[Bioundgrd] Spring Advanced Undergraduate Seminar courses

[Bob Horvitz]

January 26, 2005

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

         I am writing to inform you of the exciting Advanced 
Undergraduate Seminars courses being offered by the Department of 
Biology for the Spring 2005 term.  A complete list of the courses, 
instructors, and brief course descriptions are enclosed.  The topics 
are highly varied and encompass areas of genetics, genomics, 
biochemistry, bioinformatics, molecular biology, cell biology, 
immunology, 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 for one of these seminar courses.  Please feel 
free to contact any of the instructors to learn more about their 
courses.

***

SPRING 2004-05

7.345  Evolution of the Immune System
Instructor:  Nadia Danilova (ndanilov at mit.edu, x3-6705; laboratory of 
Lisa Steiner)
Spring 2005.  Thursdays, 1 - 3 pm.  Room 68-151.

 From early in evolution, organisms had to protect themselves from 
pathogens.  Mechanisms for discriminating self from non-self evolved 
to accomplish this task, which launched a long history of 
host-pathogen co-evolution.  The evolution of mechanisms for immune 
defence has resulted in a variety of strategies.  Prokaryotes use 
restriction endonucleases, antimicrobial peptides, and RNA 
interference for self-protection.  In multicellular organisms, 
specialized immune cells have evolved, capable of the phagocytosis of 
foreign cells as well as of self cells changed by infection or 
cancer.  Defensive mechanisms based upon germline-encoded receptors 
constitute a system of innate immunity.  In jawed vertebrates, this 
system is supplemented with a second system, known as adaptive 
immunity, which involves a specialized network of immune cells and 
organs. Adaptive immunity, in contrast to innate immunity, is based 
on the diversification of immune receptors and immunological memory 
in each individual.  In this course, we will analyze evolutionary 
pathways that have led to the development of innate and adaptive 
immunity, trace both the conserved and unique features of the immune 
response from bacteria to higher vertebrates, and identify factors, 
such as adaptive changes in pathogens, that have shaped the evolution 
of immune system.


7.346  Not offered


7.347  The Ribosome: A Most Incredible Molecular Machine
Instructors:
     Caroline Koehrer (koehrer at mit.edu, 3-1870; laboratory of Uttam RajBhandary)
     Mandana Sassanfar (mandana at mit.edu, 452-4371; laboratory of Chris Kaiser)
Spring 2005.  Wednesdays, 3-5 pm.  Room 68-151.

Can you imagine how ribosomes, which are made of proteins and RNAs 
and in electron micographs appear as thousands of tiny black dots in 
the cytoplasm, can synthesize correctly and in parallel thousands of 
distinct proteins at a rate of 15 amino acids per second? Do you 
wonder how the correct tRNAs unload their amino acids in the correct 
order in the ribosome time after time to make proteins that are 
neither too long nor too short but rather exactly as spelled as in 
the mRNA? How many proteins interact with the ribosomes and how? Do 
you know that most important antibiotics target the ribosome? Now 
with the structure of the ribosome available, the field of ribosome 
biology is more exciting than ever. Structures of the entire 70S 
ribosome, obtained by x-ray crystallography and cryo-electron 
microscopy, have revolutionized our understanding of protein 
synthesis. These structures provide a tremendous amount of 
information about the global architecture of and details of 
protein-RNA interactions within the two ribosomal subunits, as well 
as details of the interaction of the ribosome with ligands such as 
initiation factors, mRNAs, and tRNAs. In this course, we will discuss 
the structure and function of the ribosome and of many of its RNA and 
protein partners in translation. In addition to facilitating 
fundamental insights into the mechanisms of protein synthesis, the 
structure and function of the ribosome has important implications for 
applied biomedical research. We will discuss the mechanisms of action 
of antibiotics and toxins that target the ribosome, human diseases 
that result from defective protein translation, newly evolving 
approaches to drug design and new technologies in protein engineering 
to design proteins with novel properties and specific functions.


7.348  The Molecular Basis of Aging
Instructors:
     Gil Blander (gblander at mit.edu, 3-6717, 3-3567; laboratory of 
Lenny Guarente)
     Marcia Haigis (mchaigis at mit.edu, 3-6717, 3-3567; laboratory of 
Lenny Guarente)
  Spring 2004.  Thursdays, 3-5 pm.  Room 68-151.

Aging is a basic feature of the biology of humans and other 
organisms.  In certain experimental organisms aging can be postponed 
or accelerated.  This course will explore key pathways that regulate 
aging. Recent experiments in which the lifespans of simple organisms 
have been extended will be discussed.  We will consider the molecular 
mechanisms responsible for the human premature aging disorders 
Werner's Syndrome and Hutchinson-Gilford Progeria.  We will discuss 
the effect of caloric restriction, insulin-signaling, and the Sir2 
gene on lifespan extension.  In addition, we will explore the role of 
oxidative damage and the mitochondria in aging.  To allow students to 
see aging research first-hand, we will visit research laboratories 
focused on aging at MIT and at a biotechnology company.


7.349  Biological Computing: At the Crossroads of Engineering and Science
Instructor:  Julia Khodor (jkhodor at mit.edu; 324-0055; HHMI Education 
Group postdoctoral associate)
Spring 2005. Wednesdays, 1-3 pm.  (Meeting time may change; 
interested students should email instructor to confirm meeting 
schedule.)  Room 68-151.

Imagine you are a salesman needing to visit 100 cities connected by a 
set of roads. Can you do it while stopping in each city only once? 
Even a supercomputer working at 1 trillion operations per second 
would take longer than the age of the universe to find a solution by 
considering each possibility in turn. In 1994, Leonard Adleman 
published a paper in which he described using the tools of molecular 
biology - including nucleic acids, enzymes, and affinity purification 
with a biotin-avidin magnetic bead system -- to solve a smaller 
7-city example of this problem. His paper generated enormous 
scientific and public interest, and kick-started the field of 
Biological Computing. Mathematicians, computer scientists, chemists, 
biologists, and engineers came together to create a new field in 
which contributions from each are critical for the success of the 
whole. Currently Biological Computing encompasses many areas of 
active research. For example, three-dimensional self-assembly of 
molecules can be used to create stereometrical shapes or to effect 
computation. Molecule-based string rewrite systems aim to emulate 
various mathematical models of computation using DNA as rewritable 
tape.  Work in the area of exquisite detection focuses on lowering 
the number of solution molecules that can be detected, while 
whole-cell computing focuses on hijacking normal cellular processes 
for computation. We will discuss how the engineering point of view 
differs from the scientific perspective, and how each colors one's 
thinking and approach to research. We will analyze the Adleman paper, 
as well as papers that came before and after it, and critically 
examine them with an eye to identifying engineering and scientific 
aspects of each paper and the interplay between the two. Non-Biology 
majors are welcome. Care will be taken to fill in any knowledge gaps 
for both scientists and engineers.
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