BE 262 - Physical Biology Bootcamp


This course provides an intensive introduction to thinking like a quantitative biologist. Every student will build a microscope from scratch, use a confocal microscope to measure transcription in living fly embryos and perform a quantitative dissection of gene expression in bacteria. Students will then use Python to write computer code to analyze the results of all of these experiments. No previous experience in coding is presumed, though for those with previous coding experience, advanced projects will be available. In addition to the experimental thrusts, students will use “street fighting mathematics” to perform order of magnitude estimates on problems ranging from how many photons it takes to make a cyanobacterium to the forces that can be applied by cytoskeletal filaments. These modeling efforts will be complemented by the development of physical models of phenomena such as gene expression, phase separation in nuclei and cytoskeletal polymerization.

Where and When?

The course will take place in 135 Gates Thomas from September 10th through September 18th. We will begin the first morning at 8:30 am in Gates-Thomas 135 where each of you will deliver a 60 second “lightning talk” in which you quickly tell us who you are, where you are from, and what you are excited about. For these talks, send your single-slide presentation as a PDF to Rob (phillips@pboc.caltech.edu) by 5pm on Sunday, Sept. 9.

Experimental Section

  1. Order-of-magnitude Study Hall [Rob] : You can learn a lot about biology by making back-of-the-envelope estimations. In this session, you will practice making such estimates in the context of biological phenomena. In addition, you will be able to test some of your prediction by writing simulations in Python. Every student will go through this session twice during the week.
  2. Quantitative measurements of bacterial gene expression [Manuel] : Using a statistical-mechanical description of gene regulation by repression, you will make quantitative measurements of expression using wide-field epifluorescence microscopy. This will expose you to epifluorescnece microscopy, handling and preparation of bacterial samples, and deriving an expression for genetic regulation using statistical mechanics.
  3. Measuring the rate of transcription in Drosophila embryos [Jonathan and Yang Joon] : Using a clever single-transcript fluorescent reporter, you will measure the rate of transcription of a morphogen protein during the development of Drosophila embryos. You will be doing so using the state-of-the-art confocal microscopes available to all Caltech researchers in the Biological Imaging Facility.
  4. Building an optical trap or TIRF microscope from scratch [Heun Jin, Griffin, and Soichi] : Using a few rules-of-thumb about geometric optics, you will learn how optical traps and Total Internal Reflection Fluorescence (TIRF) microscopes work and put your knowledge to the test by building one from scratch. You will learn the art of aligning lasers, laying down lenses, and testing your craftsman ship on biological samples.

Experimental Schedule

Day Study Hall Bacterial Gene Expression Transcription in Drosophila Optics
Monday Sept. 10th Groups A and G Group E Group D Group F
Tuesday Sept. 11th Groups C and F Group A Group E Group D
Wednesday Sept. 12th none Group G Group C Group B
Thursday Sept. 13th Groups B and E Group D Group F Group A
Friday Sept. 14th Group D Group C Group A Group G
Monday Sept. 17th none Group F Group B Group E
Tuesday Sept. 18th none Group B Group G Group C

The sections will start at 6:30 PM in the following rooms

Experiment Location
Study Hall Gates Thomas 153
Bacterial Gene Expression Braun Basement 115
Transcription in Drosophila Braun Basement 115
Optics Broad Basement 67