The third edition of the
Physical Biology Bootcamp took place in October 2006. In this
occasion we counted with the help of Joel Swanson (University of Michigan)
as an invited instructor. Our students were a very motivated
group of graduate students, postdocs and professors from Caltech, University of Illinois at Urbana-Champaign, UCSB, UC Santa Cruz, University of Connecticut, University of Michigan and Stuttgart University.
As usual, 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 GFP photobleaching in bacteria (shown here).
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, 5 and 6:
- Advanced Projects. The
students split into smaller groups to carry out a variety of very interesting
projects.
Alberto Puliafito (UCSB) and Michael Turk (Caltech) worked with Rob on Dictyostelium development. They got some really nice pictures of its developmental stages. In particular they focused on seend the transition from spore to amoeba. They did not quite succeed because of some bacterial contamination, but they got pretty close!
Greg Huber (University of Connecticut), Justin Bois (Caltech), Songye Chen and Noah Wilson (UC Santa Cruz) worked on macrophage phagocytosis under the guidance of Heun Jin Lee (Caltech) and our visiting instructor Joel Swanson. They were interested in quantifying the forces and distribution of material during phagocytosis using optical tweezers.
Tim Schmiedl (University of Stuttgart) and Noah Ribeck (UCSD) worked with Tabita Winther and Paul Grayson (Caltech) bacteriophage DNA ejection. They focused on both in vivo and in vitro single molecule ejection experiments. Below we show E. coli with single bacteriophages attached to them.
Richard Murray, Dan Brox (Caltech) and Kipom Kim (UCSB) worked on characterizing the level of gene
expression of E. coli cells in
two different ways: by measuring single cell fluorescence using YFP and in bulk measuring LacZ activity. 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.
David Wilson (University of Michigan) and Elizabeth Villa (University of Illinois at Urbana-Champaign) ,
with the help of Lin Han (Clatech), performed in
vitro single molecule studies of DNA
looping by lac repressor using the tethered particle
method.
Day
7:
After
a great party every group gave a presentation showing everybody
what they had accomplished
during this intense week.
