IGEM team meeting notes 5 26 14

From Counter Culture Labs

Agenda[edit | edit source]

  • IP discussion with Yaasha
  • Ooh and aah over DNA distribution kit we just received from iGEM
  • Fundraising
  • DNA assembly methods

Marc - fundraising video in progress, possibly done by Wednesday Advait and Fran - (Probably) Meeting at Biocurious this Wednesday at 7:00 pm to finalize.

IP stuff[edit | edit source]

Consensus: want to keep research open but should it be selectively open? (ie, not open to incumbents who may not share their research back with the community...or should large companies have to pay a fee?)

Should we worry about market shares and competition in the future? (the Kraft monopoly scenario) Yaasha: no, if a big company starts pushing out smaller ones it will be on the basis of their innovation not ours

concerns/cultural aims of the project that extend beyond getting more vegan cheese into the world: centralization of power; environmental impact of our actions; reshape the way GMO food is regarded, handled and treated in the U.S.

Discussion about DPL option

Yaasha Sabba prefers patent option as a way to protect work done by the group and give everybody recognition as coinventors DPL is not permanent - can decide to remove it from the pool later patent office doesn't have time to look at wikis...even if you want to have it open it is good to register with the PTO and abandon it

Craig: prefers keeping everything open; brought up good point that our project does not involve novel techniques; what's goal of the team?

Miyoko (from Fairfax): Ahnon emailed Miyoko requesting help regarding producing vegan cheese once we express the protein we need to put it into something miyokoskitchen.com

Options a la Marc:

  1. File a non-provisional patent application. Get it accepted. Then

explicitly abandon the patent.

  1. File a non-provisional patent application and stop doing anything,

thus abandoning the patent.

  1. 3rd party pre-grant review: 6 month period where patent is pending;

can submit prior art; way of bringing thigs to the attention of people using PTO; but have to wait for someone else to file a patent, catch it,

and with help of a lawyer file in response to the new patent

Big Q: to patent or not to patent. Filing a provisional patent at this point would be shooting ourselves in

the foot.

What's the liklihood of an outside group affecting our group's ability to continue conducting research on this product beyond the iGEM competition?

K-casein expression in e. coli is already patented

provisional patent option: addresses 'first to file' concerns can lose the provisional if it lacks enough/appropriate information

prior art: publically announced meet up group; personal witnesses to this meeting; here is what we said in our minutes today; everything we discussed today is prior art

How do we execute the intellectual property internally? (next big hurdle)

by patenting, giving yourselves the power to say 'open' or 'closed;'

(BC or CCL or both?) conflict of interest statement prohibits any board members from being involved with projects that are not open-source

another possible issue: anyone working with a formal lab (i.e. Patrik @ LLL) will have to show their employer any patents and have it approved as well

techology transfer: additional concern associated with federally funded organizations

sub-organization with separate by-laws and small board; only purpose of this sub-org would be to hold/file provisional patents/DPL

Consensus to do 2 things:

  1. write up...
  2. attempt to either.....abandon DPL

Linda Kahl US PTO: big change; $ from patent fees no longer all going to government; much of the fees are going to US PTOs new San Jose office

Group in Ireland that has been contacting Patrik focused more on milk than the cheese have 30K in funding; backed by corporate investors (http://synbioaxlr8r.com/)

DNA Distribution Kit[edit | edit source]


To do:

  1. Go through parts list; watch videos; download excel files listing


  1. Internal databases

plasmid DB vector maps Open-source alternatives to File Maker Pro:



Fundraising[edit | edit source]

this Wednesday; somewhere in Oakland; noonish - 5 pm; Marc, Francis, etc. finishing up filming fundraising video

changing text/wording on crowd tilt page:

   writing an intro for a proposal - first sentence should explain your
entire project
   contact Jing

Fiver.com for professional voie over

Video "rough draft" link (with footage and possible music): https://docs.google.com/file/d/0B4WT2XIBrqnScmZCLUFYOTFOWlU/edit This is not so much the actual video but more of a "practice" with some good footage and a possible music choice.

Jamie: Contact David B at PETA.org Ashley: would have a problem working with PETA

this a.m. Fran posted a fundraising video on SeaFile link to video with music: https://docs.google.com/file/d/0B4WT2XIBrqnScmZCLUFYOTFOWlU/edit

DNA Assembly Methods[edit | edit source]

Craig put together an awesome power point presentation: Powerpoint: https://docs.google.com/viewer?a=v&pid=forums&srcid=MDQ3ODI0ODE4NDM3NTM4NjIyMzUBMDM5OTQ5MTk5OTAwNDIzOTE2MjcBa0Z0ZTFkd2xycGdKATQBAXYy



Traditional cloning ==

plasmid backbone: circular piece of DNA we're cloning into that has ab resistance, ORI, etc.


What RE sites can you use? RE sites can't be inside your DNA (will cute out GOI)

Stoichiometry: important consideration when determining ideal plasmid backbone:GOI ratio

If something goes wrong with ________ must use traditional cloning to fix it

Golden Gate Cloning[edit | edit source]

good for multiple sequence cloning

you design DNA overhangs to ligate multiples pieces together in a strategic orientation

no scar sequence introduced issues with scars occur when you're ligating together different protein domains

same RE used for everything; restriction site is elminated from ligated product

BioBrick approach[edit | edit source]

use a few, specific restriction enzymes

makes cloning easy if parts assembled on their own

see http://parts.igem.org/Help:Standards/Assembly

iGEM wants us to submit everything we do with BioBricks methods; different cloning methods are compatible with each other

SLIC: sequence and ligation independent cloning[edit | edit source]

one enzyme used for every reaction

multi-step process; backbone vector contains sequences intrinsic to the plasmid backbone; GOI designed with same DNA at both ends

throw in T4 DNA polymerase because it has 3' DNA exonuclease activity; eats up DNA from opposite ends of template strands

e.coli (for example) repair machinery fills in gaps after ligation

make constructs in e.coli and then express them in yeast

Gibson[edit | edit source]

three enzymes used for every reaction (more costly)

one-step process

Like SLIC except it uses T5 exonuclease (5' --> 3' activity; opposite

of T4 used in SLIC)

nicks repaired before they go into e. coli

overhangs must lack secondary structure to avoid formation of hairpins which would compete with GOI for insertion into backbone

only method with a theme song :)

GeneArt (not included in powerpoint)[edit | edit source]

Wrap-up & things to do:

  1. creating cloning strategies on paper
  2. make an excel sheet with all reagents; price break down; similar to

spreadshet for DIY cloning class

  1. update wiki with all work done individually or in groups; present

updates to group meetings

  1. finalize video and crowdtilt