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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

DATE	TOPIC
1/4	Biology by the Numbers 1	READING: PBoC Ch.2; HW1 posted
1/6	Biology by the Numbers 2
1/11	Signaling and Regulation 1
1/13	Signaling and Regulation 2
1/18	Signaling and Regulation 3
1/20	Signaling and Regulation 4
1/25	Signaling and Regulation 5
1/27	Signaling and Regulation 6
2/1	Patterns 1
2/3	Patterns 2
2/8	Membranes by the Numbers 1
2/10	Membranes by the Numbers 2
2/15	Membranes by the Numbers 3
2/17	Membranes by the Numbers 4
2/22	Photosynthesis 1
2/24	Photosynthesis 2
3/1	Photosynthesis 3
3/3	Photosynthesis 4
3/8	No class

 

Readings

1. A Feeling for the Numbers in Biology
   
   
   • Required Reading:
   
   
   • PBoC Chap. 2, 3
   
   
   • Lecture 1 (ppt)
   
   Additional reading and useful links for Lecture 1:
   • Wiebe (1998), Prokaryotes: The Unseen Majority, Proc. Natl. Acad. Sci.Vol. 95, pp. 6578-6583
     This article provides the usually neglected facts about Procaryotes.
   • Qin (2010), A human gut microbial gene catalogue established by metagenomic sequencing-Supplimentary Information, Nature 464, 59-65  
   Interesting data about how microbial populations correlate with the condition of the hosts.
   
   
   • Lecture 2 (ppt)
     
     Additional reading and useful links for Lecture 2:
     • van Oijen (2006), DNA primase acts as a molecular brake in DNA replication, Nature 439, 621-624
     This is the paper Rob discussed in class that measured the rate of replication using single-molecule methods.
     
     
   
   
2. Signaling


• Lecture 3 (ppt for lecture 3&4)
• Lecture 4 (ppt for lecture 3&4)
• Lecture 5 (ppt)
  
  Additional reading and useful links for Lecture 5:
  • Chemla (2009), High-resolution, long-term characterization of bacterial motility using optical tweezers, Nature Methods 6, 831-839
  This beautiful experiment uses optical trapping to watch the dynamics of individual bacteria undergoing tumbles and runs.
  • Cruzel (2000), An Ultrasensitive Bacterial Motor Revealed by Monitoring Signaling Proteins in Single Cells, Science 287, 1652-1657

  This paper describes measurements of the relation between the CheY-P concentration and the motor bias that Rob talked about in class.

• Lecture 6 (same as lecture 5)

Additional reading and useful links for Lecture 6:
• Alon et. al.(1999), Robustness of bacterial chemotaxis, Nature 397, 168-171

This paper is the basis of a model which reveals precise adapation as a robust phenomenon rather than dependent upon fine tuning of parameters.



3. Genes: Expression, Regulation and Management


• Lecture 7 (ppt)

Additional reading and useful links for Lecture 7:

• Neidhardt (1999), Bacterial Growth: Constant Obsession with dN/dt, JOURNAL OF BACTERIOLOGY, vol. 181, no. 24, 7405-7408
• Segal and Gaul (2008), Predicting expression patterns from regulatory sequence in Drosophila segmentation, Nature 451, 535-540
• Eran Segal and Jonathan Widom(2009), From DNA sequence to transcriptional behaviour: a quantitative approach, Nature Reviews Genetics 10, 443-456

These papers describe the use of thermodynamic models for transcription in a way that treats the nonspecific binding on a basepair by basepair basis.



• Lecture 8 (ppt same as Lecture 7)

Additional reading and useful links for Lecture 8:

• Gill and von Hippel(1989), Calculation of Protein Extinction Coefficients from Amino Acid Sequence Data, Analytical Chemistry 182, 319-326


4. Patterning in Biology


• Lectures 9&10 (ppt)

Additional reading and useful links for Lectures 9&10:

• Kondo (2010), Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation, Science 329, 1616

This article gives a perspective on current thinking about biological pattern formation.

• 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.

This is Turing's classic paper on morphogenesis which served as the basis for our treatment of the instability of reaction-diffusion systems in class."

• Julian Lewis(1998), Notch signalling and the control of cell fate choices in vertebrates,cell & developmental biology 9, 583-589.

This excellent review by Julian Lewis, one of the leading thinkers on how notch-delta signaling works, gives a qualitative explanation of such signaling and biological examples where it matters.

• David Sprinzak and Michael B. Elowitz (2010), Cis-interactions between Notch and Delta generate mutually exclusive signalling states, Nature 456, 86-90.

This elegant experiment shows how notch and delta interact both in cis and trans. Parts of this experiment served as the inspiration for the simple model we worked out in class.

 



5. Membranes by the Numbers


• Lectures 11,12,13,14 (ppt)

Additional reading and useful links for Lectures 11,12,13,14:

• Wallace, A. R. 1855. On the law which has regulated the introduction of new species. Annals and Magazine of Natural History, 2nd Series, 16:184-196.
• ON THE TENDENCY OF VARIETIES TO DEPART INDEFINITELY FROM THE ORIGINAL TYPE, by Alfred Russel Wallace written at Ternate, February, 1858

These are the two great papers of Alfred Russel Wallace that introduced his thinking on evolution.

• Theodosius Dobzhansky (1973),Nothing in Evolution Makes Sense Except in the Light of Evolution, The American Biology Teacher, March 1973, 125-129.

 



6. Photosynthesis


• Lectures 15 (ppt)

Additional reading and useful links for Lectures 15:

• Moser, et al (1992), Nature of Biological Electron Transfer, Nature 35, 796-802.

This excellent review describes the electron transfer process in proteins and has a nice description of theory ideas like those discussed in class and experiments which respond to such theories.

 

California Institute of Technology | Questions? yijuchen@caltech.edu