Team:UCSF/Notes/Bootcamp

SUMMER BOOTCAMP

Before the summer Bootcamp Raquel Gomes and the super buddies (students from UCSF iGEM 2009) came to Lincoln High School for three afterschool sessions where they taught us about synthetic biology, immunology, UCSF iGEM 2009 project and techniques the super buddies were learning in the lab. We also were given papers to read and discuss. As soon as our school year was over a two week bootcamp started at UCSF.

Week 1: June 14-18

We kicked off our summer with a brief introduction of the iGEM team and Lim Lab members after a tour of the UCSF campus. It didn’t take long for us to plunge right into lectures though. Each morning we would learn about a new topic that falls under the broader category of immunity and end with an assignments that test our understanding of that topic. The highlights of our lectures are organized with the help of the following handy table:

Seminar Topic and Highlights

Intro to Cancer and Synthetic Biology - By Raquel Gomes

A. How cancer develops

B. Synthetic Biology design

C. Introduction to topics covered during bootcamp and instructors

D. Main rules to work in lab

Immune Response - by Raquel Gomes

A. Immune cells recognize proteins on target cell surfaces using receptors.

B. The target surface proteins trigger the killing or non-killing response from the immune cells.

Cytoskeleton - by Derek Wong

A. Cytoskeletal proteins are important in forming the connection between immune cells and target cells, the immune synapse.

Cell Death - by Daniel Hostetter

A. The activation of the killing process results in...

1. Cytotoxic agents released into target cells.

2. Death signal docking on target receptors triggering apoptosis.

Intracellular signaling - by David Pincus

A. The inside of the cell is like a Rube Goldberg device

B. Writers, Erasers and Readers - kinases, phosphatases and effectors

C. Second messengers

D. Small G proteins, GTPases and ATPases

Week 2: June 21- 25

Logic Gates - by Reid Williams

A. The independent parts of proteins can be rearranged to produce a protein that acts differently.

B. These new proteins can be used to screen for the many different types of cancer and make the immune cells respond in a certain way.

C. Application: Cancer cells vary greatly in their surface protein expression (markers). We can use these markers as inputs that act as prerequisites for a certain immune cell action (i.e. killing and not killing).

Wrap-up and Intro to Team challenge - by Raquel Gomes and James Onuffer

A. Summary of everything learned during bootcamp

B. Intro to challenges

Boot camp continues onto week two. This week, our lectures focused on more of the creative aspect of synthetic biology. We learned about modularity and how parts can be put together into devices. We also studied Boolean logic and the various types of logic gates like AND or NOT gates.

Then after a summary of all the material we’ve learned over the course of boot camp, we were broken up into two groups for a team challenge. Both teams had two challenges: One was to design synthetic logic gates for cancer cell recognition and killing by cytotoxic killer cells based upon differential tumor antigen expression. The other challenge was to engineer modulators that enhanced cell mediated cytotoxicity using synthetic biology. Each group then had about two days to brainstorm, select, and tailor ideas for a final presentation to our advisers and instructors. The ideas for modulators of cell cytotoxicity were then categorized into two groups, (a) improving the cargo aspect of cell killing, and (b) improving the signaling of killing.

Each team was to come up with a few complete and practical projects under their topic. We had to look though the ideas we already had and pick out the ones we liked the best. We would then work exclusively on those ideas, finalizing and refining those ideas to present again to our instructors and advisers. After presenting, we were advised on the ideas based on feasibility within the period of time, interest, and practical application.

With a general project in mind, we began our first steps towards actually creating our projects. Before we could actually start synthesizing our parts, we needed to make primers for our parts since we were using a unique form of combinatorial cloning, Aar1 cloning. This required our parts to have both the Aar1 site and special complimentary binding sites. As we had never had any primer creating experience, we were given a lesson in how to use computer programs like APE and gene designer that would not only help with primer creation but alignments and more. We were also taught the basics of primer creation such as melting temperature and GC% content. This would all help in the weeks ahead with the various parts we had to synthesize, alignments we had to make, and more.

Ryan - add photos of bootcamp and team challenge!

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