BE 262 - Physical Biology Bootcamp

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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 begins on Monday, September 11th in 153 Gates Thomas at 8:30 AM. On our first meeting, you will all give 60-second long “lightning talks” (a single powerpoint slide) which summarizes who you are, where you’re from, and what you’re excited about. Please be sure to send your single slide as a PDF to Rob Phillips phillips@pboc.caltech.edu by Sunday, September 10th, at 5:00 PM.

Experimental Section

Each night, you and a handful of your classmates will join a TA or two in an experimental section from 6:30 PM - 10:30 PM. These sections will help cement some of the concepts and skills taught during the lecture sessions and will expose you to the wonderful facilities available at Caltech! These experimental sessions are

  1. Order-of-magnitude Study Hall [Rob, Justin, and Muir] : 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 and Franz] : 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 [Armando and Simón] : 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

By now, you should all have received information regarding your group letter assignment. Please see the table below for your night-by-night experimental section. Groups are denoted only by their letter.

Day Study Hall Bacterial Gene Expression Transcription in Drosophila Optics
Monday, Sep. 11 B, F, E A D, G C
Tuesday, Sep. 12 A, C D, G E, F B
Wednesday, Sep. 13 D, G E, F C A
Thursday, Sep. 14 No Session C B D
Friday, Sep. 15 No Session B A No Session
Saturday, Sep. 16 No Session No Session No Session E (1PM); F, G (6:30PM)

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