Team:UIUC-Illinois/Notebook/MeetingNotes
From 2012.igem.org
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<li><a name="meet8" >3/25/12</a></li> | <li><a name="meet8" >3/25/12</a></li> | ||
<li><a name="meet9" >3/27/12</a></li> | <li><a name="meet9" >3/27/12</a></li> | ||
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</div> | </div> | ||
<div id="meetingselection2" class="meetingselection"> | <div id="meetingselection2" class="meetingselection"> | ||
<center><h2>May-June</h2></center> | <center><h2>May-June</h2></center> | ||
- | + | <li><a name="meet10" >4/1/12</a></li> | |
- | <li><a name="meet11" > | + | <li><a name="meet11" >4/3/12</a></li> |
- | <li><a name="meet12" > | + | <li><a name="meet12" >4/4/12</a></li> |
- | <li><a name="meet13" > | + | <li><a name="meet13" >4/8/12</a></li> |
- | <li><a name="meet14" > | + | <li><a name="meet14" >4/14/12</a></li> |
- | <li><a name="meet15" > | + | <li><a name="meet15" >4/15/12</a></li> |
- | <li><a name="meet16" > | + | <li><a name="meet16" >4/17/12</a></li> |
+ | <li><a name="meet17" >4/22/12</a></li> | ||
+ | <li><a name="meet18" >4/24/12</a></li> | ||
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<div id="meet11" style="display:none"> | <div id="meet11" style="display:none"> | ||
<textarea rows="30" wrap="soft"> | <textarea rows="30" wrap="soft"> | ||
- | + | iGEM Advisor’s meeting | |
+ | 4/3/12 | ||
+ | Proposal presentations: | ||
+ | Uros and Adi: “Biodegradation of Polyester Polyurethane by Endophytic Fungi” | ||
+ | - Isolate the genes that degrade plastic and put them together in E. coli to | ||
+ | breakdown plastic at a commercially viable rate | ||
+ | - Alternatively, certain strains of fungi have the ability to degrade polyurethane | ||
+ | plastic. | ||
+ | - We would focus on one plastic composite to degrade. That would make the | ||
+ | project more feasible for one summer. | ||
+ | - E. coli might not be able to handle all of this. It’s been proven that the process | ||
+ | works in anaerobic and aerobic conditions, so yeast might be another object. | ||
+ | - We have the capability to build the type of filtration system necessary. | ||
+ | - Is it the best to degrade this plastic? It’s carbon sequestering. The | ||
+ | degradation of plastic would need to be coupled to something that would get | ||
+ | rid of the CO2. We could couple it to make a precursor for some new plastic. | ||
+ | We would need to repolymerize it in a type of biological recycling. | ||
+ | - Plastic is good to recycle. Another way to think about this project would be to | ||
+ | microbially recycle plastic. | ||
+ | Divya: “Transplastomic antibacterials” | ||
+ | - Plants make small molecule compounds that act as antimicrobials against | ||
+ | Gram positive bacteria. There compounds typically act in combination. | ||
+ | - Genetically modified plants would produce antimicrobials. New genes are | ||
+ | inserted into the chloroplast DNA. | ||
+ | - Use a gene gun to deliver the DNA to the cells. This way the chloroplast’s | ||
+ | double membrane is penetrated. | ||
+ | - Rate of transformation of plants is very low and growing plant tissue is difficult | ||
+ | and takes a long time. | ||
+ | - Transforming plants is a task in and of itself. We do have resources on | ||
+ | campus to do this. It would look very impressive if it actually worked. | ||
+ | - Great project, but we need some feedback from alternative sources about the | ||
+ | gene gun and plant transformation. | ||
+ | - This is a complex project for the time frame. You have to isolate the | ||
+ | compound, look at the genes, then isolate and transform. This might work as | ||
+ | a side project though, if a very simple compound was used and we changed | ||
+ | its expression levels. | ||
+ | Cara: “A Privy Understanding of E. Coli” | ||
+ | - Fecal matter is the main source of bacterial pathogens in waste. Create a little | ||
+ | package of genetically modified bacteria that would be added to a bucket that | ||
+ | would be used as a toilet. Bacteria would sanitize the fecal matter and a color | ||
+ | change would indicate full breakdown. | ||
+ | - How to focus the project: Choose one compound to degrade, look at what | ||
+ | types of bacteria/fungi/protozoans are in the mix. | ||
+ | - Animal feces might be a bigger problem than human waste. | ||
+ | - The bacteria sanitizing the fecal matter would have to compete against the | ||
+ | pathogenic bacteria already in the environment and fecal matter. | ||
+ | - Look up basillophila. | ||
+ | Announcements: | ||
+ | - In the next 2 advisor’s meetings, decide which projects are the best ideas, | ||
+ | focus on those, and represent them in groups. Have different people both | ||
+ | critique and endorse the different projects. | ||
+ | o Rank the projects. | ||
+ | - There will be one main project, and then one good side project. | ||
+ | o The side project functions as both a safety in case the primary project | ||
+ | fails, and as a continued project for the next year. | ||
+ | - Keep in mind what looks good in competition. The work we’ve put in might be | ||
+ | enough, even if there is no finished final project. But the research and | ||
+ | groundwork must be excellent in that scenario. | ||
+ | - Final advisor’s meeting is Tuesday, May 1. At this meeting the main and side | ||
+ | projects will be finalized. | ||
+ | - Next Tuesday we are meeting Dr. Robinson. | ||
+ | - April 17th, we will have a group picture for the brochure. Dress up! | ||
+ | - On Sunday’s meeting we will vote on what projects we will focus on pitching | ||
+ | again. This is the opportune time to add more to your presentation. We’re not | ||
+ | picking 2 projects, we’re picking several to re-research and reevaluate. | ||
+ | Remember, we’re objective and no project is a bad project! | ||
+ | - This Sunday Angela will also explain about the standard cloning procedure. | ||
+ | - Sunday meeting will be at 8PM in the BIF. | ||
</textarea> | </textarea> | ||
</div> | </div> | ||
<div id="meet12" style="display:none"> | <div id="meet12" style="display:none"> | ||
<textarea rows="30" wrap="soft"> | <textarea rows="30" wrap="soft"> | ||
- | + | iGEM Engineering Council | |
+ | Elections | ||
+ | 4/4/12 | ||
+ | - We removed 10 inactive groups (they had not communicated with EC for a full | ||
+ | year) | ||
+ | - Amendment passed, says candidates on co-op or study abroad can make a | ||
+ | video communication to run even if not physically present at the EC meeting. | ||
+ | - Gamma Epsilon general engineering honors society appeals to come off of | ||
+ | suspension | ||
+ | o There is drama and arguments from both sides | ||
+ | o Written, secret vote They are still on suspension. | ||
+ | - Election results: | ||
+ | o Pres: Courtney O’Connor | ||
+ | o VP: Patrick Kennedy | ||
+ | o EXPO: Elena | ||
+ | o EOH Director: Gloria Lin (voted to allow a non-engineering on EC) | ||
+ | o Director of Leadership: Steven Marks | ||
+ | o Secretary/Treasurer: Troy Meeham | ||
+ | o Dean’s Student Advisory’s Committee Director: Akash Shah | ||
+ | o Future enrichment opportunities: Kritika Jetkey | ||
+ | o EIB Director: Douglas Podgorny | ||
+ | o SITE director: Mary Kate Krouse | ||
+ | o Awards director: Samantha Tone | ||
+ | o Publicity Director: Rachel Gross | ||
+ | o Social Director: Rachel Seidner | ||
+ | o Service Director: Sara Moshaga | ||
+ | o Director of Information: Sid S. | ||
+ | o Knights of Saint Patrick: Christopher Massie | ||
</textarea> | </textarea> | ||
</div> | </div> | ||
<div id="meet13" style="display:none"> | <div id="meet13" style="display:none"> | ||
<textarea rows="30" wrap="soft"> | <textarea rows="30" wrap="soft"> | ||
- | + | iGEM weekly meeting | |
+ | 4/8/12 | ||
+ | Announcements: | ||
+ | Isiah, Lab Manager – | ||
+ | The next 2 weeks is about organizing the lab. We need to divvy up the remaining | ||
+ | work. Expect Isiah’s email about the inventory in a few days. Isiah will just finish | ||
+ | cleaning a few more things up and then the lab will be ready to go. 2 books will be | ||
+ | created, one for the glycerol stock and another for primers/buffers/ etc. There will be a | ||
+ | physical copy in lab and one digital one. | ||
+ | Cara, Social, & Anthony, Treasurer – | ||
+ | Thursday at 4 PM is the deadline for applying for SORF. WashU has not | ||
+ | responded to Cara, so we will try to use Uros’ biobrick contact. We will not be able to | ||
+ | take more than 2 trips, and 1 trip would be awesome and enough work. This trip would | ||
+ | be great for human practices and collaboration. Cara will contact Northwestern. U Mich | ||
+ | will ultimately collaborate with us, so that’s our option. We will apply for the money | ||
+ | anyways, because even if we don’t use it the money will just get reallocated back to the | ||
+ | SORF fund. The application will be about how the trip helps our human practices | ||
+ | collaboration. | ||
+ | Cara & Asha – | ||
+ | contact Courtney O ‘Connor about funding deadlines. EC funding works similarly | ||
+ | to SORF, but we need to check deadlines about that. Asha will be emailing Courtney | ||
+ | (outgoing) and Troy (incoming). | ||
+ | Results of the EC elections: | ||
+ | o Pres: Courtney O’Connor | ||
+ | o VP: Patrick Kennedy | ||
+ | o EXPO: Elena | ||
+ | o EOH Director: Gloria Lin (voted to allow a non-engineering on EC) | ||
+ | o Director of Leadership: Steven Marks | ||
+ | o Secretary/Treasurer: Troy Meeham | ||
+ | o Dean’s Student Advisory’s Committee Director: Akash Shah | ||
+ | o Future enrichment opportunities: Kritika Jetkey | ||
+ | o EIB Director: Douglas Podgorny | ||
+ | o SITE director: Mary Kate Krouse | ||
+ | o Awards director: Samantha Tone | ||
+ | o Publicity Director: Rachel Gross | ||
+ | o Social Director: Rachel Seidner | ||
+ | o Service Director: Sara Moshaga | ||
+ | o Director of Information: Sid S. | ||
+ | o Knights of Saint Patrick: Christopher Massie | ||
+ | Adi – | ||
+ | Meeting with Dr. Amos Monday at 8 am. We’re not looking at funding, but using | ||
+ | facilities instead. Website new, Alex has been sent designs from past years and he is | ||
+ | now requesting filler data and specifics on what we want included on the website. | ||
+ | Everyone should write a short bio and find a picture to send to Asha. Asha will compile | ||
+ | these and the meeting minutes to send this to Adi and Alex. Send these by Friday. We | ||
+ | actually did have a website in 2010, so that will be consulted. | ||
+ | For entrepreneurship, we need to find a faculty advisor. Bob emailed Rao’s contact, but | ||
+ | she never followed up. Angela will contact her professor who is interested in bioethics. | ||
+ | We also need to register for the entrepreneurship competition in the same way that we | ||
+ | applied to the normal iGEM competition. Apply without the membership code and | ||
+ | Courtney will approve of us later. | ||
+ | Divya – | ||
+ | practice time for undergrad research symposium will be on Tuesday. Uros, | ||
+ | Angela, and Divya will be presenting. The symposium is on April 11, from 9-3/4. It is an | ||
+ | hour poster presentation. We are now registered for quad day. | ||
+ | Bob – Has created an entirely new page to start the website from scratch. | ||
+ | Angela – | ||
+ | For the next advisor’s meeting we are meeting Dr. Gene Robison in the first floor | ||
+ | of the gatehouse. From 3-5. Dress casually, but not sloppy. At the end of the meeting if | ||
+ | time permits, Courtney will discuss how to keep a standard lab notebook for us. | ||
+ | April 28th is the chemistry outreach demos that Courtney is doing. The demos will be for | ||
+ | high schoolers. Example demos are the vomiting pumpkin (elephants toothpaste) and | ||
+ | the exploding gummibear. We will be going to Rantoul for this, but transportation is | ||
+ | providing. Ideas for demos: color changing solutions, liquid nitrogen/soap/water, make a | ||
+ | pickle battery, fire in a pumpkin. Cara will contact Dr. Ray of Chem 104 for demo ideas | ||
+ | and protocols. Concrete times and a date for practice will be announced at the next | ||
+ | advisor’s meeting. | ||
+ | Entrepreneurship and human practices needs to draft a proposal. These proposals will | ||
+ | get presented to the advisors on April 24th. On April 22nd we will practice these | ||
+ | presentations. | ||
+ | Agenda: | ||
+ | UIUC-Illinois Judging Form | ||
+ | - Bronze: submit a biobrick | ||
+ | - Silver: characterize biobrick | ||
+ | - Gold: Characterize a biobrick that is not for our team. | ||
+ | - Be sure to familiarize yourself with this! We’re going to continually consult this | ||
+ | during the summer. We are going to get a gold medal! | ||
+ | Lab updates | ||
+ | - Bhalerao: Isiah and Anthony prepared electrocompetent cells. The experiment | ||
+ | will begin Monday/Tuesday this week. | ||
+ | - Jin: Last Wednesday Dr. Jin assigned us to post-doc Dr. Lee. Tomorrow Uros will | ||
+ | meet with Dr. Lee to plan how the project will be executed. Tuesday from 9-11 | ||
+ | everyone will meet to replicate the experiment. | ||
+ | - Brad: Cara has been working hard every day. She transformed some cells with 3 | ||
+ | different plasmids that each have a his tag and then either GFP, FoA, or LacZ. | ||
+ | The LacZ failed and is being redone. | ||
+ | - Rao: Angela is working with 2 operons to see if a deletion will effect expression. | ||
+ | She tried out 4 different cloning methods. If the PUF project is done, one of 2 | ||
+ | specific cloning methods needs to be used. | ||
+ | Proposal discussion: | ||
+ | - Next Tuesday is the second proposal round. | ||
+ | - Isiah: Original idea: Use genetically modified E. coli to modify crude oil/biofuel to | ||
+ | refine/recycle oil. Naturally occurring bacteria would be used. Further research | ||
+ | indicates that time issues make this project infeasible over the summer. Current | ||
+ | research being done has revealed that it is really difficult to grow this stuff in the | ||
+ | lab. Also, one of the reagents to get the bacteria to grow is very harmful for | ||
+ | humans. | ||
+ | o Will’s feedback: For anything biodiesel look at University of Washington. | ||
+ | This is a complex proposal, so to make this successful go look at past | ||
+ | successful biodiesel projects and try to improve it/continue it slightly. | ||
+ | - Uros: Magnetic bacteria. | ||
+ | o Will: Can we use magnetic bacteria in a machine? Use b fields to control | ||
+ | the bac or use the bac to signal things through b fields. These are ideas of | ||
+ | applications. | ||
+ | - Adi: Degradation of plastic composites. | ||
+ | o Will: An Australian team has worked on this before. | ||
+ | o Potential for a great human practices project: Write reviews on different | ||
+ | topics (biofuels, sensing, etc) to help future iGEM teams orient themselves | ||
+ | each year. That way it makes it easier to see what work has been done | ||
+ | before. Also, we could devise a strategy to organize and exercise quality | ||
+ | control over the parts registry. Start with a call/teleconference survey and | ||
+ | then recompile. | ||
+ | o Stanford-Brown created a human practices website and an alumni | ||
+ | website. Max Song did this, and we’re going to try to contact him for | ||
+ | further information and collaboration. | ||
+ | - Angela: update: she has all of the PUF protein sequences and the RNA/aa info. It | ||
+ | can be synthesized by a company (time and money) or self-synthesize (2 weeks, | ||
+ | little money). University of North Carolina is researching the PUF protein and so | ||
+ | we could ask for a template DNA PUM1 gene from them. Jin’s lab could also | ||
+ | PCR out the PUM1 gene that expresses the PUF protein. So overall there are 4 | ||
+ | different sources to get the gene. Translational repressors are an application. | ||
+ | GFP can be used to characterize. Small side project – design and optimize a | ||
+ | construct for the project (to be presented in the next advisor’s meeting). | ||
+ | - Divya: looking at things with microbial properties, but not plants. Maybe yeast. | ||
+ | - Bob: Found a part that uses light to run an ATP pump. We could look into | ||
+ | photosynthetic bacteria rather than interfacing the electro-animal/slug with | ||
+ | bacteria. | ||
+ | - Uros: There are fungi/bacteria that can degrade plastic via serine hyrdolase. Yale | ||
+ | is probably going to do this project for iGEM. It’s a simple but pretty cool project. | ||
+ | We can anticipate that this will be a popular idea. Collaboration with Yale is an | ||
+ | option. | ||
+ | - Anthony: Looked into the price of the substrate ARA, but is unsure about how | ||
+ | much is needed. Also, there are troubles getting e. coli to take up the fatty acids. | ||
+ | - Asha | ||
+ | o Broad review of how tuberculosis is treated. Look for someone on campus | ||
+ | who is researching on how to treat tuberculosis/bacteria. Look for a | ||
+ | direction to research further. | ||
+ | - Cara: | ||
+ | o An Australian team has put e. coli in sewage water before. It would be a | ||
+ | 2010/2009 team. So we can look into improving that project. | ||
+ | What we will be further researching: | ||
+ | PUF project – Angela, Divya, Asha | ||
+ | Plastic degradation – Adi, Uros, | ||
+ | Fatty acid producing e. coli – Anthony, Isiah | ||
+ | E. coli waste management – Cara, Bob | ||
+ | The next time these ideas are presented – genes and a schematic should be presented. | ||
+ | Next weeks: | ||
+ | - April 10 –meeting with Dr. Robinson | ||
+ | - April 15 – general meeting to prepare for the second round of advisor’s | ||
+ | presentations | ||
+ | - April 17 – advisor’s meeting for second round of presentations | ||
+ | - April 22 – general meeting for the third round of presentations | ||
+ | - April 24 – advisor’s meeting for 3rd round, entrepreneurship and human practices | ||
+ | proposals | ||
+ | - April 29 – quick update to everyone and a quick summer plan | ||
+ | - May 1 – last meeting! The advisor’s meeting to give updates and feedback on | ||
+ | our main and side project. Entrepreneurship and human practices will also be | ||
+ | discussed. This is when we will plan our summer schedule and agenda. | ||
</textarea> | </textarea> | ||
</div> | </div> | ||
<div id="meet14" style="display:none"> | <div id="meet14" style="display:none"> | ||
- | + | <textarea rows="30" wrap="soft"> | |
+ | iGEM Saturday meeting | ||
+ | 4/14/12 | ||
+ | Project Palooza! | ||
+ | Microbial Expression and Characterization of a Sequence-specific RNA-binding Protein | ||
+ | for Translational Regulation | ||
+ | - Express PUF in prokaryotic cells and turn it into a biobrick | ||
+ | - Can we use PUF as a translational repressor? This would allow for a more | ||
+ | rapid change in protein levels. | ||
+ | - Using PUF is a relatively new idea. We would need to study how good the | ||
+ | affinity of PUF proteins are. (Binding works so that 2 amino acids interact with | ||
+ | 1 nucleotide. A 16 amino acid PUF protein recognizes 8 nucleotide | ||
+ | sequence.) | ||
+ | - Characterization: Artificial 8 base pair design for inhibition of gene expression. | ||
+ | - Optomization: Make a control, and then one nucleotide sequence with 1 one | ||
+ | bair pair off. Study the affinity of PUF to both sequences. | ||
+ | - Biobricks: 1 biobrick for each of the PUF repeats (8 in total), multiple | ||
+ | recognition sites, modular devise for translational regulation. | ||
+ | - This is a significant project, but need to look into applications. That just makes | ||
+ | it that much cooler. Compile ideas and send to Angela by Monday night. | ||
+ | Resveratrol and Piceatannol Project (Cara’s new project) | ||
+ | - Resveratrol is turned into piceatannol in the body, which then goes and alters | ||
+ | genes expressions when fat cells mature. It interacts with the insulin | ||
+ | receptors on immature fat cells, stopping them from maturing. | ||
+ | - 1) Can build piceatannol from the ground up (that’s hard.) 2) Use E. Coli to | ||
+ | metabolized piceatannol from wine/grapes/etc (but how much is actually | ||
+ | there? Is it actually efficient to do this?) 3) Put resveratrol in a medium, then | ||
+ | use E. coli that would digest it into piceatannol and secrete it. | ||
+ | o #1 and #3 have both been done. | ||
+ | - Going forward: Look at stability/solubility/degradation. Apparently piceatannol | ||
+ | also inhibits something in humans? What part of piceatannol is actually | ||
+ | interacting with the insulin receptor? (To check on this last one, contact the | ||
+ | Theorectal Biophysics group on campus to see if we can get time on their | ||
+ | computers to do some protein docking modeling.) Edit: An email update on | ||
+ | this has been sent out. | ||
+ | - Application idea: Synthesize piceatannol (somehow) so that it will work in the | ||
+ | body and be able to help maintain a healthy level of body fat. Create an E. | ||
+ | Coli system that will allow piceatannol to work in the human body.</textarea> | ||
</div> | </div> | ||
<div id="meet15" style="display:none"> | <div id="meet15" style="display:none"> | ||
- | + | <textarea rows="30" wrap="soft"> | |
+ | iGEM weekly meeting | ||
+ | 4/15/12 | ||
+ | Announcements | ||
+ | Bob – Making progress to learn wiki coding and editing. Will also try to edit the wiki with | ||
+ | current ideas and team info. | ||
+ | Adi – meeting with Joe Bradley, Angela’s contact, as a potential Entrepreneurship | ||
+ | advisor. Meeting is at Friday at 1:30. Angela will also be attending. Dr. Amos has also | ||
+ | given card access to DCL to Adi, Uros, and Angela. They also received lab tours and | ||
+ | saw the technology we now have access to. Adi is working with Alex to see how quickly | ||
+ | the website can be up and running (ideal – end of the month). Also has some contacts if | ||
+ | we decide that the PUF application should be HIV. UNC Prof. Tracie Hall will be | ||
+ | contacted to see if PUF has uses with HIV. (Contact by Angela) | ||
+ | Uros - Prof. Ha was contacted over PUF research. Emails have been gathered and | ||
+ | professors have been contacted over potential collaborations. All of the labs have been | ||
+ | quite friendly and receptive. The more opinions the better! | ||
+ | Anthony – Checking with Courtney and Melissa that the books are balanced. The | ||
+ | traveling funds we applied for are the 3 days the Friday weekend of July 13-15. (Leave | ||
+ | Friday, get back on Sunday). Busing and driving are being considered as options. | ||
+ | Asha – will be visiting the Engineering Council office to check out the availability of | ||
+ | funds for the July traveling. Also, the U Mich pres will be emailed about human practices | ||
+ | collaborations. | ||
+ | Angela – Next Sunday the President of the University of Michigan iGEM will be coming | ||
+ | to our meeting! Contacted Mat Song, last year’s human practices director, and that | ||
+ | correspondence has been sent to Asha. | ||
+ | Divya – Undergraduate Research Symposium went well! The pictures from that will be | ||
+ | posted to facebook, and a new twitter and flicker will be created for iGEM to broadcast | ||
+ | our work. During the summer, we will also have a blog on the iGEM website, | ||
+ | spearheaded by Divya and Cara. Divya will also be creating a biography of our work, | ||
+ | focusing on our opinions and perceptions of synbio before, during, and after the | ||
+ | summer. Everyone is invited to the IGB Fellows, but previous members will be | ||
+ | presenting the old E. Chiver poster. Everyone is registered though, so go grab a free | ||
+ | lunch and listen to the talk! | ||
+ | Cara – Let’s have a get together before finals! The tentative date is reading day. This | ||
+ | will probably be our last meeting/get together before dispersing for finals and until May | ||
+ | 15th. | ||
+ | Agenda | ||
+ | What’s our timeline? | ||
+ | Proposed timeline: Next Tuesday – advisor’s meeting to present our more specific | ||
+ | project proposals. Human practices and entrepreneurship should also prepare | ||
+ | presentations. April 22 – presentations to update and further refine proposals. April 24- | ||
+ | Advisor’s meeting: Human practices and entrepreneurship give formal presentations to | ||
+ | advisors. May 1 – last advisor’s meeting to discuss final plans for the summer and for | ||
+ | projects. This is the last meeting before dispersing! (In general, weekly meetings are | ||
+ | updating and planning the projects. Advisor’s meetings are for presenting and getting | ||
+ | critiques on these project ideas and plans). | ||
+ | More specific plans: | ||
+ | - Phat project: A solid plan will be developed by the last advisor’s meeting. So | ||
+ | this project will lag behind the PUF project slightly. Phat group will physically | ||
+ | meet Monday night at the UGL. | ||
+ | - Human Practices: We will go ahead with the idea of standardizing the search | ||
+ | for biobricks and past iGEM projects. | ||
+ | - Entrepreneurship: Progress does depend on what the final project will be. At | ||
+ | that point the entrepreneurship advisors will helps us make a decision about | ||
+ | what plan of action is best for the entrepreneurship competition. Once the | ||
+ | project is known and the option is chosen, the application will be a relatively | ||
+ | simple execution. Major project should be made during the summer. | ||
+ | - Wiki: Does a separate wiki need to be done for the entrepreneurship | ||
+ | competition? The wiki template will be set up, so that during the summer our | ||
+ | data will just be slotted in. This minimizes the work done during summer. | ||
+ | - PUF: further applications will be looked into. We will google + hangout on | ||
+ | Monday night to discuss the proposal presentation. Take the initiative to | ||
+ | contact UNC researchers if necessary. | ||
+ | Next advisor’s meeting! Dress up to take a formal picture (that means suits and jackets!) | ||
+ | Tentative agenda: Brief discussion of ideas for entrepreneurship and human | ||
+ | practices. Then PUF and Phat present, followed by a great deal of discussion. We will | ||
+ | also ask if it is feasible to do a main project, a side project, and the entrepreneurship | ||
+ | competition.</textarea> | ||
</div> | </div> | ||
<div id="meet16" style="display:none"> | <div id="meet16" style="display:none"> | ||
- | + | <textarea rows="30" wrap="soft"> | |
+ | iGEM Advisor’s Meeting | ||
+ | 4/17/12 | ||
+ | Project Proposals Round 2 | ||
+ | Resveratrol Metabolite Blocks Apidogenesis | ||
+ | - Why aren’t we just producing lots of resveratrol and putting it in the body? | ||
+ | The body will naturally change it into piceatannol for us. Response: Does it | ||
+ | happen in the necessary quantity and concentration? We want to make these | ||
+ | molecules more stable and more soluble in the body. | ||
+ | - Resveratrol is widely regarded as a wonderful compound to extend life and | ||
+ | help health. It’s widely researched and popular, but there is much controversy | ||
+ | about it still. | ||
+ | - How are we going to make this more soluble? Add groups to the non-active | ||
+ | sites of the molecule. Groups increase solubility, like halogenation. | ||
+ | - Do these modifications change the molecule itself? Well we can run | ||
+ | computational tests on that. We can also biologically make resveratrol | ||
+ | derivatives and test them like a pharmaceutical company. | ||
+ | o Beyond looking a solubility, computational testing might not be of much | ||
+ | help. You really need to synthesize libraries of the molecule and test | ||
+ | them. | ||
+ | - Need to look into P450 enzymes. But we want to stay away from protein | ||
+ | engineering. We can buy and test a range of enzymes though. | ||
+ | - Computational side? The molecule docking technology to do simple hydrogen | ||
+ | bond analysis is free, but for the more complex and detailed information we | ||
+ | need an expert. Courtney will consult with one person in her lab who has | ||
+ | experience in this area. | ||
+ | o The computation sounds like it is beyond the scope of the summer. | ||
+ | o Our best bet in terms of time is to just make a few analogs and test | ||
+ | them. | ||
+ | Microbial Expression and | ||
+ | - PUF works with only 8 base pairs of recognition. | ||
+ | - Where should the PUF binding site go? Let’s test a bunch of models with it in | ||
+ | various places to see which is the most effective (via visibility of YFP). | ||
+ | - Need to clearly understand the PUF mechanism. This ensures that it is | ||
+ | binding to a specific RNA sequences and not just the PolyA tail. | ||
+ | - Applications: the PUF library is obvious and useful, but could also use PUF as | ||
+ | a scaffolding tool in the style of zinc fingers. | ||
+ | - How about engineering different kinds of PUF? First need to make sure it | ||
+ | works in prokaryotes, then test the first type of PUF and optimize where the | ||
+ | binding site should be. Then and only then we should look at making different | ||
+ | versions of PUF and starting the library. | ||
+ | - For this to work at all, it is necessary to make really sure that PUF works in E. | ||
+ | coli. | ||
+ | o It is possible to make this work with cDNA. Are we sure that we can get | ||
+ | the cDNA from UNC? | ||
+ | - It is a small protein. It might be easier to just synthesize it rather than clone it. | ||
+ | We should definitely start with cDNA.</textarea> | ||
</div> | </div> | ||
<div id="meet17" style="display:none"> | <div id="meet17" style="display:none"> | ||
- | + | <textarea rows="30" wrap="soft"> | |
+ | iGEM Weekly Meeting Minutes | ||
+ | 4/22/12 | ||
+ | Announcements | ||
+ | Angela – New advisors! Kori Dunn, Angela’s graduate advisor in Prof. Rao’s lab. Prof. | ||
+ | Joe Bradley of Business and Administration is our new Entrepreneurship advisor. | ||
+ | Everyone needs to sign up for the iGEM dropbox, there are important papers and | ||
+ | documents there that are useful for everyone. We will video chat with Dr. Wong will | ||
+ | happen this Tuesday from 3-4 at the 2nd floor of the gatehouse. If the advisor’s are | ||
+ | available, we will have a normal advisor’s meeting from 4-5 (this is tentative, watch for a | ||
+ | confirmation email). Angela has received the PUF plasmid from UNC and is looking to | ||
+ | see if the transformation is successful. If the transformation is successful we will move | ||
+ | onto designing the construct. University of Michigan iGEM president is coming down | ||
+ | this week. When will we meet with him? | ||
+ | Isiah – not present, but everyone needs to send him the categorized inventory | ||
+ | information! | ||
+ | Adi – Met with Joe Bradley. PUF and Phat projects were discussed, but mainly PUF. If | ||
+ | the PUF project is successful, we will have made steps towards making a toolkit. We | ||
+ | have the option of marketing our toolkit or targeting a specific disease. Our first step is | ||
+ | intellectual property. The patent database, USPTO, and Espacenet will be searched to | ||
+ | see if any patents exist already. If we choose the business plan model, we will market | ||
+ | our team as though we are a company. We will discuss how we will start and grown our | ||
+ | company. | ||
+ | Divya – An email has been sent out about the IGB symposium. Last year’s project will | ||
+ | be presented at the poster part of the day by 2 former iGEM members. If you want free | ||
+ | breakfast and lunch, register! Our theme is “other IGB.” The brochure will be further | ||
+ | discussed with Melissa. | ||
+ | Asha – The final Engineering Council meeting of the year is next Wednesday, and the | ||
+ | retroactive summer travel funding will be discussed. Human practices has contacted | ||
+ | Northwestsern, Brown-Stanford, and University of Michigan to collaborate. Instead of | ||
+ | building a whole new website, Angela will contact Alyssa (Cornell) who is an | ||
+ | administrator of the Alumni iGEM site to see if we can create a new page on their | ||
+ | website. The point is to collaborate, not compete. In the fall we will also look into | ||
+ | potentially volunteering to teach middle schoolers/ high schoolers about synthetic | ||
+ | biology. | ||
+ | Bob – Will be working to put all of the meeting minutes up on the wiki. The website | ||
+ | looks basically the same as last time, but David has been contacted about how to make | ||
+ | the wiki look more like a website through templates. Alex and Bob will share contact | ||
+ | information to make everything look awesome. We also want to put our ideas on the | ||
+ | wiki so that we can have them available for everyone to see the time-stamp of when we | ||
+ | came up with it. | ||
+ | Anthony – Estimated budget to travel to North Carolina for next year’s IBE conference. | ||
+ | Cara – There is concern that the proposed phat project is too roundabout. A better idea | ||
+ | might be to simply mutate the cytochrome enzyme that converts resveratrol to | ||
+ | picetannol by sending it out to a company and then just testing all of the different | ||
+ | versions. Tentatively, it sounds like this is a long term project. It would be better to make | ||
+ | 1 of 2 simple constructs to test. | ||
+ | Social stuff: We will have dinner on Reading Day together. Go to one place for actual | ||
+ | food, then after to a dessert place! | ||
+ | Will’s comments – As an RSO we can set up our own poster session about our iGEM | ||
+ | projects and synthetic biology. We could do it at the end of the fall semester and invite | ||
+ | other research groups who would like to present at the end of fall semester (there aren’t | ||
+ | many symposiums at that time.) | ||
+ | Agenda | ||
+ | Bootcamp: | ||
+ | - Are we going to be ready to go into lab? Who is good at what? We need to | ||
+ | start thinking about how we are going to divvy up lab work. | ||
+ | - We need to write out specific protocols. | ||
+ | - We will partner up. | ||
+ | - We will set aside time at the beginning of the summer to simply write out | ||
+ | protocols and seriously and thoroughly learn all of the procedures. | ||
+ | - Overall, we need a good wetlab plan as soon as possible. | ||
+ | PUF stuff : | ||
+ | - The PUF sequences have been put in the iGEM dropbox. | ||
+ | - Why do we need the PUF sequences? Because we need to design primers. | ||
+ | o Yellow = 8 PUF repeats | ||
+ | o We got this from UniProt, searching for PUF1. The information from | ||
+ | this site has been put on the Word File in the dropbox. | ||
+ | o An alternative search site is the NCBI, using search “Protein”. | ||
+ | - Biobrick foundation website has lots of assembly methods. Using RFC, we | ||
+ | get the biobrick prefix and suffix for the PUF coding sequence. These | ||
+ | prefix/suffixes contains restriction sites. *****put website from the green | ||
+ | handout here ******** | ||
+ | - Plasmid backbone: pSB1c3 (this is what we submit our biobrick in). | ||
+ | pSB=plasmid synthetic biology. C= colminithol resistance. A map of this | ||
+ | backbone can be found on the parts registry to physically see the restriction | ||
+ | sites. | ||
+ | - Annotation is getting sent to everyone. | ||
+ | </textarea> | ||
</div> | </div> | ||
<div id="meet18" style="display:none"> | <div id="meet18" style="display:none"> | ||
- | + | <textarea rows="30" wrap="soft"> | |
+ | iGEM Advisor’s Meeting | ||
+ | 4/24/12 | ||
+ | Conference Call with Dr. Zefeng Wang_of UNC___ | ||
+ | - Slide #2 – 2 constructs (one with PUF binding, one without). The one without | ||
+ | the PUF binding site gives YFP because it can be translated. Dr. Wang | ||
+ | wonders if this will this work? | ||
+ | - Currently there are no papers about the prokaryotic recognition sequences. | ||
+ | Dr. Wang thinks it will not work. He recommends changing to a reporter that | ||
+ | will work. | ||
+ | - Papers suggest that PUF binds to the 3’ UTR in eukaryotic cells. We are | ||
+ | unsure of if this will work in prokaryotic cells. No one knows exactly how PUF | ||
+ | works in eukaryotes – they recruit other factors that stop translation. These | ||
+ | other factors might not exist in prokaryotes. | ||
+ | - There is a paper that claims PUF has worked in prokaryotic cells, but no | ||
+ | plasmid was included in that paper. | ||
+ | - Yeast 3 hybrid system works well in Dr. Wang’s lab. He can provide this as a | ||
+ | modular system to start with. This saves us the trouble of what if the recruiter | ||
+ | doesn’t work. | ||
+ | - Many PUF mutants can be nicely expressed in E. Coli. Some cannot be | ||
+ | expressed. | ||
+ | - We can also try ASRE – artificial site specific RNA endonuclease. But we | ||
+ | wanted to do it in E. Coli. | ||
+ | - Dr. Wang ran an experiment where PUF was used to repress Bgalactosidase. | ||
+ | The PUF binding occurred in the gene. The lower expression | ||
+ | is from RNA degradation. PUF doesn’t cut RNA, just bind it. Dr. Wang put the | ||
+ | PUF together with an endonuclease that cut the RNA when PUF bound to it. | ||
+ | But that is not PUF anymore, it’s ASRE (the name of the fusion protein). | ||
+ | - The whole ASRE complex looks like: Flag-PUF-linker-endo | ||
+ | - Dr. Wang’s lab has a library of these ASRE’s that they are willing to share with | ||
+ | us. But the paper is unpublished, so the data (if it works) needs to be treated | ||
+ | confidentially. We would not release the information to the iGEM website until | ||
+ | everything is collected and we have conveyed the results to Dr. Wang. | ||
+ | - Complications: We don’t know what the rate-limiting step yet? The binding or | ||
+ | the cut? Change design so that PUF binding site is between the RBS and the | ||
+ | gene. We put the PUF binding site multiple times to try to increase the | ||
+ | effectiveness. Could rearrange so that the reporter is under the repressor. | ||
+ | - Distance between binding and digestions sites is very close. | ||
+ | - To add multiple binding sites, where would they go? Can we add one to the 3’ | ||
+ | UTR end so that it’s after the stop codon? Does it work? | ||
+ | - Possible death mechanism: Engineer a PUF between the start codon and the | ||
+ | promoter. It’s a highly conserved region so it will stop the manufacture of | ||
+ | many proteins. | ||
+ | - We can try multiple scenarios. We want to use the existing protein and | ||
+ | change the binding site, as opposed to using mutated PUFs. | ||
+ | - Dr. Wang’s overriding concern is if/how the reporter will work. Is there any | ||
+ | natural repressor in the protein? Could use Lac I and B-galactosidase. Want | ||
+ | to arrange it so that we control gene A, gene A and YFP have inverse | ||
+ | expression. Once this works, changing modules will be easy. We will | ||
+ | investigate more cases like Lac I. | ||
+ | - Dr. Wang already sent the construct. But Dr. Wang will look into sending and | ||
+ | MTA over to Dr. Jin. | ||
+ | - Dr. Wang’s lab has every possible ASRE in a library. This is a good thing to | ||
+ | look into further down the road. Then all we would do is test the readout from | ||
+ | the different ASRE. | ||
+ | - Question about plasmid Erin sent: It is for eukaryotic expression but it does | ||
+ | replicate in E. Coli. It is PUF with another fusion that changes splicing in | ||
+ | eukaryotic cells. But now we need the new plasmid with the fusion protein | ||
+ | ASRE. | ||
+ | - Erin used a step-wise amplification system to generate the library of ASRE. | ||
+ | You can make it one-by-one, but the step-wise PCR created (in theory) all | ||
+ | possible PUF. | ||
+ | - Dr. Wang is open to collaboration and will share needed plasmids with us. | ||
+ | - Antibiotic resistance will be Amp (maybe K? depends on which backbone). | ||
+ | - The current backbone has K resistance. 3 plasmids: reporter gene with YFP | ||
+ | that is controlled by inhibitor protein. Gene 2=codes for inhibitor protein and | ||
+ | has PUF binding site. | ||
+ | - 3 markers should be enough. Although we can combine to get just 2 | ||
+ | plasmids. | ||
+ | Discussion | ||
+ | - It is clear that binding is not enough. We need the PUF binding and | ||
+ | endonuclease activity. Dr. Wang’s lab will send us their contruct. | ||
+ | - The concern right now is the location of the binding site. Can we choose one | ||
+ | or can we engineer one? | ||
+ | - There are many types of repressors to choose. We need to research which | ||
+ | would be the best choice. For next week we will remodel the construct and | ||
+ | find different repressors. Also look for a biobrick part. | ||
+ | - It’s a big help that they already have the whole PUF library. | ||
+ | - For the RBS we will use the Biobrick. This is because we want to submit a | ||
+ | standard part, so we should standardize everything. Because we have to | ||
+ | ligate everything, it’s a problematic idea to put the binding site between the | ||
+ | RBS and the gene. | ||
+ | - Other idea: Remove the loop area from the end of the mRNA. The 3’ UTR is | ||
+ | always involved in stability, so if our PUF binds on the loop it would be more | ||
+ | susceptible to the nuclease. | ||
+ | Cara’s phat project | ||
+ | - Buy resveratrol and a cytochrome P450 (several have been found, a human | ||
+ | one and a mutant Bacillus one. However the Bacillus one may not be | ||
+ | available for purchase online.) Sigma Aldrich is our potential vendor. | ||
+ | - Resveratrol ranges in price and available styles (approx $100 for 100 mg, | ||
+ | approx $300 for 500 mg) | ||
+ | - The goal is to create mutant piceatannols. So we mutate the cytochrome | ||
+ | P450 to see if we can get mutant piceatannols. | ||
+ | - It’s hard to work with cytochrome P450 in the prokaryotic system because it’s | ||
+ | made to work in eukaryotes. That’s why we can the bacillus cytochrome. | ||
+ | - Three available ways to make mutant enzymes: site specific mutagenesis by | ||
+ | a company, arichrome PCR, chemical mutagenesis | ||
+ | - Overall idea for a lab plan: We put the mutated cytochrome in the e. coli and | ||
+ | feed it resveratrol. We get a chip that binds to the insulin receptor and see | ||
+ | what has binded to our chip to see what is happening. | ||
+ | - Is this too ambitious? Or is it totally possible? There are conflicting opinions. | ||
+ | - Biggest problem is the low solubility. So all of the assays and screenings are | ||
+ | not easy. | ||
+ | - Our ideal mutant would be more soluble, because then it would avoid | ||
+ | degradation is the bloodstream. This random mutagenesis is a bit of a game | ||
+ | of luck. How many mutations do we need to go through before we find | ||
+ | something good? How many residues are there? | ||
+ | - If we have directed group addition or the making of derivatives, it might be | ||
+ | better and faster and potentially yield better results for our mutated | ||
+ | piceatannols. | ||
+ | - Feedback inhibition occurs when resveratrol and piceatannol inhibit the | ||
+ | cytochrome that creates the mutants. | ||
+ | - The painful part is where we need to evaluate each clone by an individual | ||
+ | assay. Is there a way to create a florescence detection method? This is much | ||
+ | easier. That way if the chemical is modified we see a color. Then we can do a | ||
+ | ton of wells and only examine the wells that have changed color. | ||
+ | - What is our desired endpoint? We don’t know what our final product A is. | ||
+ | We’re just looking for the best product, so how can we know for sure? | ||
+ | Extensive testing is needed. There are 2 unknowns (the enzyme and the | ||
+ | compound.) | ||
+ | - This had morphed into a pharmaceutical project, which is time consuming. | ||
+ | - Still a good side project if we can obtain and test various derivatives. | ||
+ | - Can we get constructs from people who have published? Then we can make | ||
+ | sure that it will actually work as expected in E. coli. | ||
+ | - 2 important things: We made a novel chemical and we made it in a | ||
+ | commercially viable amount (g/L). We need to engineer the cell to produce it | ||
+ | in proper amounts. So look at making P450 more stable so it can produce | ||
+ | more. | ||
+ | - Purdue paper: They did their research in cell cultures, but mentioned | ||
+ | degradation in the body. So does it degrade in the cell culture? | ||
+ | Announcements | ||
+ | -New advisors: Kori Dunn (3rd year graduate student from Prof. Rao’s lab), Amet (also a | ||
+ | 3rd year grad student from Prof. Rao’s lab), Prof. Joe Bradley for Entrepreneurship. | ||
+ | Agenda for next weekly meeting | ||
+ | - We are wrapping up for summer next week! It is important that we make the | ||
+ | most of our meeting time, so come on time and come prepared! | ||
+ | - Sunday Meeting agenda: | ||
+ | 1) Angela finishes up the biobrick talk | ||
+ | 2) Vote on projects. Do we want 2 equal projects? A main project and a | ||
+ | side project? Which one is which? | ||
+ | 3) Vote on bootcamp. Do we want a bootcamp? Will we split into pairs? | ||
+ | How long will it last and what lab procedures will we cover? | ||
+ | 4) Create a solid wetlab plan. Make one for any and all projects that we | ||
+ | have. Start simply yet thoroughly and let the gold medal guildelines | ||
+ | determine our progress. Make sure everyone is clear on this plan and | ||
+ | understands all of the constitutive components. | ||
+ | 5) Vote on vacation time. When will we reconvene for summer? Before | ||
+ | coming back to work, what should everyone have done? (Reading | ||
+ | papers, awareness of lab procedures, just take a brain break). | ||
+ | 6) If time permits, general announcements, including an update on | ||
+ | reading day’s social outing.</textarea> | ||
</div> | </div> | ||
<div id="meet19" style="display:none"> | <div id="meet19" style="display:none"> |
Revision as of 21:45, 19 June 2012