[bioundgrd] Advanced Undergraduate Seminars Spring 2009

[Nick Polizzi]

TO:     Biology Students
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 2009 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, cancer biology, neurobiology, developmental  
biology, 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 2009 semester, please check our website  
(http://mit.edu/biology/www/undergrad/adv-ugsem.html) and/or contact  
the instructors.



Spring 2009

7.344  Directed Evolution:  Engineering Biocatalysts
Instructor:  Kerry Love (kerryluv at mit.edu; 4-0727; Laboratory of  
Hidde Ploegh)
Spring 2009.  Thursdays, 11 am – 1 pm. (Class time is flexible.) 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, and Protein Engineering
Instructors:  Caroline Koehrer (koehrer at mit.edu, 3-1870; laboratory  
of Uttam RajBhandary)
Mandana Sassanfar (mandana at mit.edu, 452-4371; Education Office)
Spring 2009. Thursday, 1 – 3 pm. (Class time is flexible.)  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 all specifically target the cell’s  
translational apparatus and disrupt protein synthesis. In this  
course, we will explore the mechanisms of action of toxins and  
antibiotics, their roles in everyday medicine and the emergence and  
spread of drug resistance. We will also discuss 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.



7.346   Cancer Development, Progression and Metastasis – Is There a  
Cure in Sight?
Instructors:   Christine Chaffer (chaffer at wi.mit.edu, 8-5715;  
Laboratory of Bob Weinberg)
Christina Scheel (scheel at wi.mit.edu, 8-5176; Laboratory of Bob Weinberg)
Spring 2009. Tuesdays, 3-5 pm. (Class time is flexible.)  Room 68-151.

Despite decades of concentrated research effort, cancer remains one  
of the leading causes of death in the Western world. Generic agents,  
such as chemotherapeutics that target and kill proliferating cells,  
are still the most effective treatment for cancer patients. In the  
case of relapse, however, cancer cells usually become resistant to  
chemotherapy. To date, even with new targeted therapeutic approaches,  
advanced forms of the disease are generally incurable. Is there a  
cure in sight? Why does successful cancer therapy remain elusive?   
The answers lie, in part, in the remarkable complexity and diversity  
of the disease.  In this course, while learning to critically  
evaluate the primary research literature, we will discuss the  
fundamentals and latest discoveries in cancer research to gain an  
understanding of the hallmarks of cancer development and progression.  
We will explore the diversity in biological properties between and  
within cancer subtypes. We will discover that multiple mechanisms are  
involved in the transition from early-stage disease, usually  
consisting of discrete tumors, to late-stage disease in which the  
cancer cells have spread to distant organs. The course will provide  
an overview of the current field of cancer biology, with analyses of  
the latest experimental techniques and disease models, and will  
introduce some of the most exciting and promising research areas of  
the field.


7.347  From Molecules to Behavior:  Cell Biology of the Synapse
Instructors: Alex Chubykin (chubykin at mit.edu; 46-3301; laboratory of  
Mark Bear)
Jason Shepherd (jshephe at mit.edu; 46-3301; laboratory of Mark Bear)
Spring 2009.  Wednesdays, 1 pm - 3 pm.  (Class time is flexible.)   
Room 68-151.

The brain has an amazing capacity to store, retrieve and use  
information about past experiences.  Understanding the mechanisms  
that underlie information storage in the brain spans many disciplines  
in neuroscience, from molecules to behavior.  Neurons and their  
connections, known as synapses, are the fundamental units of  
information storage and processing in the brain.  This course will  
introduce students to current cutting-edge research concerning the  
cell biology of neurons and synapses. The course will span many  
aspects of synaptic transmission, development and plasticity.  
Specific topics will include:  (1) the molecular mechanisms of  
synapse formation during development and how abnormalities in synapse  
formation can result in cognitive disorders, such as autism and  
mental retardation; (2) the molecular mechanisms that regulate the  
functions of neurotransmitter receptors; (3) the physiology of  
synaptic transmission, including the generation and propagation of  
action potentials; (4) mechanisms of synaptic plasticity and the  
relationship of synaptic plasticity to learning and memory; and (5)  
how synaptic function is affected in neurological disorders, using  
Alzheimer's Disease as an example. We will discuss the latest tools  
that neuroscientists use to study synapses, including optical and  
genetic manipulations of synaptic transmission.  The course will rely  
on reading and analyzing original research papers from the scientific  
literature and will involve small discussion groups.  Students will  
learn how experiments  are designed, how data are obtained and how  
scientists evaluate and  interpret these data.


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