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2009-2011 Courses and Programs

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Genetics, Development and Cell Biology

Graduate Courses |500 |600 |

www.gdcb.iastate.edu/

Martin Spalding, Chair of Department
University Professor: Horner
University Professors (Emeritus): Dolphin, Stadler
Professors: Brendel, Dobbs, Enger, Gu, Henderson, Howell, Johansen, Lee, Mayfield, Oliver, P. Peterson, T. Peterson, Rodermel, Schnable, Shen, Spalding, Wurtele
Professors (Emeritus): Atherly, Bishop, Buss, Imsande, Lamotte, Miller, Pattee, Pollak, Robertson, Smith, Stewart, Swenson, Welshons
Professors (Collaborators): Link, Shoemaker, Voytas
Associate Professors: Bassham, Becraft, Chou, Colbert, Dorman, Ingebritsen, McCloskey, Powell-Coffman, Sakaguchi, Viles
Associate Professor (Adjunct): Duvick
Associate Professors (Collaborators): Danilevskaya, Tucker
Assistant Professors: Coffman, Essner, Kuhlman, Schneider, Vollbrecht, Yang, Yin
Assistant Professors (Adjunct): Ilarslan, McGrail, Muszynski
Assistant Professors (Collaborators): Buell, Hopkins, Lawrence, Sen
Lecturer: Bastawros, Krumhardt

The Department of Genetics, Development and Cell Biology (GDCB) is dedicated to biological discovery and excellence in undergraduate and graduate education. The research and teaching mission of the department is to achieve a greater understanding of fundamental principles of life by focusing on basic cellular and subcellular processes, including genome dynamics, cell structure and function, cellular response to environmental and developmental signals, and molecular mechanisms of development. Recognizing that student education is of paramount importance, GDCB strives for excellence in teaching and research. GDCB plays a leading role in undergraduate and graduate training through a variety of activities including traditional courses, undergraduate internships in research laboratories, and advanced graduate seminar and literature-based courses. Innovative approaches to learning are emphasized throughout the curriculum.

Undergraduate Study

The GDCB Department offers undergraduate majors in conjunction with other departments. Students interested in the areas of genetics, development and cell biology should major in Biology, Genetics Bioinformatics and Computational Biology (BCBio). The Biology Major is administered and offered jointly by the GDCB and EEOB departments. The GDCB faculty, together with those in EEOB and BBMB, administer and offer the Genetics Major. Each of these majors is available through the College of Liberal Arts and Sciences or through the College of Agriculture and Life Sciences. BCBio is administered by the Departments of Computer Science, GDCB, and mathematics and is available through the college of Liberal Arts and Sciences.

The Biology Major and the Genetics Major prepare students for a wide range of careers in biological sciences. Training in Biology or Genetics may lead to employment in teaching, research, or any of a variety of health-related professions. Some of these careers include biotechnology, human and veterinary medicine, agricultural sciences and life science education. BCBio majors are prepared for careers at the interfaces of biological, informational and computational sciences in the above fields. These majors are also excellent preparation for graduate study in bioinformatics, molecular genetics, cell and developmental biology, neuroscience and related fields. Faculty members in GDCB contribute to the undergraduate courses listed below. The full descriptions of these courses can be found in the Biology, Genetics and BCBio sections of the catalog.

Biol 101, 110, 111, 155, 211, 211L, 212, 212L, 255, 255L, 256, 256L, 258, 305, 305L, 313, 313L, 314, 314L, 330, 352, 394, 423, 423L, 428, 436, 444, 490, 494, 495, Gen 110, 260, 308, 410, 411, 490, 491, 495, BCBio 110, 211, 401, 402 and 442.

Graduate Study

Understanding the genetic blueprint and the functions of cells is critical to virtually all aspects of biology. The basic mission of the Department of Genetics, Development and Cell Biology is to achieve a greater understanding of fundamental principles of life. The GDCB faculty and students conduct hypothesis-driven research into the biology of animals, plants and microbes. While research in GDCB is often based on discovery and analysis of molecular mechanisms of life processes, a true understanding of living organisms will ultimately require the integration of molecular mechanisms in the context of dynamic structural components of the living cell. Thus, research efforts within GDCB use molecular, genetic, biochemical, computational and imaging techniques to study systems at increasingly complex levels of organization.

GDCB faculty contribute to a broad but integrated array of cutting-edge research topics, implementing interactive and multidisciplinary approaches that bridge conventional boundaries, and incorporating experimental and computational biology as complementary approaches. Examples include using genetics and molecular biology to investigate the cellular basis of development, or combining biochemical and computational approaches to study basic subcellular functions, signal transduction or metabolism.

The faculty in the GDCB department train graduate students in several interdepartmental majors/programs including Bioinformatics and Computational Biology, Ecology and Evolutionary Biology, Genetics, Immunobiology, Plant Physiology, Interdisciplinary Graduate Studies, Microbiology, Molecular, Cellular and Developmental Biology, Neuroscience and Toxicology. Graduate work leading to both Master of Science (M.S.) and Doctor of Philosophy (Ph.D.) degrees are available.

Prospective graduate students need a sound background in the physical and biological sciences, as well as Mathematics and English. Interested students should check the links on the GDCB web site ( www.gdcb.iastate.edu/ ) for specific admissions procedures and the latest information about individual faculty and their research programs. The interdepartmental majors and programs require submission of Graduate Record Examination (GRE) aptitude test scores. Advanced GRE scores are recommended. International students whose native language is other than English must also submit TOEFL scores with their application.

Students who are enrolled in the interdepartmental graduate majors with affiliations with GDCB are required to actively participate in seminars, research activities, and to show adequate progress and professional development while pursuing their degree. For both the M.S. and Ph.D. degrees, it is expected that research conducted by the student will culminate in the writing and presentation of a thesis or dissertation. The Graduate College, the GDCB Faculty, and the individual student's major professor and Program of Study Committee provide requirements and guidelines for study. General information about graduate study requirements can be found at the web site for the Graduate College ( www.grad-college.iastate.edu/ ) and requirements for the interdepartmental majors can be found by following the links from the GDCB web site above. Although not a formal requirement, the GDCB faculty recommends that students pursuing the Ph.D. include teaching experience in their graduate training.

Courses primarily for graduate students, open to qualified undergraduate students

GDCB 508. Biotechnology in Agriculture, Food, and Human Health. (3-0) Cr. 3. F.S.Prereq: Biol 211 and 212. Scientific principles and techniques in biotechnology. Products and applications in agriculture, food, and human health. Ethical, legal, and social implications of biotechnology. A research paper is required for graduate credit.

GDCB 510. Transmission Genetics. (3-0) Cr. 3. F.Prereq: Gen 410 or graduate standing. An in-depth investigation of the modern research practices of transmission genetics. Designed for students interested in genetic research. Topics include: Mendelian genetic analysis, analysis of genetic pathways, mutational analysis of gene function, chromosomal mechanics, gene mapping, extranuclear inheritance, human genetic analysis.

GDCB 511. Molecular Genetics. (Cross-listed with MCDB). (3-0) Cr. 3. S.Prereq: Biol 313 and BBMB 405. The principles of molecular genetics: gene structure and function at the molecular level, including regulation of gene expression, genetic rearrangement, and the organization of genetic information in prokaryotes and eukaryotes.

GDCB 512. Plant Growth and Development. (Cross-listed with MCDB, PlBio). (2-0) Cr. 2. S.Prereq: Biol 330 or a course in developmental biology; GDCB 545 or BBMB 404, 405 or GDCB 520. Plant growth and development and its molecular genetic regulation. Hormone biosynthesis, metabolism, and action. Signal transduction in plants.

GDCB 513. Plant Metabolism. (Cross-listed with PlBio). (2-0) Cr. 2. F.Prereq: Biol 330, Phys 111, Chem 331; one semester of biochemistry recommended. Photosynthesis, respiration, and other aspects of plant metabolism.

GDCB 520. Genetic Engineering. (Cross-listed with BBMB, MCDB). (3-0) Cr. 3. Alt. F., offered 2009.Prereq: Gen 411 or BBMB 405. Strategies and methods of gene cloning, restriction endonuclease mapping, southern hybridization, isolation and manipulation of plasmid DNA, and detection of specific genes in bacteria.

GDCB 528. Cellular Growth and Regulation. (Cross-listed with MCDB). (3-0) Cr. 3. Alt. F., offered 2010.Prereq: Courses in cell biology and BBMB 404, 405. Cell cycle, regulation of cell growth, cell division, membranes, transport processes, and regulation of cellular activities.

GDCB 529. Plant Cell Biology. (Cross-listed with MCDB). (2-0) Cr. 2.Prereq: Biol 313, 314, 330 or BBMB 405. Organization, function, and development of plant cells and subcellular structures.

GDCB 533. Principles of Developmental Biology. (Cross-listed with MCDB). (3-0) Cr. 3. Alt. F., offered 2009.Prereq: Biol 314. Fundamental principles in multicellular development. Emphasis on cellular and molecular regulation of developmental processes, and experimental approaches as illustrated in classical studies and current literature.

GDCB 536. Statistics for Population Genetics. (Cross-listed with Stat). (3-0) Cr. 3. Alt. F., offered 2010.Prereq: Stat 401, 447; Gen 320 or Biol 313. Statistical models for population genetics covering: selection, mutation, migration, population structure, and linkage disequilibrium. Applications to gene mapping (case-control, TDT), inference about population structure, DNA and protein sequence analysis, and forensic and paternity identification.

GDCB 537. Statistics for Molecular Genetics. (Cross-listed with Stat). (3-0) Cr. 3. Alt. S., offered 2011.Prereq: 401, 447; Gen 320 or Biol 313. Statistical models, inference, and computational tools for linkage analysis, quantitative trait analysis, and molecular evolution. Topics include; quantitative trait models, variance component mapping, interval and composite-interval mapping, and phylogenetic tree reconstruction.

GDCB 538. Computational Genomics and Evolution. (Cross-listed with BCB). (3-0) Cr. 3. Alt. S., offered 2011.Prereq: Biol 313. Introduction to evolutionary sequence analysis at the genome level. Topics include sequence alignment, phylogenetic inference, molecular clock analysis, ancestral state inference, sequence/structure relation, functional divergence and prediction, evolutionary development, genome duplication, and comparative genomics. Focus will be on data analysis and biological interpretation.

GDCB 539. Statistical Methods for Computational Biology. (Cross-listed with BCB). (2-0) Cr. 2. Alt. S., offered 2010.Prereq: BCB 568. Gu. Advanced discussion about statistical modeling of DNA and amino acid sequences, microarray expression profiles and other genome-wide data interpretation.

GDCB 542. Introduction to Molecular Biology Techniques. (Cross-listed with B M S, BBMB, BCB, EEOB, FS HN, Hort, NREM, NutrS, V MPM, VDPAM). Cr. 1. Repeatable. F.S.SS.Prereq: Graduate classification. Workshops in basic molecular biology techniques and related procedures. Satisfactory-fail only.
A. DNA Techniques. Includes genetic engineering procedures, sequencing, PCR, and genotyping. (F.S.SS.)
B. Protein Techniques. Includes fermentation, protein isolation, protein purification, SDS-PAGE, Western blotting, NMR, confocal microscopy and laser microdissection, immunophenotyping, and monoclonol antibody production. (S.SS.)
C. Cell Techniques. Includes immunophenotyping, ELISA, flow cytometry, microscopic techniques, and image analysis. (F.S.)
D. Plant Transformation. Includes Agrobacterium and particle gun-mediated transformation of tobacco, Arabidopsis, and maize, and analysis of transformants. (S.)
E. Proteomics. Includes two-dimensional electrophoresis, laser scanning, mass spectrometry, and database searching. (F.)

GDCB 544. Introduction to Bioinformatics. (Cross-listed with BCB, Cpr E, Com S). (4-0) Cr. 4. F.Prereq: Math 165 or Stat 401 or equivalent. Broad overview of bioinformatics with a significant problem-solving component, including hands-on practice using computational tools to solve a variety of biological problems. Topics include: database searching, sequence alignment, gene prediction, RNA and protein structure prediction, construction of phylogenetic trees, comparative and functional genomics.

GDCB 545. Plant Molecular Biology. (Cross-listed with MCDB, PlBio). (3-0) Cr. 3. F.Prereq: Biol 314, 330. Organization and function of plant nuclear and organelle DNA; regulation of gene expression. Methods of generating novel genetic variation. Impact of plant biotechnology on agriculture.

GDCB 556. Cellular, Molecular and Developmental Neuroscience. (Cross-listed with Neuro, B M S). (3-0) Cr. 3-4. F.Prereq: Biol 335 or Biol 436; physics recommended. Fundamental principles of neuroscience including cellular and molecular neuroscience, nervous system development, sensory, motor and regulatory systems.

GDCB 557. Advanced Neuroscience Techniques. (Cross-listed with Neuro). (2-0) Cr. 2. Alt. S., offered 2011.Prereq: Neuro 556 or equivalent course. Research methods and techniques; exercises and/or demonstrations representing individual faculty specialties.

GDCB 568. Bioinformatics II (Advanced Genome Informatics). (Cross-listed with BCB, Stat, Com S). (3-0) Cr. 3. S.Prereq: BCB 567, BBMB 301, Biol 315, Stat 430, credit or enrollment in Gen 411. Advanced sequence models. Basic methods in molecular phylogeny. Hidden Markov models. Genome annotation. DNA and protein motifs. Introduction to gene expression analysis.

GDCB 570. Bioinformatics IV (Computational Functional Genomics and Systems Biology). (Cross-listed with Com S, BCB, Stat, Cpr E). (3-0) Cr. 3. S.Prereq: BCB 567, Biol 315, Com S 311 and either 208 or 228, Gen 411, Stat 430. Algorithmic and statistical approaches in computational functional genomics and systems biology. Analysis of high throughput gene expression, proteomics, and other datasets obtained using system-wide measurements. Topological analysis, module discovery, and comparative analysis of gene and protein networks. Modeling, analysis, simulation and inference of transcriptional regulatory modules and networks, protein-protein interaction networks, metabolic networks, cells and systems: Dynamic systems, Boolean, and probabilistic models. Ontology-driven, network based, and probabilistic approaches to information integration.

GDCB 590. Special Topics. Cr. arr. Repeatable.Prereq: Permission of instructor.

GDCB 596. Genomic Data Processing. (Cross-listed with Com S, BCB). (3-0) Cr. 3. F.Prereq: Some basic knowledge of programming. Study the practical aspects of genomic data processing with an emphasis on hands-on projects. Students will carry out common data processing steps using bioinformatics tools. Topics include base-calling, raw sequence cleaning and contaminant removal; shotgun assembly procedures and EST clustering methods; genome closure strategies and practices; sequence homology search and function prediction; annotation and submission of GenBank reports; and data collection and dissemination through the Internet. Important post-genomic topics like microarray design and data analysis will also be covered.

Courses for graduate students

GDCB 632. Current Topics in Signal Transduction. Cr. 2-3.Prereq: Permission of instructor. Selected topics in signal transduction events, their molecular mechanisms and their relation to cellular processes. Topics may include cell recognition, second messenger systems, information integration and transfer, cell cycle, cell differentiation, and pattern formation.

GDCB 640. Signal Transduction. (Cross-listed with BBMB, MCDB). (3-0) Cr. 3. Alt. S., offered 2010.Prereq: GDCB 528, BBMB 404. Mechanisms and components of cellular signal transduction including receptors, G-proteins, second messengers, protein phosphorylation, other post-translational protein modifications, and transcriptional regulation.

GDCB 661. Current Topics in Neuroscience. (Cross-listed with Neuro, BBMB). Cr. 2-3. Repeatable. Alt. S., offered 2010.Prereq: Permission of instructor. Topics may include communication, hormones and behavior, neural integration, membrane biophysics, molecular and cellular neuroscience, developmental neurobiology, neuroanatomy and ultrastructure, sensory biology, social behavior, techniques in neurobiology and behavior.

GDCB 679. Light Microscopy. (Cross-listed with Micro, EEOB). (2-9) Cr. 5. Alt. F., offered 2010.Prereq: Permission of instructor. Current theories encompassing light optics and their applications for specimen preservation, paraffin and resin sectioning, general staining, histochemistry, cytophotometry, immunocytochemistry, autoradiography, image digitization, processing and presentation, and digital macro- and micrography. Limit of 10 students.

GDCB 680. Scanning Electron Microscopy. (Cross-listed with Micro, EEOB). (2-9) Cr. 5. Alt. F., offered 2009.Prereq: Permission of instructor. Current theories encompassing scanning electron optics and their applications for high and low vacuum microscopy, specimen chemical and cryopreservation methods, x-ray microanalysis, backscattered and topographic imaging, image digitization, processing and presentation. Limit of 10 students.

GDCB 681. Transmission Electron Microscopy. (Cross-listed with Micro, EEOB). (2-9) Cr. 5. Alt. S., offered 2011.Prereq: GDCB 679 and permission of instructor. Current theories encompassing electron optics and their applications for chemical and physical specimen preservation, ultramicrotomy, general staining and cytochemistry, immunocytochemistry, autoradiography, negative staining and shadowing, x-ray microanalysis, image digitization, processing and presentation.

GDCB 690. Seminar in GDCB. Cr. 1. Repeatable.Journal article critique and discussion by faculty and graduate students. Satisfactory-fail only.
A. Cellular, Molecular, and Developmental Biology
C. Neurobiology
D. Physiology
E. Evolution
F. Animal Models of Gene Therapy
H. Bioinformatics and Computational Biology

GDCB 691. Faculty Seminar. Cr. 1. Repeatable.Faculty research series.
G. Genetics. F. Prereq: Permission of instructor.
H. Bioinformatics and Computational Biology. (Same as BCB 691H).
P. Plant Development.
S. Prereq: GDCB 512 (can be taken concurrently).

GDCB 696. Research Seminar. (Cross-listed with Agron, BBMB, PlBio, Hort, For). Cr. 1. Repeatable.Research seminars by faculty and graduate students. Satisfactory-fail only.

GDCB 698. Seminar in Molecular, Cellular, and Developmental Biology. (Cross-listed with MCDB, BBMB, Micro, V MPM). (2-0) Cr. 1-2. Repeatable. F.S.Student and faculty presentations.

GDCB 699. Research. Cr. arr. Repeatable.Research for thesis or dissertation. Satisfactory-fail only.

GDCB 699I. Research. (Cross-listed with Ia LL, A Ecl, Anthr, EEOB). Cr. 1-4. Repeatable.