[Bioundgrd] Fwd: Biology Advanced Undergraduate Seminars
Janice Chang
jdchang at MIT.EDU
Wed Sep 7 22:22:24 EDT 2005
Dear Biology Undergraduates:
This is a reminder that the Biology department is offering the
following undergraduate seminars during the fall semester. The
seminars are six-unit courses, graded pass/fail, and are open to
sophomores, juniors, and seniors.
7.340 Nano-life: An Introduction to Virus Structure and Assembly
7.341 Not Just a Bag of Enzymes: DNA Dynamics in the Tiny Bacterial Cell
7.342 Evolution of the X, Y and Other Sex Chromosomes
7.343 A Love-Hate Relationship: Cholesterol in Health and Disease
7.344 Lost in Translation: From Egg to Embryo and Beyond
7.345 Diabetes and Obesity: Energy Balance and Disease
7.346 RNA Editing from A to I
If you have an interest in taking one of these seminars, but have a
schedule conflict, please feel free to contact the instructors. Email
addresses are below. Times of classes can sometimes be rescheduled.
Sincerely,
Janice
>TO: Biology Majors
>FROM: H. Robert Horvitz, Professor of Biology
>
>I am writing to inform you of an exciting course offering from the
>Department of Biology for the 2005-2006 academic year: a set of 14
>new and very current seminar courses, 7.340-7.346, Advanced
>Undergraduate Seminars. A complete list of the courses,
>instructors, and brief course descriptions are enclosed. The topics
>are highly varied and encompass areas of genetics, biochemistry,
>molecular biology, structural biology, cell biology, developmental
>biology, virology, aging, evolution, 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.
>
>To learn more about the Advanced Undergraduate Seminars to be
>offered during both the Fall 2005 and Spring 2006 semesters, please
>check our website
>(http://mit.edu/biology/www/undergrad/adv-ugsem.html), join the
>instructors for the seminars at a poster session on Registration
>Day, Tuesday, September 6 from 1-3pm in the Biology Building (68)
>lobby, and/or contact the instructors directly.
>
>
>***
>
>
>FALL 2005-2006
>
>7.340 Nano-life: An Introduction to Virus Structure and Assembly
>Instructors: Melissa Kosinski-Collins (kosinski at mit.edu, 2-1876;
>HHMI Education Group), Peter Weigele (pweigele at mit.edu, 3-3545;
>laboratory of Jon King)
>Fall 2005. Wednesdays, 11 am - 1 pm. Room 68-151.
>
>Watson and Crick noted that the size of a viral genome was
>insufficient to encode a protein large enough to encapsidate it and
>postulated that a virus shell is composed of multiples of identical
>relatively small subunits. Today, high-resolution structures of
>virus capsids reveal the products of such genetic economy to be
>highly symmetrical structures, much like a geodesic dome composed of
>protein subunits. Structures determined by X-ray crystallography and
>reconstructions from cryo-electron micrographs combined with data
>from traditional molecular approaches are beginning to reveal how
>these nano-structures are assembled. In this course, we will discuss
>basic principles of virus structure and symmetry, capsid assembly,
>strategies for enclosing nucleic acid, proteins involved in entry
>into and exit from cells, and the life cycles of well understood
>pathogens such as HIV, influenza, polio, and herpes. We will also
>review cutting-edge methods of structural biology and will
>participate in a visit to the Department of Biology's transmission
>electron microscope (TEM).
>
>7.341 Not Just a Bag of Enzymes: DNA Dynamics in the Tiny Bacterial Cell
>Instructors: Melanie Berkmen (mberkmen at mit.edu, 3-6702; laboratory
>of Alan Grossman), Lyle Simmons (simmon57 at mit.edu, 3-3745;
>laboratory of Graham Walker)
>Fall 2005. Tuesdays, 11 am - 1 pm. Room 68-151.
>
>Bacteria were among the first organisms to inhabit the earth, and
>they will probably be the last. While some bacteria are the
>causative agents of diseases such as anthrax and cholera, other
>bacteria play helpful roles, e.g., in plant development and
>antibiotic production. Studies of bacteria have been important in
>the understanding of central biological principles. For example, all
>cells possess mechanisms that ensure that each daughter cell
>inherits a full complement of genes after cell division. In humans,
>improper chromosome segregation may lead to cancer or other
>diseases. In bacteria, failed chromosome segregation results in
>death. Many bacteria must also segregate relatively small DNA
>molecules called plasmids, which can encode antibiotic-resistance
>and virulence genes. In this course, we will investigate the
>molecular mechanisms by which bacteria ensure the faithful
>segregation of their chromosomal and plasmid DNAs. For example, to
>ensure proper DNA segregation, some bacteria use an apparatus
>similar to that used for mitosis in eukaryotic cells. If a
>chromosome inadvertently gets trapped between daughter cells, a DNA
>pump is assembled at the site to help move the DNA to its correct
>destination. Fluorescence microscopy has played a pivotal role in
>studying the protein and DNA choreography involved in plasmid and
>chromosome maintenance. We will visit an MIT research laboratory
>focused on bacterial chromosome dynamics, and students will
>experience first-hand several fluorescent microscopic techniques
>used in this type of research. In addition, the class will tour the
>Novartis Institutes for Biomedical Research in Cambridge and meet
>the Novartis project leader in microbiology and infectious diseases.
>
>7.342 Evolution of the X, Y and Other Sex Chromosomes
>Instructor: Jennifer Hughes (jhughes at wi.mit.edu, 8-8420;
>laboratory of David Page)
>Fall 2005. Tuesdays, 1-3 pm. Room 68-151.
>
>You may have heard the rumor that the human Y chromosome is heading
>towards extinction or that the X chromosome is a repository for most
>of our "brainy" and "sexy" genes. While evidence is mounting to
>dispel such rumors, there is clearly a fascination in the popular
>press and the general public with the sex chromosomes. They are
>unique components of our genomes, because of their sex-specific
>distribution: females have two X chromosomes, while males have an X
>and a Y. The Y chromosome has taken on the primary role in male sex
>determination and, as a consequence, has become specialized over
>hundreds of millions of years of evolution to become a concentrated
>center for sperm-production factors. The sex chromosome system
>that we share with all mammals has been well characterized but is
>only one example of a tremendous variety of systems that are found
>in nature. In this class, we will explore the diversity of
>sex-determining mechanisms, with a focus on chromosomal systems and
>their evolution, ranging from the familiar (XX female - XY male in
>mammals and ZZ male - ZW female in birds) to the bizarre (10 Xs
>female - 5 XYs male in the duck-billed platypus). Despite this
>diversity, the evolution of sex chromosomes appears to follow a
>strikingly similar path across lineages as diverse as humans, birds,
>and insects: the member of the sex chromosome pair that is present
>in only one sex degenerates over time, losing the majority of its
>genes and shrinking in size. We will learn about the evolutionary
>theories that attempt to explain this degeneration, study
>experimental systems that allow these theories to be tested, and
>discuss the influences of such factors as lifespan, generation time,
>and even mating behavior.
>
>7.343 A Love-Hate Relationship: Cholesterol in Health and Disease
>Instructor: Ayce Yesilaltay (ayce at mit.edu; 3-8802; laboratory of
>Monty Krieger)
>Fall 2005. Thursdays, 3-5 pm. Room 68-151.
>
>After World War II, a new mysterious epidemic was killing men over
>55 like never before. To find out what was happening, researchers
>focused on a small town in Massachusetts and started the largest and
>longest epidemiological study of its kind. Our lives have not been
>the same since. The results from the Framingham Heart Study linked
>a person's blood cholesterol levels to the risk of having heart
>disease, the number one killer in western industrialized societies
>today. How could a small molecule like cholesterol, a major
>constituent of our cell membranes, be to blame? In this class, we
>will examine cholesterol's role in the cell and in the body as a
>whole, from its function as a structural component of the membrane
>to its function in signaling. We will learn that every cell is
>faced with a choice either to make cholesterol or to take it up from
>circulating blood. How does a cell know how much cholesterol is
>inside it? We will talk about the transcriptional and
>post-transcriptional mechanisms of cholesterol sensing and of
>feedback regulation in cells. We will discuss cholesterol in the
>brain and in the circulation, "good cholesterol" and "bad
>cholesterol" and how they are taken up and used in cells. We will
>consider what happens when cholesterol regulation goes awry in
>cholesterol-related human disorders and in animal models of such
>disorders. We will learn how the drugs that deal with some of these
>disorders were discovered, their targets and current strategies for
>discovering better drugs in the future.
>
>7.344 Lost in Translation: From Egg to Embryo and Beyond
>Instructor: Leah Vardy (vardy at wi.mit.edu, 8-5246; laboratory of
>Terry Orr-Weaver)
>Fall 2005. Thursdays 11 am -1 pm. Room 68-151.
>
>Have you ever wondered how an egg becomes a fly, a frog, a mouse or
>a human? Why heads are heads and tails are tails? While we look so
>different from the humble toad, given that we both use many of the
>same processes to develop. What lies at the heart of development
>includes not just our genes, but also how these genes are expressed,
>i.e., how mRNA is regulated. In this course we will explore some of
>the ways in which mRNA is regulated and see the developmental
>consequences when translation of mRNA into protein is disrupted. We
>will consider flies, frogs and mice to see how they turn on and off
>different mRNAs to meet their developmental needs. Topics will
>include mRNA localization, which is fundamental in distinguishing
>the head from the tail of a fruit fly. We will look at the
>importance of protein translation in the maturation of frog and
>mouse eggs and in the production of sperm and eggs in a
>hermaphrodite worm. We will discuss the variety of ways an embryo
>can fine-tune its mRNA expression to ensure production of a protein
>in the exact space and at the exact time required. Examples will
>include different ways to activate and suppress translation,
>including polyadenylation, the action of specific RNA-binding
>proteins and the recently discovered important role played by
>microRNAs. Finally, we will see that misregulation of translation
>plays a central role in a number of human diseases.
>
>7.345 Diabetes and Obesity: Energy Balance and Disease
>Instructor: Kelly Wong (kwong at wi.mit.edu, 8-0377; laboratory of
>Harvey Lodish)
>Fall 2005. Thursdays, 1-3 pm. Room 68-151.
>
>Do you know how your eating behavior is controlled at the molecular
>and cellular levels? How do the cells in your body determine how
>much energy they need? What mechanisms does your body activate to
>burn fat? Importantly, what happens when these processes go wrong,
>leading to diabetes and obesity? Diabetes and obesity constitute
>one of the fastest growing epidemics in the United States.
>According to the U.S. Center for Disease Control, over the last 10
>years there has been an alarming increase in the number of patients
>diagnosed with diabetes and/or obesity across the United States.
>The burden on the healthcare system imposed by diabetes was
>estimated to be $92 billion dollars of direct medical costs in 2002.
>In this course, we will discuss insulin, its signal transduction and
>the sensitivity and resistance of muscle to the actions of insulin.
>We will study the AMP-activated protein kinase, a master sensor of
>cellular energy status. We will also examine the actions of the
>hormone leptin and its role in controlling body weight and feeding
>behavior, as revealed by studies of genetically engineered mouse
>models. Besides leptin, other adipose tissue cytokines such as
>adiponectin will be discussed. Finally, we will examine the
>molecular consequences of beneficial activities, such as exercise,
>and discuss pharmacological agents that are currently being used to
>treat patients with Type II diabetes.
>
>7.346 RNA Editing from A to I
>Instructors: Ben Wong (bwong at mit.edu, 3-4704; laboratory of Alex
>Rich), Alekos Athanasiadis (alekos at mit.edu,
>alekosathanasiadis at hotmail.com, 3-4704; laboratory of Alex Rich)
>Fall 2005. Wednesdays, 1-3 pm. Room 68-151.
>
>Being human takes only about 30,000 genes, being a fruitfly takes
>about 14000 genes and being a yeast takes about 5-6,000 genes. Many
>of these genes are highly similar among these and other species. How
>is such wide range of organismal complexity achieved from a largely
>similar set of basic genes? This question has become central in
>molecular biology since the revealing of genome sequences a few
>years ago. One answer to this question appears to lie in mechanisms
>that allow single genes to encode a large number of variant products
>(usually proteins). In contrast to the classic hypothesis that one
>gene encodes one protein, post or co-transcriptional modifications
>of messenger RNA often allow single genes to generate hundreds or
>even thousands of proteins tailored to specific needs of the cells
>in different tissues or at developmental stages. RNA editing by
>dsRNA adenosine deaminases (ADARs), which convert adenosine to
>inosine, is one mechanism that generates RNA diversity present in
>organisms as diverse as primates and insects. In organisms as
>evolutionary diverse as nematode roundworms and humans, RNA editing
>has a particular role in the the central nervous system, altering
>the properties of neurotransmitter receptors and ion channels.
>Abnormalities in these activities have linked RNA editing to some of
>the most challenging and mysterious diseases, such as schizophrenia,
>depression and epilepsy. In addition, while useful for cells in
>fine-tuning protein and RNA functions, RNA editing also can combat
>viruses by altering their genomes and messages in a way that
>destroys information needed for their replication and function.
>During this course we will study ADARs, the enzymes responsible for
>A-to-I RNA editing, focusing on ADAR biochemistry and structure. The
>study of the known substrates of ADARs, mostly brain ion channels,
>will show us how editing modulates function. We will also discuss
>computational methods for identifying new ADAR substrates and the
>role that ADARs may play in molecular evolution.
>
>
>SPRING 2005-2006
>
>7.340 Molecular Mechanism of Aging
>Instructors: Danica Chen (danicac at mit.edu, 2-4140; laboratory of
>Lenny Guarente), Agnieszka Czopik (czopik at mit.edu, 3-3567;
>laboratory of Lenny Guarente)
>Spring 2006. Thursdays, 1-3 pm. Room 68-151.
>
>Aging is a degenerative process that results in decreased viability
>and increased susceptibility to diseases. This course will focus on
>molecules and molecular pathways that regulate the aging process,
>such as the insulin-signaling pathway and members of the Sir2 gene
>family. We will discuss the molecular mechanism of calorie
>restriction, the only known dietary regimen that extends the
>lifespans of a variety of organisms. Other topics will include the
>human premature aging disorders Werner's Syndrome and
>Hutchinson-Gilford Progeria, the role of oxidative damage and the
>mitochondria in aging, and the effects of metabolism on aging. We
>will explore the reciprocal effects of aging and immunity at the
>cellular and molecular levels and the ways these effects may be
>relevant to human biology. The class will be concluded with tours of
>a research laboratory at MIT and a biotech company both focused on
>aging.
>
>7.341. Virus-Host Interactions: A Molecular Arms Race Important for
>Cell Biology and Disease
>Instructor: Richard Jenner (rjenner at wi.mit.edu, 8-7181; laboratory
>of Rick Young)
>Spring 2006. Tuesdays 3-5 pm. Room 68-151.
>
>Viruses are tiny genetic entities that lie in between living and
>non-living things. Consisting of DNA or RNA protected in a protein
>shell, viruses are inert until they come alive inside a host cell.
>Viruses travel lightly with very few proteins and genes, instead
>hijacking cellular proteins to replicate themselves. The cell
>responds with an armament of antiviral proteins, attacking many
>aspects of viral replication. Viruses in turn express specialized
>proteins that act to block this host antiviral response. During this
>course, we will examine multiple examples of this molecular arms
>race between virus and host. We will learn about viruses that remain
>undetected within cells and the thousands of viral elements that we
>all carry within our genomes. We will also discuss how the battle
>between viruses and human cells causes diseases such as AIDS and
>cancer and what the study of virology teaches us about normal
>cellular functions.
>
>7.342 The RNA Revolution
>Instructors: Rickard Sandberg (sandberg at mit.edu, 3-7039; laboratory
>of Chris Burge), Michael Stadler (stadler at mit.edu, 3-7039;
>laboratory of Chris Burge)
>Spring 2006. Thursdays, 3-5 pm. Room 68-151.
>
>Recent findings have revolutionized our view of the roles of RNA in
>biology. For example, short non-coding RNAs (microRNAs and short
>interfering RNAs) play key roles in development and cancer by
>regulating gene expression. The biology of short non-coding RNAs and
>their importance in these processes will be topics for this course.
>In addition, the mechanism of alternative splicing explains in part
>how humans can express 500,000 different proteins with only 25,000
>genes. Alternative splicing, the process by which exons are joined
>in different combinations to generate multiple variants of a gene,
>is estimated to affect about 75% of all human genes. We will discuss
>how alternative splicing diversifies the human protein repertoire,
>influences sex determination and courtship behavior in fruit flies
>and when disrupted can cause diseases such as spinal muscular
>atrophy. Attention will also be given to catalytic RNAs that act in
>the ribosome during protein synthesis. In each session we will
>critically evaluate both the experimental and the computational
>techniques used in the primary literature to foster an understanding
>of their strengths and limitations. This course will give you an
>overview of the exciting newly emerging roles for RNA.
>
>7.343 Takin' Out the Trash: Quality Control in Cellular Processes
>Instructors: Peter Chien (pchien at mit.edu; laboratory of Tania
>Baker), Eric Spear (espear at mit.edu; laboratory of Chris Kaiser)
>Spring 2006. Wednesdays, 3-5 pm. Room 68-151.
>
>Messenger RNAs are synthesized from a DNA blueprint, the proteins
>resulting from these messages are produced using the complex
>machinery of the ribosome, and finally these proteins must attain
>their proper mature folded state. Although this process is
>extraordinarily accurate, care must be taken by the cell to cope
>with the inevitable mistakes that occur along this long and
>complicated pipeline. To this end, the cell has evolved a broad
>range of mechanisms to ensure the quality of the final protein
>product. For example, improperly folded proteins are often
>recognized as aberrant and subsequently degraded, relieving the cell
>of the potentially detrimental effects of a non-functional and
>abnormal protein. In this class, we will discuss some of the many
>mechanisms used for cellular quality control. We will consider the
>stresses that can generate such aberrant protein products and how
>the cell continuously fights these challenges. The recognition of
>misfolded proteins and how these proteins are targeted to the
>degradative machinery will also be discussed. We will consider both
>prokaryotic and eukaryotic quality control, drawing attention to the
>similarities between these two systems as well as highlighting
>differences between them. The importance of these quality control
>mechanisms will be emphasized throughout the course by discussing a
>number of relevant human diseases, including cystic fibrosis,
>Huntington's Disease, and certain types of cancer.
>
>7.344 Toxins, Antibiotics, 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 2006. Tuesdays, 1-3 pm. Room 68-151.
>
>What do the lethal poison Ricin, Diphtheria toxin, and the widely
>used antibiotic tetracycline have in common? They all inhibit
>protein synthesis by targeting the cell's translation machinery. Why
>is Ricin such a powerful toxin? How does it work? If Diphtheria
>toxin and tetracycline also inhibit translation, why do they have
>such different consequences? How does resistance to antibiotics like
>tetracycline arise? In this course, we will explore the mechanisms
>of action of toxins and antibiotics that specifically target
>components of the translational apparatus leading to the disruption
>of protein synthesis. We will discuss the roles of these antibiotics
>and toxins in everyday medicine, the emergence and spread of drug
>resistance, and how we might overcome this increasing problem by
>identifying new drug targets and designing new drugs. We will also
>discuss how the detailed understanding of the structure of the
>ribosome and the translation machinery has led to new technologies
>in protein engineering and promising applications for human therapy.
>
>7.345 Jellyfish, FRET and Quantum Dots: Illuminating Biology with
>Fluorescent Probes
>Instructors: Andrew Dutton (adutton at mit.edu, 2-2826; laboratory of
>Barbara Imperiali), Bianca Sculimbrene (sculimbr at mit.edu, 2-2826;
>laboratory of Barbara Imperiali)
>Spring 2006. Wednesday 1-3 pm. Room 68-151.
>
>Significant advances in biology have occurred through the use of
>fluorescence techniques. The sensitivity and selectivity of
>fluorescent probes has advanced our understanding of human diseases
>and of many other areas of biology by allowing the study of proteins
>within living cells. This course will focus on fluorescence
>spectroscopy as a powerful probe to study biological systems. We
>will first discuss fluorescence and methods to fluorescently label
>biomolecules. Examples of the in vitro chemical labeling of proteins
>and the hijacking of naturally-occurring fluorescent proteins, such
>as GFP (a green fluorescent protein from jellyfish), will be
>considered. Recent examples will be used to demonstrate the power of
>fluorescence methods at the frontier of biological research. We will
>learn how Fluorescence Resonance Energy Transfer (FRET), quantum
>dots and single-molecule experiments have impacted fields such as
>cancer biology and infectious disease. This course will endow
>students with the ability to understand and critically evaluate the
>primary literature, which is fundamental to advanced careers in
>science and medicine. Fluorescence technologies lie at the interface
>of chemistry and biology, and we hope that any student interested in
>either of these areas will find the information taught in this
>course extremely useful.
>
>7.346 How Abnormal Protein Folding Causes Alzheimer's, Parkinson's,
>Mad Cow and Other Neurodegenerative Diseases
>Instructor: Atta Ahmad (giftee6 at mit.edu, 3-3707; laboratory of Vernon Ingram)
>Spring 2006. Thursdays, 11 am - 1 pm. Room 68-151.
>
>The cause of both Alzheimer's Disease (AD) and Parkinson's Disease
>(PD) is abnormal deposition of proteins in brain cells. In addition,
>there are 20 other neurological diseases caused by similar protein
>deposition. Millions of people suffer from these diseases. The
>latest research shows that these diseases arise as a consequence of
>a specific series of molecular events. First, a protein assumes a
>non-native sticky "misfolded state." Two or more such sticky
>proteins associate together to generate a multi protein "oligomeric
>state." These oligomers can associate with each other or can recruit
>newly formed sticky proteins, thereby growing into bigger
>thread-like structures called "amyloid fibrils." These fibrils can
>deposit either inside or outside brain cells, disrupting normal
>biological functions and resulting in neuronal cell death. Depending
>on the region of the brain affected, this cell death leads to
>visible symptoms, such as memory loss, loss of cognitive ability,
>abnormal muscular movements, involuntary shaking and, in many cases,
>death. In this course, we will discuss the processes that trigger
>protein aggregation (such as, mutations and environmental effects)
>with an emphasis on Alzheimer's Disease, Parkinson's Disease and Mad
>Cow Disease. The methods used to study the processes of aggregation
>(e.g., fluorescence spectroscopy, circular dichroism, infrared
>spectroscopy, transmission electron microscopy, confocal microscopy)
>will be discussed. We will consider the consequences of the aberrant
>proteins on cellular processes. We will also discuss potential
>targets for intervening with these processes and approaches that
>could lead to possible treatments for these disorders.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.mit.edu/pipermail/bioundgrd/attachments/20050907/278d8f05/attachment.htm
More information about the bioundgrd
mailing list