Bootcamp

From 2009.igem.org

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(New page: '''iGEM 2009 Curriculum planning''' '''iGEM 2009 Bootcamp Draft Syllabus''' '''Monday, June 15''' '''Introduction:''' (Ben) · Welcome, overview of subject area · ...)
 
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'''iGEM 2009 Curriculum planning'''
'''iGEM 2009 Curriculum planning'''
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'''iGEM 2009 Bootcamp Draft Syllabus'''
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A two week long intensive program where thirty years worth of cell biology is condensed into four hour lectures, and taught to high school students, international students, and buddies alike. We met every morning at 9am, took an hour long lunch break at one, and either had more lectures in the afternoon or learned new lab techniques. We were also assigned various homework assignments. We had to use what we learned in the lectures by answering homework questions, and we also had journal clubs where we read and discussed scientific papers.
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'''Introduction:'''
'''Introduction:'''
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(Ben)
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('''Ben''')
·      Welcome, overview of subject area
·      Welcome, overview of subject area
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·      Start with a blank diagram of a polarized cell.  We'll add "parts" to the cell as we discuss in subsequent modules.
·      Start with a blank diagram of a polarized cell.  We'll add "parts" to the cell as we discuss in subsequent modules.
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(Oliver)
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('''Oliver''')
·      Review central dogma.  Proteins as basic “parts” for cellular function.  Introduce concept of protein domains as independent modules.
·      Review central dogma.  Proteins as basic “parts” for cellular function.  Introduce concept of protein domains as independent modules.
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·      Concept of model organisms, neutrophils and dicty
·      Concept of model organisms, neutrophils and dicty
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(Pincus)
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('''Pincus''')
·      How to read a scientific paper.
·      How to read a scientific paper.
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(Pincus)
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('''Pincus''')
·      Lead Journal Club discussion.  
·      Lead Journal Club discussion.  
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(Arthur)
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('''Arthur''')
·      What is the cytoskeleton? What are its functions?
·      What is the cytoskeleton? What are its functions?
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·      How does actin generate force on membranes?
·      How does actin generate force on membranes?
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·      How do (we think) cells crawl? (Briefly mention how bacteria chemotax)
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·      How do (we think) cells crawl?
   
   
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Toolbox parts:
 
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Journal Club (pr):
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Journal Club:
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(Arthur)
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('''Arthur''')
Paper: Actin microfilament dynamics in locomoting cells.
Paper: Actin microfilament dynamics in locomoting cells.
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(Delquin)
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('''Delquin''')
·      Intro to signal transduction I: Cells need to communicate signals from the outside to the inside.
·      Intro to signal transduction I: Cells need to communicate signals from the outside to the inside.
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(Ben)
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('''Ben''')
·      GPCR signaling in chemotaxis.
·      GPCR signaling in chemotaxis.
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Parts to add to figure: GPCRs, heterotrimeric G proteins (α, β, γ subunits)
Parts to add to figure: GPCRs, heterotrimeric G proteins (α, β, γ subunits)
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Toolbox parts:
 
   
   
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Journal Club:
Journal Club:
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(Ben and/or Delquin)
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('''Ben and/or Delquin''')
Paper: The receptors and coding logic for bitter taste.
Paper: The receptors and coding logic for bitter taste.
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(Pincus)
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('''Pincus''')
·      Intro to signal transduction II: second messengers, scaffolds, adaptors, intracellular signaling proteins, cascades
·      Intro to signal transduction II: second messengers, scaffolds, adaptors, intracellular signaling proteins, cascades
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(Oliver)
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('''Oliver''')
·      Lipid kinases/phosphatases: (modulators of PIP2/PIP3 interconversion)
·      Lipid kinases/phosphatases: (modulators of PIP2/PIP3 interconversion)
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Parts to add to figure: PI3K, PTEN, SHIP2
Parts to add to figure: PI3K, PTEN, SHIP2
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Toolbox parts:
 
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Journal Club:
Journal Club:
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(Oliver)
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('''Oliver''')
Paper:  G Protein Signaling Events Are Activated at the Leading Edge of Chemotactic Cells
Paper:  G Protein Signaling Events Are Activated at the Leading Edge of Chemotactic Cells
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Signal processing/Decision making (cont’d): Iowa
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Signal processing/Decision making (cont’d): '''Iowa'''
·      Common currencies of signaling: GTPases
·      Common currencies of signaling: GTPases
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Parts to add: Rac, Rho, Cdc42, GEFs, GAPs
Parts to add: Rac, Rho, Cdc42, GEFs, GAPs
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Toolbox parts:
 
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Journal Club:
Journal Club:
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(Iowa)
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('''Iowa''')
Paper:  An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways.
Paper:  An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways.
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Synthetic Biology (how do we plan to change things?)
Synthetic Biology (how do we plan to change things?)
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(Wendell?)
 
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(Ben)
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('''Ben''')
Paper:  Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors.
Paper:  Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors.
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TEAM CHALLENGE ALL DAY (pizza lunch provided,  Buddy meeting during lunch hour?)
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TEAM CHALLENGE ALL DAY  
   
   

Latest revision as of 23:59, 14 October 2009

iGEM 2009 Curriculum planning

A two week long intensive program where thirty years worth of cell biology is condensed into four hour lectures, and taught to high school students, international students, and buddies alike. We met every morning at 9am, took an hour long lunch break at one, and either had more lectures in the afternoon or learned new lab techniques. We were also assigned various homework assignments. We had to use what we learned in the lectures by answering homework questions, and we also had journal clubs where we read and discussed scientific papers.


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?


Parts to add to figure: dendritic actin networks, lamellipodia, filopodia, acto-myosin networks




Wednesday, June 17


Journal Club:

(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)



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



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



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?)



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



Thursday, June 25


TEAM CHALLENGE Presentations

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