MATH 499 VIGRE Seminar: Mathematical Models in Developmental Biology

Meeting:  Tuesday, 4 pm, Herman Brown Hall, 4th Floor

Spring 2006 Tentative Schedule:

 

T January 17th

 

Organizational Meeting

T January 24th

 

Heather

Drosophila Development

T January 31st

 

Tim

Protein System Program

T February 7th

 

Diane

Papers 1), 2), & 3)

T February 14th

 

Trevor

Papers 4) & 5)

T February 21st

 

Tim

Papers 6) & 7)

T February 28th

 

 

Program data/results/discussion

T March 7th

Katri

Papers 8), 9)

 

T March 14th

 

Spring Break

T March 21st

Nick

Papers 10), 11)

T March 28th

Heather

Results update, comparison of data with published papers

T April 4th

 

 

 

T April 11th

 

 

 

T April 18th

 

 

 

T April 25th

 

 

 

End of Semester

 

 


Fall 2005 presentations

Spring 2005 presentations

Fall 2004 presentations

 

Papers

1)      Dynamics of Drosophila embryonic patterning network perturbed in space and time using microfluidics - Diane

2)      Morphogens: precise outputs from a variable gradient - Diane

3)      Morphogen gradient from a noisy source - Diane

4)      The interpretation of morphogen gradients - Trevor

5)      Diffusion and scaling during early embryonic pattern formation - Trevor

6)      Finding the center reliably: robust patterns of developmental gene expression - Tim

7)      Dynamic control of positional information in the early Drosophila embryo – Tim

8)      Bicoid determines sharp and precise target gene expression in the Drosophila embryo - Katri

9)      Shaping BMP morphogen gradients in the Drosophila embryo and pupal wing - Katri

10)  Engineering gene networks to emulate Drosophila embryonic pattern formation - Nick

11)  BMP signalling: synergy and feedback create a step gradient - Nick

12)  Topology and robustness in the Drosophila segment polarity network –

 

 

Protein System Program

 

Here’s the good coefficient files we have found for the 4-protein system:

Bestset8.coeff

Bestset13.coeff

 

Questions we’d like to answer:

 

  1. Is this actually a 3-protein system?
  2. Is it robust to other initial conditions (vary bicoid by small random perturbations, etc.)?
  3. Is it scale invariant?
  4. Can we locally vary parameters?

 

 

Basic ‘How-To’

 

What are we studying?

In this seminar, we are looking at models for the genetic regulatory network that serves as the basis for Drosophila segmentation.  We are studying some of the basic models for this process, as well as reading current biological research papers.  We are also looking at exploring this new notion of robustness, hoping to mimic the naturally stable biological system in a mathematical model. 

 

Requirements

 

1 credit hour = attend weekly seminars AND present one paper

3 credit hours = attend weekly seminars, present one paper, AND work on a project over semester

 

Interested?

Email Heather Hardway (hardway at rice.edu) or TJ Hitchman (theron at math.rice.edu)

 

Conferences/Summer Opportunities for Undergraduates

47th Annual Drosophila Research Conference – March 29th – April 2nd, 2006, right here in Houston!

Santa Fe Institute – REU, summer school

2006 Undergraduate Summer Research Program in Mathematical Biology – Penn State Erie

PCMI – Park City Utah/IAS summer program in low dimensional topology

Mathematical and Theoretical Biology Institute – summer program

Systems Biology Dynamics – summer program at McGill University

Mathematical Biosciences Institute – summer program

NIH – summer internship program

 

 

Resources

PowerPoint of Drosophila Development 101

Timetable of early Drosophila development

FlyMove

FlyBase

Reinitz Lab Homepage