MCDB 3990: Systems Biology for Biologists!

Learning Lounge Hours: The lounge (Porter B0054) should be open from 9AM to 11PM Mondays through Fridays.  It is a good place to work, that is study and read) and talk biology. 

Mike's Office Hours:  I am typically available for drop ins from 1 to 3PM on Mondays and Fridays.
    Syllabus:  Spring 2014

    Class Date

    Topics to be covered, papers to be read BEFORE class

    week 1


    Tuesday, 14 January

    Course introduction and logistics: topics, pedagogy, projects, grading

    Where are you (and I) coming from?
    Reading papers and using nb  [nota bene link]


    Uri Alon: introduction to systems biology 


    In class exercise and discussion

    Thursday, 16 January

    Thinking about biology and biological systems: components and interactions

    — read BEFORE class using NB (google drive folder)

    1. Mayr - What makes biology unique

    2. Hogan - The end of science revisited

    3. Kitano - Systems biology: a brief overview

    4. Vendeville et al - An inventory of the bacterial macromolecular components and their spatial organization


    In class exercise:: Consider transcription and translation: what factors are involved in controlling the rate of gene expression?  

    week 2


    Tuesday, 21 January

    Thinking transcription

    — read BEFORE class using NB 

    1. Hagen et al., Transcriptional dynamics

    Thursday, 23 January

    PhET applet on gene expression

    Thinking translation

    — read BEFORE class using NB 

    1. Novoa and de Pouplana - Speeding with control: codon usage, tRNAs, and ribosomes

    2. Gollnick - Regulation of the Bacillus subtilis trp operon by an RNA-binding protein 


    In class exercise

    week 3


    Tuesday, 28 January

    The lac operon

    — read BEFORE class using NB 

    1. Vilar e al., - Modeling network dynamics: the lac operon, a case study

    2. Hammar et al., The lac repressor displays facilitated diffusions in living cells

    3. Cournac & Plumbridge - DNA looping in prokaryotes: experimental and theoretical approaches. 


    (optional)  van Hoek & Hogeweg: The effect of stochasticity on the lac operon: an evolutionary perspective 


    Thursday, 30 January

    Chemotaxis in bacteria

    — read BEFORE class using NB 

    1. Berg & Tedesco, Transient response to chemotactic stimuli in E. coli

    2. Berg & Brown, Chemotaxis in E. coli analyzed by three-dimensional tracking

    3. Ulon et al., Robustness in bacterial chemotaxis

    week 4


    Tuesday, 4 February

    Virtual lab on chemotaxis and bacterial behaviors

    review of video project topics. 

    Thursday, 6 February

    Chemotaxis 

    — read BEFORE class using NB 

    4. Parkinson & Houts, Isolation and behavior of E. coli deletion mutants lacking chemotaxis functions


    Social systems in bacteria

    — read BEFORE class using NB 

    1. Budrene & Berg, Complex patterns formed by the motile cells of E. coli. 

    2. Park et al., Motion to form a quorum

    week 5


    Tuesday, 11 February

    Social systems in bacteria - part 2

    — read BEFORE class using NB 

    3. West et al., The social life of microbes

    4. Weber & Buceta Dynamics of the quorum sensing switch: stochastic and non-stationary effects


    Hour physics: What makes a old (or bad) youtube science video

    Alice and Bob: How can atoms exist?

    Thursday, 13 February

    Social systems in bacteria part 3

    — read BEFORE class using NB 

    5. Refardt et al., Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection

    6. Travisano & Velicer,  Strategies of microbial cheater control

    7. Dandekar et al, Bacterial quorum sensing and metabolic incentives to cooperate

    week 6


    Tuesday, 18 February

    Systems as interacting organisms and generations

    — read BEFORE class using NB 

    1. Trivers, Parent-Offspring conflict

    2. Albo et al., Worthless donations: male deception and female counter play in a nuptial gift-giving spider. 

    Thursday, 20 February

    Social systems: Dicytostelium

    — read BEFORE class using NB

    1. Nagano, Modeling the model organism Dictyostelium 

    2. Ho et al., Kin recognition protects cooperators against cheaters. 
    3. Raguso, Small molecules mediate bacterial farming by social amoeba.

    week 7


    Tuesday, 25 February

    Community Effects

    — read BEFORE class using NB 

    1. Standley et al., eFGF and its mode of actin in the community effect during Xenopus myogenesis

    2. Bolouri & Davidson. The gene regulatory network basis of the "community effect" and analysis of a sea urchin example. 

    Thursday, 20 February

    Review of current state of story board  

    CreatureCasts and Feynman on magnets

    week 8


    Tuesday, 4 March

    Embryonic patterning - Xenopus

    — read BEFORE class using NB 

    1. Moon & Kimelmann. From cortical rotation to organizer gene expression: toward a molecular explanation of axis specification in Xenopus

    2. Ben-Zvi et al., Scaling of the BMP activation gradient in Xenopus embryos

    Thursday, 6 March

    Embryonic patterning - Drosophila

    — read BEFORE class using NB 

    1. Lynch & Roth. The evolution of dorsal-ventral patterning mechanisms in insects

    2. Sanson. Generating patterns from fields of cells


    supplement:  Green and Akam: Evolution of the pair rule gene network: insights from a centipede.

    week 9


    Tuesday, 11 March

     Noisy networks

    — read BEFORE class using NB 

    1. Eldar & Elowitz; Functional roles for noise in genetic circuits

    2.  Sanchez & Golding. Genetic Determinants and cellular constraints in noisy gene expression

    3. Ansel et al., Cell-to-cell stochastic variation in gene expression is a complex genetic trait. 


    sup:  Spudich & Koshland:  Non-genetic individuality: chance in the single cell

    sup: Lestas et al, Fundamental limits on the suppression of molecular fluctuations.    

    Thursday, 13 March

    Noisy network part 2  :  

    — read BEFORE class using NB 

    1. Levine, Lin & Elowitz. Functional roles of pulsing in genetic circuits.


    First draft of background paper on video project. 

    week 10


    Tuesday, 18 March


    review for midterm exam

    Thursday, 20 March

     MIDTERM EXAM

    week 11


    Tuesday, 1 April

    Cancer— read BEFORE class using NB 

    1. Axelrod et al., Evolution of cooperation among tumor cells. 

    2. Alfarouck et al., Tumor acidity as evolutionary spite


    Presentation and review of project story boards

    Thursday, 3 April

    Cancer part 2 — read BEFORE class using NB 

    3. Burrell and Swanton: The evolution of the unstable cancer genome

    4. Lu et al., Genome evolution predicts genetic interactions in protein complexes and reveal cancer drug targets.

    week 12


    Tuesday, 8 April

    REVIEW Storyboards

    Thursday, 10 April

    REVIEW Storyboards

    week 13


    Tuesday, 15 April

    Developmental networks part 2 — read BEFORE class using NB 

    Final storyboard


    Adachi et al., Context-depedent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells.

    Thursday, 17 April

    Immune networks 

    — read BEFORE class using NB 

    1. Matzinger, The danger model: a renewed sense of self


    supplement: Osborn and Olefsky, The cellular and signaling networks linking the immune system and metabolism in disease

    week 14


    Tuesday, 22 April

    Metabolic networks 

    — read BEFORE class using NB 


    1. Radokivits et al., 2010. Genetic Engineering of Algae for Enhanced Biofuel Production


    supplemental: 

    Jeong et al., The large-scale organization of metabolic networks

    Ravasz et al., Hierarchical organization of modularity in metabolic networks.

    Thursday, 24 April

    (maybe) Tanouchi et al., Programmed cell death in bacteria and implications for antibiotic therapy. 


    Classroom presentations (sign up by emailing Mike)

    week 15


    Tuesday, 29 April

    Classroom presentations (sign up by emailing Mike)

    Thursday, 1 May

    Classroom presentations (sign up by emailing Mike):  Final course roundup!


    Course Description: This three credit course is designed to introduce MCDB majors (and others) to the behavior of various biological systems a semi-quantitative way.  

    While many systems biology courses (and books) appear to have been designed for people with a high level of mathematical competency and confidence, that will not be our approach.  We will approach systems more qualitatively - discussing specific biological behaviors.  The goal is that after this you will be able to approach and analyze any new system you meet (in the wild). 

    What does that mean in practice?  There will not be too much lecturing, but rather you will be expected to have read the papers assigned before class; we will discuss observations, methods, and implications in class by working through various scenarios.  

    To encourage you in your reading, we will be using the nota bene (NB) system [link], and you will be assigned into smaller groups of 4 to 5 people each.  Using NB you will be able to post and respond to comments and questions from other members of your group (and I will be able to tell whether you have read the papers!) 

    This course may be different from what you are be used to.
    • There is no textbook. All study materials are pdfs available through the web site. 
    • You are expected to have read and worked through the study materials before class; 
      a substantial percentage (10%) of your grade
       will depends upon it.
    • Class time is used primarily for questions, discussion, and tutorials; be prepared to answer questions in class.
    • In addition to one exams (midterm), a substantial portion of your grade will be based on a video presentation and supporting paper you will generate.  This will be challenging and rewarding exercise, and we will spend significant amounts of time on your project in class during the second half of the semester.  
    Course Google Drive Folder:   Google Drive Folder

    Course projects and grading:     

    The midterm exam will be held in class and consist of approximately 3 essay type questions.  

    The final project will consider of a 10 minute video on a particular, systems related project together with a 5 to 10 page paper describing your thinking and research on the project. 

    You will also receive a grade based on your reading and participation in classroom discussions. 


    Course policies:  

    Students with disabilities:  If you qualify for 
    accommodations because of a disability, please submit 
    a letter to me from Disability Services in a timely manner 
    so that your needs may be addressed.

    Disability Services determines accommodations based 
    on
    documented disabilities. Contact: 303-492-8671 - 

    Willard 322 or through this web-link 

    Religious observances, Classroom behavior, 
    Sexual Harassment, and the Honor code: