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Physical Biology Bootcamp

February 2006

The second Physical Biology Bootcamp took place in February 2006. In this edition we counted with the help of Julie Theriot (Stanford University) as an invited instructor. Our students were a very motivated group of graduate students, postdocs and professors from Brandeis University, University of Washington, UPenn, UCLA, MIT, UCSD, Caltech, Brown University and the Curie Institute.

We started by exploring the Size and Rate of Things in order to get a feeling for biological scales and orders of magnitude. From there we moved to DNA Science, where the students were introduced for the first time to concepts and tools of Molecular Biology. The last two days were dedicated to more advanced projects each group performed independently.

Several Matlab Tutorials were carried out during the week to introduce the students to image analysis. At the end of each day we all got together to discuss the results of the day. The Bootcamp culminated with presentations given by all groups and a big party!

Bootcamp Schedule

Day 1:

- The Size of Things. An important step in understanding new scientific concepts is learning the scales of the problem. Over what spatial scales do biological processes occur? How much energy is consumed? In our courses be always begin by looking at various cells and organisms to discern the overall size, sizes of organelles, and rates of whole-cell and intracellular movement, using a variety of light and fluorescence microscopy techniques.


- The Rate of Things. Just like in The Size of Things, here we try to get the students acquainted to the time scales of biological processes. We looked at the time of cell division of E. coli and Yeast, development of Sea Urchin and Dictyostelium and motility of C. elegans, among other organisms.


Days 2 and 3:

- DNA Science. Molecular biology has progressed at an amazing rate in the last two decades yeilding a set of tools that allow us to manipulate DNA in a very controlled way. The aim of this section of the courses is to show a set of examples of the different tools that can be used to solve a wide variety of problems. Our claim is that, at least when dealing with E. coli, it is mostly about asking the right question rather than developing new techniques.







Days 4 and 5:

- Advanced Projects. The students split into smaller groups to carry out a variety of very interesting projects.

Odisse Azizgolshani (graduate student, UCLA) and Bill Klug (professor, UCLA) built an optical tweezer setup, characterized it and trapped DNA attached to a bead. This was done with the help of David Wu, Heun Jin Lee and Frosso Seitaridou.

Eric Klavins (professor, University of Washington) and Julie Theriot built a device to characterize Keratocyte Galvanotaxis, how they move in response the the presence of an electric field.

Ashok Prasad (graduate student, Brandeis University), Dhananjay Tambe (graduate student, Brown University) and Vivek Shenoy (professor, Brown University) and Julie Theriot studied the motility of the pathogen Listeria, which hijacks its host actin polymerization machinery to propel itself through the cytoplasm.

Brian Ross (graduate student, MIT) and John Beausan (graduate student, UPenn), with the help of Seth Blumberg and Lin Han, performed in vitro single molecule studies of DNA looping by lac repressor using the tethered particle method.

Erol Levin (postdoc, UCSD) and Josh Martin (graduate student, Brandeis University) worked on characterizing the level of gene expression of single GFP expressing E. coli cells in three different ways. This project was ment to shed some light into how quantitative one can be with gene expression, how much does the message depend on the messenger.

Pierre Sense (professor, Curie Institute) and Dan Reeves (graduate student, Brandeis University) worked on characterizing lipid membrane mechanics. One particular question they tried to answer is how does the presence of different lipid rafts, or domains, change the elastic properties of lipid vesicles?


Day 6:

After a great party every group gave a presentation showing everybody what they had accomplished during this intense week.



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