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Course Listings:
ST 590A Bioinformatics I
This
introductory course provides a broad overview for bioinformatics
students who will take additional courses in statistical genetics,
bioinformatics and computer science. It introduces empirical genomic
science students to statistical and computational facets of genomic
science and provides them with a collection of data analysis and
management skills. At the end of the course, students should have
an appreciation of the basic problems facing genomic scientists,
the roles that bioinformatics plays in the solution of these problems,
a basic understanding of bioinformatics methodologies, and skills
using key genomic science computer equipment.
ST 590C Bioinformatics II
Bioinformatics
II is intended primarily for graduate students pursuing degrees
in the Bioinformatics area. The primarily goal of the course is
to provide in-depth training in a variety of bioinformatics topics.
At the end of the course, students should be prepared to initiate
independent research in some area of bioinformatics and to provide
technical support to research groups in the genomic sciences.
The course is divided into five major sections: sequence alignment,
identifying patterns, evolution and phylogeny, structure prediction
and miscellaneous topics.
PP 610 or 810G Journal Club
Both
masters and doctoral students will attend the combined weekly
journal club in bioinformatics and functional genomics. Students
will be required to present one paper from the current literature
each semester. Each week, there will be two 25-minute presentations
in which speakers describe and critique recent articles from the
scientific literature. Participants include graduate students,
faculty, postdoctoral associates and technicians. Doctoral students
will take the one-credit course four times.
____ 893 Doctoral Supervised Research (course prefix varies)
Preq:
Doctoral Student
Instruction
in research and research under the mentorship of a member of the
Graduate Faculty.
____ 895 Doctoral Dissertation Research (course prefix varies)
Preq:
Doctoral Student
Dissertation research credits
____
899 Doctoral Dissertation
Preq: Doctoral Student
For
students who have completed eight semesters and all credit hour requirements,
including the oral preliminary examination, and are writing and
defending their dissertations. You must receive approval from
the Director of Graduate Programs before registering for this
course.
BCH
701 Macromolecular Structure
Preq:
BCH 453 or BCH 553; a course in physical chemistry highly recommended
Introduction
to the current understanding and methods used for the study of
structures, thermodynamics and conformational dynamics of proteins,
nucleic acids and membranes.
BCH
703 Macromolecular Synthesis and Regulation
Prerequisite:
BCH 453 or BCH 553
Biochemistry
of DNA replication, transcription, RNA processing and translation.
Development of key concepts, techniques and applications relating
to mechanisms and regulation of these processes by analysis of
primary literature.
BCH
705 Molecular Biology of the Cell
Preq:
BCH 701 or BCH 703
Regulation
of cellular processes, membrane structure and function, signal
transduction, protein trafficking/sorting, secretion, photosynthesis
and nitrogen fixation.
BCH
751 Biophysical Chemistry
Preq:
BCH 451 or equivalent; one semester of physical chemistry
Fundamental
and practical aspects of biological macromolecular structure,
thermodynamics, hydrodynamics, kinetics and spectroscopy with
emphasis on mechanisms in functionally important structural transformations.
BCH/GN
761 Advanced Molecular Biology of the Cell
Preq:
BCH 703 and 705
An
advanced treatment involving integrated approaches to biological
problems at the molecular level, encompassing biochemistry, cell
biology and molecular genetics. Broad, multidisciplinary approaches
to solving research problems in biology and the critical study
of primary scientific literature, the development of a research
proposal, oral presentations and class discussions.
BCH
763 Biochemistry of Hormone Action
Preq:
BCH 705 or GN 757
Study
of well-defined models of steroid and protein hormone action via
lectures, assigned readings and discussions. Students add breadth
to the course and depth to their own understanding by searching
the literature and writing or lecturing about a particular hormone
of their own choosing.
BCH/GN
768 Nucleic Acids: Structure and Function
Preq:
BCH 701 and 703
An
advanced treatment involving integrated approaches to biological
problems at the molecular level, encompassing biochemistry, cell
biology and molecular genetics. Broad, multidisciplinary approaches
to solving research problems in biology and the critical study
of primary scientific literature, the development of a research
proposal, oral presentations and class discussions.
BO
710 Plant Anatomy
Preq:
BO 200
Study
of plant cells, ultrastructure, cell types, tissues, organs and
patterns of growth and differentiation.
BO
712 Plant Morphogenesis
Preq:
Six hours of botany equivalent to BO 400 and BO 421
Review
and synthesis of factors involved in development of plant form.
Demonstration of levels of control from the molecular to whole
organism by tissue culture experiments.
CBS
750 Veterinary Medical Virology I
Preq:
Veterinary Medical Virology I
Discussion
of basic principles of animal virology and the relationship of
viruses to diseases in domestic animals.
CBS
751 Pathogenic Bacteriology and Mycology
Preq:
MB 411, graduate standing and consent of instructor
Lecture
covering pathogenic bacteria and fungi important in medicine.
Lectures supplemented by laboratory exercises providing students
the opportunity to learn basic characteristics of these microorganisms
and how they are isolated, cultivated and identified.
CS
720 Molecular Biology in Plant Breeding
Preq:
CS(GN,HS) 741, GN 701, GN 702, GN 703
Theory
and principles of molecular biology applied to plant breeding.
Experimental approaches to induce genetic change, cytoplasmic
recombination, haploid utilization and potentials of molecular
techniques for solving breeding problems.
CSC
530 Computational Methods for Molecular Biology
Preq:
CSC 311 Coreq: CSC 505
Computer
algorithms supporting genomic research: DNA sequence comparison
and assembly, hybridization mapping, phylogenetic reconstruction,
genome rearrangement, protein folding and threading.
FOR
710 Quantitative Forest Genetic Methods
Preq:
GN 509, ST 701
Fundamental
principles and procedures for partitioning experimental variance,
estimating parameters of interest from different mating schemes
and experimental designs and their uses in making tree breeding
decisions.
FS
725 Fermentation Microbiology
Preq:
BCH 451, MB 401
Fermentation bioprocessing and characteristics, function and ecology
of responsible microorganisms. Fermentative activities, growth
responses and culture interactions related to metabolism, physiology
and genetics of lactic acid bacteria and selected yeasts and molds.
Current developments in starter culture technology and genetics;
application to food and industrial fermentations.
____ 693 Master's Supervised Research (course prefix varies)
Preq:
Master's Student
Instruction
in research and research under the mentorship of a member of the
Graduate Faculty.
____ 695 Master's Thesis Research (course prefix varies)
Preq:
Master's Student
Thesis research credits
____ 699 Master's Thesis Preparation (course prefix varies)
Preq:
Master's Student
For
students who have completed all credit hour requirements
and are writing and defending their thesis. You must receive approval
from the Director of Graduate Programs before registering for
this course.
GN
701 Molecular Genetics
Preq:
GN 411
A
discussion of the structure and function of genetic material at
a molecular level. Consideration of both prokaryotic and eukaryotic
systems. The aim is to describe genetics in terms of chemical
principles.
GN
702 Cellular and Developmental Genetics
Preq:
GN 701 or consent of instructor
Regulation
of genes involved in cellular function, differentiation and development
in eukaryotes. Presentation
of biological systems and model organisms used to study genetic
control of cellular and developmental processes.
GN
703 Population and Quantitative Genetics
Preq:
GN 411, ST 501
Mutation
and origin of genetic variation. Measuring genetic variation in
natural populations. Gene and genotype frequencies. Hardy-Weinberg
equilibrium. Values, means, genetic and environmental variance,
heritability of quantitative traits. Random genetic drift and
inbreeding. Natural and artifical selection. Theory and tests
of models of maintenance of genetic variation. Molecular evolution
of genes and proteins. Genome evolution.
GN
710 Eukaryotic Regulatory Mechanisms
Preq:
GN 701
Detailed
analysis of mechanisms regulating eukaryotic gene expression in
plants, animals and smaller eukaryotes. Molecular interactions
responsible for controlling gene function with emphasis on transcription.
GN/FOR
725 Forest Genetics
Preq:
GN 411 or consent of instructor
Application
of genetic principles to silviculture, management and wood utilization.
Emphasis
on variation in wild populations, the bases for selection of desirable
qualities and fundamentals of controlled breeding.
GN/FOR
726 Advanced Topics in Quantitative Genetics
Preq:
GN(FOR) 725, GN(ST) 770 or GN(ANS) 713 or consent of instructor
Advanced
topics in statistics and population genetics pertinent to current
research problems in genetics with special applications to forestry.
Basic
statistical and genetic theory reviewed as bases for intensive
study of selection theory and experimental and mating design evaluation.
Study of genetics of natural populations for evolutionary interest
as well as for their implications to breeding theory.
GN
750 Developmental Genetics
Preq:
GN 701, GN 702
Action
and regulation of genes and gene-products in development and differentiation.
Examples
from microorganisms, plants and animals. Emphasis on molecular
and biochemical aspects of mechanisms controlling gene expression
in eukaryotic cell differentiation.
GN/ST
756 Computational Molecular Evolution
Preq:
GN 411 and ST 511 or consent of instructor
Phylogenetic
analyses of nucleotide and protein sequence data. Sequence
alignment, phylogeny reconstruction and relevant computer software.
Prediction of protein secondary structure, database searching,
bioinformatics and related topics. Project required.
GN
820E Professionalism and Ethics
Lead
discussions of the principles of research ethics and dilemmas
in the contemporary research environment.
GN
735 (temporary number GN 810G) Introduction to Genomic Science
This course is designed to introduce students from a variety of
backgrounds to the scope and methodology of genomic science. The
emphasis will be on empirical approaches to the underlying biology,
science statistical and technological detail will be provided
in other courses. It is envisaged that 20-40 students may take
the course each fall semester, including students from departments
diverse as statistics, genetics, crop science, biochemistry, entomology
and engineering. The syllabus is likely to be divided into four
modules.
After
introducing sequencing and mapping technology, these modules will
cover:
- the
aims, specific methods and findings of the major genome projects
(bacterial, human, plant and animal);
- approaches
to documenting genome expression from single gene analysis to
SAGE, differential display and microarray hybridization;
- functional
genomics, including an introduction to applied genomics, dealing
with topics such as parasitology, advanced plant and animal
breeding and pharamacogenetics.
MB
714 Microbial Metabolic Regulation
Preq:
MB 351, BCH 451 (Credit in both MB 414 and MB 714 is not allowed)
An
integrative perspective on bacterial physiology and metabolism
through analysis of metabolic regulatory functions.
MB
718 Introductory Virology
Preq:
BCH 451 or GN 411 or MB 351
Introduction
to principles of virology including: classification and nomenclature,
epidemiology, structure, genome replication, gene expression strategies
and cellular infection cycle. Major groups of viruses including
those with DNA genomes and positive-sense or negative-sense RNA
genomes.
MB/BO/GN/PP
730 Fungal Genetics and Physiology
Preq:
BCH 451, BO 775, GN 411 or PP 501
Basic
concepts of genetics and physiology of fungi, with emphasis on
saprophytic and plant pathogenic mycelial fungi. Current literature
on evolution, cell structure, growth and development, gene expression,
metabolism, sexual and asexual reproduction and incompatibility
systems. Laboratory exercises on mutant isolation, sexual and
parasexual analysis, genetic transformation, and RFLP and isozyme
analysis.
MB/IMM/PHY 751 Immunology
Preq:
BCH 451, GN 411, MB 351
Introduction
to mechanisms of immunity in man and animals. Emphasis on interactions
between cells of the immune system in production of immune responses
and the molecules in control of these interactions.
PO/CBS
756 Immunogenetics
Preq:
MB 501C or MB 751 or consent of instructor
Basic
concepts of the immune system. Genetic
basis of the immune response including immunoglobulin genetics,
major histocompatibility complexes and their role in the immune
response, the molecular basis of the immune system and effector
mechanisms.
MB/GN
758 Prokaryotic Molecular Genetics
Preq:
BCH 451 or BCH 551, GN 411, MB 401
Structure
and function in prokaryotic molecular genetics, with emphasis
on mutations and mutagenic pathways, transcriptional and translational
regulation, RNA processing, DNA replication and recombination
and characterization of recombinant DNA molecules. Applications
of genetic and recombinant DNA techniques to microbial processes,
including strain construction and enhancement of gene expression.
MB/GN
760 Experimental Microbial Genetics
Preq:
BCH 561, GN 411, MB 351
Laboratory-oriented
presentation of current methodologies and concepts in molecular
microbial genetics and their application to strain construction,
plasmid and phage manipulations, mutagenesis, cloning and genetic
engineering of microorganisms.
MB/CBS/IMM
783 Advanced Immunology
Preq:
CBS 753 or VMM 815 or MB 751 or equivalent or consent of instructor
The
ontogeny and phylogeny of self and non-self recognition. Emphasis
on basic mechanisms evolved during the evolution of the species.
Speciality areas such as immunology of reproduction and genetic
regulation of the immune response.
PP
729 Plant Pathogenesis
Preq:
PP 501, BCH 551, BO 751, consent of instructor
Infection
processes, alterations in photosynthesis, respiration, nitrogen
metabolism, vascular function and growth regulator function. Biochemical
nature of the weapons utilized by pathogens in pathogenic attack
and defensive mechanisms employed by the hosts in resisting attack
and resultant dynamic interactions.
PP
732 Genetics of Host-Parasite Interactions
Preq:
BCH 451, GN 411, MB 401 or consent of instructor
Concept-oriented
approach to an understanding of host-parasite genetic interactions
from molecular through population levels. In-depth consideration
of gene action, gene-for-gene interactions, co-evolution, pathogen
virulence, host defense, gene flow in populations and other current
topics.
PP/BO/MB
775 The Fungi
Preq:
BO 200 or equivalent
Overview
of the fungi within framework of a survey of major classes.
ST
501 Experimental Statistics for Biological Sciences I
Preq:
ST 311 or graduate standing
Basic
concepts of statistical models and use of samples; variation,
statistical measures, distributions, tests of significance, analysis
of variance and elementary experimental design, regression and
correlation, chi-square.
ST
701 Experimental Statistics For Biological Sciences II
Preq:
ST 511
Covariance,
multiple regression, curvilinear regression, concepts of experimental
design, factorial experiments, confounded factorials, individual
degrees of freedom and split-plot experiments. Computing laboratory
addressing computational issues and use of statistical software.
ST
741 Statistical Theory I
Coreq:
MA 425 or MA 511 and MA 405
Probability
tools for statistics: description of discrete and absolutely continuous
distributions, expected values, moments, moment generating functions,
transformation of random variables, marginal and conditional distributions,
independence, order statistics,multivariate distributions, concept
of random sample, derivation of many sampling distributions.
ST
742 Statistical Theory II
Preq:
ST 741; Coreq:
MA 426 or MA 512
General
framework for statistical inference. Point estimators: biased
and unbiased, minimum variance unbiased, least mean square error,
maximum likelihood and least squares, asymptotic properties. Interval
estimators and tests of hypotheses: confidence intervals, power
functions, Neyman-Pearson lemma, likelihood ratio tests, unbiasedness,
efficiency and sufficiency.
ST
743 Linear Models and Variance Components
Preq:
MA 405, ST 741; Coreq:
ST 742
Theory
of estimation and testing in full and non-full rank linear models.
Normal theory distributional properties. Least squares principle
and the Gauss-Markoff theorem. Estimability and properties of
best linear unbiased estimators. General linear hypothesis. Application
of dummy variable methods to elementary classification models
for balanced and unbalanced data. Analysis of covariance. Variance
components estimation for balanced data.
ST/GN
757 Statistics for Molecular Quantitative Genetics
Preq:
ST 512 and GN 703 or ST 721
Genetic
mapping data. Linkage map reconstruction, quantitative genetical
models. Statistical
methods and computer programs for mapping quantitative trait loci
and estimating genetic architecture of quantitative traits.
ST
793 Advanced Statistical Inference I
Inference
with emphasis on definition of statistical models, construction
and use of likelihoods, and general estimating equations. Comparison
of inference methods based on jackknife, bootstrap, and normal
approximations. Rank and permutation tests and concepts from robust
inference.
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