Dwarf tobacco?

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Sebastian Cocioba

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Jan 31, 2014, 12:36:21 AM1/31/14
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Does anyone have any dwarf tobacco seeds? Im growing some petite Havana but they are actually not so petite...my lab space is limited so any dwarf mutant if the Nicotiana genus would be quite welcome. Thanks!

PS I hate arabidopsis.

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

Cory Tobin

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Jan 31, 2014, 2:08:34 AM1/31/14
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How big is too big? I have some tobacco that gets about 1 to 1.5 feet
tall. I'm not sure if it's actually a dwarf variety or if I'm just
stunting the growth by planting in small pots. But even if I am just
stunting it, it's able to flower and produce viable seeds.

-cory

Koeng

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Jan 31, 2014, 4:21:41 PM1/31/14
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Any particular reason you like tobacco over arabidopis? Sorry, I am not really into plant biotech so I don't know a lot of the differences

-Koeng

Nathan McCorkle

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Jan 31, 2014, 4:35:11 PM1/31/14
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On Fri, Jan 31, 2014 at 1:21 PM, Koeng <koen...@gmail.com> wrote:
> Any particular reason you like tobacco over arabidopis? Sorry, I am not
> really into plant biotech so I don't know a lot of the differences

Maybe because it's a commercial crop more data exists? More commercial
value if the inventor comes up with some awesome GMO?

Cathal Garvey

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Jan 31, 2014, 4:44:08 PM1/31/14
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I imagine a modified tobacco with pest or fungal resistance would be big
money, but then you'd be one of the bad guys for helping make more
cigarettes in the world. :)
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Nathan McCorkle

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Jan 31, 2014, 10:36:07 PM1/31/14
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On Fri, Jan 31, 2014 at 1:44 PM, Cathal Garvey
<cathal...@cathalgarvey.me> wrote:
> I imagine a modified tobacco with pest or fungal resistance would be big
> money, but then you'd be one of the bad guys for helping make more
> cigarettes in the world. :)

'Better Cigarette' GMO? Throw some caffeine in there, pull in the
coffee market. Mellow Methyl Salicilate 'natural menthol' smokes, or
Intelligent Isoamyl Acetate (aka Bursting Banana) flavor. Some
biosynthetic combustion product that scrubs carcinogens from the
smoke.

This is fun!

Cathal Garvey

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Feb 1, 2014, 6:09:28 AM2/1/14
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Just remove the nicotine and you'll have my support. Same flavour,
useful for people quitting, and fewer health effects.

If you borrowed some inspiration from marijuana and packed the smoke
full of antioxidants and antiinflammatories, you might even counteract
the negative effects of the smoke itself.

New DIYbio project for Sebastian: "Safe Ciggie"?
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Nathan McCorkle

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Feb 1, 2014, 11:19:03 PM2/1/14
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On Sat, Feb 1, 2014 at 3:09 AM, Cathal Garvey
<cathal...@cathalgarvey.me> wrote:
> Just remove the nicotine and you'll have my support. Same flavour,

Isn't tobacco's use primarily medicinal? Do people like the flavor that much?

Sebastian Cocioba

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Feb 2, 2014, 12:08:01 AM2/2/14
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As always great commentary but to get back to the question about the
reason behind tobacco its actually quite simple. Nicotiana tabacum and
its subsequent cultivars are fantastic tools for plant transformations.
It grows quickly, agrobacterium loves it (high but not too high
phenolic exudates), but most importantly it regenerates very fast. One
of the big roadblocks to agrobacterium mediated transformations is the
lack of a reliable regeneration system. Even if the agro does a stellar
job at transferring its T-DNA into the wounded plant tissue, if you
can't successfully select for transgenic tissue and then make a
functioning plant out of it what's the point? I managed to get a stable
transformant rooted and happy in 4-5 weeks time. The seeds take a bit
longer to get in comparison to Arabidopsis but the seeds are larger,
easier to handle, and plentiful. The plant is also not so sensitive to
temperature and humidity fluxes as Arabidopsis but will need optimal
conditions for the leaf to be beefy enough for transient expression
experiments like agroinfiltration by injection. My favorite trait is
honestly the seed properties. Its not dust like Arabidopsis. If you
ever worked with the plant and have even slightly longish hair and it
happens to be a dry cold day, static will be your nemesis. The seed
dust clings to everything and is tricky to surface sterilize. With
tobacco I just put a wet paper towel saturated in 70% ethanol in front
of the laminar hood, sprinkle some tobacco seeds on it, remoisten the
towel and allow for the paper to dry. I repeat this once more and I end
up with surface sterilized seeds that have never in my 5+ years of
tissue cultures ended up contaminated. Its just so much more
manageable. Plus the plant gives off a nice aroma (not at all like dry
cured tobacco cigars) and the flowers are pretty. The leaves do get a
bit sticky due to some oil secretions but you win some you lose some.

Either way I really like it as a model organism and can't see myself
switching to Arabi any time in the future. I've developed protocols for
many different species but tobacco is by far the easiest...second only
to the classic African violet.

As for the commercial aspect, I really am not interested in making
tobacco any more desirable. I know too many people especially in my
family whose lives got snuffed out due to chain smoking. I know that's
an extreme example but I'd rather not. Last thing I want is to have the
smokers on my back about being the bad guy (Pro-GMO and "part of the
problem") too.

Im leaning towards expression research so in my quest ill end up with
some pretty fluorescent tobacco plants that I plan to line my shelves
with. A few UV LED strips and Ill be happy. If this whole PEG kit works
ill probably make it use tobacco so everyone can make their own
fluorescent plants. The GFP E. Coli of plant biotech. My dream is that
by the time Im done, people will look at plant engineering (at least in
its simplest form) as trivial. I can already hear the hipsters say they
were transforming plants before it was cool.

:P

PS: enclosed is a picture of one of my grow racks spilling over with
tobacco plants. Its safe to say I need more space. I may remove the
middle shelf and grow from the bottom to the top of the second shelf.


Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D From: Nathan McCorkle
Sent: 2/1/2014 11:19 PM
To: diybio
Subject: Re: [DIYbio] Re: Dwarf tobacco?
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Alex

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Feb 2, 2014, 12:27:35 AM2/2/14
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Very cool, Sebastian! I have a similar setup but, unfortunately, my plants are all currently dead! Haha I have my sights set on some tobacco next and just need to get my hands on some seed.

Your plants look great!

Alex

Andrew Willoughby

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Feb 2, 2014, 12:44:21 AM2/2/14
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Where are you doing this? I'm a high school senior and it's my dream to do plant biotech. I'm trying to make college fit that.

John Griessen

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Feb 3, 2014, 9:44:28 AM2/3/14
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On 02/01/2014 11:08 PM, Sebastian Cocioba wrote:
> As for the commercial aspect, I really am not interested in making
> tobacco any more desirable.

It could become desirable as a GMO factory. Maybe it's evolved ability to create
nicotine while still thriving will even help with creating other side benefit drugs,
oils, plastics precursors, etc....

Cathal Garvey

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Feb 3, 2014, 9:52:38 AM2/3/14
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Well, I can imagine that if you chop the head off that biosynthetic
chain, you'll end up with a pretty optimised precursor pathway for other
alkaloids (nicotine is alkaloid, right?).

The problem is, nobody will hear "nicotine free", they'll just hear
"tobacco". It's a sure-fire, ironclad, guaranteed way to end up being
accused of trying to shill GMO ciggies.
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John Griessen

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Feb 3, 2014, 11:24:28 AM2/3/14
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On 02/03/2014 08:52 AM, Cathal Garvey wrote:
> The problem is, nobody will hear "nicotine free", they'll just hear
> "tobacco". It's a sure-fire, ironclad, guaranteed way to end up being
> accused of trying to shill GMO ciggies.

But are the ones listening the same group? As for tool users for GMO
research, will they care if it is tobacco? If anti tobacco
activists shout that tobacco-based researchers are promoting tobacco,
will it cause trouble for users of laboratory plants, or even factory-greenhouse plants?

Sebastian Cocioba

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Feb 3, 2014, 1:40:11 PM2/3/14
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As a tool I LOVE tobacco. I use it to express stuff all the time. To
make it the focus of GM in and of itself is a different story.
Exploiting it for tools is one thing, making it a better crop is
another. Plus USDA, EPA, and FDA approval is millions of dollars.

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D From: John Griessen
Sent: 2/3/2014 11:24 AM
To: diy...@googlegroups.com
Subject: [DIYbio] gen mod tobacco?
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Nathan McCorkle

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Feb 3, 2014, 7:06:13 PM2/3/14
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On Mon, Feb 3, 2014 at 6:52 AM, Cathal Garvey
<cathal...@cathalgarvey.me> wrote:
> Well, I can imagine that if you chop the head off that biosynthetic
> chain, you'll end up with a pretty optimised precursor pathway for other
> alkaloids (nicotine is alkaloid, right?).
>
> The problem is, nobody will hear "nicotine free", they'll just hear
> "tobacco". It's a sure-fire, ironclad, guaranteed way to end up being
> accused of trying to shill GMO ciggies.

Why are (GMO or not) cigarettes a bad thing? I thought the tobacco /industry/
was evil, not the plant.

Nicotine in the plant probably acts as a natural pesticide as well, so
leaving its pathway alone while augmenting others might be helpful for
keeping it competitive in the fields.

Andrew Willoughby

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Feb 3, 2014, 2:41:11 PM2/3/14
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Caffeine...

Sebastian Cocioba

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Feb 4, 2014, 11:49:01 AM2/4/14
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I have a personal lab at home in NYC and will soon be moving it to a
business address. I've built my lab specifically for plant biotech and
all was procured through eBay and university auctions. Its amazing how
well set up you can get with a little patience and some negotiating. I
don't think I've spent more than $4k in total but have the value of a
few tens of thousands.

Like I've mentioned previously, the limiting factor in doing plant
biotech DIY or otherwise is agrobacterium regulations. Im working on a
way to eliminate the need for bacteria in plant transformations all
together and make it available as a kit or open source protocol using
commercially available ingredients. This just put even more fire under
my ass to get this to work.

If you have any questions just ask. I'd love to help make your research
dream a little more tangible. Its super rare to find people that are
interested so by all means ask away! :)

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D From: Andrew Willoughby
Sent: 2/4/2014 9:22 AM
To: diy...@googlegroups.com
Subject: RE: [DIYbio] Re: Dwarf tobacco?
Where are you doing this? I'm a high school senior and it's my dream
to do plant biotech. I'm trying to make college fit that.

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Koeng

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Feb 4, 2014, 12:15:57 PM2/4/14
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Andrew Willoughby

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Feb 4, 2014, 12:18:36 PM2/4/14
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Well here's a copy of the email I sent to NY Botanic's email address:

I stumbled upon your website from a poster on the DIYbio google group/mailing list. Sorry if I try to take this opportunity to mine you for questions; plant biotech is my dream. 

Are public plant biotech labs common? Google searches don't seem to turn up much.

Is there anyway I can browse your research? (Papers that is)

I've applied to a disgusting amount of schools, 7 with plant science/ biotech/ bioengineering -ish programs:

University of Illinois @ Urbana-Champaign: Bioengineering and Horticulture
Colorado School of Mines: Bio E

Cornell: Plant Science

CalTech: BioTech

University of Southern California: Biotech, with a botany research focus

Colorado State University: Horticulture

University of Oklahoma: Botany

Are any of these schools widely recognized in this field? It's hard to find any kind of reliable source analyzing a school's academic quality in botany. I guess not enough people are interested, sadly.

If getting a job in a lab like NY Botanics, what other jobs are out there for plant scientists/ plant biotech-people? I'm strongly considering double majoring in Chemical Engineering as well to be more hireable.

Is there any other advice anyone out there can give a stressed out 18 year old trying to decide, if not the rest of his life, then the what opens the door to it?

So are you working on making gene guns more efficient? If I remember correctly from watching the Glowing Plant project's videos, you don't need the agrobacterium if the gene gun works.
Is agrobacterium regulated because of horizontal gene transfer-phobia?

I'm sure I'll think of a few more questions
Andrew Willoughby

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Sebastian Cocioba

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Feb 4, 2014, 12:22:04 PM2/4/14
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Not to go off topic but how will they ship agro across state lines without an APHIS permit? Its still considered regulated.


Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

From: Andrew Willoughby
Sent: 2/4/2014 12:18 PM
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scoc...@gmail.com

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Feb 4, 2014, 2:05:47 PM2/4/14
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My humblest apologies Andrew! I think the email was either snagged in my spam net or I simply didn't get a chance to write back. The poster was me. I use my Gmail account to post to DIY bio so I can keep tabs on what's important and interesting (DIY Bio) versus the crap ton of biotech supplier ads and the occasional business email that floods my NYB inbox. Truly sorry that I didn't get a chance to write back!

I don't want to make my work seem like something its not. I work from my home lab soon to be pro lab in a separate location. I started a company because I had a few ideas I wanted to work on while trying to generate some income for the lab. I began with orchid micropropagation and sold to a few hotel chains in the local NYC area but that all stopped when I fell in love with plant genetic engineering. I decided to turn the company into a non-income generating R&D model until I do manage to make something worth selling. Im almost entirely self taught aside from an almost finished BS from Stony Brook University so I cant really advise on whats best from an academic stand point. Im doing this all on my own which is terrifying since if I mess up its all on me but liberating since I don't have to be pressured by a PI or grant deadline etc. Its a hobby that turned semi-pro…nothing special.

As far as agrobacterium and my knowledge of it is concerned, strains like GV3101 EHA105 etc are up for deregulation but until then its treated as a plant pathogen and thus BSL1-2 grey area. In some cases under specific conditions it can and will transfect mammalian cells. Moving plant pathogens or material carrying such across state lines in the USA is a felony. I have absolutely no clue how on earth Glowing Plant Project people got around this…or did they disclaim everything in superfine print? Wild type agrobacterium transfers oncogenes that produce similar cytokine compounds that trigger cell proliferation (cancer). The hormones they code for (genes IaaM, IaaH, and IPT from the Ti plasmid) are also considered carcinogens but in large concentrations. Until the proper authorities concluded beyond any doubt that the disarmed strains are in fact disarmed and can in no way transfer their genes to other things (which would defeat the purpose of agro) they will keep the bacteria regulated to a degree.

As for my “research”, I have nothing formal published yet but expect a small article to be done soon. My focus is on using polyethylene glycol as a means of transforming plants and more importantly the plastid (chloroplasts). Gene guns are expensive to buy and expensive to shoot. The DIY derivatives are unreliable at best and known pressures for plastid transformation is in excess of 1000 PSI so that kind of pressure I would avoid. Its also very inefficient. About 5% transformants in comparison to the 80%+ with agro but it can only target the nucleus. The use of alternative carrier nanoparticles like tungsten tend to be slightly to severely bioavailable or bioreactive which may induce defensive apoptosis. Either way in my opinion the gene gun and agro are not the answer but a convenient solution to genetic engineering in higher plants. I like PEG and protoplasts but they are tough to handle. Im working on making the process as fool proof as possible. Worst case Ill try to publish it in PLoS ONE or just a detailed entry on openwetware.org.

I'm trying to organize my life so that I can have time to post to my blog which is or will be 100% plant biotech. For now I post religiously on Facebook so you can friend me if you’d like and follow my rants, anecdotes, and cooking-show-like protocols.

Sent from Windows Mail

Alex

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Feb 4, 2014, 2:37:11 PM2/4/14
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Sebastian,

I share similar interests to you and Andrew. I'm a complete noob but have friend requested you on Facebook.

Thanks,
Alex P

Cory Tobin

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Feb 4, 2014, 4:57:11 PM2/4/14
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> CalTech: BioTech
>
> Are any of these schools widely recognized in this field? It's hard to find
> any kind of reliable source analyzing a school's academic quality in botany.

I work in Caltech's only plant lab so I would say that, no, Caltech in
general is not recognized as a powerhouse in plant genetics / botany.
I suppose my PI is a pretty big deal in Arabidopsis development but
the university overall is mainly known for physics.

If you stop by Caltech to visit let me know and I'll show you around our lab.

-cory

Nathan McCorkle

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Feb 4, 2014, 5:20:49 PM2/4/14
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My University (Rochester Institute of Technology) had a greenhouse
and a few plant classes that were ALWAYS full, I didn't even get to
take the plant cloning class because it was so popular :(

I remember the main plant professor was from Urbana-Champaign for his
MS and PhD.

The field is definitely tougher if you don't want to work for Monsanto
or the other agro-giants, that said, those are the exact companies
you'd want to intern for because they're leaders in the field.

There are also opportunities in Government National Labs, including
biofuel and timber and crop research.

I'm not sure what you're stressing out about, but try to realize that
nothing comes quickly in life, and that modern science is building on
about 2500 of strong R&D, going back about 10000 years total. What I
mean is that there's A LOT TO LEARN, and it really does take years and
years. This might seem boring, especially compared to sci-fi movies,
but that's just how learning works today. This isn't as much of a
limitation as you think, in fact it's essential to evolution, it's up
to every new generation to re-check the 'facts' of history to make
sure there aren't errors, and often innovate with a new take on old
ideas.

Even though I've often wanted to 'get school done with', it's really
amazing that there's SO MUCH TO LEARN, knowing civilization is so old
and to see the progression just in written history... and also knowing
that there was an even longer amount of time before civilization
existed. If learning 'everything' was quick, life might seem more like
an explosive combustion reaction than a nice calm campfire.

Anyway, definitely check out the DIY genegun, reproducing those
results would be a great first project for someone with a fresh mind
like you!
https://labitat.dk/wiki/File:Rudiger_Trojok_gene_gun_hack-v01.pdf
> https://groups.google.com/d/msgid/diybio/CAKSQMN5LGC0xbcegdVb%3DYWYmXQb%3DQ%2Bm63q2zCg7LvK8jxRkVzg%40mail.gmail.com.
>
> For more options, visit https://groups.google.com/groups/opt_out.



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Andrew Willoughby

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Feb 4, 2014, 7:23:54 PM2/4/14
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Sebastian: I added you on facebook, rants are fine with me; I'm very interested. Why would you want to change plastid DNA instead of just the plant's own DNA? I guess if it's shorter, it's easier to understand. But is it always smaller? A lot of ferns if I remember correctly have enormous genomes because they're so old with many duplicate parts. Why isn't plastid DNA gigantic? Maybe I just don't now enough about DNA...Science classes at my school are kind of a joke, everything I know I learned on the internet.
Cory: If I went to CalTech, is it possible to get into that lab? Or is it full?
Nathan: I love thinking about how long agriculture has been going on. Recently I've been getting interested in the
biodiversity of the wild relatives of our crop plants; especially with possible uses in disease resistance.

Cory Tobin

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Feb 4, 2014, 7:46:06 PM2/4/14
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> Cory: If I went to CalTech, is it possible to get into that lab? Or is it full?

You said you're 18 so I imagine you're applying for undergrad studies.
Usually the undergrads at caltech start doing research after their
first or second year. The procedure would be to email my PI and
express interest in working in the lab. He doesn't personally mentor
students so he would ask the grads and postdocs in the lab if anyone
wants to take on a student to mentor. If someone has time to mentor
you then you would be invited to work in the lab. In general, this is
the procedure for undergrads getting spots in research labs. Some
larger labs have more formal procedures for applying, but usually you
just email professors a few months in advance and ask.

-cory

Andrew Willoughby

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Feb 4, 2014, 7:58:37 PM2/4/14
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A few months in advance during my first year?



-cory

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Cathal Garvey

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Feb 5, 2014, 9:32:51 AM2/5/14
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> Im working on a
> way to eliminate the need for bacteria in plant transformations all
> together and make it available as a kit or open source protocol using
> commercially available ingredients. This just put even more fire under
> my ass to get this to work.

Go team eliminating awkward stuff from biohacking! :)
Can't wait to see more, and I, likewise, am totally OK with unstructured
rants. Get that blog going somewhere I can RSS-feed it!
Please help support my crowdfunding campaign, IndieBB: Currently at
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