that it's easy to extract it from dandelion04:14
genehackerpolyethylene04:14
kanzure-_because you don't have to do SDS-PAGE bullshit04:14
genehackerSDS PAGE?04:14
genehackerok04:14
kanzure-_SDS PAGE is usually how you do protein purification04:14
kanzure-_but it's some complicated gel steps or something04:14
genehackerso let's make some DNA polymerases04:14
kanzure-_why?04:15
kanzure-_oh04:15
genehackerthe type of things needed for PCR04:15
kanzure-_yeah that's a good idea04:15
genehackerheh dandelions though04:15
kanzure-_transgenic production of Tac polymerase. ok.04:15
kanzure-_yeha04:15
kanzure-_*yeah04:15
kanzure-_they grow basically everywhere04:15
genehackerI was thinking any polymeras04:15
kanzure-_so get a pot with some soil and a lamp04:15
kanzure-_do you know the transformation protocol for agrobacterium?04:16
kanzure-_I recently found this neat freeze-thaw protocol04:16
kanzure-_with a add-the-new-DNA step in between or something04:16
genehackerperhaps we should modify them so they don't express those tufts of fiber on the seeds...04:16
genehackerhmmm...04:16
genehackertry DNA hack04:17
genehackerI saw something on their about argobacter transformation04:18
genehacker http://web.archive.org/web/20070309143649rn_1/www.accessexcellence.org/RC/AB/BA/Transforming_Plants.html04:20
kanzure-_http://heybryan.org/books/papers/Increasing%20plant%20susceptibility%20to%20Agrobacterium%20infection%20by%20overexpression%20of%20the%20Arabidopsis%20nuclear%20protein%20VIP1.pdf04:22
kanzure-_Increasing Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP104:22
kanzure-_Increasing Light strongly promotes gene transfer from Agrobacterium tumefaciensto plant cells04:23
kanzure-_http://heybryan.org/books/papers/New%20biotechnological%20applications%20of%20coconuts.pdf04:23
kanzure-_http://heybryan.org/books/papers/Light%20strongly%20promotes%20gene%20transfer%20from%20Agrobacterium%20tumefaciensto%20plant%20cells.pdf04:24
genehackercoconuts?04:27
genehackerheh04:27
kanzure-_yep.04:27
kanzure-_just add plasmid vector to coconut milk.04:27
genehackerso what other proteins do we need04:28
genehackerI'd say let's see if we can synthesize taq first then work on other stuff04:28
kanzure-_the proteins required to do natural competence04:28
kanzure-_MagA, for MRI reporter genes04:29
kanzure-_mechanoreceptors, for magnetic guiding of cells04:29
kanzure-_chlorohopdins-2 for laser-activation of neurons04:29
genehackerbut first let's make a DNA synth04:29
kanzure-_hrm.04:29
kanzure-_do you have the sequence to taq?04:29
genehackerso we don't have to buy the DNA sequence04:29
genehackerno04:29
genehackerbut ncbi.org does04:29
genehackernah04:30
genehackerwait04:30
kanzure-_then also insulin, dopamine, various other neurotransmitters04:30
kanzure-_key opium proteins for a few bucks in the pocket04:30
genehackerhahahaha04:31
genehackeris there any law against it?04:31
kanzure-_I'm sure.04:31
genehackerbah04:31
kanzure-_I think it would be cheaper to buy the oligos over the internet, but I'm still interested in making a synthesizer04:33
genehackerI like self-sufficiency04:34
kanzure-_of course.04:36
genehackerhey we could build a biolistic gun to transform plants04:36
kanzure-_out of what04:36
genehackerthe first biolistic guns were modified BB guns04:36
genehackerPVC04:36
genehackerpipe fittigns04:36
kanzure-_do you mean ballistic?04:37
genehackerbiolistic, ballistic, same thing04:38
genehackerjust biolistic is more specific04:38
genehackerthough gene guns tend to be super-high velocity helium gas guns04:40
genehackerThe earliest custom manufactured geneguns (fabricated by Nelson Allen) used a 22 caliber nail gun cartridge to propel an extruded polyethylene cylinder (bullet) down a 22 cal. Douglas barrel. A droplet of the tungsten powder and genetic material was placed on the bullet and shot down the barrel at a lexan "stopping" disk with a petri dish below. The bullet welded to the disk and the genetic...04:41
genehacker...information blasted into the sample in the dish with a doughnut effect (devastation in the middle, a ring of good transformation and little around the edge). The gun was connected to a vacuum pump and was under vacuum while firing.04:41
kanzure-_wah, I don't want to have to build a vacuum pump04:42
genehackerthen you use helium as a propellent or something like that04:42
genehackerhttp://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/McDonald/Gene_gun.html04:44
kanzure-_if we can find a root that drips out recombinant proteins, then that would be ideal04:50
kanzure-_there are some organisms that grow in simple media and secrete stuff into the liquid medium, but I'm not entirely sure that's the best of ideas04:50
kanzure-_root dripping would be awesome.04:50
genehackerhmmmm04:50
kanzure-_berries would be ok maybe.04:50
kanzure-_ooh04:56
kanzure-_rhizosecretion04:56
fennzuh. 11 am04:57
fennmore like 1004:57
kanzure-_right04:57
kanzure-_what is zuh? is it like guh?04:57
fennsure04:57
kanzure-_10:30.04:58
kanzure-_tomorrow it's produce disassembly stuff. next week is gear optimization (probably the last one on gear stuff since albert is gone)04:58
kanzure-_*is leaving04:58
kanzure-_*product04:58
fennoh this is a 'give a presentation' lab meeting04:58
fenndo you guys ever actually sit down and talk about what you're all doing?04:59
kanzure-_nope04:59
kanzure-_heh04:59
kanzure-_we sit down one-on-one04:59
kanzure-_but that's not quite the same thing04:59
kanzure-_we talk about what we're doing in the other lab though .. if that counts.05:00
genehackerwoo hoo, they sequenced some of flu05:17
genehacker*swine flu05:18
genehackerMKAILVVMLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK05:19
genehackerLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELRE05:19
genehackerQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSK05:19
genehackerSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQ05:19
genehackerEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK05:19
genehackerGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTG05:19
genehackerMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKR05:19
genehackerIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG05:19
genehackerCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASS05:19
genehackerLVLVVSLGAISFWMCSNGSLQCRICI05:19
kanzure-_yeah.05:20
genehackerhttp://www.google.com/search?q=MKAILVVMLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK+LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELRE+QLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSK+SYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQ+EGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK+GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTG+MVD05:20
genehackerGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKR+IENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG+CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASS+LVLVVSLGAISFWMCSNGSLQCRICI&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a05:20
genehackerhmmmm....05:20
genehackerpreliminary data?05:20
genehackerhttp://www.iayork.com/Temp/SwineFluOnlyAlign.txt05:21
genehackerdamn where's the sequence05:21
genehackerhttp://stephan-zielinski.com/dwa/2009/04/28/swine-flu-ha-as-ambient-music/05:21
genehackerall I can find is this05:21
kanzure-_I posted a link to diybio05:22
kanzure-_or someone else did05:23
genehackerhmmmm....05:23
genehackernow how do I do sequence comparison again05:23
kanzure-_what do you want to do? homology analysis?05:23
genehackercompare with other stuff05:24
genehackermultiple sequence alignment05:24
genehackerthat sorta stuff05:24
kanzure-_you need to say something in particular.05:24
kanzure-_alignment?05:24
genehackeryeah05:25
kanzure-_or do you want to just look for homologues or something?05:25
kanzure-_alignment is something you do before you submit the sequence05:25
genehackeras in compare it to other flu viruses05:25
kanzure-_what do you want to get as a result of the comparison05:25
fennblast search05:26
fennor try to use clustal if you're comparing specific things05:26
genehackerhttp://www.ncbi.nlm.nih.gov/nuccore/FJ96697005:26
genehackerOseltamivir_resistance sensitive?05:26
genehackerwhat does that mean?05:26
genehackeroh we're good05:27
fennadamantane resistant!05:27
fennwe can use this to wipe out those russian supersoldiers05:27
kanzure-_the gorillas?05:27
genehackerhahahah05:28
fennomega red, etc05:28
genehackerchemical it's based on is essentially a subunit of diamond05:28
kanzure-_what are these plastic sleeve bioreactor thingies?05:29
fennhow does duckweed growth compare to algae?05:31
genehackerplastic sleeve bioreactors?05:31
genehackeryou mean like with big bags of plastic05:32
fennwp says 10 to 30 tons per hectare year05:32
kanzure-_er, people are using these mist reactors for roots in a different way. I was hoping they were hanging roots and the roots would drip my recombinant proteins.05:32
katsmeow-afk10 tons dry?05:34
kanzure-_ah, "root exudation"05:34
fennmost proteins dont drip05:34
kanzure-_what about in a sap05:35
genehackermaple trees?05:48
kanzureno, I don't want to have to grow trees06:26
fenni dont quite understand your message to diybio re: inventory lists06:52
fenndid someone make a bio lab inventory?06:52
ybitkanzure, where did the cell membrane diagram svg come from?08:07
facefaceI think you guys may have discussed this before, but what about a 'nano printing press' for DNA sysnthesis?08:23
facefacewith DNA bases (or mimetic molecules) covalently linked to moveable supports, like little arms, that could be 'typeset' for opposite strand DNA synthesis08:24
facefacesomehow the device could interface with DNAPol, allowing it to do the synthesis step. After each reaction the arm could be retracted and the arm complementart to the next base could be inserted08:25
facefacewash repeat08:26
facefaceof course it would be really cool if you didn't have to wash... any one got references for nano-mechanically controlled enzyme kinetics?08:26
facefacei.e. fix the enzyme, let it run, jam a rod in the active site, retract rod, repeat08:27
facefaceno grim simily intended08:27
facefacei.e. can you deactivate an imobilized enzyme mechanically? second, can you alter enzyme specificity mechanically? i.e. DNApol for synth.08:28
facefaceI remember a lot about programmable DNA pol in the chan.08:28
facefacep.s. can someone improve this for me? http://en.wikipedia.org/wiki/DNA_microarray#Fabrication08:29
fenni see what you mean.. like a line printer08:29
fennthe problem is how do you get the information into the enzyme08:29
facefacefenn: yeah, like a little printing press08:29
fennmy idea was to use three 'antennae' to pick up monochromatic light signals08:29
fennalso, instead of a line printer it'd print one base at a time08:30
facefacefenn: the idea was to induce a mechanical change in the enzyme?08:30
fennyes08:30
fenna 'conformational change' as the biologists like to have it08:31
facefacefenn: that makes more sense, but I was also thinking of 'typesetting' a chunk of DNA at a time08:31
facefacefenn: right08:31
fennbut chunking doesn't gain anything at all08:31
facefaceI see what your saying08:31
fennyou want to make a fake template strand08:32
fenni'm talking about hijacking the polymerase08:32
facefacefenn: I also think that modified DNApol could be used for sequencing, i.e. if it went through specific conformational change depending on the base it was at08:32
fennanyway, i dont see how you're going to be able to build a fake template in the first place08:32
facefacefenn: yeah, roughly two different ideas, both using immobilized base mimetics on a physically moveable support08:32
fenngosh when did everything get so difficult08:33
facefacefenn: right, constructing the template sequence is as hard as synthesizing the DNA (potentially)108:33
facefacewhats that?08:33
* fenn just spent 3 hours designing a blinky light for a bike.. and he's nowhere close to done08:34
faceface;-)08:34
facefacekeep at it!08:34
fennnow, normally i'd just use a microcontroller08:34
fennbut stupid me decided to do it on stripboard08:34
fennbecause i have been playing with this stripboard cad program08:34
facefacecool08:35
fennand now i'm all confused whether i'm looking at it mirrored or not08:35
fennbecause i cant figure out how to label the 555 footprint08:35
fennoh, duh, nevermind08:36
fennnow i see you're supposed to edit the footprint08:36
fennnot like i expect anyone to notice any errors or anything http://imagebin.org/4723910:50
fennif you can even figure out wtf is going on.. it's based on this http://ourworld.compuserve.com/homepages/Bill_Bowden/555exp.gif10:51
genehackerhttp://www.mrdv.org/experiences.html12:09
genehackerinteresting12:09
genehackerhttp://www.foresight.org/nanodot/?p=302012:13
genehackerreprap is nanotech?12:14
kanzurefaceface: there have been some papers on PDMS for DNA synthesis, btw. nanoimprint lithography, etc.13:58
facefacePDMS?13:58
kanzurefenn: we had partial inventory lists.14:00
kanzurefenn: I don't understand your imagebin diagram thingy. is that supposed to be a circuit? what's with the fat line widths?14:00
kanzurefaceface: yes. 14:00
kanzuresee this14:01
kanzurehttp://heybryan.org/books/papers/Oligonucleotide%20on-chip%20synthesis%20using%20PDMS%20stamp.pdf14:01
facefacekanzure: no, I meant, what are PDMS?14:05
facefaceSwine flu virus kills child in US 14:06
kanzureit's a polymer that cures when exposed to light14:06
facefaceI knew this woudl start happening as soon as they said 'we should expect this to happen'14:06
facefaceseems all news hapens that way now...14:06
facefacewe should expect to see... bang .. it happens... I guess I should expect it14:06
facefacekanzure: right14:07
* kanzure goes down to eat14:16
kanzurehttp://jscms.jrn.columbia.edu/cns/2009-04-14/vaidyanathan-citizenscience14:47
myelinzarthis is so stupid15:23
myelinzarhttp://openwetware.org/wiki/Talk:DIYbio:Equipment15:23
myelinzarwhy is he doing this.15:23
* myelinzar throws a rock at Bill15:23
myelinzarhttp://heybryan.org/books/papers/design-utility-search.png16:47
myelinzarhttp://heybryan.org/diagrams/symbolic-regression-design.png17:46
myelinzarbehold! my mad diagramming skillage17:46
kanzurehttp://www.youtube.com/watch?v=Ascql_RoeBU has a nice video composition of feet18:29
kanzurebipedal octopus disguised as a rolling coconut18:30
kanzureTowards a spiderman suit18:59
kanzurehttp://heybryan.org/books/papers/Towards%20a%20Spiderman%20suit%20-%20large%20invisible%20cables%20and%20self-cleaning%20releasable%20superadhesive%20materials.pdf18:59
kanzurehm, I think I can bike from my apartment to my dorm22:31
kanzureer, to the university22:31
kanzureabout six miles, so 12 mi a day. that sounds doable.22:31
kanzure-duzt: Were you able to find the parts you needed?22:49
kanzure-"We are very encouraged by these results, which show that oral delivery of a23:11
kanzure-therapeutic dose of small, interfering RNA (siRNA) to a specific cell type in an23:11
kanzure-animal model is possible, and that evidence of gene silencing using this23:11
kanzure-delivery system is measurable," said Dr. Czech.23:11
duztkanzure ya23:21
duzti also got a book that has all sorts of cheap designs for bio equipment23:21
duztlow costs methods for pcr or something like that23:22
kanzure-is that the name of the book?23:26
kanzure-hm. guttation.23:49
duztkanzure: http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.amazon.com%2FLow-Cost-Approach-PCR-Appropriate-Biomolecular%2Fdp%2F0195119266&ei=uOf4SdrtHNjHtgeeydy1Dw&usg=AFQjCNFcXLh4FHsgJVoByF766ugtayeO7Q23:50
duzterr23:50
kanzure-phyllosecretion23:54
kanzure-oh, that's from leaves.23:55

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