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Physical Biology Bootcamp

October 2006

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.


Eric Peterson (Clatech) and Joel Varley (UCSB) worked with Tristan on electrophysiology of gramacidin.


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.



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