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.
