Team:Virginia United/Team

Who we are

Where we're from

Virginia United is a regional team between Virginia Tech, University of Virginia, Virginia Commonwealth University, Bluefield State College, and Virginia State University. The team members spent their summer spread between labs at Virginia Tech, University of Virginia, and Virginia Commonwealth University working towards a common project.

Regional Team

The Virginia United Team was created as a collaborative effort between five schools, University of Virginia, Virginia Commonwealth University, Virginia Polytechnic Institute and State University (Virginia Tech), Bluefield State College, and Virginia State University. We divided up and worked on separate parts of the project in three different locations in the state and maintained communication through constant emails, Skype calls, and face to face regional meetings. Collaborating on a project of this magnitude with this many people involved was in itself an experimental endeavor that challenged us to develop a project and maintain strong communication and organizational skills that are vital to the interdisciplinary component of synthetic biology. Not only did each individual have something unique to offer to the team, but so did each individual university based on their access to resources that other schools might have lacked. Perhaps one of the most vital components of this project is what we learned from working together to help develop a project that we would not have been able to accomplish individually. Having gained a better understanding of how research can be conducted in a huge group setting has provided us with the experience that will really become instrumental in our future in research and in particular synthetic biology as the need for collaborative projects between schools, states, and even countries becomes a normal part of the research world.

Collaborations with Other Teams

We helped the software team create a program that can analyze a construct's DNA sequence and design oligo primers that can be used for USER fusion. Our team helped by explaining how USER fusion works, explaining optimal length of primers, and explaining optimal melting temperatures for the primers. USER fusion is a method for splicing together long strands of DNA and is convenient for construct assembly.

VA United Boot Camp

In order to become acquainted with the members of each sub team, the Va United team held a boot camp at the beginning of the summer starting June 1 and ending on June 4. In addition to getting to know one another the team also discussed an overview of our project. To bring each team member up to speed in the field of synthetic biology, daily laboratory projects were planned including construct assembly, screening, and analysis. Each day, guest speakers, including advisors from each institution, lectured on important points in the growing field of synthetic biology and instilled excitement in all the students. The FBI visited the Virginia United students to lecture on safety and discretion while participating in research and provided a workshop to help conceptualize their lecture’s importance. In summary, the boot camp provided an exciting environment for team bonding and offered an environment conducive for thinking and learning.

Here is a basic outline of the days

June 1 11:00-12:00: Welcome, Introductions, Outline of Week (VBI Conference Center) 12:00-1:00: Lunch provided (Pizza Hut) (VBI Lobby) 1:00-2:00: Lecture: Steve Fong (VCU) - synthetic biology (Fralin) 2:00-3:30: Discussion: Review and Discuss Project (Fralin) 3:30-4:00: Discussion: Outline of Labwork (Fralin) 4:00-4:30: Labwork: Start overnight cultures (Fralin) 4:30-6:00: Students Find, Read, and Summarize Papers in pairs (Fralin) 6:00-8:00: Group Dinner (not provided) 8:00-10:00: Student Literature Presentations and Discussion (Fralin)

June 2 8:00-8:30: Breakfast provided (Muffins and Fruit) (Fralin) 8:30-12:00: Labwork: Minipreps, assembly, transformation (Fralin) 12:00-1:00: Lunch provided (Jimmy Johns) (Fralin) 1:00-2:00: Inchan Kwon (UVA) (Fralin) 2:00-4:00: Continue Labwork 4:00-5:00: Campus Tour (Weather Permitting) (Fralin) 5:00-6:00: Project Discussion/Parts Sequence Collection Continued (Fralin) 6:00-8:00: Group Dinner (not provided) 8:00-10:00: Research Past iGEM Projects and Discussion (Fralin)

June 3 8:30-9:00: Breakfast provided (Panera bagels) (Fralin) 9:00-10:00: Lecture: John Tyson (VT) - modeling of cellular processes (Fralin) 10:00-11:00: Workshop: Mathematical Modeling (Matt Lux) (Fralin) 11:00-12:00: Continued project discussion or campus tour (alternate time) (Fralin) 12:00-1:00: Lunch provided (Kroger) (Fralin) 1:00-2:00: Lecture: Jean Peccoud (VT) (Fralin) 2:00-3:00: GenoCAD Workshop - Introduction to Grammars (Laura Adam) (Fralin) 3:00-3:30: GenoCAD Workshop - GenoCAD Tutorial (Matt Lux) (Fralin) 3:30-5:00: GenoCAD Workshop - iGEM Project in GenoCAD (Matt Lux) (Fralin) 5:00-6:00: LABWORK: Pick colonies, grow in 96-well plates w/ and w/o aTc (Fralin) 6:00-8:00: Dinner (not provided) 8:00-10:00: Present Past iGEM Projects and Discussion (Fralin)

June 4
8:30-9:00: Breakfast provided (Doughnuts) (VBI Lobby)
9:00-10:00: Biosecurity aspects of synthetic biology, Edward You, Supervisory Special Agent, Federal Bureau of Investigation (VBI Conference Center)
Abstract: Amidst the increased attention and the diversity of views within the U.S. Government on biosecurity, the FBI Weapons of Mass Destruction Directorate has proactively engaged in outreach activities to promote science, safety and security within academia. Supervisory Special Agent Edward You will provide a presentation which will explore the nature of risk, review current policy discussions to minimize those risks, and suggest actions to improve the collaborative environment to promote research and education in the biological sciences while minimizing potential national security risks. 10:00-12:30: Biosecurity Table Top Exercises (simulating biosecurity incidents through discussions guided by FBI agents) (VBI various) 12:30-1:30: Lunch provided (Macadoos) (VBI Lobby) 1:30-2:30: Ryan Senger (VT) - whole-cell modeling (Fralin) 2:30-5:00: LABWORK Measure fluorescence using flow (Melissa Makris) (Vet School) Measure fluorescence using plate reader (Matt Lux) (VBI) Measure fluorescence using microscope (Dave Ball) (VBI) 5:00pm: Dinner at Matt's The goal is to assemble a simple device using BioBricks. Since we only have 1 week, the BioBrick parts have already been transformed and grown on plates. During the week, students will start liquid cultures for each part, miniprep the plasmids, digest the plasmids, ligate the digested DNA, transform the assembled device, grow the new cells, and measure their results.

The device contains three BioBrick parts: a TetR generator (BBa_I732084), a Ptet controlled GFP (BBa_I13522), and a vector expressing RFP (BBa_J04450). The TetR generator expresses the TetR transcription factor, which represses the Ptet promoter. The inducer aTc can be added to the growth media and block TetR from repressing the Ptet promoter. Thus, the Ptet controlled GFP will show a response in GFP level based on the presence or absence of aTc. The RFP expressing vector provides a positive control for the assembly because those vectors that do not properly digest can be identified by their expression of RFP, which can be seen by eye.

June 1 Start liquid cultures from pre-made plates (Inoculation protocol) June 2 Perform miniprep on liquid culture to prepare the plasmid DNA (miniprep protocol) 3A BioBrick assembly (BioBrick Assembly Manual) Restriction Enzyme Digestion Ligation Transform cells and plate (Transformation protocol) June 3 Pick colonies and start liquid cultures (Inoculation protocol) Create cultures of (a) non-transformed cells (control), (b) transformed cells w/ aTc (+aTc), and (c) transformed cells aTc (-aTc) June 4
Make glycerol stock (Glycerol stock protocol) Measure fluorescence in 3 rotating groups: Station 1: Melissa Makris: flow cytometer (VT Vet School) Station 2: David Ball: fluorescent microscopy (VBI) Station 3: Matt Lux: plate reader (VBI)

Not only did we get to meet one another at this “boot camp”, but we also learned a lot of important things that helped us throughout the summer. Each speaker that we had helped us to understand a different aspect of the field, and each day that we worked in the lab the more familiar we became with the techniques that we would be using throughout the summer.

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