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Bootcamp
From 2009.igem.org
iGEM 2009 Curriculum planning
iGEM 2009 Bootcamp Draft Syllabus
Monday, June 15
Introduction:
(Ben)
· Welcome, overview of subject area
· Review concept of sensor/actuator systems (Input -> Processing -> Output).
· Start with a blank diagram of a polarized cell. We'll add "parts" to the cell as we discuss in subsequent modules.
(Oliver)
· Review central dogma. Proteins as basic “parts” for cellular function. Introduce concept of protein domains as independent modules.
· Tree of life.
· Concept of model organisms, neutrophils and dicty
(Pincus)
· How to read a scientific paper.
Tuesday, June 16
(Pincus)
· Lead Journal Club discussion.
· Paper: Green fluorescent protein as a marker for gene expression.
Output (cell movement, shape change):
(Arthur)
· What is the cytoskeleton? What are its functions?
· Actin: What it is, how it works, stuctures it forms, how it's regulated
· Cellular responses that involve shape change
· Common theme: cytoskeletal regulation
· How does actin generate force on membranes?
· How do (we think) cells crawl? (Briefly mention how bacteria chemotax)
Parts to add to figure: dendritic actin networks, lamellipodia, filopodia, acto-myosin networks
Toolbox parts:
Wednesday, June 17
Journal Club (pr):
(Arthur)
Paper: Actin microfilament dynamics in locomoting cells.
Input (receptors and signals):
What initiates the process of shape change or movement?
(Delquin)
· Intro to signal transduction I: Cells need to communicate signals from the outside to the inside.
· Receptors (types), ligands, how receptors relay signals to the inside of the cell.
· GPCR signaling: canonical model
· Basic pharmacology concepts (agonist, antagonist, inverse agonist)
(Ben)
· GPCR signaling in chemotaxis.
· Gs, Gi, Gq pathways (G12/13)
· Hypothesis: Gi pathway important for chemotaxis signaling (micropipette movie)
Parts to add to figure: GPCRs, heterotrimeric G proteins (α, β, γ subunits)
Toolbox parts:
Thursday, June 18
Journal Club:
(Ben and/or Delquin)
Paper: The receptors and coding logic for bitter taste.
Signal processing/Decision making (what is the cell's "computer" or brain?):
How are cytoskeletal responses regulated?
(Pincus)
· Intro to signal transduction II: second messengers, scaffolds, adaptors, intracellular signaling proteins, cascades
· Common currencies of signaling: kinases
(Oliver)
· Lipid kinases/phosphatases: (modulators of PIP2/PIP3 interconversion)
Parts to add to figure: PI3K, PTEN, SHIP2
Toolbox parts:
Friday, June 19
Journal Club:
(Oliver)
Paper: G Protein Signaling Events Are Activated at the Leading Edge of Chemotactic Cells
Signal processing/Decision making (cont’d): Iowa
· Common currencies of signaling: GTPases
· GTPase cycle, GEFs and GAPs
· Small G proteins: Rac, Rho, Cdc42
· GTPase signaling and the cytoskeleton
Parts to add: Rac, Rho, Cdc42, GEFs, GAPs
Toolbox parts:
Monday, June 22
Journal Club:
(Iowa)
Paper: An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways.
Synthetic Biology (how do we plan to change things?)
(Wendell?)
Tuesday, June 23
Journal Club (pre-assigned questions for groups of 2):
(Ben)
Paper: Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors.
Collect individual project ideas, 5PM.
Wednesday, June 24
"Winner" of project ideas HW announced. List of ideas, parts, etc. distributed. Teams assigned.
TEAM CHALLENGE ALL DAY (pizza lunch provided, Buddy meeting during lunch hour?)
Thursday, June 25
TEAM CHALLENGE Presentations
