BIOLOGY
Professors:
Janice Naegele, Chair; Barry Chernoff, Earth and
Environmental Sciences; Frederick Cohan; J. James Donady; Laura B.
Grabel; Michael Weir; Jason S. Wolfe
Associate Professors: Ann
Campbell Burke, Stephen Devoto, John Kirn, Sonia Sultan
Assistant Professor: Gloster
B. Aaron Jr., Michael S. Singer
GRADUATE PROGRAM
The Biology Department offers graduate work
leading primarily to the degree of doctor of philosophy. A master of arts degree
may be awarded under certain conditions.
Possible fields of concentration for Ph.D.
candidates include cell biology, developmental biology and genetics;
neuroscience and behavior; ecology, evolution and environmental biology; and
informatics and modeling. Descriptions of research programs in the department
can be found at http://www.wesleyan.edu/bio/.
Although the primary emphasis is on an
intensive research experience culminating in a thesis, the student will also be
expected to acquire, through an individual program of courses, seminars, and
readings, a broad knowledge of related biological fields. The low
student-faculty ratio in the department ensures close contact between faculty
and students. Research seminars are offered by students, faculty, and invited
outside speakers; additional courses and lectures of interest offered by other
departments are also available to biology students. All graduate students have
the opportunity for some undergraduate teaching in favorable circumstances and
with faculty supervision. Teaching assistants are involved primarily in
preparing materials for, and assisting in, laboratory courses, tutoring, and
evaluating student work. In the later years of the PhD program, a limited amount
of classroom teaching may be offered to those qualified. Students are encouraged
to spend a summer at the Marine Biological Lab in Woods Hole, Cold Spring
Harbor labs, or another institution offering specialized graduate courses.
Funds are available to support this work.
REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY
The PhD is a research
degree, demanding rigorous scholarly training and creativity; the result is an
original contribution to the candidate's field.
Courses:
A program of study for the first two years will be worked out by the student and
a faculty committee at the time of matriculation. This program will take into
account the student's proposed field of interest and prior background in biology
and related sciences. No specific courses are required but rather, a
subject-matter requirement. Before taking the qualifying examination, all
students must have at least one course above the introductory level (at Wesleyan
or elsewhere) emphasizing a modern approach to each of the following areas:
genetics; evolution, population biology; physiology, neurobiology, behavior;
cell biology, developmental biology; biochemistry, molecular biology. The
adequacy of the courses that have been taken at other institutions will be
evaluated by the faculty committee through its meeting with the student.
Students with focus in bioinformatics may substitute upper-level courses (200,
300, or 500) in two areas of computer science. All graduate students must take a
minimum of two advanced-level (300 or 500) courses within the
Biology Department. At least one of these should be taken during the student's
first year. Departmental and interdepartmental seminars will be included in the
program, and additional individual reading in particular areas may also be
required.
Research.
First-year students are exposed to
research in the department through two one-semester lab rotations or research
practica. Toward the end of each semester of the first year, each student will
meet with an evaluation committee of the faculty to review progress and to
discuss any modification of the proposed schedule. Students do research in
fields of specialization described above. In some fields such as informatics
and modeling, students can be jointly mentored by a faculty member in Biology
and a faculty member in a related field such as Computer Science.
Preliminary qualifying
examination. A qualifying
examination will be taken before the end of the second year. The examination is
designed to test the student's knowledge of biology and ability to think
critically. It includes a written research proposal, followed by an oral
examination to discuss the proposal and evaluate the student's breadth in
biology. The examination will be administered by four faculty members of the
department (or associated departments), chosen by the student and his or her
research advisor. The examining committee will include the research advisor and
one member who does research in a field clearly outside the student's area of
special interest. All students should be familiar with the use and capabilities
of the University's computer facilities. Knowledge of a computer programming
language or a foreign language will be recommended to those students for whom it
is likely to be of benefit.
Dissertation.
The most important requirement is a
PhD thesis, an original contribution to biology, that merits publication. The
candidate will receive advice and guidance from the thesis director but must
demonstrate both scientific competence and originality. Normally, the candidate
will choose a thesis topic, after consultation with appropriate faculty, during
the second year of graduate work. A thesis committee of three members, chosen by
the student and thesis advisor, will meet with the student and advisor at least
twice a year to review progress. This committee determines when sufficient
experimental work has been completed and must approve the final written
document.
Teaching:
A minimum of three semesters as a teaching assistant is required.
The department offers courses at the 200 and
300-level that may be appropriate for our graduate students, summarized as
follows. Complete descriptions can be found at http://www.wesleyan.edu/course.
BIOL210 Genomics: Modern Genetics, Bioinformatics, and the
Human Genome Project
BIOL212 Principles and Mechanisms of Cell Biology
BIOL213 Behavioral Neurobiology
BIOL214 Evolution
BIOL218 Developmental Biology
BIOL220 Conservation Biology
BIOL221 Human Genetics
BIOL222 Issues in the Health Sciences
BIOL223 Integration of Life Science Learning and Clinical
Experience
BIOL224 Hormones, Brain and Behavior
BIOL227 Microscopic Cell Anatomy and Physiology
BIOL231 Microbiology
BIOL232 Immunology
BIOL235 Comparative Vertebrate Anatomy
BIOL245 Cellular Neurophysiology
BIOL247 Laboratory in Neurophysiology
BIOL228 Health and Disease in Human Populations - An
Introduction to Epidemiology
BIOL249 Neural Systems and Behavior
BIOL250 Laboratory in Cellular and Molecular Neurobiology
BIOL254 Comparative Animal Behavior
BIOL261 Ecology
BIOL265 Bioinformatics Programming
BIOL268 Contemporary Environmental Issues
BIOL290 Plant Form and Diversity
BIOL306 Tropical Ecology and the Environment
BIOL312 Conservation of Aquatic Ecosystems
BIOL314 Topics in the Biology of Aging
BIOL321 The Cell in
Development
BIOL323 Experimental Embryology
BIOL330 Cell Biology of Aging and Disease
BIOL344 Biological Structure
BIOL345 Developmental Neurobiology
BIOL348 Animal Orientation and Migration
BIOL351 Approaches to Understanding the Neurobiology of
Learning and Memory
BIOL369
Pattern and Process in Macroevolution
BIOL500 Graduate Pedagogy
The elements of good teaching
will be discussed and demonstrated through lectures, practice teaching sessions,
and discussions of problems encountered in the actual teaching environment. The
staff consists of faculty and experienced graduate students. An integral part
of the course is a required one-day workshop BEFORE the first day of formal
classes.
Credit: 0.50
Fall 2005
BIOL501/502 Individual
Tutorial, Graduates
A sequence of laboratory
research projects in different fields; the type and duration are decided upon an
individual basis. For first-year graduate students only.
Credit: 1.00
BIOL505/506 Cell and
Developmental Journal Club I
Presentation and active
discussion of a series of current research articles in the field of cell and
developmental biology from journals.
Credit: 0.25
Fall (BIOL 505) and Spring (BIOL
506)
BIOL507/508 Evolution Journal
Club I
Presentation and active
discussion of current research articles in evolutionary biology. Each semester
the class will choose one theme within evolutionary biology to be the focus of
discussion. Themes from recent semesters have included: genome-based evolution
studies, co-evolution, speciation, phylogenetic approaches for investigating
natural selection, the role of competition in evolution, the evolution of
host-parasite relationships, and the evolution of behavior. Articles for
discussion generally come from the journals.
Credit: 0.25
BIOL509/510 Neuroscience
Journal Club I
Presentation and discussion of
current research articles in the field of neuroscience from journals including
Neuron, J. Neuroscience, Science, Nature, and Brain, Behavior and Evolution.
Credit: 0.25
Fall (BIOL 509) and Spring (BIOL
510)
BIOL511/512 Group Tutorial,
Graduate
Credit: 1.00
BIOL514 Topics in the Biology
of Aging
This is a seminar course which
focuses in depth on a specific topic of emerging research interest in an
important area of the biology of aging. In addition to faculty lectures,
students will be expected to maintain a schedule of reading in the primary
scientific literature, give oral presentations in class, and participate
actively in class discussions. Graduate students will be expected to be
particularly rigorous in their analytical approach to experimental design.
Credit: 1.00
BIOL516 Plant-Animal
Interactions
This course will explore the
ecology and evolution of interactions between plants and animals, including
mutualism (e.g. pollination, frugivory) and antagonism (e.g. herbivory,
granivory), that are central to the functioning of ecosystems and the generation
of biodiversity. The format will be seminar-style, involving reading,
discussion, and student presentations of key papers on chosen topics.
Credit: 1.00
Spring 2006
BIOL518 Nature and Nurture:
The Interplay of Genes and Environment
In this advanced seminar, we
consider how genes and environment interact to shape the development and
behavior of organisms, including humans. After an initial series of lectures and
discussions on classic and current readings, the class will consist of in-depth
student presentations and discussion.
Credit: 1.00
Fall 2005
BIOL524 Neuropharmacology
The molecular mechanisms
underlying the adaptive (and sometimes maladaptive) nature of brain function are
beginning to be elucidated. This course is designed to provide the student with
an understanding of the major signaling pathways involved in normal brain
function and in neurological disorders. The course will initially introduce the
student to the major signaling pathways in the brain, followed by their
involvement in learning and memory, and neurological and psychiatric disease.
Topics will include: 1) cell biology of the neuron synaptic transmission,
neurotransmitters, 2) modulation of synaptic transmission, 3) tyrosine kinases,
4) G protein-coupled receptors serotonin, dopamine, acetylcholine, opiate
receptors, 5) neuronal plasticity gene induction, immediate early genes,
neurogenesis, 6) cell death and AIF pathways, 7) molecular mechanisms in
learning and memory integration of MAP kinase and CREB pathways, and 8)
molecular mechanisms of psychiatric diseases.
Credit: 1.00
BIOL527 Evolutionary and
Ecological Bioinformatics
Bioinformatic analysis of gene
sequences and gene expression patterns has added enormously to our understanding
of ecology and evolution. For example, through bioinformatic analysis of gene
sequences, we can now reconstruct the evolutionary history of physiology even
though no traces of physiology exist in the fossil record. We can determine the
adaptive history of one gene and all the gene's descendants. We can now
construct the evolutionary tree of all of life. Bioinformatics is particularly
promising for analysis of the ecology and biodiversity of microbial communities,
since well over 99% of microorganisms cannot be cultured--our only knowledge of
these organisms is through analysis of their gene sequences and gene expression
patterns. For example, even when we cannot culture most of a microbial
community, we can determine which metabolic pathways are of greatest
significance through analysis of community-level gene expression. All these
research programs are made accessible not only by breakthroughs in molecular
technology, but also by innovation in the design of computer algorithms. This
course, team-taught by an evolutionary biologist and a computer scientist, will
present how bioinformatics is revolutionizing evolutionary and ecological
investigation, and will present the design and construction of bioinformatic
computer algorithms underlying the revolution in biology.
Credit: 1.00
Fall 2005
BIOL533 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.
Identical with: MB&B533
Credit: 0.50
BIOL537 The Origins of
Bacterial Diversity
Wherever there is life, there
are bacteria. Free-living bacteria are found in every environment that supports
eukaryotes, and no animal or plant is known to be free of bacteria. There are
most likely a billion or more species of bacteria, each living in its unique
ecological niche. This course will explore the origins of bacterial
biodiversity: how bacteria evolve to form new species that inhabit new
ecological niches. We will focus on how the peculiarities of bacterial sex and
genetics facilitate bacterial speciation. Topics will include the
characteristics of bacterial sex, why barriers to genetic exchange are not
necessary for speciation in bacteria, the great potential for formation of new
bacterial species, the evolutionary role of genetic gifts from other species,
and the use of genomics to identify ecologically distinct populations of
bacteria.
Credit: 1.00
BIOL540 Issues in Development
and Evolution
This is an advanced course
exploring the relationship between embryonic development and morphological
evolution. The course will include a combination of lectures, discussion and
student presentations of papers chosen from the primary literature. Subjects
covered will include broad, fundamental issues such as the concept of homology;
developmental characters and phylogeny, as well as the evolutionary significance
of specific developmental phenomena such as animal segmentation, direct
development, and major morphological transitions in evolution.
Credit: 1.00
Spring 2006
BIOL543 Muscle and Nerve
Development
We will examine the structure
and function of muscle cells, the development of muscle cell identity, the
development of motor neurons, and the interactions between nerve and muscle that
lead to a functioning neuromuscular system. The course will focus primarily on
vertebrate model systems such as chick, mouse, and fish. We will also examine
human diseases, including muscular dystrophies and related neuromuscular
disorders.
Credit: 1.00
BIOL550 Bioinformatics and
Functional Genomics
The exciting new fields of
genomics and bioinformatics are bringing together the complementary disciplines
of biology and computer science. With the sequencing of the human genome and the
genomes of several model organisms, the door has opened to using new
computational and modeling approaches to understanding genome function in
organisms.
This
focused-inquiry course will interweave the discussion of biological and
informatic topics focusing on computational issues and tools used in the
interdisciplinary fields. Possible topics include the application of alignment
algorithms to the analysis of genomic sequences, cluster analysis of
micro-arrays of gene expression, and the prediction of RNA secondary structures
using dynamic programming methods.
Credit: 1.00
BIOL557 Advanced Research
Seminars in Biology
This course focuses on the
specific research projects of the individual graduate students in the Biology
Department, and it comprises student presentations and discussion including the
department faculty, graduate students and interested undergraduates. Background
readings for each session may include relevant papers from the literature. The
course offers a forum for presenting new results and exploring new ideas, as
well as for providing researchers with feedback and suggestions for solving
methodological problems. It also provides an opportunity for undergraduate
majors and new graduate students in the program to become familiar with the wide
range of biological research taking place in the Department.
Credit: 0.50 (Students sign up
in Fall only.)
Fall 2005 and Spring 2006
BIOL575 Topics in Neurobiology:
Cell Death in Development and Disease
This course consists of a weekly
meeting, which includes a lecture on a topic by the Instructor and a student-led
discussion. The major readings are current journal articles and reviews.
Students will prepare oral presentations on the assigned readings, lead
discussions and write a grant proposal on their topic. Prior to each meeting,
the presenters must meet with the Instructor to review and practice their
presentation. The course will include a selection of current studies that
clearly illustrate the biochemical and genetic causes of cell death and how it
relates to development or disease of the nervous system. Topics range across
model systems and different CNS regions. The relevance of basic research on
cell death to understanding and treating neurodegenerative diseases is also
discussed.
Credit: 1.00
BIOL580 Experimental Design
This specialized course for
graduate and undergraduate students provides an in-depth analysis of a current
research program in biology. The course will include background lectures,
student presentations of projects within the research program, as well as
analysis of recent publications describing possible future directions for
research.
Credit: 0.50
BIOL591/592 Advanced Research
Investigation of special
problems leading to a dissertation or thesis.
Credit: 1.00
NS&B501/502 Individuate
Tutorial, Graduate
Credit: 1.00
NS&B524 Neuropharmacology
Identical with: BIOL324
Credit: 1.00
NS&B543 Muscle and Nerve
Development
Identical with: BIOL543
Credit: 1.00
NS&B575 Topics in Neurobiology:
Cell Death in Development and Disease
Identical with: BIOL575
Credit: 1.00
NS&B591/592 Advanced Research,
Graduate
Credit: 1.00
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