Physical Biology Laboratory

In September 2007 we joined forces with Joel Swanson (University of Michigan), Elaine Bearer (Brown University), Michael Roukes (Caltech), and Scott Fraser (Caltech), and hosted the first bootcamp for the incoming bioengineering class at Caltech as part of their orientation. Joining us were also students from UCLA as well as postdocs from Caltech. This six day crash course was intended to expose bootcampers to both advanced techniques in microscopy and molecular biology as well as cutting edge research projects pursued in our lab and various other labs at Caltech. The bootcampers participated in an advanced Matlab course and learned about particle tracking, creating composite images, curve fitting and more, and also learned about Vector NTI, a useful software tool for designing experiments in molecular biology. We also heard talks by Joel, Elaine and our own Dr. Heun Jin Lee. The days were long but exhilarating, and the course culminated on the sixth day when bootcampers reported the discoveries that they made in their individual projects while wearing their choice of special costume! Here is a quick glance ats what we did.

Day 1:

- Microscopy: 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 image shows bovine endothelial cells. Their tubulin is stained with Bodipy FL goat-antimouse IgG and the F-actin is stained with Texas Red X-Phalloidin. The nucleous is stained with DAPI (but is not shown in this image).

- Microscopy: 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 some pond scum (video below), Drosophila melanogaster, C. elegans, Dictyostelium, and bacteria and yeast.

- Spectrometry: Examining the rate of things. We can infer much about the rate of biological processes not just by directly observing them through a microscope, but also through less direct measurements, such as monitoring the optical density of a population of growing cells. Much can be deduced about the physiology of bacterial cells just by monitoring how population density changes over time. In this part of the bootcamp we set to recreate one of the most famous experiments in biology conducted by Jaques Monod that suggested the notion that bacterial cells do not waste resources to make proteins if they are not needed. The idea in this experiment is to place E. coli cells in a medium where the organic source is the limiting factor and is composed of a mixture of two carbohydrates, such as glucose and lactose. E. coli will first utilize the preferred energy source (glucose in this case) while suppressing proteins required utilization of the second sugar. Once glucose is exhausted form the medium the cell will undergo a lag period where it needs to synthesize the proteins required for intake and digestion of the second carbon source (lactose). Once these enzymes are produced exponential growth is resumed and the cells continue to double, albeit at a lower doubling rate. In the figure shown the bootcampers demonstrate the diauxic shift for various inoculation volumes of starter E. coli cultures growing in a glucose/lactose medium.

Day 2:

- 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.

The goal of these two days was to take bacteria that, because of a plasmid they were carrying, turned blue in the presence of a sugar, and alter that plasmid such that the bacteria fluoresced red or green instead. In the process the students learned the essential molecular biology techniques of the Polymerase Chain Reaction (PCR), restriction digest, gel electrophoresis, ligation, and transformation via electroporation. A side project performed in parallel allowed them to also explore the relatively new technique of quantitative PCR (qPCR): students already familiar with basic PCR used a qPCR machine and a fluorescent DNA label to track the formation of the PCR product in real time, while those unfamiliar with the basic technique performed a "pseudo-quantitative" PCR procedure that consisted of removing samples from the PCR reaction every few cycles and running these samples on an agarose gel. They could then use the image-analysis techniques they learned during the Bootcamp Matlab tutorials to quantify the intensity in the bands on the gel and demonstrate the exponential growth of product that typifies PCR reactions.

Throughout these two days an emphasis was placed on the students truly understanding the reasoning behind the techniques, rather than mindlessly following fully worked-out procedures; therefore they were required, for example, to use the restriction enzymes' manufacturer's website to design digests, and to use the parameters given in the ligation manual to calculate how much of each component to add to the reaction.

- Quantitative PCR . To analyze the PCR amplification of the target gene in a more accurate way some of the bootcampers that were familiar with conventional PCR monitored this reaction by means of Quantitative PCR or QPCR for short. Here a fluorescent stain for dsDNA is added to the reaction and enables us to monitor the number of replicates as the cycle progresses. The figure above shows the amplification plots of the targets (early) and no targnet controls (late).