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APh/BE 162 - Physical Biology Laboratory

Course Instructor: Rob Phillips

[ Course Information | Readings | Protocols and Handouts | Useful Links | Important Model Organisms | Contact Information | Student Webpages | ]

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Image processing results in a wealth of quantitative information; here a lipid bilayer vesicle is deformed using a micropipette to garner information about its mechanical properties. Fourier analysis (blue and red lines) and edge finding (green lines) reveal geometric features of the deformed vesicles for further analysis. (c) Tristan Ursell/Rob Phillips

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Course Information

• Make up lecture section I: Monday 1/30 from 2:30pm to 6:30pm
• Make up lecture section II: Wednesday 1/25 from 2:30pm to 6:30pm
• Class outline (pdf)
• General Meeting: Wednesday -- 3 pm to 5 pm, 040 Keck
• Section I: Friday -- 1 pm to 5 pm, 040 Keck
• Section II: Tuesday -- 2:30 pm to 6:30 pm, 040 Keck

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Readings

• Measuring protein concentration
  
  • Edelhoch H; Spectroscopic Determination of Tryptophan and Tyrosine in Proteins, Biochemistry, Jul 1967; 6(7):1948-54.
    
  • Gill SC and von Hippel PH; Calculation of Protein Extinction Coefficients from Amino Acid Sequence Data, Anal Biochem, 1989; 182:319-326.
    

• DNA Science
  
  • Lutz R and Bujard H; Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements, Nucleic Acids Research, 1997; 25(6):1203-10.
    
  • Peters JE, Thate TE and Craig, NL; Definition of the Escherichia coli MC4100 Genome by Use of a DNA Array, Journal of Bacteriology, Mar 2003; 185(6):2017–2021.
    

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Useful Links

• Amino Acid Data
• The Protein Databank (PDB)
• Review of 2D Diffusion
• Beer's Law - Tutorial
• Spectra Database - (amino acids, fluorophores, etc)

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Important Model Organisms

• Model Organisms for Biomedical Research @ NIH
• Dictyostelium
• C. elegans
• Drosophila melanogaster

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Protocols and Handouts

• Microscopy and Spatial Calibration
• Beta-Galactosidase Kinetic Assay
• Electroformation of Bilayer Vesicles
• Image Analysis with Matlab Tutorial
• DNA Science
  • Week 1: Restriction Digests, PCR and Gel Electrophoresis
    
    • Restriction Endonucleases Assay
    • Invitrogen Accuprime PFX Supermix Protocol
      
  • Week 2: Gel Extraction, Ligation and Transformation
    
    • Qiagen QIAquick Spin Handbook
      
    • Roche Rapid DNA Ligation Kit Protocol
      

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Student Webpages

• The Rate and the Size of Things
  • David and Michael
    
  • Siyang and Guilherme
    
  • Oren and Nick
    
  • Alex, Jin-Hong and Eileen
    

• DNA Science
  • Alex, Jin-Hong and Eileen
    
  • Siyang and Guilherme
    
  • David and Michael
    

• Final Projects
  • Nick: Manipulation of the Lac Promoter
    
  • Siyang and Guilherme: Membrane Mechanics
    
  • David, Oren and Michael: Pattern Formation
    
  • Alex, Jin-Hong and Eileen: Gene Expression and Microtubule Polymerization
    

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Contact Information

Rob Phillips
159 Broad
x3374
phillips AT pboc.caltech.edu

Tristan Ursell
71 Broad
x8889
natsirt AT caltech.edu

Hernan Garcia
157 Broad
x3106
hgarcia AT caltech.edu

Joanne Ramirez
132 Broad
x3333
joannear AT caltech.edu