IGEM:UCSF/2007/Plan

Teahing Framework

The iGEM team will be composed High school and undergraduates. To have an effective effort over this short time (8-10 weeks) our strategy will be to focus the first half of the program on a well-scripted didactic and teaching lab program, while the second half of the program will focus on independent generation and implementation of novel and creative ideas. Thus the summer program will have three major components.

1. Didactic Program

Presentations by teaching staff. This will include some printed material as well as short seminars/discussions. Will be focused on getting them up to speed with rationale and methods that will be used in the teaching labs. Tentative assignments are listed below – can be changed!

Why

• Synthetic Biology [Sergio]
• Cell signaling and MAP kinase pathways [David]
• Adaptation: Chemotaxis and Vision [WAL]
• Pathogens as synthetic biologists [WAL]

How

• Yeast as a system & Cloning strategies [Sergio]
• Reading behavior (FACS, microscopy, western) [Noah]
• Manipulating yeast MAPK pathways [Caleb, Sergio]
• Modeling reactions (e.g. adaptive systems) [Hana]

(ACTION ITEM: write up handouts for each; key papers – GET TO WAL BY 5/22 FOR EDITING)

2. Teaching Labs

Primary goal will be to give kids hands-on experience to get them up to speed. We will design simple projects, but ones that have some aspect of interesting and novel synthetic biology.

Overall Teaching Project Goals

• TECHNOLOGY:

Develop platform for rapid combinatorial construction of modular cellular circuits based on type IIs fragments Develop bacterial factors as parts to precisely modulate eukaryotic cell signaling pathways

• SYSTEMS DESIGN & ENGINEERING:

Can we design simple kinase circuits capable of adaptation? Explore parameter robustness of different circuit architectures Explore architecture, linkage differences (different feedback points – e.g. MAPKK vs MAPK, reversible vs. irreversible negative feedback)

Teaching Experimental “Lab”

(Break up into three groups – make a set of negative feedback circuits using three part type IIs ligation using components we have premade) – test if make, test behavior:

• negative feedback loop @ MAPKK: YopJ (RFP-zip) recruited to Ste5 or Pbs2 (irrev. Modifies MAPKK); expressed from pFig1 and pSTL1
• negative feedback loop @ MAPK: OspF (RFP-zip) recruited to Ste5 or Pbs2 (irrev modifies P-MAPK); expressed from pFig1 and pSTL1
• Double negative feedback loop @MAPK: pSte5 or pCyc -YopH-zip-phosphodependent degron-RFP

NEED TO PREMAKE AND TEST THESE PARTS [Sergio]

Teaching Computational “Lab”

MATLAB simulation of simple adaptation circuit using a few parameter sets [Hana, David, Ala, Ryan, Noah]

NEED TO SET THIS UP IN A SIMPLE WAY WHAT COMPUTERS, HOW MANY?

3. Discussion/Brainstorming/Project Generation

Weekly meetings

Present and discuss classic papers in synthetic biology and past years iGEM projects (online) Weekly Homework assignments: come up with novel, creative ideas including novel applications, behaviors, circuit implementations, parts, construction and screening/assay technologies.

Independent Project Generation: Weeks 4-8

If we get to this point: Great! By this time we could have gone over a few cycles of discussing their ideas, and some might be maturing into doable things (related to the “concepts and parts” they have used in the starters). For the second half of the program we will focus on helping the students refine and implement some of these ideas both computationally and experimentally. The students will be instructed to think broadly and creatively, but to work within the constraints of the type IIs parts that we have available.