IGEM team meeting notes 5 26 14: Difference between revisions
(Created page with "May 19th 2014 = Agenda = == Introductions == Patrik: Bio Jamie: Biotech student at BCC Rebecca: Graduate student. Synthetic biology, science fiction and history of science...") |
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May 19th 2014 |
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= Agenda = |
= Agenda = |
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* IP discussion with Yaasha |
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== Introductions == |
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* Ooh and aah over DNA distribution kit we just received from iGEM |
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* Fundraising |
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* DNA assembly methods |
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Marc - fundraising video in progress, possibly done by Wednesday |
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Patrik: Bio |
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Advait and Fran - (Probably) Meeting at Biocurious this Wednesday at |
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Jamie: Biotech student at BCC |
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7:00 pm to finalize. |
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Rebecca: Graduate student. Synthetic biology, science fiction and |
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history of science. |
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Shashank: Studying salt tolerance in plants |
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Advait: Middle schooler interested in biology |
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Mallory on Zoom |
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Fran (not on Zoom, only this document): Nursing student learning about |
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biology. |
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= IP stuff = |
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== Brief intro to project for new people == |
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wiki: https://wiki.counterculturelabs.org/index.php/Vegan_cheese |
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Consensus: want to keep research open |
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== Announcements == |
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but should it be selectively open? (ie, not open to incumbents who may |
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not share their research back with the community...or should large |
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companies have to pay a fee?) |
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Should we worry about market shares and competition in the future? (the |
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Kraft monopoly scenario) |
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Yaasha: no, if a big company starts pushing out smaller ones it will be |
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on the basis of their innovation not ours |
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concerns/cultural aims of the project that extend beyond getting more |
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vegan cheese into the world: |
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centralization of power; |
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environmental impact of our actions; |
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reshape the way GMO food is regarded, handled and treated in the U.S. |
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Discussion about DPL option |
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== Updates from sub-projects == |
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Yaasha Sabba prefers patent option as a way to protect work done by the |
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What happened in the last week? A brief overview. |
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group and give everybody recognition as coinventors |
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DPL is not permanent - can decide to remove it from the pool later |
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patent office doesn't have time to look at wikis...even if you want to |
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have it open it is good to register with the PTO and abandon it |
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Craig: |
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=== Fundraising === |
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prefers keeping everything open; |
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Fran: Video script is written and Craig provided some very helpful |
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brought up good point that our project does not involve novel |
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initial comments. I will give recording another shot in the morning, and |
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techniques; |
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then upload a version with no music soundtrack and one with a music |
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what's goal of the team? |
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soundtrack to solicit further comments. I am committed to getting this |
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recording done tomorrow. Anybody should feel free to take a crack at it, |
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though, I don't want to hog the project. |
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Miyoko (from Fairfax): |
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In any case, once the next iteration of the recording is done, we will |
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Ahnon emailed Miyoko requesting help regarding producing vegan cheese |
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still need a lot of input about photos, stock footage, any |
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once we express the protein we need to put it into something |
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captions/titles, etc. |
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miyokoskitchen.com |
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Options a la Marc: |
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Finding good stock footage has been challenging! Easiest route to good |
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# File a non-provisional patent application. Get it accepted. Then |
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footage to layer into the video might just be to take it ourselves with |
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explicitly abandon the patent. |
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cell phones or other devices. |
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# File a non-provisional patent application and stop doing anything, |
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thus abandoning the patent. |
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# 3rd party pre-grant review: 6 month period where patent is pending; |
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can submit prior art; way of bringing thigs to the attention of people |
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using PTO; but have to wait for someone else to file a patent, catch it, |
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and with help of a lawyer file in response to the new patent |
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Big Q: to patent or not to patent. |
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=== Molecular biology === |
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Filing a provisional patent at this point would be shooting ourselves in |
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the foot. |
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What's the liklihood of an outside group affecting our group's ability |
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Craig presents on cloning. |
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to continue conducting research on this product beyond the iGEM |
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competition? |
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K-casein expression in e. coli is already patented |
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Many vectors have multiple cloning sites: A series of restriction |
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endonuclease sites. |
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provisional patent option: addresses 'first to file' concerns |
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You amplify your gene using PCR or cut it out of another plasmid, |
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can lose the provisional if it lacks enough/appropriate information |
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matching restriction sites and ligate it into the plasmid. |
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prior art: publically announced meet up group; personal witnesses to |
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Meh, I can't pay attention and take notes. Here's the presentation: |
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this meeting; here is what we said in our minutes today; everything we |
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https://docs.google.com/viewer?a=v&pid=forums&srcid=MDQ3ODI0ODE4NDM3NTM4NjIyMzUBMDM5OTQ5MTk5OTAwNDIzOTE2MjcBa0Z0ZTFkd2xycGdKATQBAXYy&authuser=0 |
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discussed today is prior art |
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How do we execute the intellectual property internally? (next big |
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https://www.youtube.com/watch?v=WCWjJFU1be8 |
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hurdle) |
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by patenting, giving yourselves the power to say 'open' or 'closed;' |
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=== |
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Cheese making === |
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Miyoko Schinner - vegan chef and TV host, has written books on vegan |
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cheese and has signed up on our meetup list. I'll (Ahnon) contact her |
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directly.... just sent her em via meetup. |
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(BC or CCL or both?) conflict of interest statement |
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=== Background research == |
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prohibits any board members from being involved with projects that are |
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not open-source |
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another possible issue: anyone working with a formal lab (i.e. Patrik @ |
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== Break out into sub-groups == |
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LLL) will have to show their employer any patents and have it approved |
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as well |
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techology transfer: additional concern associated with federally funded |
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=== IP Issues discussion === |
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organizations |
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Marc: should definitely patent, and do defensive license; willing to |
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write up draft asap |
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sub-organization with separate by-laws and small board; only purpose of |
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Patrik: fastest way to get most people eating vegan cheese would be |
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this sub-org would be to hold/file provisional patents/DPL |
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patent the heck out of it, show it can be made cheaper than cow's milk, |
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and sell the IP to Kraft. - If that is the *only* issue we care about. |
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Consensus to do 2 things: |
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Mallory: if you open everything, then groups with most resources will |
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# write up... |
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get the upper hand |
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# attempt to either.....abandon DPL |
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Mallory was basically making the argument that big incumbent corps will |
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take what we made and make lots of profits. |
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Linda Kahl |
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=== Fundraising === |
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US PTO: big change; $ from patent fees no longer all going to |
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government; much of the fees are going to US PTOs |
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new San Jose office |
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Group in Ireland that has been contacting Patrik |
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Patrik: If we have a fundraiser we really should put a lot of effort |
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focused more on milk than the cheese |
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behind it. |
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have 30K in funding; backed by corporate investors |
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Ahnon: needs to contact Amyris again |
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(http://synbioaxlr8r.com/) |
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Patrik: needs to contact Bruce German to ask about companies working on |
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breast milk nutritional supplements |
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Advait: |
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http://www.ncbiotech.org/research-grants/research-funding/biotechnology-research |
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- too late to apply, maybe next year |
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Advait: http://www.gofundme.com/ |
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http://www.rockethub.com/ |
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http://peerbackers.com/ |
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Jamie and Marc will contact PETA office in Oakland (do they have contact |
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with Patrick Brown as well?P |
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Shashank: Viz. Amyris, saw Greg Warner at BioCurious today. Shashank - |
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please remind Greg to join the iGEM team! I don't think he' son our |
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mailing list yet. Do you have an email for him? Maybe the one I've been |
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using doesn't work -- Patrik He was away on vacation..i have a |
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netcom.com email.will forward a note to both of you...-s |
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gwerner@ix.netcom.com - yeah, the ix.netcom one is the one I've been |
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using |
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= DNA Distribution Kit = |
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http://www.gofundme.com/ |
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http://scistarter.com/ |
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https://experiment.com/ |
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=== Molecular biology === |
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iGEM DNA distribution kit: |
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http://parts.igem.org/Help:2014_DNA_Distribution |
http://parts.igem.org/Help:2014_DNA_Distribution |
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To do: |
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Proposed goals for upcoming week: |
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# Go through parts list; watch videos; download excel files listing |
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components/details |
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# Internal databases |
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plasmid DB |
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vector maps |
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Open-source alternatives to File Maker Pro: |
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http://www.osalt.com/filemaker |
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http://alternativeto.net/software/filemaker-pro/ |
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= Fundraising = |
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this Wednesday; somewhere in Oakland; noonish - 5 pm; Marc, Francis, |
|||
etc. finishing up filming fundraising video |
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changing text/wording on crowd tilt page: |
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writing an intro for a proposal - first sentence should explain your |
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entire project |
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contact Jing |
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Fiver.com for professional voie over |
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Video "rough draft" link (with footage and possible music): |
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https://docs.google.com/file/d/0B4WT2XIBrqnScmZCLUFYOTFOWlU/edit |
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This is not so much the actual video but more of a "practice" with some |
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good footage and a possible music choice. |
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Jamie: Contact David B at PETA.org |
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Ashley: would have a problem working with PETA |
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this a.m. Fran posted a fundraising video on SeaFile |
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link to video with music: |
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https://docs.google.com/file/d/0B4WT2XIBrqnScmZCLUFYOTFOWlU/edit |
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= DNA Assembly Methods = |
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Craig put together an awesome power point presentation: |
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Powerpoint: |
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https://docs.google.com/viewer?a=v&pid=forums&srcid=MDQ3ODI0ODE4NDM3NTM4NjIyMzUBMDM5OTQ5MTk5OTAwNDIzOTE2MjcBa0Z0ZTFkd2xycGdKATQBAXYy |
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linkers |
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== |
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Traditional cloning == |
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plasmid backbone: circular piece of DNA we're cloning into that has ab |
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resistance, ORI, etc. |
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http://help.teselagen.com/manual/section/8/ |
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What RE sites can you use? RE sites can't be inside your DNA (will cute |
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out GOI) |
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Stoichiometry: important consideration when determining ideal plasmid |
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backbone:GOI ratio |
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If something goes wrong with ________ must use traditional cloning to |
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fix it |
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== Golden Gate Cloning == |
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good for multiple sequence cloning |
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you design DNA overhangs to ligate multiples pieces together in a |
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strategic orientation |
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no scar sequence introduced |
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issues with scars occur when you're ligating together different protein |
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domains |
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same RE used for everything; restriction site is elminated from ligated |
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product |
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== BioBrick approach == |
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use a few, specific restriction enzymes |
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makes cloning easy if parts assembled on their own |
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see http://parts.igem.org/Help:Standards/Assembly |
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iGEM wants us to submit everything we do with BioBricks methods; |
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different cloning methods are compatible with each other |
|||
== SLIC: sequence and ligation independent cloning == |
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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 |
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== Gibson == |
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* Finalize construct design |
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* Plan initial experiments necessary to get "band on a gel" verification |
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of casein and kinase expression |
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* Make list of all required reagents, tools and other consumables, |
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including gBlocks and primers |
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* Reach out to companies asking for donated reagents (and plasmids from |
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DNA 2.0) |
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three enzymes used for every reaction (more costly) |
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=== Cheese making === |
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one-step process |
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= Tasks = |
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Like SLIC except it uses T5 exonuclease (5' --> 3' activity; opposite |
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== juul == |
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of T4 used in SLIC) |
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nicks repaired before they go into e. coli |
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* Look more closely at DPL. Follow up with Linda Kahl and Brewster |
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Kahle. |
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* Follow up with Rusty to see if he can help with video / equipment |
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* Find the best plasmid for us to order from addgene (but check the |
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biobrick dna distribution list first) |
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overhangs must lack secondary structure to avoid formation of hairpins |
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== Patrik == |
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which would compete with GOI for insertion into backbone |
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only method with a theme song :) |
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* Follow up with Bruce German Re: milk protein companies |
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* |
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== GeneArt (not included in powerpoint) == |
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== Jamie == |
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Wrap-up & things to do: |
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* contact PETA and other vegan organization |
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# creating cloning strategies on paper |
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# make an excel sheet with all reagents; price break down; similar to |
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spreadshet for DIY cloning class |
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# update wiki with all work done individually or in groups; present |
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updates to group meetings |
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# finalize video and crowdtilt |
Latest revision as of 10:47, 25 May 2019
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:
- File a non-provisional patent application. Get it accepted. Then
explicitly abandon the patent.
- File a non-provisional patent application and stop doing anything,
thus abandoning the patent.
- 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:
- write up...
- 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]
http://parts.igem.org/Help:2014_DNA_Distribution
To do:
- Go through parts list; watch videos; download excel files listing
components/details
- Internal databases
plasmid DB vector maps Open-source alternatives to File Maker Pro:
http://www.osalt.com/filemaker
http://alternativeto.net/software/filemaker-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
linkers
==
Traditional cloning ==
plasmid backbone: circular piece of DNA we're cloning into that has ab resistance, ORI, etc.
http://help.teselagen.com/manual/section/8/
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:
- creating cloning strategies on paper
- make an excel sheet with all reagents; price break down; similar to
spreadshet for DIY cloning class
- update wiki with all work done individually or in groups; present
updates to group meetings
- finalize video and crowdtilt