APh162: Physical Biology LaboratoryWinter 2006When: W, 3:00 PM.Who: You and me (Rob Phillips, x 3374, [email protected], 159Broad). The TAs for the course are Hernan Garcia, x3106, [email protected] Broad and Tristan Ursell x 8889, [email protected] 71 Broad. JoanneRamirez ([email protected]) is the Lab Manager and will be helping uswith many different aspects of the course. I am always happy to see you, butwith certainty, the best way to contact me is by email. After that, the bestapproach is to schedule a time to see me through my assistant, Katie Miller(x6337, [email protected], 138 Broad).Where: 040 Keck, subbasementWhat: See below!How: We will meet once per week in the lab and once per week as a group.You will have weekly presentations as well as hand in a CD each week withyour ”write up”. The particular due dates will be worked out as we go along.Probably there will only be a total of 4 times when you hand in your work.Course Philosophy: This course is the experimental counterpart of APh161:Physical Biology of the Cell. The basic idea of both courses is to pursue theexciting opportunities that exist at the interface between biology and moretraditional quantitative sciences. In particular, the ambition of these coursesis to use quantitative tools to investigate biological systems. The idea ofalmost all of the experiments is that there will be a core part of the experi-1ment where we suggest a concrete measurement or procedure. However, onceyou have accomplished that, almost all of the labs will permit (and we willSTRONGLY encourage) open ended exploration on your part - in some ways,this is the most serious aspect of the course – you need to take the ball andrun with it. We are expecting you to talk to us and to think and explore.In all cases, the experiments will culminate in measurements. This meansthat when you report the outcome of your experiment, you should have quan-tified the results. We will be using Matlab repeatedly as the basis of ouranalysis and we will conduct some tutorials as a group on how to do imageanalysis and data manipulation.1 Tentative Course OutlineThe course outline given below is intended to provide an overall s ense of thetopics we will cover and the general flow of the course. Certain individualtopics might be added or deleted as I see fit.1. Weeks 1 and 2: Biology - A Feeling for the Numbers• Spatial scales. The size of things - molecules, macromolecularassemblies, organelles, cells, tissues, organisms. Using microscopyto examine the sizes of biological structures.• Temporal scales in cells. How fast? Measurements of the rateof processes such as enzyme action, the cell cycle and embryonicdevelopment.2. Weeks 3-6: DNA Science• Manipulating DNA. restriction enzymes, gel electrophoresis, bac-terial transformation.• Fluorescence in E. coli. Bioinformatics. Putting genes for fluores-cent proteins into bacteria and observing the resulting response.3. Weeks 7-10: Advance d Projects• Cytoskeletal Polymerization. Single molecule and bulk measure-ments of the rate of polymerization of cytoskeletal polymers.2• Quantification of Gene Expression. Single cell and bulk measure-ment of the level of gene expression in cells.• Optical Tweezers or TIRF. Build your own optical tweezers set upand measure the trap stiffness. Build your own TIRF microscope.• Lipid Bilayer Mechanics Measurement of the mechanical proper-ties of lipid bilayers. Examination of the segregation properties ofmulticomponent lipid
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