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5024: POPULATION & COMMUNITY ECOLOGY:  Population dynamics, interspecific interactions, succession, and diversity of plants and animals. Quantitative approaches emphasized. Ecology course required. (3H,3L,4C).

5034: ECOSYSTEM DYNAMICS:  Application of a systems perspective to functional characteristics of ecosystems. Laboratory: computer simulation of ecosystem dynamics. Pre: MATH 2015, CS 1014. (3H,3L,4C).

5044: AQUATIC ECOTOXICOLOGY:  Techniques for evaluating polluted aquatic ecosystems, including laboratory toxicity testing and field biological monitoring, and the development of criteria for maintaining water quality. (2H,2C).

5054: HAZARD EVALUATION OF TOXIC CHEMICALS:  Discussion of philosophical issues in the development of standards for control of toxic chemicals in freshwater, including site-specific examples, application of current control methods, recovery of damaged ecosystems, and government regulations. Pre: 5044. (2H,2C).

5064 (ALS 5064) (BCHM 5064) (PPWS 5064): SEMINAR IN MOLECULAR CELL BIOLOGY & BIOTECHNOLOGY:  Review and discussion of current problems and literature in molecular cell biology and biotechnology by students, VPI&SU faculty and outside speakers. Students give formal presentations of research results or current literature. May be taken on pass-fail basis. Students enrolled in the MCBB Ph.D. option will be required to give one formal presentation on an A-F basis. Graduate status in participating MCBB departments required. (1H,1C).

5074 STREAM ECOLOGY:  Application of ecological principles to running water environments.  Recitation: critical assessment of contemporary literature and research themes associated with stream ecosystems.  Graduate standing required.  (3H, 4C)

5084 GROUNDWATER ECOLOGY:  Application of hydrologic and ecological principles to groundwater environments to address the biodiversity and processes of subsurface aquatic ecosystems.  Recitation:  assessment of primary literature directed at the ecology of groundwater systems.  Graduate standing required.  (3H, 4C)

5094 STABLE ISOTOPES IN ECOLOGY:  Application of stable isotope methods and interpretations to studies of ecosystem structure and function.  Recitation:  critical assessment of contemporary literature and research themes associated with applications of stable isotopes to ecological research.  Graduate standing required.  (3H, 4C)

5104 ADVANCED DEVELOPMENTAL BIOLOGY:  Morphological, physiological and molecular events in embryological and developmental systems, including regulation at the level of transcription, translation, and enzyme or hormone activation.  Review of the current literature.  Pre resiquite: Graduate standing required.  (4H, 4C)

5114G ADVANCED GLOBAL CHANGE ECOLOGY: Human alterations of climate, landscapes and biogeochemical cycling influence ecological structure and functioning at the global scale. Such changes have the potential to disrupt natural and managed ecosystems with potentially significant biological and economic impacts. This course will examine the influences of these global changes on the ecosystem processes and biodiversity, drawing on paleo- and contemporary examples. Current and future potential feedbacks between biological systems and the global environment will also be addressed. Pre-requisite: Graduate Standing required.  (4H, 4C)

5134G ADVANCED EVOLUTIONARY GENETICS:  Genetic variation, agents of change in gene frequencies, molecular evolution, mechanisms of speciation, ecological speciation. Comparison of theoretical models with natural and laboratory populations. Graduate standing required. (4H, 4C)

5154 EXERCISES IN GRANTSMANSHIP: All aspects of obtaining grant funding in the sciences. Grant writing, ethics, development of proposals for national funding agencies, the peer review system, and participation in a mock grant panel meeting. Pre-requisite: Graduate Standing required. (3H, 3C)

5164: BIOLOGY SEMINAR LAB:  A practicum in the preparation and presentation of formal scientific seminars. Graduate standing required. (3L,1C).

5174: GRADUATE SEMINAR:  Offered in the major subdisciplines of biology. Pass/Fail only. (1H,1C).

5184 PROKARYOT RECOMBINANT PROTEINS:  Concepts of bacterial recombinant protein expression, purification, and handling. Protein bioinformatics resource and the functional characterists of proteins with biochemical and biophysical techniques. Discussion of research articles related to class topics. Pre-requisite: Graduate Standing required. (3H, 3C

5214 BIOMACROMOLECULAR STRUCTURE:  Analysis of biomacromolecular interactions using X-ray crystallography data. Acquisition, processing, refinement, and validation of biomacromolecular structures. Conformational search methods. Simulation of folding/unfolding thermodynamics. Use of protein structure databases. Pre-requisite: Graduate Standing required. (3H, 3C)

5304 (PPWS 5304): PLANT STRESS PHYSIOLOGY:  Analysis of physiological responses of agricultural and native plants to environmental stresses such as extremes of temperature, availability of water and nutrients, and presence of air pollutants. Emphasis on linking stress caused changes in carbon gain, water loss, nutrient utilization, and energy balance with changes in growth. Laboratory to introduce equipment and research approaches used in greenhouse and field studies. (3H,3L,4C).

5314 ADVANCED PLANT ECOLOGY: The ecology of terrestrial plants in natural systems including major plant functional types, macromolecular plant ecology, behavior of populations, responses of plant communities to disturbance, vegetation analysis, and ordination; discussion of current research papers. Pre-requisite: Graduate Standing required. (4H, 4C)

5384 (GEOL 5384): MORPHOMETRICS:  Study of shape and size in fossil and modern organisms with strong focus on quantitative methods and digital image analysis. Covers analytical methods (multivariate methods, Fourier analysis, geometric morphometrics), image processing, and software training (SAS, SAS/IML, and Imaging Software). Pre: STAT 5004, GEOL 5374. (2H,3L,3C).

5404: NEUROETHOLOGY: Overview of Neuroethology, the study of the neural basis of animal behavior. Topics include: organization of the nervous system, control and coordination of movement, sensory transduction, visual and auditory prey detection and recognition, visual communication, matched filters/predictive coding of sensory information, learning templates, computational maps, sensory integration, behavioral plasticity, spatial cognition, neural plasticity, and lateralization of neural function. (3H, 3C)

5634: MICROBIAL PHYSIOLOGY:  The study of the structure, function and metabolic activities of prokaryotic microorganisms. Topics covered include cell composition and growth, metabolic unity and diversity, patterns of regulation, transport mechanisms, environmental sensing and response and cellular differentialtion processes. Students will give presentations and critically analyze current literature in the field. (4H,4C).

5664G ADVANCED VIRIOLOGY: Classification, structure, replication, and pathogenesis of viruses of animals, plants and bacteria. Epidemiology, prevention, and treatment. Pre-requisite: Graduate Standing required. (3H, 3C)

5674G ADVANCED PATHOGENIC BACTERIOLOGY: Characteristics of bacteria that cause human disease, nature of infectious processes, virulence factors, epidemiology, resistance, immunization. Review of publications in the current literature related to data and statistical analysis and methods. Graduate standing required. (4H, 4C)

5734 ADVANCED INFLAMMATION BIOLOGY: Cellular and molecular pathways controlling human responses to inflammatory challenges. Regulation of immune cells during inflammation. Interaction of host cells and tissues with environmental risk factors that cause inflammation. Pathogenesis of inflammatory diseases including cardiovascular diseases, diabetes, multi-organ failure, neurological diseases and sepsis. Therapeutic intervention of inflammatory diseases. Discussion of current literature. Integrative approached to study of inflammation will be critically evaluated and synthesized. Pre-requisite: Graduate Standing required. (4H, 4C)

5804G ADVANCED PROKARYOTIC DIVERSITY:  The study of the vast array of physiological, morphological, and behavioral properties of prokaryotes, i.e., the Bacteria and the Archaea, that enables them to compete successfully in nature and, in many instances, to complement each other. Topics covered include the modern classification of prokaryotes and show how their widely diverse properties have contributed to a better understanding of cell and molecular biology and biochemistry, how they have been useful in industry and agriculture, and how they are important for continued life in our biosphere. Graduate standing required. (3H, 3C)

5844 ADVANCED PROTEOMICS AND BIOLOGICAL MASS SPECTROMETRY: Introduction to mass spectrometry (MS) instrumentation and advanced proteomic methods for systems biology applications. Peptide mass fingerprinting, tandem MS, quantitation, phospho/glyco proteomics, and bioinfomatics tools for evaluation and interpretation of mass spectrometry data. Includes three 4-hour lab sessions. Pre-requisite: Graduate Standing required. (3H, 4C)

5854G ADVANCED CYTOGENICS:  Structure and function of eukaryotic chromosomes, with emphasis on (i) use of model systems to study specific chromosomes substructures or functions; (ii) techniques used to indentify and classify both normal and aberrant chromosomes; and (iii) diseases caused by defective chromosome structure and/or function. Pre-requisite: Graduate Standing required (3C, 3H)

5864 PHYSICAL CHEMISTRY OF THE CELL:  Applications of classical thermodynamics, chemical kinetics, and ststistical mechanics in molecular and cellular processes. Pre-Requisite: Graduate Standing required (3H, 3C)

5884 MOLECULAR BIOLOGY OF THE CELL:  Current concepts of the molecular organization of animal and plant cells. Topics include membrane structure and function, organelle biosynthesis and function, intracellular signaling, the cytoskeleton, the cell cycle, tissue formation and modern experimental methodologies. (3H, 3C)

5694 (CSES 5694): SOIL BIOCHEMISTRY:  Comprehensive presentation and analysis of the biochemistry of soil humic acid formation, physicochemical properties of humic substances, and interactions of soil humic substances with toxic organics and metals. Microbial degradation of organics, including pesticides, and the fate of genetically engineered microbes in soil. Pre: 4684, 4694. (2H,3L,3C).

5974: INDEPENDENT STUDY:  Pass/Fail only. Variable credit course.

5984: SPECIAL STUDY:  Variable credit course.

5994: RESEARCH & THESIS:  Variable credit course.

6004: TOPICS IN ECOLOGY & SYSTEMATICS:  Reading and discussion in a specific area of ecology and systematics. Topic will vary, and course may be taken for credit more than once. Background in ecology or systematics required. Variable credit course.

6014: TOPICS IN EVOLUTIONARY BIOLOGY:  Readings and discussion in a specific area of evolutionary theory, ecological genetics, or molecular evolution. Topics will vary, and course may be taken for credit more than once. Background in genetics and population biology required. Variable credit course.

6024 (ALS 6024) (BCHM 6024) (PPWS 6024): TOPICS IN MOLECULAR CELL BIOLOGY & BIOTECHNOLOGY:  Specific areas such as the molecular biology of plant and animal disease resistance, of photosynthesis, of oncogenes, of organelle assembly, and of growth and development, structure and function of polyamines and of proteases will be discussed. Students will give presentations and critically analyze current literature. May be repeated. Variable credit course. Pre: BCHM 5214.

6064: TOPICS IN FRESHWATER ECOLOGY:  Readings and discussion in a specific area of freshwater ecology, including species interactions, and community level functions. Topics will vary, and course may be taken for credit more than once. Variable credit course. Pre: 4004.

6084: TOPICS IN CELL AND DEVELOPMENTAL BIOLOGY: Readings and discussion of a focused area of cellular and developmental biology, including cell signaling, cell cycle, differentiation and morphogenesis, cytoskeletal regulation and cell death. Topics vary each semester and course may be repeated with different content up to a maximum of 12 credits. Graduate standing required.  (3H, 3C)

6404: TOPICS IN VERTERBRATE BIOLOGY:  Readings and discussion in a specific area of vertebrate biology. Topic will vary, and course may be taken for credit more than once. Background in vertebrate biology required. Variable credit course.

6644: TOPICS IN MICROBIAL GENETICS:  Readings and discussion in a specific area of microbial genetics, including temperate bacteriophage, insertion elements and transposons, gene function in prokaryotic microorganisms, and mechanisms of genetic recombination. Topic will vary and course may be taken for credit more than once. Pre: 4624. (3H,3C).

6704 (VMS 6704): TOPICS IN IMMUNOLOGY:  Readings and discussion in a specific area of immunology. Topic will vary and course may be taken for credit more than once. Pre: 4704. (3H,3C).

6984 SPECIAL STUDY: Variable credit course.

7994: RESEARCH & DISSERTATION:  Variable credit course.

Advanced Undergraduate Courses (BIOL)

The following 4000-level courses have been approved for graduate credit:

4004: FRESHWATER ECOLOGY: Interactions of physical, chemical, and biological properties of freshwater ecosystems. Senior standing required. Pre: 2804. (3H,3L,4C).

4014: ENVIRONMENTAL TOXICOLOGY:  Discussion of ecotoxicological and philosophical issues in the development of standards for control of toxic chemicals in freshwater, including site-specific examples, application of current control methods, recovery of damaged ecosystems, and government regulations. Pre: 2804. (2H,2C).

4044 (GEOG 4044): BIOGEOGRAPHY:  A survey of the field of biogeography. A study of the factors influencing the distribution of plants and animals approached from ecological, historical, and cultural perspectives. Human influence on biotic patterns, such as crop domestication, habitat alteration, species introductions and extinctions, management issues, and environmental change, is a primary force. Pre: 2804 or GEOG 1104. (3H,3C).

4104: DEVELOPMENTAL BIOLOGY: Morphological, physiological, and molecular events in embryological and developmental systems, including regulation at the level of transcription, translation, and enzyme or hormone activation. Pre: 2004. (3H,3C).

4134: EVOLUTIONARY GENETICS:  Genetic variation, Hardy-Weinberg equilibrium, agents of change in gene frequencies, molecular evolution, mechanisms of speciation. Comparison of theoretical models with natural and laboratory populations. Pre: 2004. (3H,3C).

4314: PLANT ECOLOGY (WRITING INTENSIVE):  Introduction to ecology of terrestrial plants including major plant functional types, behavior of populations, responses of plant communities to disturbance, vegetation classification, and ordination. Laboratory covers methods for measuring and analyzing natural vegetation, and setting up field and greenhouse experiments. This is a writing intensive course. Even years. Pre: (2304 or 2804 or FOR 3314). (3H,3L,4C).

4354 (ENT 4354): AQUATIC ENTOMOLOGY:  Biology and taxonomy of insects and other macroinvertebrates most commonly encountered in freshwater environments. Selected aspects of biology, such as habitat, feeding, locomotion, and life history. Identification of individual taxa, mostly at family and genus level. Significance of these organisms in aquatic ecology, pollution monitoring, and natural resource management.  Pre: (1005, 1006), (1015, 1016) or (1105, 1106, 1115, 1116). (3H,3L,4C).

4404: ORNITHOLOGY:  Biology of birds, including functional anatomy, systematic, evolutionary history, behavior, and ecology. Laboratory on systematic, anatomy, and field experience in the areas of behavior and ecology. Pre: 2504. (3H,3L,4C).

4434: MAMMALOGY:  Biology of mammals including evolution, systematic, anatomy, physiology, and ecology. Laboratory on systematic, morphology, zoogeography, and diversity of North American mammals. Pre: 2504.  (3H,3L,4C).

4474: ETHOLOGY:  An evolutionary and ecological approach to animal behavior, drawing on behavioral genetics, endocrinology, neurophysiology, and behavioral ecology to explain how and why the behavior of an organism is adapted to its environment. Pre: 2504. (3H,3C).

4484 (ENT 4484) (FIW 4484): FRESHWATER BIOMONITORING:  Concepts and practices of using macroinvertebrates and fish to monitor the environmental health of freshwater ecosystems. Effects of different types of pollution and environmental stress on assemblages of organisms and underlying ecological principles. Role of biological studies in environmental regulation. Study design, field and laboratory methods, data analysis and interpretation, verbal and written presentation of results. Pre: (2804), (4004 or 4354 or ENT 4354 or FIW 4424 or FIW 4614). (3H,3L,4C).

4524: ENVIRONMENTAL ANIMAL PHYSIOLOGY:  Physiological adaptations to environmental factors, emphasizing vertebrate organ systems. Evolutionary and acclimatory processes will be considered. Must have prerequisites or instructor's permission. Writing intensive. Odd years. Pre: 3404. (3H,3C).

4534: COMPARATIVE ENDOCRINOLOGY (WRITING INTENSIVE):  Physiology of endocrine systems, emphasizing vertebrates but including invertebrates. Mechanisms of hormone action, physiologic roles of hormones, and overall integration. Must have prerequisites or instructor's permission. Pre: BIOL 3404. (3H,3C).

4554 (ALS 4554): NEUROCHEMICAL REGULATION: Neurochemical transmission within the vertebrate brain will be examined. Emphasis will be placed on the chemical coding underlying the control of various behaviors and how these systems can be modified by various drugs or diet. Pre: (3404 or ALS 2304), (CHEM 2535). (3H,3C).

4574 (ALS 4574): SOCIAL BEHAVIOR OF BIRDS AND MAMMALS:  Animal behavior from the viewpoint of group organization during the life cycle of the organism. Emphasis is on adaptive mechanisms as they relate to the behavior-physiology-genetic interaction. Pre: 1106. (2H,2C).

4604 (FST 4604): FOOD MICROBIOLOGY:  Role of microorganisms in food borne illness and food quality, spoilage, and preservation. Control and destruction of microorganisms in foods. Pre: 2604, 2614. (3H,3L,4C).

4624: MICROBIAL GENETICS:  Molecular genetics of bacteria and their associated plasmids and phages. Pre: 2004, 2604. (3H,3C).

4644: MICROBIAL MOLECULAR GENETICS AND PHYSIOLOGY LABORATORY:  Introduction to classical and molecular methods used for the study of bacterial genetics and physiology. Laboratory exercises cover analysis of patterns of gene regulation; assay of enzymatic activities; mutagenesis followed by selection, screening, and physiological characterization of mutant strains; genome database utilization; and large scale fermentation. Pre: 4624. (1H,6L,3C).

4664: VIROLOGY:  Classification, structure, pathogenesis, host response, and replication strategies of viruses of bacteria, plants, and animals, stressing mechanisms elucidated by molecular biological techniques. Pre: 3774, BCHM 4116. (2H,3C).

4674: PATHOGENIC BACTERIOLOGY:  Characteristics of bacteria that cause human disease, nature of infectious processes, virulence factors, epidemiology, resistance, immunization, diagnostic bacteriology. Pre: 2604, 2614. (3H,3L,4C).

4704: IMMUNOLOGY:  Immunochemistry of antigens and antibodies, serological reactions, chemistry of complement, control of immunity, immune response of an intact animal. Pre: 2104 or CHEM 2536. (3H,3C).

4714: IMMUNOLOGY LABORATORY: Serological and immunobiological techniques used to interpret the consequences of an immune response. Pre: 4704. (3L,1C).

4774: MOLECULAR BIOLOGY LAB:  An introduction to recombinant DNA methods, including restriction endonuclease digestion, gel electrophoresis, cloning, Southern blotting, polymerase chain reaction, sequencing and analysis of reporter gene expression in transgenic organisms. BIOL 3774 may be taken as a co requisite with 4774. Pre: 3774. (1H,6L,3C).