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MOLECULAR BIOLOGY AND BIOCHEMISTRY
Professors:
Anthony Infante, Donald Oliver
Associate Professors:
Scott Holmes, Michael McAlear, Ishita Mukerji, Chair
Assistant Professors:
Manju Hingorani, Robert P. Lane
GRADUATE
PROGRAM
Students in the Molecular Biology and Biochemistry
Department study the molecular mechanisms of biological processes using the
tools of molecular biology, genetics, biochemistry, and biophysics.
The graduate program of the Department of
Molecular Biology and Biochemistry is designed to lead to the degree of doctor
of philosophy. A master of arts degree is awarded only under special
circumstances. The emphasis of the program is on an intensive research
experience culminating in a thesis. The program of study also includes a series
of courses covering the major areas of molecular biology, biochemistry, and
biophysics, journal clubs in which current research is discussed in an informal
setting, practica designed to introduce first-year students to the research
interests of the faculty, and several seminar series in which distinguished
outside speakers participate. The low student-faculty ratio allows programs to
be individually designed and ensures close contact between the student and the
faculty. All graduate students also have an opportunity to assist in teaching
undergraduate courses. A concentration in molecular biophysics supported by a
training grant from the National Institutes of Health is available for students
with interest in both the physical and life sciences. The department
currently has 24 graduate students, and the graduate program is an integral part
of the department offerings. Graduate students serve as teaching assistants in
undergraduate courses and upper-level courses and seminars. Graduate students
typically enjoy fruitful interactions with upper-level undergraduates performing
research.
REQUIREMENTS FOR THE DOCTOR OF
PHILOSOPHY DEGREE
Courses.
Ideally, incoming students will have completed courses in general biology, cell
and molecular biology, genetics, biochemistry, general chemistry, organic
chemistry, physical chemistry, calculus, and a computer language. Deficiencies
in any of these areas would normally be made up in the first year. A core
curriculum of graduate courses in the following areas is given on a two-year
cycle: nucleic acid structure, biosynthesis and its regulation, regulation of
gene expression, structural mechanisms and energetics of protein-nucleic acid
interactions, protein structure and folding, protein trafficking in cells,
physical techniques, molecular genetics, the cell cycle, biological spectroscopy
and molecular, biochemical and cellular basis of cancer and other human
diseases. Additional graduate course electives are also available. Within this
general framework individual programs of study tailored to fit the student's
background and interests are designed in consultation with the graduate
committee and the student's advisor.
Qualifying examinations.
The criteria for admission to candidacy for the
PhD will be performance in courses, aptitude for research, a written qualifying
examination at the end of the third semester, and the oral defense of an
original research proposal by the middle of the fourth semester.
Teaching.
Normally, three to four semesters of teaching
are required.
Areas of Research. Research areas
include the mechanisms of DNA replication and repair, centrosome and telomere
function, gene regulation and DNA-protein interactions genome organization and
structure, protein structure-function relationships, and protein trafficking
between cell compartments. These research topics are integral to our
understanding of how cells become specialized during development, and how genes
and proteins interact in genetic networks. A
molecular/biochemical/biophysical-level approach to these topics will also
contribute important medical insights. For example: 1) DNA replication, repair,
and chromosome function are important fields for cancer research; 2) gene
regulation and chromosome structure are important for stem cell biology; 3)
protein structure-function relationships are critical for a host of
neurodegenerative diseases; and 4) genetic pathways reveal consequences of
mutations that underlie most genetics disorders. Our department is therefore
focused on the fundamental genetic components of a cell, and our aim is to
further understanding of how these components interact to produce complex
phenotypes in the organism.
Facilites. The department is housed in a modern
air-conditioned building. Major times of instrumentation for molecular
biological analysis include an Applied Biosystems DNA synthesizer, a microarray
hybridization chamber, a Perkins-Elmer real time PCR machine, a gel-scanning
densitometer/phosphorimager, and an Evans and Sutherland Picture System 350 for
visualizing ethidium bromide-stained gels. Analytical instrumentation includes
Varian400 and 500 MHz nuclear magnetic resonance (NMR) spectrometers, a laser
Raman spectrometer with UV resonance Ruman capability, a time-correlated single
photon counting flourescence setup, a ThermoElectron Deca XP Plus ion trap mass
spectrometer equipped for reversed-phase electrospray tandem mass spectrometry,
a Brechbuehler helium pressure cell for loading microcapillary columns, several
UV-visible spectrometer, a stopped flow kinetics system, two high-performance
liquid chromatography system, two standard steady-state fluorometers, and a
Jasco circular dichroism (CD) spectrometer. Cell biological imaging
equipment includes a Zeiss Axioplan fluorescence microscope equipped with
CFP/YFG/GFP/Rhodamine filter sets and a Zeiss MRM Digital camera, a Zeiss
confocal microscope and a digital camera, and transmission and scanning electron
microscopes. Additional major equipment includes several scintillation counters,
multiple preparative ultracentrifuges, a fermenter, environmental chambers,
multiple cold rooms, and a photographic darkroom equipped with an XOMAT film
developer. There are multiple computers throughout the building available in the
graduate computer room and in faculty member laboratories.
MOLECULAR BIOPHYSICS
The department of Chemistry and Molecular Biology and
Biochemistry offer an interdepartmental certificate program in molecular
biophysics supported by a training grant from the National Institutes of Health.
This program is designed to prepare students for research and careers that
combine interests in the physical and life sciences. Interested students are
encouraged to consult David Beveridge in the Chemistry Department or Ishita
Mukerji in the MB&B Department.
MB&B500 Graduate Pedagogy
Identical with: BIOL500
Credit: 0.50
Fall 2005
MB&B501/502 Individual Tutorial, Graduate
Credit: 1.00
MB&B504 Selected Topics in Modern Biology
A seminar primarily concerned with papers taken
from current research publications designed for, and required of, graduate
students; one 90-minute meeting each week.
Credit: 0.25
MB&B505 Mechanisms of DNA Damage/Repair and
Related Diseases
Identical with: MB&B305
Credit: 1.00
Spring 2006
MB&B507 Molecular Biophysics Journal Club I
Identical with: CHEM307
Credit: 0.50
Fall 2005
MB&B508 Molecular Biophysics Journal Club II
Identical with: CHEM308
Credit: 0.50
Spring 2006
MB&B510 Selected Topics in Molecular Genetics
This is a half semester course. It will be
offered in the second half of the semester. This is an intensive course
consisting of lectures and discussions of selected topics in molecular biology
and genetics. Topics will vary from year to year.
Credit: 0.50
MB&B511 Group Tutorial, Graduate
Credit: 0.25
MB&B512 Molecular, Proteomic and Cell
Biological Analysis of Telomere Composition and Function
This course will focus on a critical feature of
the eukaryotic cell known as the telomere, or linear chromosome end. We will
discuss the diverse set of critical molecular mechanisms affected by and
involving telomeres including chromosome segregation, cellular aging, meiotic
gamete production, and cancer progression. We will also focus on the physical
architecture of the telomere, how this architecture dynamically alters in
different biological contexts, and the types of molecules known to associate
with telomeres in multiple model organisms including yeast and human cells. An
emphasis will be placed on experimental strategies used for identifying new
components of the telomere complex and for understanding telomere function
during normal and diseased cellular states.
Credit: 0.50
Fall 2005
MB&B516 Topics in DNA Replication
The rapid accumulation of knowledge concerning
DNA replication embraces biochemical, genetic, and physiological aspects of such
replication, as well as their implications for determining the structure and
function of DNA. This one-half semester course will deal with current aspects of
DNA replication with a strong biochemical emphasis on its enzymology. Topics
will include DNA precursors and their control, initiation and the function of
initiation proteins, individual replication enzymes and the enzymology of the
replication fork, termination of replication, and regulation of replication.
Credit: 0.50
MB&B519 Structural Mechanisms of
Protein-Nucleic Acid Interactions
Identical with: CHEM519
Credit: 0.50
MB&B520 Topics in Nucleic Acid Structure
This course focuses on the principles of nucleic
acid structure. The scope of this course is to go beyond the common DNA
structures such as B-DNA and A-DNA helical structures. The course will
concentrate on other DNA structural motifs like branched DNA, supercoiled DNA,
triplex DNA and quadruplex DNA. Physical characterization of these structures as
well as the functional implication of these structures (in terms of DNA
replication, transcription, telomeres, etc.) will be discussed extensively.
Discussion will also center on the forces that stabilize these structures, such
as H-bonding and stacking interactions. The course will also cover other
important DNA structural motifs such as curved or bent DNA as found in A-tracts
and the relevance of these structures in promoter recognition and gene
expression. Important RNA structures, such as ribozymes and pseudoknots will
also be discussed. We will also discuss the significance of DNA structural
motifs in eukaryotic genomes and the application of bioinformatic tools to
search for these motifs.
Credit: 0.50
MB&B521 Aspects of the Biochemistry of Cancer
This course will discuss some of the classical
and current observations concerning alterations in biochemical metabolic
pathways that occur upon cellular transformation. The mechanism of action of
various mitogens such as growth factors and phorbal esters and their effects on
protein phosphorylations, changes in membrane components and alterations in
carbohydrate metabolism are among the topics.
Credit: 1.00
MB&B522 Mechanisms of Protein Trafficking
within Cells
This is a half-semester course. It will be
offered the first half of the semester. This course surveys mechanisms of
membrane protein topogenesis and protein secretion starting with E. Coli and
progressing to eucaryotic cells.
Credit: 0.50
MB&B523 Energetics and Mechanisms of
Protein-Nucleic Acids Interactions
Identical with: CHEM523
Credit: 1.00
MB&B525 Energetics of Protein-Nucleic Acid
Interactions
Identical with: CHEM525
Credit: 0.50
MB&B527 Topics in Chromatin Structure
This course will investigate the structure of
the eukaryotic chromosome and consider how that structure influences fundamental
biological processes such as recombination, DNA replication, chromosome
segregation and gene expression. We will also examine the elements necessary
for maintaining and propagating chromosomes, including telomeres, centromeres,
and replication origins. We will use primary sources from scientific literature
and a discussion format to appreciate current approaches, conclusions, and
unresolved issues in the field. This is a half semester course. It will be
taught the first half of the semester.
Credit: 0.50
MB&B528 Topics in Eukaryotic Genetics:
Transcription
This half semester course will follow two
principle themes: we will examine the use of genetic methods in current
biological research, and apply these methods to address questions about the
regulation of gene expression in eukaryotes. Our examination of transcriptional
regulation will lead us into the related topics of gene organization, chromosome
structure, and signal transduction.
Credit: 0.50
Fall 2005
MB&B529 Advanced Microbiology
This course will deal with new exciting concepts
in microbiology that can not be considered in an undergraduate course. Topics
will include the Biosphere, space, (exomicro-biology) environmental topics
involving pollution, Biolfilms, and microbes as geological agents, industrial
microbiology, new concepts in pathogenicity of microbes and viruses, and
evolution.
Credit: 0.50
MB&B530 Molecular and Cellular Basis of Human
Diseases
This course shall cover the molecular, genetic,
cellular and biochemical aspects of selected human ailments. Topics will
include aging, atherosclerosis, osteoporosis, diabetes, obesity and Alzheimer's
Disease.
Credit: 1.00
Spring 2006
MB&B531 The Genomics of Evolution, Adaptation,
and Regulation
Identical with: MB&B331
Credit: 1.00
MB&B532 Structure-Function and Kinetics of DNA
Metabolic Enzymes
The key to understanding how enzyme catalysts
work is to understand their structure and properties, and the kinetics and
thermodynamics of their reactions. In this course you will learn how the
principles of kinetics and thermodynamics are used to investigate the mechanisms
of action of these biological machines. The focus, in particular, will be on
learning the workings of enzymes responsible for DNA replication, repair, and
recombination.
Credit: 0.50
MB&B533 Gene Regulation
The MBB department is focused on the molecular
and biochemical pathways that lead to cellular phenotype. Integral to our
understanding of these pathways is elucidating how biological information is
integrated - specifically, how the cell considers all of the various inputs,
integrates these signals, and produces predictable cellular outcomes. This
course will be the first offered in the MBB department in which the central
theme is how biological information is integrated. Specifically, we will focus
on the integration that takes place in the cell nucleus. Here, information
about the developmental status of a cell, presented in the nucleus in the form
of combinations of transcription factors, is integrated at gene promoters to
produce predictable patterns of gene expression. We will cover three important
and emerging topics in gene regulation: 1) how promoters function as integrated
circuits, 2) how the histone (i.e., epigenetic) code may compensate for a
curiously low level of apparent genetic instruction as to which transcription
factors should bind to which promoters, and 3) how microarray technology leads
to a whole-systems view of gene co-regulation. These topics in gene regulation
are an emerging focal point in the Human Genome Project.
Credit: 0.50
MB&B537 Molecular Basis of Pathogenicity
This course will focus on a variety of new
concepts concerning the molecular and genetic basis of pathogenicity emphasizing
organisms that may be used for Bioterrorism as well as others that have played
an important role in human illnesses. Bacteria and viruses will be covered.
Credit: 1.00
MB&B539 Gene Regulation
This is a 1/2 semester course (Tuesday,
September 13, thru Tuesday October 25). Discussion of topics in the regulation
of eukaryotic gene expression such as: Transcription factors and their mode of
action; enhancers; silencers; locus control region and insulators; and the role
of nucleosome positioning and chromatin structure. In addition, several
illuminating systems such as the response to steroid hormones or heat shock; the
control of yeast mating type; muscle differentiation and MyoD; and homeoproteins
in development will be examined. Control of gene expression by RNA processing,
stability or translation will be briefly considered. Emphasis throughout the
course will be placed on the experimental methods that have given us our current
understanding of the regulation of gene expression.
Credit: 0.50
MB&B544 Gene Expression: The Translation Step
and Its Control
This course will cover problems of current
research interest in molecular biology with special emphasis on the synthesis,
structure, and functions of RNA; the synthesis of proteins; the control of
post-transcriptional genetic activities; and the transfer of genetic
information. These topics are discussed as they may relate to the mechanisms
underlying hormonal regulation, embryonic development and cellular
differentiation.
Credit: 0.50
MB&B550 Bioinformatics and Functional Genomics
Identical with: BIOL350
Credit: 1.00
MB&B557 Research Seminars in Molecular Biology
Weekly informal presentations by graduate
students about their research projects. This includes description of
experimental outline, technical details, problems that are encountered and
possible solutions. The active informal discussion among the participants is
designed to generate communication skills, new ideas, interpretations and
introduce novel techniques that would aid the graduate student. There will also
be formal seminars of more advanced research projects intended as an exercise in
public speaking and a comprehensive presentation. A summary of the work
accomplished during the practicum (MB&B 501, 502) will be expected of first year
students. A sixty minute meeting every week is planned. (This course is
required of all graduate students).
Credit: 0.25
Fall 2005
MB&B558 Research Seminars in Molecular Biology
Weekly formal presentations by graduate students
about their research projects. This includes description of experimental
outline, technical details, problems that are encountered and possible
solutions. The active discussion among the participants is designed to generate
communication skills, new ideas, interpretations and introduce novel techniques
that will aid the graduate student. There will also be formal seminars on more
advanced research projects intended as an exercise in public speaking and a
comprehensive presentation. A summary of the work accomplished during a
practicum will be expected of first year students. A 60-minute meeting every
week is planned. (This course is required of all graduate students.)
Credit: 0.25
Spring 2006
MB&B570 Multi-Dimensional Nuclear Magnetic
Resonance Spectroscopy
Identical with: CHEM570
Credit: 0.50
MB&B575 The Cell-Division Cycle and Cancer
This course will cover a broad range of topics
that are related to the process of cell division. We will discuss how the cell
cycle is executed and regulated in a variety of eukaryotic systems. Major
consideration will be applied to discussions of cancer and the defects in
cell-division regulation that underlie this disease. Some of the topics
include: growth factors, signaling pathways, apoptosis, cyclin-dependent kinases
as cell-cycle regulators, transcriptional and post-transcriptional control of
cell cycle genes, DNA replication, DNA damage checkpoints, and tumor
suppressors.
Credit: 0.50
MB&B581 Physical Chemistry for Life Scientists
Identical with: MB&B381
Credit: 1.00
MB&B585 Seminar in Molecular Biology
This course includes the presentation and
discussion of recent findings in the field of molecular biology.
Credit: 0.25
Fall 2005
MB&B586 Seminar in Molecular Biology
This course includes the presentation and
discussion of recent findings in the field of molecular biology.
Credit: 0.25
Spring 2006
MB&B587 Seminar in Biological Chemistry
Identical with: CHEM587
Credit: 0.25
Fall 2005
MB&B588 Seminar in Biological Chemistry
Identical with: CHEM588
Credit: 0.25
Spring 2006
MB&B589 Advanced Research for BA/MA Students
Intensive investigation of special research
problems leading to a BA/MA thesis.
Credit: 1.50
MB&B591/592 Advanced Research Graduate
Credit: 1.00
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