Jun 16, 2024  
Rensselaer Catalog 2008-2009 
Rensselaer Catalog 2008-2009 [Archived Catalog]


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Head: Susan P. Gilbert

Accelerated Program Head: Michael H. Hanna

Graduate Admissions Coordinator: Jody Malm
Department Home Page: http://j2ee.rpi.edu/biology

For two decades, the science of biology has been undergoing revolutionary change. Many problems once handled only descriptively are now analyzed at the molecular level. With this trend expected to continue, Rensselaer has developed  undergraduate and graduate programs to train students for the biological challenges of the future including advances in healthcare and environmental sustainability and resource management.

All areas of biology require knowledge of chemistry, physics, and mathematics as well. The undergraduate biology curriculum, therefore, trains students in the fundamentals of the life sciences and the chemistry and physics of the life processes, providing the background necessary for professional training in research or medicine. Options are available to prepare students for careers in applied biology and in industry. Programs of study in biology may also be combined with specific options in biochemistry, biomedical engineering, bioinformatics, biophysics, biotechnology (genetic engineering), chemical engineering, computer science, management, mathematics, microbiology, and technical communications.

Research and Innovation Initiatives

Biochemistry and Biophysics
The study of fundamental problems in modern biochemistry and molecular biochemistry employ a variety of advanced techniques. Current work at the gene and protein levels is being applied in cell biology and physiology. For example, research in this area includes developing computer models of how the lens accommodates the human eye. Studies on the lens protein alpha crystallin include biochemical and biophysical characterization. Novel molecular genetics approaches are used to compare properties of alpha crystallin to members of the small heat shock protein family. Additional studies include investigation of how muscle is organized to power locomotion and how variation between muscle fiber types is generated. Current investigations of structure/function relations of myosin use molecular biology and genetic techniques. Recent research focuses include the application of nuclear magnetic resonance (NMR) spectroscopy to study important and interesting problems in neuroscience and aging, e.g. Alzheimer’s disease, the most common senile dementia. These studies focus on the important roles of membrane proteins in signaling and transport.

Bioinformatics and Molecular Biology
Research in bioinformatics and molecular biology includes both computational work and applications using molecular genetic approaches. In the computational sphere, design and application of database research and sequence alignment algorithms, molecular modeling, and simulation are used in studies ranging from structural characterization of biomedically relevant proteins to studies of basic protein folding mechanisms.

Protein folding mechanisms are studied using modeling and data mining from genomic and structural databases. Molecular genetic approaches are used to test the prediction of modeling studies, to design and produce probes, and to obtain sequence information for novel genes. Three laboratories are involved in engineering novel proteins or activities of existing proteins, using molecular gene manipulations.

Microbiology and Ecology
In this program, faculty and their students are conducting ecological, molecular, and genetic studies. Both basic and applied research projects are available, sometimes within the same laboratory. Ecological studies include freshwater ecology and biotransformation of organic compounds. Molecular studies include work on nitrogen fixing symbiotic bacteria and bacteria living in the environment using recombinant DNA technology, and overlap in some cases with genetic studies of prokaryotes and eukaryotes. Vibrio cholerae, the agent of the disease cholera, is indigenous in aquatic environments which serve as the reservoir for infection of humans. Studies are aimed at understanding the physiology and biochemistry that gives Vibrio cholerae the ability to propagate through the external environment. In addition, the Darrin Fresh Water Institute at Lake George is well-equipped for studies in microbial ecology. A semester of study at Lake George is offered as part of the curriculum.

Cellular, Developmental, and Molecular Biology
Research in these areas is a high priority in the Biology Department. The vast majority of labs in the department utilize molecular and/or genetic approaches in their studies. Several areas in cellular biology are prominently featured. The first focuses on the biochemical control of cytoskeletal organization, microtubule dynamics, cell polarity, and cell differentiation. The second is centered on microtubule interactions with motor proteins and the cell cortex in neural cells. The third is concerned with signal transduction mechanisms controlling cell-cell interactions during tumor cell migration. The fourth focuses on stem cell growth and regulation in the context of tissue engineering. Two undergraduate laboratory courses that teach basic research techniques in these areas is available, and students are encouraged to work in research labs upon completion of this course. A fifth research laboratory focuses on human neurobiology, particularly the molecular, genetic, and cellular mechanisms involved in normal brain development and diseased conditions such as Joubert Syndrome where a novel gene from patients with the disease has been mapped and cloned.

Model organisms are utilized to study developmental and cellular phenomena. Research using the nematode worm Caenorhabditis elegans as a model system is focused on the developmental functions of the conserved GTP-binding proteins, the septins. Septins are studied for their role in cytokinesis in fungi and animals, and are implicated in some cancers and neurodegenerative diseases. Research in one laboratory with the fruit fly Drosophila melanogaster focuses on a family of proteases, the matrix metalloproteinases (MMPs). In vitro these proteins cleave most extracellular matrix components and in vivo, increases in MMP expression correlate with some cancer and inflammatory diseases. Research in another laboratory utilizing Drosophilia includes studies exploiting their genetic properties and transgenic techniques to express a specific myosin, and moving up in scale to protein expression and function, muscle mechanics, and whole organism studies. Research utilizing zebra fish makes it possible to study the organization, regulation, and function of the neural circuits in the central nervous system that coordinate environmental responses such as the startle response.

Interdisciplinary Programs

See also Biochemistry/Biophysics, and Bioinformatics and Molecular Biology, under the Interdisciplinary Programs and Research section.

Accelerated Program

The Biology Department offers highly motivated students interested in the medical profession the opportunity to combine undergraduate and graduate study to reduce the number of years spent in academic study.

Undergraduate Programs

Undergraduate students may pursue either a baccalaureate program or an accelerated degree program. Both of these degree programs are explained on the next page.

Graduate Programs

The biology research laboratories at Rensselaer are equipped for graduate study and projects in Biochemistry & Biophysics, Bioinformatics & Computational Biology, Biotechnology, Cell Biology & Cell Signaling, Microbial Ecology, Geomicrobiology, & Environmental Biology, Molecular Genetics & Developmental Biology, and Neurobiology & Behavior. In addition, cooperative programs with other organizations provide a wider range of research possibilities. Rensselaer’s Darrin Fresh Water Institute at Lake George offers a program on lake ecosystem analysis involving field, laboratory, and computer analysis of biological, chemical, and physical data. An active program in biochemistry and biophysics is jointly sponsored with the Chemistry, Physics, Mathematics, and Chemical Engineering Departments. Students must complete a core curriculum that includes courses in general biochemistry and molecular biology and pass a qualifying exam. During the first year students must complete three laboratory rotations with different faculty as part of their research training. Qualified students may take a candidacy examination in their special area of interest and proceed to the Ph.D. under the guidance of the candidacy committee. The detailed curriculum is tailored to the student’s background and special interests.

Master’s Programs

Thirty credit hours of course work are necessary to complete the M.S. program. A minimum of six credits and a maximum of nine must be in research. Of the remaining credits, 15 must be in graduate-level courses. A thesis based on an original research project is required.

Doctoral Programs

Candidates for the Ph.D. must satisfy the requirements of the graduate evaluation committee (GEC), pass the qualifying exam, and pass a candidacy exam. The latter consists of a written and an oral portion, and should usually be taken during the second year of full-time study. A degree candidate also must submit a dissertation based on an original research project. The GEC requires a high level of performance in selected courses and research, and reports its findings each year of full-time study. Additionally, all doctoral candidates are required to participate in teaching for one academic year under the supervision of a faculty member. The student thus gains experience teaching should he or she select an academic career. Sixty credit hours past the M.S. degree are required.

Minor Programs

The Biology Department offers a minor in biology.  Biology majors may elect to complete minors in biochemistry/biophysics or astrobiology.  See the section on biochemistry and biophysics for requirements for the biochemistry/biophysics minor.  Requirements for the biology and astrobiology  minors are given below.

Course Descriptions

Courses directly related to all Biology curricula are described in the Course Description section of this catalog under the department code BIOL.

Faculty * 


Boylen, C.W.—Ph.D. (University of Wisconsin); microbial ecology, physiological effects of starvation on microorganisms.

Diwan, J.J.
—Ph.D. (University of Illinois); cell physiology, bioenergetics.

Dordick, J.—Ph.D. (Massachusetts Institute of Technology); biochemical engineering, enzyme technology, bioseparations.

Garcia, A.E. —Ph.D. (Cornell University); mathematical and computational analysis in cellular and molecular biology.

Gilbert, S.P. —Ph.D. (Dartmouth College; structure and mechanisms of microtubule-based molecular motors involved in cell motility and cytoskeletal dynamics.

Koretz, J.F.—Ph.D. (University of Chicago); structural biophysics of protein aggregation, computer modeling.

Lindhardt, R.—Ph.D. (John Hopkins University); medicinal chemistry and biocatalysis, carbohydrate chemistry.

Makhatadze, G. —Ph.D. (Moscow Physico-Technical Institute) experimental and computational design of thermostable proteins, thermodynamics of protein-ligand interactions.

McDaniel, C.N.—Ph.D. (Wesleyan University); plant development and cell culture.

Nierzwicki-Bauer, S.A.
—Ph.D. (University of New Hampshire); plant molecular biology, subsurface microbiology.

Palazzo, R.E.—Ph.D. (Wayne State University); cellular organization, cell replication, cell motility, development and cancer.

Roy, H.
—Ph.D. (The Johns Hopkins University); plant molecular biology and biochemistry.

Zuker, M.—Ph.D. (Massachusetts Institute of Technology); algorimths for predicting RNA and DNA secondary structure.

Research Professors

Bedard, D.—Ph.D. (University of Chicago); environmental microbiology and ecology, microbial molecular biodegradation of halogenated aromatics.

Lister, B.—Ph.D. (Princeton University); ecology, undergraduate education.

Associate Professors

Bystroff, C.—Ph.D. (University of California, San Diego); genomics, protein structural prediction.

Hanna, M.H.—Ph.D. (University of Illinois); directed evolution of proteins, scientific teaching.

Plopper, G.—Ph.D. (Harvard University); signal transduction in tumor cell biology and tissue engineering.

Assistant Professors

Barquera, B.—Ph.D. (National Autonomous University of Mexico); bioenergetics of Vibrio cholerae.

Ferland, R.I. —Ph.D. (University of Rochester); Joubert Syndrome, learning and memory, genetics, neuroscience.

Finger, F.—Ph.D. (Yale University); analysis of septin function in C. elegans development.

Ligon, L.A. —Ph.D. (University of Virginia); neurobiology, cytoskeleton and motor proteins, microtubule/cortex interaction.


Page-McCaw, A.—Ph.D. (Massachusetts Institute of Technology); genetic and molecular analysis of matrix metalloproteinases during development in Drosophila melanogaster.

Page-McCaw, P.—Ph.D. (Massachusetts Institute of Technology); genetic analysis of learning and memory in the zebrafish, Danio rerio.

Swank, Douglas—Ph.D. (University of Pennsylvania); structure/function relations of myosin.

Wang, Chunyu—Ph.D. (Cornell University): NMR spectroscopy,  neuroscience and aging, Alzheimer’s disease.

Professors Emeritus

Ehrlich, H.L.—Ph.D. (University of Wisconsin); microbial ecology, biotransformation and biodegradation of natural polymers and pesticides, biotechnology.

Parsons, R.H.—Ph.D. (Oregon State University); cellular physiology, epithelial transport.

Pfau, C.J.—Ph.D. (Indiana University); molecular biology of animal viruses, antiviral drugs.

Associate Professor Emeritus

Clersceri, L.S.—Ph.D. (University of Wisconsin); microbial ecology, biotransformation and biodgradation of natural polymers and pesticides, biotechnology.

Research Assistant Professors


McCallum, S.A.—Ph.D. (University of Virginia); MMR, structure determination.

Morgan, J.—Ph.D. (California Institute of Technology); energy transduction. 

Paluh, J.L.—Ph.D. (Stanford University); cell cycle and cytoskeleton, stem cell biology.

Adjunct Faculty


Belfort, Marlene—Ph.D. (University of California at Irvine); developmental genetics and bioinformatics, introns.



* Departmental faculty listings are accurate as of the date generated for inclusion in this catalog. For the most up-to-date listing of faculty positions, including end-of-year promotions, please refer to the Faculty Roster section of this catalog, which is current as of the May 2008 Board of Trustees meeting.

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