Genetics and Genomics courses for first-year students
AGR 5307 Molecular Genetics for Crop Improvement
Introduction into concepts and applied aspects of plant molecular and cellular biology that allow students to understand and discuss strategies for crop improvement through biotechnology. Instructor – Altpeter, 3 credits, taught every spring.
AGR 5321C Genetic Improvement of Plants
Genetic basis for crop improvement including methods for improving crop yield, pest resistance, and adaptability. Emphasis on manipulating genetic variability in self- and cross-pollinate, annual and perennial crop plants. Overview of plant biotechnology and molecular breeding techniques. Instructor – Quesenberry, 3 credits, taught every fall.
AGR 6322 Advanced Plant Breeding
Theory and use of biometrical genetic models for analytical evaluation of qualitative and quantitative characteristics, with procedures applicable to various types of plant species. Instructor – Kenworthy, 3 credits, taught in Spring of even years.
AGR 6325L Plant Breeding Techniques
Examination of various breeding techniques used by agronomic and horticultural crop breeders in Florida. Field and lab visits to active plant breeding programs, with discussion led by a specific breeder each week. Hands-on experience in breeding programs. Instructor – Kenworthy, 1 credit, taught in Spring of odd years.
ANG 6532 Molecular Genetics of Disease
This course will examine the molecular genetics of disease in humans. The completion of the human genome sequence, the availability of high-throughput, next-generation sequencing platforms, and public databases of genetic variants have greatly accelerated the discovery of genes involved in disease, leading to breakthroughs in diagnosis and treatment. We will discuss a range of genetic disorders from single-gene recessive defects (e.g. myotonic dystrophy and alpha 1-antitrypsin deficiency) to complex diseases (e.g. diabetes and Alzheimer’s). Methods to isolate genes involved in disease (e.g. whole genome scans and linkage disequilibrium), genetic testing, and types of treatment (e.g. gene therapy) will be discussed. We will also discuss the ethical, legal and social issues associated with genetic investigation of human health and disease. Instructor – Connie Mulligan, email@example.com, 3 credits
ANG 6592 Seminar in Molecular Anthropology
The purpose of this class is to examine current applications of molecular data to questions of human evolution and population genetics. Emergence of modern Homo sapiens, Neanderthal genetics, reconstruction of human migrations, and evidence of natural selection on the human genome are among the topics discussed in detail. Examples of ancient DNA studies, admixture, and molecular genetics of human disease are also briefly discussed. Data types include mitochondrial DNA, Y chromosome, nuclear DNA, and various –omic datasets, including genomic, exomic, transcriptomic, etc. Instructor – Connie Mulligan, firstname.lastname@example.org, 3 credits.
BOT 6935 Sect. 1E96 – Evolutionary Processes
This 3 credit graduate seminar course will focus on understanding how the major forces of evolution (natural selection, genetic drift, mutation, and migration) influence both patterns of genetic variation within populations, inferences about population structure, and the speciation process. The course is intended for MS or PhD students (in the FLMNH, Biology, Genetics, PMCB, SNRE or other graduate programs) interested in an introduction to the principals of population genetics and evolution. We will read Will Provine’s excellent book “The Origins of Theoretical Population Genetics” which in spite of its title is a real page-turner (the author was Betty Smocovitis’s thesis advisor), along with modern primary literature. I anticipate that we will cover topics including F-statistics, detecting selection and local adaptation, the evolution of sex chromosomes, and speciation genetics. The final choice of topics will depend upon the interests of the enrolled students.
ENY 5820 Insect Molecular Genetics
You will learn the basic terms and concepts associated with genetic manipulation of insects and the use of molecular genetic methods to solve problems in entomology involving sex determination, insect behavior, systematics, ecology, and transformation of pest and beneficial insects. The course will enable you to identify literature for additional study on specific topics.
General Description The course emphasizes the fundamental concepts behind several molecular methods, such as the polymerase chain reaction (PCR), cloning, sequencing, genomic libraries and Southern and Northern blots, to answer interesting questions of interest to entomologists. The course is organized into three components and is intended to provide people with little previous experience in molecular genetics with an introduction to concepts, terminology and applications of these powerful tools.
Email: email@example.com, Phone: 352-273-3961; Fax: 392-0190
GMS 5905 Introduction to phylodynamics: A practical approach to molecular phylogenetics of pathogens
By the end of the course the students will have a solid understanding of the basic principles of molecular evolution, tree-building algorithms (distance, maximum likelihood and Bayesian based methods), molecular clocks theory, and coalescence theory. They will also be able to analyze real molecular sequence data (using HIV and HCV data sets) with the MEGA5 and BEAST software programs, to infer maximum likelihood and Bayesian trees, calibrate a molecular clock and use coalescence models to investigate the demographic history of microbial epidemics and the relationship between intra-host viral evolution and pathogenesis. Instructor: Marco Salemi, firstname.lastname@example.org, 3 credits.
GMS 6014 – Applications of Bioinformatics in Genetic Research
This course is designed to help graduate students in molecular biology or related disciplines to understand the basis of bioinformatics applications, and to develop the necessary skills that will enable them to use these tools accurately and creatively in their research.
GMS 6231 – Genomics and Bioinformatics
Principles of genomic characterization and bioinformatic analysis of eukaryotes, including an overview of analytical platforms, computational tools, experimental design, analysis methods and databases used to study DNA sequence, gene expression and protein levels. The course aims at providing an understanding of the principles of genomic analysis of eukaryotes at various levels (DNA, mRNA and protein), and of the bioinformatics methods used for this purpose.
GMS 6232 – Advanced Applications of Bioinformatics in Genetic Research
A special topic course designed for students who want to gain more hands-on experience in applying bioinformatics and computational approaches to solve real research problems. This course focuses on programming and the development of new software tools to solve biological problems (as opposed to simply using existing tools).
GMS 6233 Quantitative models of protein evolution and phylogenetics
Please join us for this two-unit course, emphasizing the study of the theoretical principles underlying models of protein evolution, as used in phylogenetic analysis. Through this course students will develop a critical understanding of the biological principles and mathematical tools used to model protein evolution in inferring phylogenetic relations. The students will learn about the principles and assumptions underlying these models and will study their applications in current phylogenetic methods. The course will consist of interactive lectures in a socratic format and will be tailored to the progress of the students. This formal course should be useful to all graduate students interested in phylogenetic methods and the biology and evolution of proteins (e.g., Genetics and Genomics, Biology, IDP). The instructor is a computational biologist with training in theoretical population genetics, evolutionary theory and bioinformatics. Instructor – Luciano Brocchieri, 2 credits.
GMS 7795 Drosophila Neurogenetics: From Development to Function
This 5-week (1-module) course will provide a comprehensive and detailed introduction to contemporary research on the genetics of Drosophila neurobiology. The course will be divided in three major sections covering: (A) the development of the CNS, (B) the dissection of neural circuits in the adult brain, and (C) the genetic basis of complex behaviors. This comprehensive course will provide graduate students with a strong background on the genetic pathways that control the development of the CNS, the generation of brain circuits, and complex behaviors. The target audience for this course is second year IDP students of the Neuroscience and Genetics concentrations, and Master students from the Biotechnology and Biomedical Engineering programs. Only the core course GMS 6001 will be required, although basic genetics and neuroscience courses will be helpful. Instructors – Fernandez-Funez, Rincon-Limas, 1 credit.
HOS 5743 Phytochemicals in Food and Health
This course is focused on applied biotechnology. It examines the nature and properties of phytochemicals in fruits and vegetables including their taxonomic distribution, potential roles in human disease prevention/health promotion, biosynthesis and degradation, enzymes, genes and case studies of select plant breeding or metabolic engineering efforts.
Instructor: Dr. Bala Rathinasabapathi, email@example.com 3 credits, taught even years, Summer B semesters, Pre-req: BCH 4024 or equivalent
MCB 5303L Microbial Genetics Lab ISIS 3298 02 Shanmugam
MCB 6937 Ancestral Reconstruction
We will learn about the uses and methods for reconstructing ancestral protein (and nucleotide) sequences, with the side-goal of producing a set of ancestral sequences for your research, so bring your data and interesting questions (or we’ll develop them as we go). 2 credits.
PCB 5136L Techniques Microbiology Lab ISIS 0897 03 Preston
PCB 5530 Plant Molecular Biology and Genomics
The course has four modules. The first two modules focus on building student understanding of basic principles and foundational knowledge of molecular mechanisms controlling plant growth, development and adaptation. The second two modules introduce students to current genomics technologies, data and analyses with the goal of stimulating students to think critically and creatively about current research questions. Instructors – Altpeter, Hanson, Davis, Peter, 3 credits.
PCB 6555 Introduction to Quantitative Genetics
This course is intended for students of all disciplines who are interested in genetic principles and biometric evaluation of characters that exhibit continuous variation in natural populations or breeding programs. This course will introduce graduate students to concepts, theory and methods in quantitative genetics with emphasis in applications for breeding programs and statistical analysis of genetic experiments. The course is designed for both MS and Phd graduate students in the following disciplines: plant or anuimal genetics; plant or anumal breeding; molecular gentics or biotechnology; conservation biology in botany, zoology or fisheries. http://sfrc.ufl.edu/people/faculty/gezan/ (offered odd years, Spring)
PHA 6427 Pharmacogenetics of Drug Metabolism and Transport
Pharmacogenetics/pharmacogenomics is the study of how an individual’s genetic inheritance affects the body’s response to drugs. This course will examine factors that affect drug response including genetics, as well as, additional factors such as environment, diet, age, and concurrent drug therapy and health status. Methods important to pharmacogenomics research will be presented. The course will use a combination of lectures and student-led discussion of recent papers from the primary literature. The goal of this course is to provide students an understanding of pharmacogenetics/pharmacogenomics in the context of variability in drug response and the application of pharmacogenetics to drug development and drug treatment.
PHA 6449 Pharmaogenomics
Pharmacogenomics is the study of how an individual’s genetics influences responses to drugs. This course will focus on pharmacogenetics and pharmacogenomics research design, including utilization of key knowledge from the human genome and HapMap projects, candidate gene, versus genome-wide approaches, other considerations in design of human pharmacogenomics investigations, and approaches to defining functional effects of pharmacogenetic candidates. The course will use a combination of lectures, discussions of assigned literature, projects and student-led presentations. The goal of this course is to provide students with the knowledge and skills to undertake pharmacogenomics research. 2 credits.
ZOO 6927 (may be classified as PCB also) Population Genetics
Topics: Population and quantitative genetics. Theory of gene frequency dynamics within and between populations. Deterministic and stochastic processes in evolution.
Instructor – Charles Baer, 4 credits.
ZOO 6927 Comparative Genomics of Eukaryotes
The course will be based upon readings from the literature and a class project focused on three complete and assembled animal genomes (three as yet unpublished crocodilian genomes). We will complete some readings and develop interesting analyses that can be conducted by comparing these genomes with each other and with other available genomes. Instructor – Edward Braun, 3 credits
Journal clubs/seminars (generally 1 credit):
BCH 7410 Advanced Gene Regulation
This is a literature based course that involves one hour lectures by faculty followed by the presentation and discussion of current literature in the field of gene regulation, chromatin structure, and epigenetics. Instructor – Jorg Bungert
GMS 6012 Human Genetics
This course will cover a variety of topics in human genetics that builds on the content of GMS 6001 genetics section. Thus, it will focus on the most relevant recent discoveries, new tools in human genetics, complex genetic situations, and novel mechanisms in the context of human disease, using clinical examples. There may be a small group activity. Prerequisite: GMS 6001, or permission of Instructor (Peggy Wallace). This course is geared toward IDP Ph.D. students (1st year or beyond), particularly those in the Genetics concentration, but other students are welcome provided they have a good understanding of basic genetics and molecular biology.
GMS 6013: Developmental Genetics
This course is a combined lecture and seminar format that covers current topics in the molecular genetic mechanisms of vertebrate embryonic development. Instructors: Cohn and Harfe. Offered in Spring of even numbered years
GMS 6015 Human Genetics II
This course will survey current advanced topics of human genetics, emphasizing novel tools, mechanisms, and applications in medicine. Prerequisite: graduate-level knowledge of genetics and molecular biology (e.g. GMS6001 and GMS6012). Please contact the course director, Dr. Margaret (Peggy) Wallace (firstname.lastname@example.org), to further clarify if you have any question about whether your background is appropriate for the course. This course usually enrolls students from multiple programs, with different background coursework and experiences.
MCB 7922 JOURNAL COLLOQUY
This fall, the Microbiology & Cell Science department is proud to offer a journal colloquium in scientific writing for graduate students. In this colloquium, we will analyze primary research articles, not from a scientific perspective but from the perspective of literary structure. We will determine precisely how modern biological research articles are constructed and how the different parts combine to clearly convey (or not) the scientific findings. The colloquium is being facilitated by a practicing biological scientist with experience in literary analysis and critique. This course will make you a better reader and writer. We will probably meet Thursdays at 4pm, so consider that when planning your schedule.
ZOO 6927 Seminar in Molecular Evolution
This course consists of a “journal club”, where two students every Thursday will each select a different article for the class to read beforehand for discussion during either period 5 or 6. The chosen articles can be from any area of comparative genetics and genomics. For example, in the past, students have chosen papers on coalescent methods for inferring phylogenies; next generation sequencing technology for comparative biology; human origins and historical population growth/migrations; statistical and computer models of molecular evolution; protein evolution, function, and structure; hidden Markov models, evolution, and bioinformatics; sex chromosome evolution; and the like. Indeed, a distinct strength of the course is the opportunity to review studies from different areas outside of one’s discipline. Instructor – Miyamoto, 2 credits.
Courses not for credit:
Core concepts in biomanufacturing and quality systems
Designed for the development of skills required for success in today’s biotechnology industry, this course covers two tracks: “Processes & Facilities” and “Regulatory Affairs, Quality Assurance, & Quality Control.” Using a blend of hands-on applications and lectures, course instructors integrate core concepts of processes and facilities with quality compliance to build a solid understanding of the development, manufacture, testing, and release-for-sale of a regulated product.
AREAS OF FOCUS
Students will be asked to apply project management skills in the production and regulation of a standard biotechnology-based process.Each student will complete both tracks of study in Processes & Facilities as well as Regulatory Affairs, QA, and QC. An industry recognized certificate documenting 24 hours of blended hands-on experience and lecture, will be issued upon completion.
Who should attend:
This course is intended for current employees in biotechnology, or individuals who are interested in entering a career in the biotechnology industry.
For more information or any questions, contact Lori Wojciechowski: 386.462.3181, email@example.com, Website: http://www.cerhb.ufl.edu/education-center