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courses</title></head><body>
<div><font color="#000000">January 26, 2005</font></div>
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<div><font color="#000000">TO: Biology
Majors</font></div>
<div><font color="#000000">FROM: H. Robert Horvitz,
Professor of Biology</font></div>
<div><font color="#000000"><br></font></div>
<div><font color="#000000">
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.</font></div>
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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.</font></div>
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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.</font></div>
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<div><font color="#000000"><b>SPRING 2004-05</b></font></div>
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<div><font color="#000000"><b>7.345 Evolution of the Immune
System</b></font></div>
<div><font color="#000000">Instructor: Nadia Danilova
(<u>ndanilov@mit.edu</u>, x3-6705; laboratory of Lisa
Steiner)</font></div>
<div><font color="#000000">Spring 2005. Thursdays, 1 - 3 pm.
Room 68-151.</font></div>
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<div><font color="#000000">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.</font></div>
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<div><font color="#000000"><br></font></div>
<div><font color="#000000"><b>7.346 Not offered</b></font></div>
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<div><font color="#000000"><b>7.347 The Ribosome: A Most
Incredible Molecular Machine</b></font></div>
<div><font color="#000000">Instructors:</font></div>
<div><font color="#000000"> Caroline Koehrer
(<u>koehrer@mit.edu</u>, 3-1870; laboratory of Uttam
RajBhandary)</font></div>
<div><font color="#000000"> Mandana Sassanfar
(<u>mandana@mit.edu</u>, 452-4371; laboratory of Chris
Kaiser)</font></div>
<div><font color="#000000">Spring 2005. Wednesdays, 3-5 pm.
Room 68-151.</font></div>
<div><font color="#000000"><br></font></div>
<div><font color="#000000">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.</font></div>
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<div><font color="#000000"><br></font></div>
<div><font color="#000000"><b>7.348 The Molecular Basis of
Aging</b></font></div>
<div><font color="#000000">Instructors:</font></div>
<div><font color="#000000"> Gil Blander
(<u>gblander@mit.edu</u>, 3-6717, 3-3567; laboratory of Lenny
Guarente)</font></div>
<div><font color="#000000"> Marcia Haigis
(<u>mchaigis@mit.edu</u>, 3-6717, 3-3567; laboratory of Lenny
Guarente)</font></div>
<div><font color="#000000"> Spring 2004. Thursdays, 3-5
pm. Room 68-151.</font></div>
<div><font color="#000000"><br></font></div>
<div><font color="#000000">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.</font></div>
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<div><font color="#000000"><br></font></div>
<div><font color="#000000"><b>7.349 Biological Computing: At the
Crossroads of Engineering and Science</b></font></div>
<div><font color="#000000">Instructor: Julia Khodor
(<u>jkhodor@mit.edu</u>; 324-0055; HHMI Education Group postdoctoral
associate)</font></div>
<div><font color="#000000">Spring 2005. Wednesdays, 1-3
pm. </font><font color="#FF0000"><b> (Meeting time may change;
interested students should email instructor to confirm meeting
schedule.)</b></font><font color="#000000"> Room
68-151.</font></div>
<div><br></div>
<div><font color="#000000">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.</font></div>
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