[bioundgrd] Spring 2008 Biology Advanced Undergraduate Seminars

[Nicholas Polizzi]

December 18, 2007

TO:     		Biology Majors
FROM:   	H. Robert Horvitz, Professor of Biology

   I am writing to inform you of the exciting Advanced Undergraduate  
Seminar courses being offered by the Department of Biology for the  
Spring 2008 term.  A complete list of the courses, instructors, and  
brief course descriptions are enclosed.  The topics are highly varied  
and encompass areas of biochemistry, molecular biology, microbiology,  
developmental biology, immunology, ecology, biotechnology and human  
disease. A student can take any number of these courses.  The  
courses, which generally involve four to eight students, are for 6  
units, graded pass/fail, and meet two hours each week.  The focus is  
on reading and discussing the primary research literature.  Most  
courses have two short written assignments.  Some include field trips  
to MIT research laboratories or to commercial sites using  
technologies discussed in the courses.  The level of each course will  
be tailored to the students who enroll.  Because of the small size of  
these courses, we expect students not to drop these courses once they  
have begun.

         These courses offer a number of special features:  small  
class size, a high degree of personal contact with the instructor, a  
focus on the primary research literature, and an opportunity to  
discuss current problems in biology interactively.  I believe these  
courses greatly enrich an undergraduate’s experience.  There are  
limited alternative opportunities available to undergraduates to  
interact closely with instructors who are experienced full-time  
researchers; to learn to read, understand, and analyze primary  
research papers; and to engage in the type of stimulating discussions  
and debates that characterize how science is really done.  Most  
advanced MIT undergraduates (generally juniors and seniors) have been  
sufficiently exposed to the basics of biology to be able to read the  
primary literature and appreciate both methodologies and cutting-edge  
advances.  These courses have two goals:  first, to expose students  
to the kind of thinking that is central to contemporary biological  
research; and second, to impart specific knowledge in particular  
areas of biology.  These courses are designed to be intellectually  
stimulating and also to provide excellent preparation for a variety  
of future careers that require an understanding both of what modern  
biology is and of how it is done.  Students who have taken Advanced  
Undergraduate Seminars in the past (different specific courses, same  
general design) have been enormously enthusiastic about their  
experiences.

          I am writing to you before Registration Day to encourage  
you to consider enrolling in one of these seminar courses.  Please  
feel free to contact any of the instructors to learn more about their  
courses. To learn more about the Advanced Undergraduate Seminars to  
be offered during the Spring 2008 semester, please check our website  
(http://mit.edu/biology/www/undergrad/adv-ugsem.html) and/or contact  
the instructors.



Spring 2007-2008

7.341  Under the Radar Screen: How Pathogens Evade Immune Surveillance
Instructors: Gijsbert Grotenbreg (grotenbreg at wi.mit.edu; 4-2081;  
laboratory of Hidde Ploegh) John Antos (antos at wi.mit.edu; 4-2081;  
laboratory of Hidde Ploegh)
Spring 2008. Wednesdays, 3 pm - 5 pm. Room 68-151.

Why are infectious diseases such as HIV, mycobacterium tuberculosis,  
malaria or influenza thriving today and killing millions of people  
each year? These diseases are threats because our immune system  
sometimes fails. Although we are equipped to effectively counter most  
attacks from the microbial world, some pathogens have developed ways  
to evade both our innate and adaptive immune barriers to ensure their  
own survival. The strategies used by these viruses, bacteria or  
parasites are numerous, but all target specific branches and pathways  
of our immune defenses. In this course, we will explore the specific  
ways by which microbes defeat our immune system and the molecular  
mechanisms that are under attack (Toll-like receptors, the ubiquitin/ 
proteasome pathway, MHC I/II antigen presentation). Through our  
discussion and  dissection of the primary research literature, we  
will analyze numerous aspects of host-pathogen interactions. We will  
particularly emphasize the experimental techniques used in the field  
and how to read and understand research data. Technological advances  
in the fight against microbes will also be discussed, with specific  
examples. These sessions will highlight the interplay among different  
disciplines of biology and the fact that much can be learned about  
the fundamental properties of our immune system through the study of  
immune evasion.



7.342  Developmental and Molecular Biology of Regeneration.
Instructor:  Christian Petersen (petersen at wi.mit.edu; 324-2132;  
laboratory of Peter Reddien)
Spring 2008.  Thursdays, 3 pm - 5 pm.  Room 68-151.

Regeneration is widespread throughout the animal kingdom.   
Remarkably, planarian flatworms and hydra can regenerate an entirely  
new body.  Salamanders can regenerate entirely new limbs, and fish  
can regenerate fins, spinal cords, and even heart tissue.  Mammals  
can regenerate digit tips, liver, and hair.  Mammals also maintain  
blood, skin and gut throughout adulthood.  How does a regenerating  
animal “know” what is missing? How are stem cells or differentiated  
cells used to create new tissues during regeneration?  We will take a  
comparative approach to explore this fascinating problem by  
critically examining classic and modern scientific literature about  
the developmental and molecular biology of regeneration.  We will  
learn about conserved developmental pathways that are necessary for  
regeneration, and we will discuss the relevance of these findings for  
human medicine.



7.343  Sophisticated Survival Skills of Simple Microorganisms:   
Bacterial Stress Responses and their Relevance to Ecology, Health and  
Industry
Instructor: Adrienne Dolberry (dolberry at mit.edu, 3-8686; laboratory  
of Penny Chisholm)
Spring 2008. Thursdays, 11 am - 1 pm.  Room 68-151.

The ability of bacterial cells to acclimate to unfavorable growth  
conditions has allowed such “simple” microorganisms to thrive in  
environments uninhabitable by more complicated forms of life.  By  
studying bacteria such as Escherichia coli, Bacillus subtilis and  
others under conditions of extreme heat, artic temperatures, high  
light and acidic surroundings, researchers have identified and  
characterized genes involved in the acclimation of such  
microorganisms to and survival under stressful environments.  How  
might organisms that are experts in cold acclimation, such as species  
of Psychrobacter bacteria from the Artic, help us to identify life on  
Mars?  What types of cellular morphologies do pathogenic Escherichia  
coli assume when they contaminate your apple cider?  How do  
starvation and light stresses control primary energy production in  
lakes and ponds?  In this course, we will discuss the microbial  
physiology and genetics of stress responses in aquatic ecosystems,  
astrobiology, bacterial pathogenesis and the food industry.  We will  
learn about classical and novel methods utilized by researchers to  
uncover bacterial mechanisms induced under both general and  
environment-specific stresses.  Finally, we will compare and contrast  
models for bacterial stress responses to gain an understanding of  
distinct mechanisms of survival and of why there are differences  
among bacterial genera.



7.344  Directed Evolution: Engineering Biocatalysts
Instructor:  Kerry Love (klove at wi.mit.edu, 4-2081; laboratory of  
Hidde Ploegh)
Spring 2008.  Thursdays, 1-3 pm.  Room 68-151.

Enzymes, nature’s catalysts, are remarkable biomolecules capable of  
extraordinary specificity and selectivity.  These characteristics  
have made enzymes particularly attractive as an alternative to  
conventional catalysts in numerous industrial processes.  Oftentimes,  
however, the properties of an enzyme do not meet the criteria of the  
application of interest.  While biological evolution of an enzyme’s  
properties can take several million years, directed evolution in the  
laboratory is a powerful and rapid alternative for tailoring enzymes  
for a particular purpose.  Directed evolution has been used to  
produce enzymes with many unique properties, including altered  
substrate specificity, thermal stability, organic solvent resistance  
and enantioselectivity – selectivity of one stereoisomer over  
another.  One example is the improvement of the catalytic efficiency  
of glutaryl acylase, an important enzyme in the manufacturing of semi- 
synthetic penicillin and cephalosporin.  The technique of directed  
evolution comprises two essential steps: mutagenesis of the gene  
encoding the enzyme to produce a library of variants, and selection  
of a particular variant based on its desirable catalytic properties.   
In this course, we will examine what kinds of enzymes are worth  
evolving and the strategies used for library generation and enzyme  
selection.  We will focus on those enzymes that are used in the  
synthesis of drugs and in biotechnological applications.



7.345  Antibiotics, Toxins, Protein Engineering and The Ribosome
Instructors: Caroline Koehrer (koehrer at mit.edu, 3-1870; laboratory of  
Uttam RajBhandary) Mandana Sassanfar (mandana at mit.edu, 452-4371;  
Education Office)
Spring 2008. Wednesdays, 1 – 3 pm. Room 68-151.

The lethal poison Ricin (best known as a weapon of bioterrorism),  
Diphtheria toxin (the causative agent of a highly contagious  
bacterial disease), and the widely used antibiotic tetracycline have  
one thing in common: they specifically target the cell’s  
translational apparatus and disrupt protein synthesis. The ribosome,  
the function of which is to synthesize all proteins within a cell,  
has emerged as a prime drug target. Over the past decade, we have  
gained new and fundamental insight into the molecular workings of the  
ribosome, an amazing macromolecular machine. In this course, we will  
explore the structure and function of the ribosome. We will discuss  
the various mechanisms of action of toxins and antibiotics, their  
roles in everyday medicine, and the emergence and spread of drug  
resistance. We will also talk about the identification of new drug  
targets and how we can manipulate the protein synthesis machinery to  
provide powerful tools for protein engineering and potential new  
treatments for patients with devastating diseases, such as cystic  
fibrosis and muscular dystrophy.

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