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Detailed Information

Programs of Study

It is an exciting time to be in Rensselaer’s Department of Biology. There is a shift in emphasis toward interdisciplinary research, with new initiatives directed toward biotechnology, environmental sciences, integrative systems biology, nanotechnology, and stem cell and tissue engineering and regeneration. The Department is growing, with a number of new faculty members and an aggressive recruitment plan during the next five years. Faculty members and students engage in cutting-edge research in state-of-the-art laboratories and facilities, including the brand new $100-million Center for Biotechnology and Interdisciplinary Studies with core facilities and instrumentation for cellular, biochemical, and biophysical approaches to life science research. With excellent leadership, an outstanding faculty, dedicated staff members, bright students eager to explore, and modern facilities, the Department is at the forefront of groundbreaking research efforts in this vitally important field.

Rensselaer’s Department of Biology offers both Ph.D. and M.S. degree programs. Currently, there is a Ph.D. program in biology and another new Ph.D. program in biochemistry and biophysics. The M.S. degree programs require 30 credit hours beyond the bachelor’s degree, and the Ph.D. requires 72 credit hours beyond the bachelor’s degree.

Research Facilities

Research is supported by state-of-the-art facilities and equipment, including the Rensselaer Libraries, whose electronic information system provides access to collections, databases, and the Internet from campus and remote terminals; the Rensselaer Computing System, which permeates the campus with a coherent array of more than 7,000 nodes of distributed laptops, desktops, advanced workstations, and servers; a shared toolkit of applications for interactive learning and research and high-speed Internet connectivity; one of the country’s largest academically based, class 100 clean-room facilities; high-performance campuswide computing facilities that allow for serial or parallel computation; and five core laboratories for molecular biology, proteomics, bioimaging, and tissue engineering.

Rensselaer’s research capabilities have been enhanced with the addition of the Computational Center for Nanotechnology Innovations (CCNI). The result of a $100-million collaboration with IBM and New York State, the CCNI is the world’s most powerful university-based supercomputing center and a top 10 supercomputing center of any kind in the world. The CCNI is made up of massively parallel Blue Gene supercomputers, POWER-based Linux clusters, and Opteron-based clusters, providing more than 100 teraflops of computational muscle and approximately a petabyte of shared online storage.

The Department maintains extensive research and instructional laboratories that house special and unique equipment developed for specific studies as well as extensive analytical and optical instrumentation, minicomputers, and microcomputers. The Biochemistry and Molecular Biology Teaching Laboratory includes a walk-in cold room and is equipped with facilities for modern molecular biology, gene expression, DNA sequencing, protein purification, plate reader–based screening assays, and state-of-the-art separation technology. The Bioinformatics Laboratory is equipped with twenty Silicon Graphics workstations, distance delivery apparatus, and audiovisual equipment. It is connected via a high-speed network to local Challenger and Origin 2000 servers and provides local access to high-speed RAID drives for searches of the most generally important biological sequence and structure databases. Available software includes some of the most powerful and generally used searching, sequence alignment, and analysis software, which are accessible through GCG seqlab and other formats, as well as molecular visualization, modeling, and dynamics packages from Molecular Simulations. Available software includes Vector NTI and Tripos packages.

Several research areas involve participation and cooperation with other departments, including the Departments of Biomedical Engineering, Chemistry and Chemical Biology, Earth and Environmental Science, and Economics, and a number of Rensselaer’s major interdisciplinary and independent collaborative facilities, including the Center for Biotechnology and Interdisciplinary Studies, Darrin Fresh Water Institute, Wadsworth Center, Ordway Research Institute, and Genomics Institute.

Rensselaer’s Center for Biotechnology and Interdisciplinary Studies provides a platform for collaboration among many diverse academic and research disciplines to enhance discovery and encourage innovation. Key areas of emphasis include drug discovery and development, regenerative medicine, and functional materials and devices, all of which build upon the fundamental disciplines of systems biology, biocatalysis, computational biology, and tissue engineering. The core research facilities within the center contain laboratories for molecular biology, analytical biochemistry, microbiology, live-cell imaging, single-molecule detection, optical trapping, atomic force microscopy, tissue and cell culture, proteomics, and scientific computing and visualization. The center contains an 800-MHz and 600-MHz nuclear magnetic resonance (NMR) spectrometers and the computing and visualization infrastructure needed to model molecular structure at the atomic level.

The Darrin Fresh Water Institute (DFWI) conducts research that increases public awareness of environmental issues and contributes to answers for tough questions concerning the protection of land, water, and air. The DFWI is well known for its all-encompassing study of freshwater systems and ecological processes. This institute provides Rensselaer students and faculty members as well as visiting scientists the opportunity to study a number of ecosystems and to conduct research on important environmental problems. There are facilities on the RPI campus, at the lakeside Adirondack field station in Bolton Landing, and at a remote monitoring station.

Wadsworth Center is the most comprehensive state health laboratory in the country. Research is conducted through four divisions: environmental disease prevention, genetic disorders, infectious disease, and molecular medicine. Ordway Research Institute, Inc., is a not-for-profit, freestanding corporation with specific research themes–cancer, genomics/pharmacogenetics, emerging infections and host defense, and neural and vascular biology–and a mission to translate basic science observations into therapeutics. Core research facilities are an infrastructure of laboratories and equipment for flow cytometry, hollow fiber research, microscopy, pharmacokinetics and pharmacodynamics modeling, signal transduction, and target and drug discovery. The Genomics Institute, an Ordway Research Institute center of research, is a collaboration between the Wadsworth Center and Albany Medical College. This institute targets research for better health by the discovery of genetic approaches for the understanding of mammalian development and disease in order to design new treatment answers.

Financial Aid

Financial aid is available in the forms of teaching and research assistantships and fellowships, which include tuition scholarships and stipends. Graduate teaching and research assistantships carry a minimum stipend of $22,000 and a full-tuition scholarship. All fellowship awards are calendar-year awards for full-time graduate students.

Cost of Study

Full-time graduate tuition for the 2008–09 academic year is $36,950. Other costs (estimated living expenses, insurance, etc.) are projected to be about $13,680. Therefore, the cost of attendance for full-time graduate study is approximately $50,630. Part-time study and cohort programs are priced differently. Students should contact Rensselaer for specific cost information related to the program they wish to study.

Living and Housing Costs

Graduate students at Rensselaer may choose from a variety of housing options. On campus, students can select one of the many residence halls and immerse themselves in campus life or choose from a select number of apartments designed for graduate students only. There are abundant, affordable options off campus as well, many within easy walking distance.

Student Group

Of the 1,176 graduate students, 29 percent are women, and 92 percent are full-time with 75 percent of fulltime graduate students studying at the doctoral level.

Student Outcomes

Rensselaer’s graduate students are hired in a variety of industries and sectors of the economy and by private and public organizations, the government, and institutions of higher education. Their starting salaries average $74,807 for master’s degree recipients and $82,750 for Ph.D. recipients.

Location

Located just 10 miles northeast of Albany, New York State’s capital city, Rensselaer’s historic 275-acre campus sits on a hill overlooking the city of Troy, New York, and the Hudson River. The area offers a relaxed lifestyle with many cultural and recreational opportunities, with easy access to both the high-energy metropolitan centers of the Northeast–such as Boston, New York City, and Montreal, Canada–and the quiet beauty of the neighboring Adirondack Mountains.

The Institute

Recognized as a leader in interactive learning and interdisciplinary research, Rensselaer continues a tradition of excellence and technological innovation dating back to 1824. Rensselaer has five schools–Architecture, Engineering, Management, Science, and Humanities and Social Sciences–that offer more than 100 graduate programs in over forty-eight disciplines that attract top students, researchers, and professors. The discovery of new scientific concepts and technologies, especially in emerging interdisciplinary fields, is the lifeblood of Rensselaer’s culture and a core goal for the faculty, staff, and students. Fueled by significant support from government, industry, and private donors, Rensselaer provides a world-class education in an environment tailored to the individual.

Applying

The admission deadline for the fall semester is January 1. Basic admission requirements are the submission of a completed application form (available online), the required application fee ($75), a statement of background and goals, official transcripts, official scores on the GRE General Test, TOEFL or IELTS scores (if applicable), and two recommendations. It is recommended that applicants also submit scores for the GRE Subject Test in Biology.

The Faculty and Their Research

• Blanca Barquera, Assistant Professor; Ph.D., National Autonomous University of Mexico. Na+ bioenergetics in bacteria from global gene expression; bacterial physiology; mechanistic biochemistry of energy-transducing proteins; pathogen adaptation for host infection.
• Donna L. Bedard, Research Professor; Ph.D., Chicago. Molecular environmental microbiology; environmental biotechnology.
• Chris Bjornsson, Director, Microscopy and Imaging Core Facility Center for Biotechnology and Interdisciplinary Studies; Ph.D., Manitoba. Characterizing and minimizing the brain’s reactive responses to neural prosthetic device insertion.
• Charles Boylen, Professor and Associate Director of Darrin Fresh Water Institute; Ph.D., Wisconsin. Ecosystem function and alteration by human interaction with the environment.
• Christopher Bystroff, Associate Professor; Ph.D., California, San Diego. Bioinformatics, protein folding, and design; computational biology.
• Lenore S. Clesceri, Associate Professor Emeritus; Ph.D., Wisconsin. Natural polymer degradation and transformations of synthetic organics.
• Joyce J. Diwan, Professor; Ph.D., Illinois at Chicago. Development of an integrated package of computer-based learning tools for teaching biochemistry of metabolism in a studio format.
• Jonathan Dordick, Howard P. Iserman Professor; Ph.D., MIT. Protein-material interactions; biocatalysis in drug discovery and human toxicology, bioengineering, and nanobiotechnology.
• Henry L. Ehrlich, Professor Emeritus; Ph.D., Wisconsin–Madison. Bacterial oxidation of Mn(II) and reduction of Mn(IV), in particular as it applies to the development and fate of marine ferromanganese concretions and the possible bacterial origin of Mn(IV) oxide in calcareous deposits along the western shore of the Dead Sea.
• Russell J. Ferland, Assistant Professor; Ph.D., Rochester. Basic mechanisms of neurodevelopment and neurological disease.
• Fern Finger, Assistant Professor; Ph.D., Yale. Septins; Caenorhabditis elegans septins, emphasizing functions in nervous system and organ development and crosstalk between the septin and actin cytoskeletons.
• Angel E. Garcia, Sr. Constellation Chaired Professor in Biocomputation and Bioinformatics; Ph.D., Cornell. Theoretical and computational aspects of the structure, dynamics, and stability of biological molecules.
• Susan P. Gilbert, Professor and Department Head; Ph.D., Dartmouth. Structure and mechanisms of microtubule-based molecular motors involved in cell motility and cytoskeletal dynamics.
• Michael H. Hanna, Associate Professor; Ph.D., Illinois at Urbana-Champaign. Microbiology, molecular biology: directed gene/protein evolution.
• Jane F. Koretz, Professor; Ph.D., Chicago. Modeling the human visual process.
• Lee Ligon, Assistant Professor; Ph.D., Virginia. Cytoskeleton organization and dynamics in development and in neuronal, cancer, and stem cells using live-cell imaging and biochemistry.
• Robert J. Linhardt, Ann and John H. Broadbent Jr. ’59 Sr. Constellation Professor of Biocatalysis and Metabolic Engineering and Acting Director of the Center for Biotechnology and Interdisciplinary Studies; Ph.D., Johns Hopkins. Glycobiology; glycomics; chemoenzymatic synthesis; microanalysis and high-throughput screening.
• Bradford Lister, Research Professor and Director, Anderson Center for Innovation in Undergraduate Education; Ph.D., Princeton. Ecology; undergraduate education.
• George I. Makhatadze, Chaired Constellation Professor in Biocomputation and Bioinformatics; Ph.D., Institute of Protein Research. Protein engineering and design; experimental and computational studies of biomacromolecular interactions.
• Scott McCallum, Research Assistant Professor; Ph.D., Virginia. Identifying macromolecular interactions that have key roles in major diseases, including cancer, and that can be utilized in the design of drug and protein therapeutics.
• Joel Morgan, Research Assistant Professor; Ph.D., Caltech. Molecular mechanism of energy transduction in biological systems.
• Sandra A. Nierzwicki-Bauer, Professor and Director, Darrin Fresh Water Institute; Ph.D., New Hampshire. Microbiology of freshwater systems; invasive species; acid-impacted Adirondack lakes.
• Addrea Page-McCaw, Assistant Professor; Ph.D., MIT. Protease-mediated cell-cell signaling and tissue remodeling in Drosophila.
• Patrick Page-McCaw, Assistant Professor; Ph.D., MIT. Zebrafish as a model system for sensory-motor integration and brain development.
• Robert E. Palazzo, Professor and Provost; Ph.D., Wayne State. Cell biology and biochemistry of centrosomes.
• Janet L. Paluh, Research Assistant Professor; Ph.D., Stanford, Cell cycle and the cytoskeleton; G2/M/G1 and asymmetry mechanisms in yeast; microenvironment of human embryonic stem cells.
• Mark D. Platt, Director, Proteomics Core Facility, Center for Biotechnology and Interdisciplinary Studies; Ph.D., Virginia. Development of novel proteomic approaches; applications of biological mass spectrometry.
• George E. Plopper, Associate Professor; Ph.D., Harvard. Development; cell differentiation; tissue formation; tissue engineering; wound healing; tumorigenesis and metastasis; cell-extracellular matrix interactions; integrin-mediated signaling; signal transduction; cell polarity.
• Harry Roy, Professor; Ph.D., Johns Hopkins. Development of muscle cells; sea urchin rRNA synthesis; biochemistry of ATP synthesis in chloroplasts and structure and biogenesis of the chloroplast enzyme ribulose bisphosphate carboxylase.
• Susan Sharfstein, Assistant Professor; Ph.D., Berkeley. Mammalian cell biotechnology and bioprocessing focused on recombinant biopharmaceutical production.
• Douglas M. Swank, Assistant Professor; Ph.D., Pennsylvania. Muscle physiology and motor protein biophysics.
• Chunyu Wang, Assistant Professor; Ph.D., Cornell; M.D., Peking Union Medical College. Solution NMR spectroscopy of protein structure and dynamics in Alzheimer’s disease with special emphasis on amyloid beta-peptide and membrane proteins, mechanisms, and applications of protein splicing.
• Michael Zuker, Professor; Ph.D., MIT. Development of algorithms to predict RNA and DNA secondary structure by free energy minimization using empirically derived thermodynamic parameters.
• Research Groups
• Biochemistry and Biophysics: Several biology faculty members, all of whom are members of the interdepartmental Center for Biophysics, have research projects in the areas of biochemistry and biophysics. Many of these projects have goals that are both fundamental and applied. One project is examining changes in patterns of gene expression associated with adaptation to different conditions by Vibrio cholera, the organism responsible for the disease cholera. Aging of the human crystalline lens is being studied, including loss of the ability to focus (accommodate). Experiments at a molecular level are characterizing alpha-crystallin, a small heat shock protein that is the major protein of the mammalian lens. The role of chaperones in assembly of the photosynthetic enzyme Ribulose Bisphosphate Carboxylase/Oxygenase (RuBisCO) is also being examined. Studies are being pursued to understand the mechanochemistry of kinesin, myosin, and dynein molecular motors that generate movements and remodel the cytoskeleton. The bioinformatics studies of nitric oxide synthase (NOS) are being combined with spectroscopic studies (e.g., electron paramagnetic resonance and circular dichroism), thermodynamic and kinetics experiments, and site-directed mutagenesis to elucidate mechanisms of catalysis and regulation of this enzyme. Research in one laboratory has goals relating to enzyme technology. Projects include the study of enzymatic catalysis under extreme conditions and the enzymatic synthesis of polymeric materials. Biochemical research in one laboratory focuses on heparan sulfate proteoglycans. Kinetics and thermodynamics of interactions of carbohydrates with proteins are being studied using biophysical approaches such as calorimetry, spectroscopy, X-ray crystallography, and molecular modeling. The internal structure of mitochondria is being characterized using electron tomography and computer modeling. The structure of the outer mitochondrial membrane channel VDAC is also being determined using cryoelectron microscopy with 2-D crystals. Faculty: Barquera, Bystroff, Dordick, Gilbert, Koretz, Ligon, Linhardt, Makhatadze, McCallum, Morgan, Nierzwicki-Bauer, Swank, Wang.
• Bioinformatics and Computational Biology: Statistical models and molecular simulations are being applied to predict protein structures and protein folding pathways. A hidden Markov model for sequence-structure correlations has been developed, along with methods for predicting inter-residue contacts and helix propensities of short peptides. Collaborative research involves protein structure predictions based on gene sequence alignments. Results of these studies, along with experiments utilizing approaches of biochemistry and molecular genetics, have advanced understanding of the structural basis of the function and regulation of isoforms of the enzyme nitric oxide synthase (NOS). Algorithms to predict RNA and DNA secondary structure are being developed by free energy minimization, using empirically derived thermodynamic parameters. Computed partition functions, for systems containing two molecules that can fold as well as hybridize with each other, allow prediction of melting curves. The Bioinformatics Center, a joint initiative of Rensselaer and the Wadsworth Center of the New York State Department of Health, provides additional opportunities for collaborative research. Faculty: Bystroff, Garcia, Makhatadze, Platt, Wang, Zuker.
• Biotechnology: Several projects being carried out by biology faculty members, alone or in collaboration with members of other departments, are aimed at developing new technology or useful products. Many patents and patent applications have resulted from this research. New methods for site-directed mutagenesis and combinatorial chimeragenesis have been developed. These are being used in collaborative research aimed at directed evolution of small heat shock proteins. In another project, a database of naturally occurring plasmids has been developed. Biocatalysts with unique activities and selectivities are being generated, and biomolecules are being incorporated into nanostructures and composites. Other research is using combinatorial and high-throughput biocatalysis for drug discovery. Biochips containing heparan sulfates are being prepared for screening of the mouse glycome. Carbohydrates equivalent to tumor antigens are being synthesized for potential use in cancer vaccines. Faculty: Barquera, Boylen, Bystroff, Dordick, Gilbert, Ligon, Nierzwicki-Bauer, Linhardt, A. Page McCaw, Platt, Plopper, Swank, Wang.
• Cell Biology and Cell Signaling: The centrosome, the organelle that directs formation and organization of the cellular microtubule network, is being characterized using isolated and reconstituted centrosomes. Some experiments are aimed at elucidating genetic and biochemical mechanisms that control replication of the centrosome in relation to cell-cycle events. How intracellular signaling pathways are modulated in response to interaction of cells with the extracellular matrix is being examined in two biology laboratories. Differentiation relating to interaction of mesenchymal stem cells with extracellular matrix proteins is being studied, along with regulation of migration of breast cancer cells across lung endothelium. Another project is defining the role of plasma membrane integrins in mediating cell responses to changes in the extracellular microenvironment. Experiments are aimed at elucidating roles of matrix constituents in regulating tissue maintenance and repair, as well as tumor progression. Faculty: Ferland, Finger, Gilbert, Ligon, A. Page-McCaw, Palazzo, Paluh, Plopper, Swank.
• Educational Innovation: Faculty members are also engaged in developing computer-based courseware and formats for studio teaching. Many of these educational innovations have been evaluated for student perceptions and learning outcomes. Papers describing these innovations, and/or the learning materials themselves, have been successfully subjected to peer review. A resource of expertise is the Anderson Center for Innovation in Undergraduate Education, directed by a biology faculty member. Web-based materials for the studio-format teaching of courses in biochemistry, human physiology, genetics, and ecology have been developed and tested. Undergraduate laboratory courses have also been revised to incorporate independent inquiry-based learning, including the design and execution of experiments, preparation of the data for poster presentation, and publication. Faculty: All.
• Microbial Ecology, Geomicrobiology, and Environmental Biology: Members of the Biology Department work in areas of microbial ecology, geomicrobiology, and environmental biology. In addition, other faculty members use microbes as model systems or for gene expression. The Darrin Fresh Water Institute, administered by a member of the Department, has modern facilities for research relating to aquatic biology and the environment. An interdepartmental Environmental Science degree program has fostered collaborative interactions, particularly with members of the Earth and Environmental Science and Economics Departments at Rensselaer. Tools of molecular biology are being used to identify bacteria of ancient lineage in subsurface sediments, to characterize aquatic phytoplankton communities, and to detect the presence of zebra mussel veligers in water samples. Other studies focus on the identification and molecular genetics of cyanobacteria that grow in symbiotic association with the aquatic fern Azolla. One laboratory is identifying and characterizing microorganisms in aquatic sediments that have enzymatic capabilities for oxidizing or dechlorinating PCBs. A goal is to use such organisms or enzymes derived from them to degrade contaminant PCBs. Another project is focusing on the molecular ecology of microbial communities in hot springs. Physiological responses of microorganisms and aquatic angiosperms to environmental stress, such as that arising from acid rain, are being studied. Ecological alteration of regional lakes by introduction of exotic invasive plant species is also being examined. The research addresses broad issues of the environment, such as biodiversity and challenges to sustainability. Faculty: Barquera, Bedard, Boylen, Ehrlich, Lister, Nierzwicki-Bauer.
• Molecular Genetics and Developmental Biology: Research relating to molecular genetics and developmental biology takes advantage of several model organisms, including the fruit fly Drosophila melanogaster, the nematode worm C. elegans, zebrafish, and gene knockout mice. Experiments, utilizing the nematode worm C. elegans as a model system, are elucidating developmental functions of septins, which are GTP-binding proteins involved in cytokinesis, and are implicated in human cancers and neurodegenerative diseases. Directed evolution of small heat shock proteins (chaperones) is a goal of one project that involves collaborative interactions of several faculty members. Using in vitro recombination, chimeric genes are being assembled from fragments of genes for naturally occurring heat shock proteins. These are expressed and assayed. Developmental roles of matrix metalloproteases are being studied in the fruit fly Drosophila melanogaster. These proteases, which have important signaling roles, are increased in inflammatory diseases and cancer. Another model system, the larval zebra fish, is being for studies of developmental genetics and neuroscience. Neural circuits involved in the highly conserved startle response are being characterized, and genes involved in habituation to startle identified. Mammalian genes that influence development, differentiation, and behavior are being examined using mice as a model system. Mouse behaviors are being correlated with specific genes, and mouse models of human behavioral conditions and diseases are being created using transgenic and gene knockout approaches. Faculty: Ferland, Finger, A. Page-McCaw, P. Page-McCaw, Swank.
• Neurobiology and Behavior: Members of the Biology Department, with additional collaborators, are involved in neurobiological research. Several different model systems are being used for studies ranging from the cell biology of nervous system development to elucidating the molecular bases of animal behavior. The functions of septin-family GTPases in axonal migration during nervous system development are being studied in the nematode worm, C. elegans. Septins are evolutionarily conserved proteins implicated in Parkinson’s and other neurodegenerative diseases. Experimental approaches include in vivo studies of nervous system development and locomotory behavior as well as cell biological studies of axonal migration using primary cultures of embryonic worm neurons. The startle response, a highly conserved behavior, is being studied in another model system, the larval zebra fish. Approaches include quantitative assays of startle behavior, characterization of the neural circuits involved in the startle response, and identification of genes required for the naive startle response and for habituation to startle. Genetic polymorphisms that influence learning and memory, anxiety and fearfulness, and left-right laterality in the brain are being studied in the mouse. Mouse behaviors are being correlated with specific genes, and mouse models of human behavioral conditions and diseases are being created using transgenic and gene knockout approaches. Faculty: Ferland, Finger, Ligon, A. Page-McCaw, P. Page-McCaw.

Correspondence and Information

Rensselaer Polytechnic Institute
Jody Malm, Admissions Coordinator
Department of Biology
1W14 Jonsson-Rowland Science Center
110 8th Street
Troy, New York 12180
Telephone: 518-276-2808
Email: malmj@rpi.edu