S26: Quantitative Microbiology

Physics 176/276 

Instructor: Prof. Terry Hwa; Urey 7222
e-mail: 
Time Mon/Tu/Fri   6 – 7:20 pm 
Location MYR-A 2702
Office Hour: by appointment.
Course URL: this page (https://matisse.ucsd.edu/courses/s26-quant-microb/)
Grade 4 problem sets (to be posted below);
soln evaluated in class (Mon/Tues  6-7:20pm)
Preferred
prerequisite:		 math through ordinary differential equation; undergrad thermodynamics & statistical mechanics; intro to molecular biology; or consent of instructor.

Course description

Reference Books

Course outline

  • Intro: central dogma, gene regulatory network, and bacterial physiology
  • Protein-DNA interactions: equilibrium, kinetic, cooperatively
  • Gene regulation: cooperativity and combinatorial regulation
  • stochastic gene expression; genetic circuits with feedback
  • Bacterial growth physiology: growth laws, growth and size control
  • Bacterial metabolism: catabolite repression, diauxic shift, metabolic overflow
  • Bacterial motility and chemotaxis
  • Effect of the environment

Course activity (tentative) [calendar]

  Date Topics assignment
L1 Mon, Mar 30

Intro to quantitative biology;
review of molecular microbiology [note] [recording]
ref: Monod, 1949 

  
L2 Tu, Mar 31 Protein-DNA interaction I:  thermodynamics & specificity [note] [recording] 
refs: Berg & von Hippel, 1986; 1987; 1988; Fields et al, 1997; Gerland et al, 2002
 HW1 on L1-L3 due on Friday April 10
L3 Fri, Apr 3 Protein-DNA interaction II: kinetic accessibility [note] [recording]
refs: Berg, Winter, von Hippel, 1981;
Winter, Berg, von Hippel, 1981
  
L4 Mon, Apr 6

transcriptional regulation I: intro & simple models of activation & repression [note] [recording]
refs: Bintu et al, 2005a; Bintu et al, 2005b

  
L5 Tu, Apr 7 Transcriptional regulation II:  
Cooperative control [note] [recording]
  
L6 Fri, Apr 10
zoom ID:
858 534 7263

Transcriptional regulation III: 
Combinatorial control (theory) [note] [recording]
ref: Buchler et al, 2003

  
  Mon, Apr 13
zoom ID:
858 534 7263
 HW 1 discussion
(meet in Urey 6120)		 HW2 on L4-L7 due on Friday April 24
L7 Mon, Apr 20
zoom ID:
858 534 7263
 Transcriptional regulation IV: 
Combinatorial control (expt) [note] [recording]
ref: Kuhlman et al, 2007