--- Day changed Wed Apr 29 2009
00:17 < kanzure> cis-action: hey
00:17 < kanzure> sorry, I had a meeting with someone
00:23 < kanzure-> I}ruid: hey.
00:41 < kanzure-_> so, the first protein worth expressing would be GFP, which could be done with a kit
00:41 < kanzure-_> but beyond that I'm not quite sure
00:41 < kanzure-_> hey Splicer_. talking about agrobacterium.
02:02 < kanzure-_> http://pubs.caes.uga.edu/caespubs/pubcd/images/B1286-17.jpg
02:02 < kanzure-_> crown gall
02:03 < kanzure-_> http://www.ag.ndsu.edu/pubs/plantsci/crops/a1219-3.jpg
02:08 < kanzure-_> http://forestpests.org/rootbutt.html
02:19 < cis-action> finally back
02:20 < kanzure-_> hi
02:29 < cis-action> uh oh gotta leave again
02:51 < kanzure-_> hahah
02:51 < kanzure-_> "the mammary gland: bioreactor for the production of recombinant proteins"
02:51 < kanzure-_> YES
02:52 < 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.
02:57 < 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)
03:22 < kanzure-_> http://en.wikipedia.org/wiki/Lemna
03:22 < kanzure-_> search for "secrete"
03:23 < 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]
03:47 < kanzure-_> genehacker: transgenic protein expression in mammary glands
03:58 < kanzure-_> fenn: are you going to show up tomorrow?
04:01 < genehacker> hahahahhahahahaha
04:01 < genehacker> is that the llama one?
04:01 < kanzure-_> no
04:01 < genehacker> link?
04:02 < kanzure-_> one moment
04:04 < genehacker> llamas  actual produce microantibodies which are great for a lot of things
04:04 < kanzure-_> http://heybryan.org/books/papers/The%20mammary%20gland%20-%20bioreactor%20for%20the%20production%20of%20recombinant%20proteins.pdf
04:04 < kanzure-_> but actually I've been thinking of using dandelions for protein expression
04:04 < kanzure-_> because of the specific composition of the latex/plastic from the plant
04:05 < kanzure-_> and transfectability by agrobacterium
04:05 < 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.pdf
04:06 < genehacker> dandelions?
04:07 < genehacker> what do we want to produce first off?
04:07 < genehacker> illegal neuroenhancers perhaps?
04:08 < genehacker> http://craphound.com/overclocked/Cory_Doctorow_-_Overclocked_-_Printcrime.html
04:08 < kanzure-_> what illegal neuroenhancers?
04:09 < genehacker> there are none as of yet...
04:09 < kanzure-_> so ...
04:10 < genehacker> what?
04:10 < genehacker> why  dandelions?
04:10 < kanzure-_> because it's easy.
04:10 < kanzure-_> you can eat them.
04:10 < kanzure-_> you can extract the latex
04:11 < genehacker> latex for what?
04:12 < kanzure-_> do you not know where plastic comes from?
04:13 < genehacker> yes I do
04:13 < genehacker> it comes from
04:13 < genehacker> oil
04:13 < genehacker> are you talking about making stuff like PE?
04:13 < genehacker> in 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?
04:14 < kanzure-_> I don't care about polyester really- although that would be neat
04:14 < kanzure-_> more interested in other proteins more than anything
04:14 < kanzure-_> the thing is that it's easy to extract it from dandelion
04:14 < genehacker> polyethylene
04:14 < kanzure-_> because you don't have to do SDS-PAGE bullshit
04:14 < genehacker> SDS PAGE?
04:14 < genehacker> ok
04:14 < kanzure-_> SDS PAGE is usually how you do protein purification
04:14 < kanzure-_> but it's some complicated gel steps or something
04:14 < genehacker> so let's make some DNA polymerases
04:15 < kanzure-_> why?
04:15 < kanzure-_> oh
04:15 < genehacker> the type of things needed for PCR
04:15 < kanzure-_> yeah that's a good idea
04:15 < genehacker> heh dandelions though
04:15 < kanzure-_> transgenic production of Tac polymerase. ok.
04:15 < kanzure-_> yeha
04:15 < kanzure-_> *yeah
04:15 < kanzure-_> they grow basically everywhere
04:15 < genehacker> I was thinking any polymeras
04:15 < kanzure-_> so get a pot with some soil and a lamp
04:16 < kanzure-_> do you know the transformation protocol for agrobacterium?
04:16 < kanzure-_> I recently found this neat freeze-thaw protocol
04:16 < kanzure-_> with a add-the-new-DNA step in between or something
04:16 < genehacker> perhaps we should modify them so they don't express those tufts of fiber on the seeds...
04:16 < genehacker> hmmm...
04:17 < genehacker> try DNA hack
04:18 < genehacker> I saw something on their about argobacter transformation
04:20 < genehacker>  http://web.archive.org/web/20070309143649rn_1/www.accessexcellence.org/RC/AB/BA/Transforming_Plants.html
04:22 < kanzure-_> http://heybryan.org/books/papers/Increasing%20plant%20susceptibility%20to%20Agrobacterium%20infection%20by%20overexpression%20of%20the%20Arabidopsis%20nuclear%20protein%20VIP1.pdf
04:22 < kanzure-_> Increasing Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP1
04:23 < kanzure-_> Increasing Light strongly promotes gene transfer from Agrobacterium tumefaciensto plant cells
04:23 < kanzure-_> http://heybryan.org/books/papers/New%20biotechnological%20applications%20of%20coconuts.pdf
04:24 < kanzure-_> http://heybryan.org/books/papers/Light%20strongly%20promotes%20gene%20transfer%20from%20Agrobacterium%20tumefaciensto%20plant%20cells.pdf
04:27 < genehacker> coconuts?
04:27 < genehacker> heh
04:27 < kanzure-_> yep.
04:27 < kanzure-_> just add plasmid vector to coconut milk.
04:28 < genehacker> so what other proteins do we need
04:28 < genehacker> I'd say let's see if we can synthesize taq first then work on other stuff
04:28 < kanzure-_> the proteins required to do natural competence
04:29 < kanzure-_> MagA, for MRI reporter genes
04:29 < kanzure-_> mechanoreceptors, for magnetic guiding of cells
04:29 < kanzure-_> chlorohopdins-2 for laser-activation of neurons
04:29 < genehacker> but first let's make a DNA synth
04:29 < kanzure-_> hrm.
04:29 < kanzure-_> do you have the sequence to taq?
04:29 < genehacker> so we don't have to buy the DNA sequence
04:29 < genehacker> no
04:29 < genehacker> but ncbi.org does
04:30 < genehacker> nah
04:30 < genehacker> wait
04:30 < kanzure-_> then also insulin, dopamine, various other neurotransmitters
04:30 < kanzure-_> key opium proteins for a few bucks in the pocket
04:31 < genehacker> hahahaha
04:31 < genehacker> is there any law against it?
04:31 < kanzure-_> I'm sure.
04:31 < genehacker> bah
04:33 < kanzure-_> I think it would be cheaper to buy the oligos over the internet, but I'm still interested in making a synthesizer
04:34 < genehacker> I like self-sufficiency
04:36 < kanzure-_> of course.
04:36 < genehacker> hey we could build a biolistic gun to transform plants
04:36 < kanzure-_> out of what
04:36 < genehacker> the first biolistic guns were modified BB guns
04:36 < genehacker> PVC
04:36 < genehacker> pipe fittigns
04:37 < kanzure-_> do you mean ballistic?
04:38 < genehacker> biolistic, ballistic, same thing
04:38 < genehacker> just biolistic is more specific
04:40 < genehacker> though gene guns tend to be super-high velocity helium gas guns
04:41 < genehacker> The 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.
04:42 < kanzure-_> wah, I don't want to have to build a vacuum pump
04:42 < genehacker> then you use helium as a propellent or something like that
04:44 < genehacker> http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/McDonald/Gene_gun.html
04:50 < kanzure-_> if we can find a root that drips out recombinant proteins, then that would be ideal
04:50 < 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 ideas
04:50 < kanzure-_> root dripping would be awesome.
04:50 < genehacker> hmmmm
04:50 < kanzure-_> berries would be ok maybe.
04:56 < kanzure-_> ooh
04:56 < kanzure-_> rhizosecretion
04:57 < fenn> zuh. 11 am
04:57 < fenn> more like 10
04:57 < kanzure-_> right
04:57 < kanzure-_> what is zuh? is it like guh?
04:57 < fenn> sure
04:58 < 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 leaving
04:58 < kanzure-_> *product
04:58 < fenn> oh this is a 'give a presentation' lab meeting
04:59 < fenn> do you guys ever actually sit down and talk about what you're all doing?
04:59 < kanzure-_> nope
04:59 < kanzure-_> heh
04:59 < kanzure-_> we sit down one-on-one
04:59 < kanzure-_> but that's not quite the same thing
05:00 < kanzure-_> we talk about what we're doing in the other lab though .. if that counts.
05:17 < genehacker> woo hoo, they sequenced some of flu
05:18 < genehacker> *swine flu
05:19 < genehacker> MKAILVVMLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK
05:19 < genehacker> LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELRE
05:19 < genehacker> QLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSK
05:19 < genehacker> SYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQ
05:19 < genehacker> EGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK
05:19 < genehacker> GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTG
05:19 < genehacker> MVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKR
05:19 < genehacker> IENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG
05:19 < genehacker> CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASS
05:19 < genehacker> LVLVVSLGAISFWMCSNGSLQCRICI
05:20 < kanzure-_> yeah.
05:20 < genehacker> http://www.google.com/search?q=MKAILVVMLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK+LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELRE+QLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSK+SYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQ+EGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK+GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTG+MVD
05:20 < genehacker> GWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKR+IENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG+CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASS+LVLVVSLGAISFWMCSNGSLQCRICI&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a
05:20 < genehacker> hmmmm....
05:20 < genehacker> preliminary data?
05:21 < genehacker> http://www.iayork.com/Temp/SwineFluOnlyAlign.txt
05:21 < genehacker> damn where's the sequence
05:21 < genehacker> http://stephan-zielinski.com/dwa/2009/04/28/swine-flu-ha-as-ambient-music/
05:21 < genehacker> all I can find is this
05:22 < kanzure-_> I posted a link to diybio
05:23 < kanzure-_> or someone else did
05:23 < genehacker> hmmmm....
05:23 < genehacker> now how do I do sequence comparison again
05:23 < kanzure-_> what do you want to do? homology analysis?
05:24 < genehacker> compare with other stuff
05:24 < genehacker> multiple sequence alignment
05:24 < genehacker> that sorta stuff
05:24 < kanzure-_> you need to say something in particular.
05:24 < kanzure-_> alignment?
05:25 < genehacker> yeah
05:25 < kanzure-_> or do you want to just look for homologues or something?
05:25 < kanzure-_> alignment is something you do before you submit the sequence
05:25 < genehacker> as in compare it to other flu viruses
05:25 < kanzure-_> what do you want to get as a result of the comparison
05:26 < fenn> blast search
05:26 < fenn> or try to use clustal if you're comparing specific things
05:26 < genehacker> http://www.ncbi.nlm.nih.gov/nuccore/FJ966970
05:26 < genehacker> Oseltamivir_resistance sensitive?
05:26 < genehacker> what does that mean?
05:27 < genehacker> oh we're good
05:27 < fenn> adamantane resistant!
05:27 < fenn> we can use this to wipe out those russian supersoldiers
05:27 < kanzure-_> the gorillas?
05:28 < genehacker> hahahah
05:28 < fenn> omega red, etc
05:28 < genehacker> chemical it's based on is essentially a subunit of diamond
05:29 < kanzure-_> what are these plastic sleeve bioreactor thingies?
05:31 < fenn> how does duckweed growth compare to algae?
05:31 < genehacker> plastic sleeve bioreactors?
05:32 < genehacker> you mean like with big bags of plastic
05:32 < fenn> wp says 10 to 30 tons per hectare year
05:32 < 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.
05:34 < katsmeow-afk> 10 tons dry?
05:34 < kanzure-_> ah, "root exudation"
05:34 < fenn> most proteins dont drip
05:35 < kanzure-_> what about in a sap
05:48 < genehacker> maple trees?
06:26 < kanzure> no, I don't want to have to grow trees
06:52 < fenn> i dont quite understand your message to diybio re: inventory lists
06:52 < fenn> did someone make a bio lab inventory?
08:07 < ybit> kanzure, where did the cell membrane diagram svg come from?
08:23 < faceface> I think you guys may have discussed this before, but what about a 'nano printing press' for DNA sysnthesis?
08:24 < faceface> with DNA bases (or mimetic molecules) covalently linked to moveable supports, like little arms, that could be 'typeset' for opposite strand DNA synthesis
08:25 < faceface> somehow 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 inserted
08:26 < faceface> wash repeat
08:26 < faceface> of course it would be really cool if you didn't have to wash... any one got references for nano-mechanically controlled enzyme kinetics?
08:27 < faceface> i.e. fix the enzyme, let it run, jam a rod in the active site, retract rod, repeat
08:27 < faceface> no grim simily intended
08:28 < faceface> i.e. can you deactivate an imobilized enzyme mechanically? second, can you alter enzyme specificity mechanically? i.e. DNApol for synth.
08:28 < faceface> I remember a lot about programmable DNA pol in the chan.
08:29 < faceface> p.s. can someone improve this for me? http://en.wikipedia.org/wiki/DNA_microarray#Fabrication
08:29 < fenn> i see what you mean.. like a line printer
08:29 < fenn> the problem is how do you get the information into the enzyme
08:29 < faceface> fenn: yeah, like a little printing press
08:29 < fenn> my idea was to use three 'antennae' to pick up monochromatic light signals
08:30 < fenn> also, instead of a line printer it'd print one base at a time
08:30 < faceface> fenn: the idea was to induce a mechanical change in the enzyme?
08:30 < fenn> yes
08:31 < fenn> a 'conformational change' as the biologists like to have it
08:31 < faceface> fenn: that makes more sense, but I was also thinking of 'typesetting' a chunk of DNA at a time
08:31 < faceface> fenn: right
08:31 < fenn> but chunking doesn't gain anything at all
08:31 < faceface> I see what your saying
08:32 < fenn> you want to make a fake template strand
08:32 < fenn> i'm talking about hijacking the polymerase
08:32 < faceface> fenn: 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 at
08:32 < fenn> anyway, i dont see how you're going to be able to build a fake template in the first place
08:32 < faceface> fenn: yeah, roughly two different ideas, both using immobilized base mimetics on a physically moveable support
08:33 < fenn> gosh when did everything get so difficult
08:33 < faceface> fenn: right, constructing the template sequence is as hard as synthesizing the DNA (potentially)1
08:33 < faceface> whats that?
08:34  * fenn just spent 3 hours designing a blinky light for a bike.. and he's nowhere close to done
08:34 < faceface> ;-)
08:34 < faceface> keep at it!
08:34 < fenn> now, normally i'd just use a microcontroller
08:34 < fenn> but stupid me decided to do it on stripboard
08:34 < fenn> because i have been playing with this stripboard cad program
08:35 < faceface> cool
08:35 < fenn> and now i'm all confused whether i'm looking at it mirrored or not
08:35 < fenn> because i cant figure out how to label the 555 footprint
08:36 < fenn> oh, duh, nevermind
08:36 < fenn> now i see you're supposed to edit the footprint
10:50 < fenn> not like i expect anyone to notice any errors or anything http://imagebin.org/47239
10:51 < fenn> if you can even figure out wtf is going on.. it's based on this http://ourworld.compuserve.com/homepages/Bill_Bowden/555exp.gif
12:09 < genehacker> http://www.mrdv.org/experiences.html
12:09 < genehacker> interesting
12:13 < genehacker> http://www.foresight.org/nanodot/?p=3020
12:14 < genehacker> reprap is nanotech?
13:58 < kanzure> faceface: there have been some papers on PDMS for DNA synthesis, btw. nanoimprint lithography, etc.
13:58 < faceface> PDMS?
14:00 < kanzure> fenn: we had partial inventory lists.
14:00 < kanzure> fenn: I don't understand your imagebin diagram thingy. is that supposed to be a circuit? what's with the fat line widths?
14:00 < kanzure> faceface: yes. 
14:01 < kanzure> see this
14:01 < kanzure> http://heybryan.org/books/papers/Oligonucleotide%20on-chip%20synthesis%20using%20PDMS%20stamp.pdf
14:05 < faceface> kanzure: no, I meant, what are PDMS?
14:06 < faceface> Swine flu virus kills child in US 
14:06 < kanzure> it's a polymer that cures when exposed to light
14:06 < faceface> I knew this woudl start happening as soon as they said 'we should expect this to happen'
14:06 < faceface> seems all news hapens that way now...
14:06 < faceface> we should expect to see... bang .. it happens... I guess I should expect it
14:07 < faceface> kanzure: right
14:16  * kanzure goes down to eat
14:47 < kanzure> http://jscms.jrn.columbia.edu/cns/2009-04-14/vaidyanathan-citizenscience
15:23 < myelinzar> this is so stupid
15:23 < myelinzar> http://openwetware.org/wiki/Talk:DIYbio:Equipment
15:23 < myelinzar> why is he doing this.
15:23  * myelinzar throws a rock at Bill
16:47 < myelinzar> http://heybryan.org/books/papers/design-utility-search.png
17:46 < myelinzar> http://heybryan.org/diagrams/symbolic-regression-design.png
17:46 < myelinzar> behold! my mad diagramming skillage
18:29 < kanzure> http://www.youtube.com/watch?v=Ascql_RoeBU has a nice video composition of feet
18:30 < kanzure> bipedal octopus disguised as a rolling coconut
18:59 < kanzure> Towards a spiderman suit
18:59 < kanzure> http://heybryan.org/books/papers/Towards%20a%20Spiderman%20suit%20-%20large%20invisible%20cables%20and%20self-cleaning%20releasable%20superadhesive%20materials.pdf
22:31 < kanzure> hm, I think I can bike from my apartment to my dorm
22:31 < kanzure> er, to the university
22:31 < kanzure> about six miles, so 12 mi a day. that sounds doable.
22:49 < kanzure-> duzt: Were you able to find the parts you needed?
23:11 < kanzure-> "We are very encouraged by these results, which show that oral delivery of a
23:11 < kanzure-> therapeutic dose of small, interfering RNA (siRNA) to a specific cell type in an
23:11 < kanzure-> animal model is possible, and that evidence of gene silencing using this
23:11 < kanzure-> delivery system is measurable," said Dr. Czech.
23:21 < duzt> kanzure ya
23:21 < duzt> i also got a book that has all sorts of cheap designs for bio equipment
23:22 < duzt> low costs methods for pcr or something like that
23:26 < kanzure-> is that the name of the book?
23:49 < kanzure-> hm. guttation.
23:50 < duzt> kanzure: 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=AFQjCNFcXLh4FHsgJVoByF766ugtayeO7Q
23:50 < duzt> err
23:54 < kanzure-> phyllosecretion
23:55 < kanzure-> oh, that's from leaves.