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General Information

Textbooks

	Physical Biology of the Cell by Phillips, Kondev and Theriot ISBN: 0815341636
	A Feeling for the Numbers in Biology by Ron Milo and Rob Phillips This book is in the early stages of being written and is meant to complement the recently developed BioNumbers website.  We will be periodically posting pdfs from this book for you to read.

 

Syllabus

• 2010 Syllabus (PDF)
  
  

  DATE	TOPIC (click for slides and suggested reading)
  1/5	A Feeling for the Numbers in Biology 1	READING: PBoC Ch.2; HW1 posted
  1/7	A Feeling for the Numbers in Biology 2
  1/12	Signaling 1
  1/14	Signaling 2	HW1 due, HW2 posted
  1/19	Signalling 3
  1/21	Signalling 4	HW2 due, HW3 posted
  1/26	Genes: Expression, Regulation and Management 1
  1/28	Genes: Expression, Regulation and Management 2	HW3 due, HW4 posted
  2/2	NO CLASS
  2/4	NO CLASS
  2/9	Patterning in Biology 1
  2/11	Patterning in Biology 2	HW4 due 2/12 at 5 pm
  2/16	Light and Life 1	HW5 posted
  2/18	Light and Life 2
  2/23	Rob's summary
  2/25	Biological Miscellany (guest lecture)	HW5 due 2/26 at 5 pm; HW6 posted
  3/2	Biological Miscellany (guest lecture)
  3/4	Biological Miscellany (guest lecture)	HW6 due 3/5 at 5 pm
  3/9	Biological Miscellany (guest lecture)

 

Readings

1. A Feeling for the Numbers in Biology
   
   
   • Required Reading:
   
   
   • PBoC Chap. 2
   
   
   • Lecture 1 (pptx/ppt/pdf)
   
   Additional reading and useful links for Lecture 1:
   • Transeau E.N.  (1926) The accumulation of energy by plants.  The Ohio Journal of Science.  26 (1): 1-9.
   • Jorgensen P., Nishikawa J.L., Breitkreutz B.-J., and Tyers M. (2002) Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast.  Science 297: 395-400.
   This paper and the next reveal careful measurements of eukaryotic cell size distributions.
   • Tzur A., Kafri R., LeBleu V.S., Lahav G., and Kirschner M.W. (2009) Cell Growth and Size Homeostasis in Proliferating Animal Cells.  Science 325: 167-171.
   • Crane H.R. (1950) Principles and Problems of Biological Growth. The Scientific Monthly: 376-389.
   This is the article Rob mentioned in class about uneven objects (like matchboxes) forming into helices.
   • Malstrom J., Beck M., Schmidt A., Lange V., Deutsch E.W., and Aebersold R. (2009) Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans.  Nature 460: 762-765,  and supplementary information.  
   This article, cited in the slides, gives a census of the proteins in a spirochete (the supplementary information has the figure in the slides).
   
   
   • Lecture 2 (pptx/ppt/pdf)
     
     Additional reading and useful links for Lecture 2:
     • Prentis J.J. (1996) Thank you, Boltzmann, that Your Constant is So Small.  The Physics Teacher 34: 392-397.
     • Anderson C. (2008) The end of theory: will the data deluge make the scientific method obsolete?
     This is the Wired article Rob mentioned in class.
     
     
   
   
2. Signaling


• Lecture 3 (pptx/ppt/pdf)


Additional reading and useful links for Lecture 3:
• http://www.bmb.psu.edu/nixon/micro401/overview.htm
This webpage gives an introduction to two-component signal transduction systems and to some useful links.

• Greenfield D., McEvoy A.L., Shroff H., Crooks G.E., Wingreen N.S., Betzig E., and Liphardt J. (2009) Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Bio 7(6): e1000137.



• Lecture 4 (pptx/ppt/pdf)


Additional reading and useful links for Lecture 4:


• Lecture 5 (pptx/ppt/pdf)


Additional reading and useful links for Lecture 5:
• Keymer J.E., Endres R.G., Skoge M., Meir Y., and Wingreen N.S. (2006) Chemosensing in Escherichia coli: Two regimes of two-state receptors. PNAS 103 (6): 1787-1791.
This paper forms the theoretical basis for the main substance of our discussion of chemotaxis.
• Sourjik V. and Berg H.C. (2002) Receptor sensitivity in bacterial chemotaxis. PNAS 99 (1): 123-127.
This paper forms the experimental basis for the main substance of our discussion of chemotaxis.

• Pollard T.D. and Borisy G.G. (2003) Cellular motility driven by assembly and disassembly of actin filaments. Cell 112: 453-465.
• Bray D. (2002) Bacterial chemotaxis and the question of gain.  PNAS 99 (1): 7-9.


• Lecture 6 (pptx/ppt/pdf)


Additional reading and useful links for Lecture 6:
• Neidhardt, F.C. (1999) Bacterial Growth: Constant Obsession with dN/dt. J. Bacteriol. 181 (24): 7405-7408.
• Wei Y., Liu T., Sazinsky S.L., Moffet D.A., Pelczer I., and Hecht M.H. (2003) Stably folded de novo proteins from a designed combinatorial library.  Protein Science 12:92-102.
• Bamford D.H., Grimes J.M., and Stuart D.I. (2005) What does structure tell us about virus evolution? Curr Opin Struct Biol 15(6): 655-63.
• Qian B., Powers T.R., and Breuer K.S. (2008) Shape transition and propulsive force of an elastic rod rotating in a viscous fluid.  PRL 100: 078101.


3. Genes: Expression, Regulation and Management


• Lecture 7 (pptx/ppt/pdf)


Additional reading and useful links for Lecture 7:

• Blainey P.C., van Oijen A.M., Banerjee A., Verdine G.L., Xie X.S. (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. PNAS 103(15): 5752-7, and the movie Rob mentioned.


• Lecture 8 (pptx/ppt/pdf)


Additional reading and useful links for Lecture 8:

• Zenklusen D., Larson D.R., and Singer R.H. (2008) Single-RNA counting reveals alternative modes of gene expression in yeast.  Nat. Struct. and Molec. Biol. 15 (12): 1263-71.
• Golding I., Paulsson J., Zawilski S.M., Cox E.C. (2005) Real-time kinetics of gene activity in individual bacteria.  Cell 123: 1025-1036.


4. Patterning in Biology


• Lectures 9 and 10 (pptx/ppt/pdf)


Additional reading and useful links for Lectures 9 and 10:

• Turing A.M. (1952) A Chemical Basis for Morphogenesis.  Philosophical Transactions of the Royal Society of London.  Series B, Biological Sciences 237 (641): 37-72.
5. Photosynthesis


• Lectures 11 and 12 (pptx/ppt/pdf)


Additional reading and useful links for Lectures 11 and 12

• Dobzhansky T. (1973) Nothing in biology makes sense except in the light of evolution. The American Biology Teacher 125-129.


6. Rob's course summary


• Lecture 13 (pptx/ppt/pdf)


7. Biological Miscellany


• Lecture 14 (Franz Weinert) (pdf)


• Lecture 15 (Martin Linden) (pdf)


• Lecture 16 (Rob Brewster) (pptx/ppt/pdf)


• Lecture 17 (Christoph Haselwandter) (pptx/ppt/pdf)
• Notes

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