(Skip to menu.)

Physical Biology Laboratory - Bootcamp June 2007

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

---

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

---

Course Information

• Bootcamp Schedule (pdf) and (xls)
• Marked Caltech Map (pdf): This is a Caltech map. Highlighted in red are the four building where we will be working. The names of the building and the room numbers are given on the lower right corner.

---

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.
    

---

Useful Links

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

---

Important Model Organisms

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

---

Protocols and Handouts

• Microscopy and Optics & Size of Things
  • Microscopy and Optics
    • Microscopy and Spatial Calibration (pdf)
    • A brief explanation about fluorescence microscopy (pdf)
    • Some basics on digital imaging and CCD cameras (pdf)
    • This is a condensed tutorial by Newport (pdf)
    
    
  • Size of Things
    • Lab Manual "Size of Things" (pdf)
    • Data sheet for the slide of bovine pulmonary cells (pdf)
    • Some useful protocols related to the preparation of samples (media, plates, etc) (pdf)
• Rate of Things
  • Lab Manual "Rate of Things" (pdf)
  • Some useful protocols related to the preparation of samples (media, plates, etc) (pdf)
  • Image Analysis with Matlab Tutorial
  • http://snowdome.caltech.edu/aph162/APh162-2007/Matlab/ Go to this link to access the files that are used at the particle tracking tutorial. You will need to use the class username and password
• DNA Science
  
  • Restriction Digests, PCR and Gel Electrophoresis
    
    • Restriction Endonucleases Assay
    • Invitrogen Accuprime PFX Supermix Protocol
      
    • Useful protocols for working with DNA (pdf)
    • Brief description of all the methods (PCR, transformation, etc.) that we will be using for this part of the course (pdf)
  • Gel Extraction, Ligation and Transformation
    
    • Qiagen QIAquick Spin Handbook
      
    • Roche Rapid DNA Ligation Kit Protocol
      
    • Useful protocols for working with DNA (pdf)
    • Brief description of all the methods (PCR, transformation, etc.) that we will be using for this part of the course (pdf)
• Projects
  • Haloferax volcanii -- Isolation of Mononucleosomal DNA and Creation of DNA Library
    
    • Cultivation of Haloferax volcanii, and a protocol for the isolation of its mononucleosomal DNA
      
    • Cloning the mononucleosomal DNA to create a library of nucleosome specific DNA sequences
      
    • Solutions to prepare
      
    • Media preparation
      
      

---

Navigation