Graduate Bulletin

Courses in Biology

Bio 501 Special Topics in the Biological Sciences (1-3)

This course will examine emerging trends in biological sciences. New information emerging from recent studies will be stressed.

Bio 504 Cell Biology I (3)

One of two courses on the structural and functional organization of the cell that may be taken in sequence or independently (see Bio 505). This course covers the extracellular matrix, adhesion receptors, cytokines, the actomyosin and microtubule-based cytoskeleton, and membrane- cytoskeleton interactions, in the control of growth, differentiation and the cell cycle, and cytoplasmic structures and motility. Prerequisite: Biochemistry course equivalent to Bio 365.

Bio 505 Cell Biology II (3)

Second of two courses on the structural and functional organization of the cell that may be taken in sequence or independently (see Bio 504). This course covers membrane organization, permeability, channels and active transport, intracellular membrane systems, intracellular transport and secretion, receptors and endocytosis, intracellular signaling, and oxidative phosphorylation and photosynthesis. Prerequisite: Biochemistry course equivalent to Bio 365.

Bio 509 Introduction to Biological Materials (3)

Investigation of the structure, function, and material properties of non-living biological products (e.g., insect and plant cuticles, mineralized shells, bone). Particular attention to developmental control on the cellular and other levels; term paper, class presentation required. Prerequisite: Graduate standing.

Bio 510 Laboratory and Environmental Safety (1)

This course will cover the basics of several aspects of Environmental Health and Safety with an emphasis on laboratory safety. The course will include discussion on various federal and state regulations as they apply to environmental health and safety. The following topics will be reviewed: lab safety and the OSHA lab safety standard "Occupational Exposure to Hazardous Chemicals in Laboratories", OSHA Hazard Communication Standard, New York State Right-to-Know Law, EPA and DEC air and water pollution regulations including regulations on hazardous waste, occupational safety, biosafety including OSHA's "Occupational Exposure to Bloodbone Pathogens" standard, radiation safety, fire safety and personal protective equipment. One lecture per week, plus additional flexible time is required. Permission of Instructor. Open to matriculated graduate students only.

Bio 511 Population Genetics (3)

Advanced course for first and second year students needing a comprehensive survey of population-genetics theory and practical applications. Topics covered include random-genetic drift, the Hardy-Weinberg equilibrium, natural and artificial selection, mutation, gene flow, and population structure. Emphasis on modern molecular and computer techniques for data acquisition and analysis will be strong. Problem solving and algebraic manipulations will be required. Prerequisites: Bio 2l2 and Mat 113 or the equivalent.

Bio 513 Modern Use of Light Microscopy (3)

The light microscope as a powerful observational, analytical, and quantitative research tool. Practical use of the microscope is emphasized. Topics include image formation, polarized light, interference and fluorescence microscopy, video techniques for image enhancement, analysis and recording, and specimen preparation and experimental manipulation. Prerequisite: Consent of instructor.

Bio 514 Biotechnology Laboratory (2)

Introduction to technology used to study concepts in molecular and cellular biology. One literature-based paper is required. Prerequisite: Bio 365 or permission of instructor.

Bio 515a Responsible Conduct and Skills in Research (1)

Seminar course on good scientific practices and ethical principles that guide scientific research. Topics include: introduction to ethical reasoning, how to give a talk, laboratory safety, scientific record keeping, conflict of interest, scientific misconduct, how to avoid plagiarism, use of animals and humans in research, human genomic research and the protection of privacy and confidentiality, funding opportunities for graduate students, and skills in the use of computer and printed information retrieval sources. Required for all matriculated graduate students. Not open to non-matriculated graduate students.

Bio 515b Responsible Conduct and Skills in Scientific Communication (1)

Seminar course on good scientific practices and ethical principles that guide scientific research. Topics include: effective communication, writing and submitting a scientific paper, peer review, writing grants, ethics of scientific communication, preparing effective and ethical illustrations, use of reference data bases, attending conferences. Overview of skills and training qualifications reflected in current job and postdoctoral opportunities. Students are required to make presentations. Required of all matriculated graduate students. Not open to non-matriculated graduate students. Prerequisite: Bio 515a or permission of the instructor.

Bio 517a Current Literature in Forensic Biology I (1)

Students will research the literature on assigned topics and discuss research and issues of historic and contemporary importance in forensic biology.

Bio 517b Topics in Forensic Science (1)

Students will research the literature on assigned topics and discuss research and issues of historic and contemporary importance in forensic biology.

Bio 518 (Gog 518, Inf 508) Ecological Modeling (3)

This course introduces various theoretical and mathematical approaches to modeling ecological and environmental data through computer-based exercises in the application of existing models and the development of new models. Modeling topics cover animal population models, vegetation models, and large scale landscape models, as well as model applications in decision making. This course is geared towards demystifying models and providing students with the confidence and skills to apply this very useful tool to research projects. Prerequisites: Statistics and either General Ecology, Environmental Analysis, Environmental Studies or equivalent or permission of instructor.

Bio 519 (Ant 512) Human Population Genetics (3)

The genetics of human populations with emphasis on the application of the principles of population genetics to human groups, particularly concerning inbreeding, selection, drift, flow, and the structure of human populations. Prerequisite: Ant 502 or permission of instructor.

Bio 521 Cell and Molecular Developmental Neurobiology (3)

The cellular and molecular basis of neural development. Students will analyze and discuss the current scientific literature on pattern forming events underlying the regional organization of the nervous system, on neuronal and glial cell differentiation, and on the establishment and maintenance of neuronal connections. Prerequisite: Bio 504, 505 or consent of instructor.

Bio 522 Forensic DNA Analysis Laboratory (10)

The overall goal of this forensic laboratory course is to provide students with the theoretical foundation and tools to perform DNA analysis on mock evidence employing methods commonly used in today’s accredited forensic laboratories. Students will learn the theory and practice of forensic DNA analysis; past and current state-of-the-art-technologies; legal issues and statistical analyses. Students will perform analytical procedures that include DNA extraction, DNA quantification, PCR-based methods, multiplex amplification of STR loci, capillary electrophoresis of amplified products, and analysis, interpretation and reporting of single source and mixture data samples. Prerequisite: Permission of instructor.

Bio 523 Biochemistry and Biomolecular Structure (3)

One of the four courses required of incoming graduate students in the cell, molecular, developmental, and neural biology core area. This course includes an introduction to biophysical chemistry; protein structure, folding and function; nucleic acid structure, folding and function; and protein-DNA interactions. Prerequisite: Biochemistry course equivalent to Bio 365.

Bio 524 Advanced Molecular Biology (3)

Biosynthesis and function of biological macromolecules. Current work on the different species of RNA and RNA-containing structures in the cell, DNA synthesis in chromosome replication, protein synthesis, and control mechanisms operating at the levels of nucleic acid and protein synthesis. Two 1 1/2-hour lecture periods per week. Given spring semester only. Prerequisites: Bio 301; 111N or equivalent; Chm 342 or Bio 365, Chm 343 or Bio 367, or Chm 440A,B or equivalents.

Bio 526 Chemical Biology: Basic Principles (3)

Biochemical mechanisms underlying biological function of macromolecules. Thermodynamic and kinetic aspects of enzyme reaction, especially those involved in nucleic acid and protein metabolism, and of other biological processes. The principles underlying sequence determination, modification, and synthesis of nucleic acids and proteins. Also open to advanced undergraduates. Prerequisite(s): General biology and chemistry or consent of instructor.

Bio 530A Biodiversity and Conservation: Theoretical Issues (4)

Review of principles of ecology with respect to their potential application to biological conservation. Drawing from examples of conservation management problems, students will examine theoretical and empirical evidence from population, community, and ecosystem ecology, and evaluate current and projected strategies for preserving biological diversity in regional and in globally prominent ecosystems. This is a companion course for Bio 530B. Two lectures plus one discussion per week. Prerequisite: Graduate standing or permission of instructor.

Bio 530B Biodiversity and Conservation: Policy Issues (4)

Survey of approaches to environmental planning and public policy analyses that directly pertain to biological conservation. Students will review economic, political, and legal approaches to policy analysis. In discussions, they will explore strategies for introducing ecological information and conservation needs into the public policy forum. This is a companion course for Bio 530A. Two lectures plus one discussion per week. Prerequisite: Graduate standing or permission of instructor.

Bio 533 Advanced Population-Community Ecology (4)

Major concepts in population dynamics and the structure and evolution of communities. Topics include niche partitioning, competition theory, population cycles, population regulation, optimization theory, the community matrix, species packing, and species diversity. Emphasis on current research. Three class periods each week plus one additional hour each week of seminar devoted to an in-depth analysis of current research papers. Open only to graduate students. Prerequisites: Bio 320 or equivalent and graduate student status.

Bio 539 Comparative Functional Genomics (3)

This course will provide students with a comprehensive review of concepts, goals and methods of genome analysis. Besides reviewing both classical and molecular genetics and comparatively analyzing model organisms, and gene and protein families, we will also examine relevant technological advances including large-scale genomic analysis, map-based cloning and transgenic technology. Prerequisite: graduate status.

Bio 540 Principles of Bioinformatics (3)

This course is intended for graduate students in the Biological Sciences and will introduce students to various aspects of modern computational techniques in Biology. Emphasis will be placed on problems in molecular biology. Students will learn various computational techniques, existing implementations of the most common algorithms, and how to create their own implementations. Prerequisites: Permission of instructor.

Bio 541 Molecular Neurobiology (3)

The molecular biology of learning and memory, neural development and disease. The course will relate the structure and function of receptors, second messengers, cytoskeletal proteins, transcription factors and gene structure to their roles in the nervous system. Students will be required to write a research proposal on a question of their choosing. Prerequisite: graduate standing or consent of instructor.

Bio 542 Restoration Ecology (3)

Restoration ecology seeks to enhance natural recovery of damaged ecosystems. Through lectures and readings, we review the science and practice of ecological restoration, with emphasis on application of ecological principles. In addition to other course assignments, graduate students will be required to produce a research proposal for a possible restoration project. Prerequisites: Graduate standing and coursework in ecology.

Bio 543 Restoration Ecology Laboratory (1)

Demonstrations and laboratory exercises will explore tools for the design, implementation, and assessment of restoration projects in a variety of habitats. As the principal assignment, student teams will prepare a design plan for a restoration project. As an added course requirement, graduate students will be required to produce professional quality reports describing team projects. Prerequisites: Enrollment in Restoration Ecology.

Bio 545 Experimental Ecology (3)

Ecological concepts are demonstrated with experimental manipulations and comparative assessment techniques. Local wetlands are studied; the focus is on the effects of invasive species. Ecological assessment skills are developed in the field and laboratory. Lectures couple fundamental and applied topics, balancing understanding of ecological principles with realistic environmental problem solving. Discussion group examines classic and current literature. Students oversee research and prepare a technical report that becomes part of the record for a municipal wetland. Prerequisites: Bio 320 or equivalent, graduate status and permission of instructor.

Bio 547 Cellular Aspects of Neurophysiology: Lecture (3)

Electrophysiology of nerves and muscles. Topics include excitable membranes, synaptic transmission, pacemaker potentials, lateral inhibition, and the vertebrate visual system. Prerequisite: Consent of instructor.

Bio 548 Cellular Aspects of Neurophysiology: Laboratory (4)

Standard electrophysiological techniques for both intra- and extracellular recordings. Experience with a number of standard preparations used in neurophysiology. Prerequisites: Bio 547 and consent of instructor.

Bio 549 Neurotransmitters (3)

Examination of the mechanisms and concepts of chemical transmission, emphasizing the regulatory mechanisms controlling synthesis, release, reuptake, and receptor activation for each of four classes: monoamines, acetylcholine, amino acids, and peptides. Neurotransmitter-related diseases and the involvement of transmitters and transmission in developmental processes such as synaptogenesis and synaptic stabilization. Prerequisite: Graduate standing or consent of instructor.

Bio 550 Cellular Basis of Neuroanatomy: Lecture (3)

An examination of neuroanatomical methods and their cellular basis. Topics include the structure of neurons and glia, axoplasmic transport, receptor binding, and a variety of classic and modern techniques, such as the Golgi method, Nissl and Myelin stains, tract-tracing methods, immunocytochemistry, and intracellular dye injection. Prerequisite: Consent of instructor.

Bio 551 Cellular Basis of Neuroanatomy: Lab (2)

The student is given hands-on experience with a variety of classic and modern neuroanatomical techniques, such as fixation, embedding, sectioning, tract-tracing, autoradiography, enzyme histochemistry, the Golgi method, Nissl and myelin stains, and immunocytochemistry. Prerequisites: Bio 550 and consent of instructor.

Bio 555 Plant Ecology (3)

Current research and theoretical background in the field of plant ecology will be explored. Topics include population and community dynamics, evolution of life history traits, physiological responses to environmental stresses, plant-animal interactions, and the role of vegetation in ecosystem processes. Prerequisite: General Ecology/Field Biology or permission of instructor.

Bio 556 Plant Ecology Laboratory (1)

Field and Laboratory studies will explore experimental and analytical technique used in plant ecology. Topics include population dynamics, community patterns, plant-animal interactions, and vegetation mapping. Graduate students will conduct independent research projects. Pre or co-requisite: ABIO555

Bio 560 Neural Basis of Behavior (3)

The neural basis of innate and learned behaviors in vertebrates and invertebrates will be examined. Emphasis will be placed on sensory processing, reflexive behavior, fixed action patterns, rhythmic behaviors and simple learned behavior amenable to analysis at the neuronal level including analysis of membrane electrical activity, chemical synaptic activity and neuromodulation. An oral class presentation and term paper are required. Prerequisites: Bio 341, Neurobiology or equivalent, permission of instructor.

Bio 567 Optimization Theory in Animal Behavior (3)

Optimization techniques with applications to current problems in behavioral ecology. Classical univariate and multivariate unconstrained optimization, lagrange theory and evolutionary stable strategies, dynamic programming, and optimal control theory. Techniques may change, depending on advances in the field and the interests of participants. Prerequisite: A course in ecology or behavior.

Bio 575 Forensic Biology (3)

Students will learn forensic biological procedures for human identification employing methodologies and instrumentation used in today’s crime labs. Students will learn how to: 1) identify biological stains on mock evidence; 2) collect, package and store biological evidence for subsequent DNA profiling; 3) extract and quantify human DNA; 4) utilize DNA amplification and computer-assisted genetic analysis of STR’s; 5) apply a statistical weight to the STR DNA match results; and 6) present the test results in a final case report and as an expert witness in a mock criminal trial. One laboratory and one, one hour lecture per week plus additional flexible time as required. Prerequisite: Permission of instructor.

Bio 599A Laboratory Rotation I (3)

First year graduate students in the molecular, cellular, developmental, and neural biology core area are required to enroll in this course. For the first 4 weeks, students will visit laboratories to discuss possible rotation projects and meet weekly with the course coordinator to discuss their progress in finding a lab. Students will then spend seven-weeks in a laboratory rotation working on a project assigned by the respective faculty member. All placements in laboratories will be arranged in consultation with and approved by the course coordinator. S/U grading.

Bio 599B Laboratory Rotation II (3)

First year graduate students in the molecular, cellular, developmental, and neural biology core area are required to enroll in this course. This course consists of rotating in laboratories for successive seven-week periods working on a project assigned by the respective faculty members. All placements in laboratories will be arranged in consultation with and approved by the course coordinator. S/U grading.

Bio 600 Topics in Evolution (1-4)

Bio 601 Topics in Ecology (1-4)

Bio 602 Topics in Cell Biology (1-4)

Bio 603 Topics in Genetics and Molecular Biology (1-4)

Bio 604 Topics in Physiology (1-4)

Bio 605 Topics in Developmental

Biology (1-4)

Bio 606 Topics in Parasitology (1-4)

Bio 607 Topics in Plant Biology (1-4)

Bio 608 Topics in Animal Biology (1-4)

Bio 610 Topics in Biophysics and Biochemistry (1-4)

Bio 611 Topics in Population Biology (1-4)

Bio 612 Topics in Theoretical Biology (1-4)

Bio 613 Research Techniques in Biology (1-4)

The theory and practice of research techniques in biology. Prerequisites: Consent of instructor and department chair.

Bio 614A (Bms 614A) The Theory and Technique of Electron Microscopy: Lecture (2)

Instrumentation theory (e.g., electron optics, image formation, etc.), including several of the new electron microscopes, as well as introduction to image interpretation and reconstruction techniques. Prerequisites: Special arrangement and permission of instructor.

Bio 614B (Bms 614B) The Theory and Techniques of Electron Microscopy: Lab (2)

Laboratory periods involve specimen preparation including fixation, embedding, sectioning, training, and photography along with whole-mount specimen preparation for TEM and SEM. Prerequisites: Special arrangement and permission of instructor.

Bio 615 Biotechnology Development (3)

This course studies the ways in which scientists apply results produced by basic research to create new methods or products to solve human problems. Initially, students will study cases organized around nanoscale biological phenomena or processes emulated by technologies. Subsequently, they will be exposed to general issues in innovation as applied to biotechnology. These studies will help them to understand the process of getting from thoughts to things. A forward engineering approach is emphasized, with topics ranging from cognitive psychology to business practice. Prerequisite: Bio 524 or permission of the instructor.

Bio 617 Molecular Evolution (3)

The theory, history, and practice of molecular evolution and phylogenetic tree building will be covered. Major insights and discoveries in the field will be discussed. Students will learn to use computers for genetic database searching, sequence alignment, and tree building. Students will analyze data sets relevant to their research interests. Prerequisite: Consent of instructor.

Bio 620 Tutorial in Computing and Bioinformatics (3)

This course will provide hands-on training in methods of computer-assisted bioinformatics, with specific application to biological research. Topics include: data mining, sequence retrieval, DNA and protein sequence alignment, molecular evolution and phylogenetic analysis, population genetics and analysis of genetic variation within species, comparative genomics of model organisms, and computer-based visualization and analysis of macromolecular structures. Prerequisite: graduate status.

Bio 622 Tutorial in Imaging and Microscopy (3)

This course will include lectures, demonstrations and hands-on exercises to introduce the fundamental principles underlying microscopy and imaging. Topics include: bright and dark field, phase contrast, differential interference, fluorescence and confocal scanning microscopes as well as video and digital image processing and analysis. Prerequisite: graduate status.

Bio 623 Biomolecular Structure (3)

Study of the structure and folding of proteins and nucleic acids and the interactions between these biomolecules. Topics include secondary and tertiary structure classification, thermodynamics of folding and reassociation, hydrophobicity scales, surface area and volume calculations, coulombic surfaces, measurment of kinetic and thermodynamic parameters of biomolecular interactions, and the nature of the forces governing biomolecular interactions. Prerequisite: Bio 523

Bio 627 Courtroom Testimony for Forensic Scientists (1)

The goal of this course is to prepare students to present scientific evidence to members of jury and court. Students will learn the rules of criminal and civil procedure applicable to expert witnesses. They will learn how to translate highly technical and complex concepts from the sciences (biology, chemistry, and human population genetics) into language that can be understood clearly by members of the court. Special attention will be given to the ethical issues confronting the expert witness as well as issues relating to establishing the weight of the evidence through the application of statistical methods. Prerequisite: Permission of instructor.

Bio 629 Advanced Genetics (3)

This course will provide an overview of concepts and techniques in genetics and their use in answering fundamental questions in biology. The lectures will focus primarily on studies carried out in model organisms such as yeast, C. elegans, Drosophila, and mouse (human) to illustrate the power of forward and reverse genetics as experimental tools. Genomic approach based on the completely sequenced genomes will be also discussed. Prerequisites: Bio 524 or equivalent or permission of instructor.

Bio 630 Topics in Biodiversity, Conservation and Policy (1)

Presentations and discussions of contemporary issues and literature relating to biodiversity, conservation, and policy. Prerequisite: permission of instructor.

Bio 633 Ecology, Evolution, and Behavior Seminar (0)

Seminars and discussions of the current literature in ecology, evolution, and animal behavior. Required of all graduate students in the EEB program during each semester of residence.

Bio 650 MCDN Graduate Research Seminar (0)

This course is a seminar series attended by all graduate students and faculty in the MCDN core area (Molecular, Cellular, Developmental and Neural Biology) . Each Ph.D. student beyond the first year will present one formal seminar per academic year on his/her research.

Bio 681 Seminar in MCDN (0)

This course will consist of student presentations based on papers from the current literature of the field. Specific seminar topics will be announced in advance of pre-registration. May be repeated for credit. Prerequisite: permission of instructor

Bio 682 Seminar in EEB (0)

This course will consist of student presentations based on papers from the current literature of the field. Specific seminar topics will be announced in advance of pre-registration. May be repeated for credit. Prerequisite: permission of instructor

Bio 697 Graduate Research (2-12)

Individual, independent experimental or theoretical research in biology. By permission of chair of the department Graduate Programs Committee. Credits may be transferred to Bio 699 or Bio 899 if admitted to a degree program. S/U graded.

Bio 698 Internship in Forensic Biology (6)
The student will complete a project in forensic biology laboratory under the supervision of a mentor. The student will research the literature to identify a problem in forensic biology, develop an approach to its solution utilizing the scientific method, and document the aims, results, and conclusions in a substantial written report which will be examined by a committee of two members approved by the Department Graduate Committee. Prerequisites: Bio 514, 575 and permission of instructor.

Bio 699 Master's Research (2-12)

Original research in biology leading to the preparation of a thesis in partial fulfillment of the master's degree. Open to students enrolled in a master's program in biology.

Bio 898 Doctoral Research (3-12)

Original experimental or theoretical research in biology for students officially accepted in the Ph.D. program in biology, and leading to the preparation of a dissertation. Residence credit earned in this course becomes applicable upon satisfactory completion of all other requirements established for the Ph.D. in biology.

Bio 899 Doctoral Research (1-12)

Required of all candidates completing the Ph.D. in biological sciences. Prerequisite: advancement to doctoral candidacy in biological sciences. Does not count towards the 60 credit requirement for graduation.