Biology and Biotechnology
Material in this course focuses on biological (especially microbiological) systems by which materials and energy can be interconverted (e.g., waste products into useful chemicals or fuels). The processes are dealt with at the physiological and the system level, with emphasis on the means by which useful conversions can be harnessed in a biologically intelligent way. The laboratory focuses on measurements of microbial physiology and on bench-scale process design.
Strategies for optimization of bioprocesses for scale-up applications. In addition to the theory of scaling up unit operations in bioprocessing, students will scale up a bench scale bioprocess (5 liters) including fermentation and downstream processing to 55 liters. Specific topics include the effects of scaling-up on: mass transfer and bioreactor design, harvesting techniques including tangential flow filtration and centrifugation, and chromatography (open column and HPLC). Recommended courses include BB 3055 Microbial Physiology and BB 4070/560 Separations of Biological Molecules, as a working knowledge of the bench scale processes will be assumed. Otherwise, instructor permission is required.
This seminar course will examine what is known about ecological responses to both natural and human-mediated environmental changes, and explore approaches for solving ecological problems and increasing environmental sustainability. Areas of focus may include, and are not limited to, conservation genetics, ecological responses to global climate change, sustainable use of living natural resources, and the environmental impacts of agricultural biotechnology. Recommended background: BB 1045, BB 2040, ENV 1100. This course will be offered in 2014-15 and in alternating years thereafter.
Students are exposed to various issues related to integrity in doing research to enable development of an appropriately reasonable course of action in order to maintain integrity on a variety of research-related performance and reporting activities. These activities include, but are not limited to data fabrication, authorship, copyright, plagiarism, unintended dual use of technology, and responsibilities towards peers who may request your confidential review or feedback. The course will use class discussion, case studies, and exercises to facilitate an understanding of the responsibilities of scientists to their profession. Students may receive credit for either BB 551 or a BB 570 course entitled Research Integrity in the Sciences but not both.
This course will cover key elements to writing successful grant proposals and manuscripts. This includes project development, identification of funding agencies or journals, proposal and manuscript writing and editing, as well as aspects of the submission and review process. Students will be expected to develop a NIH/NSF style postdoctoral proposal outside their dissertation field and participate in a mock proposal review panel. Students are expected to complete this course prior to their Qualifying Exam. Students may receive credit for either BB 552 or a BB 570 course entitled Scientific Writing and Proposal Development but not both.
This applied course introduces students to the basics of experimental design and data analysis. Emphasis will be placed on designing biological experiments that are suitable for statistical analysis, choosing appropriate statistical tests to perform, and interpreting the results of statistical tests. We will cover statistical methods commonly used by biologists to analyze experimental data, including testing the fit of data to theoretical distributions, comparisons of groups, and regression analysis. Both parametric and non-parametric tests will be discussed. Students will use computer packages to analyze their own experimental data. Students may receive credit for either BB 553 or a BB 570 course entitled Experimental Design and Statistics in the Life Sciences but not both.
This course is offered every semester covering different topics, both basic and applied, in Biology and Biotechnology and rotates among the faculty. Students read and discuss the literature in relevant topics.
This course is arranged with an individual faculty member within the student?s discipline. The graduate student is involved in the development of course materials, such as a syllabus, projects, or quizzes, and course delivery, such as lecturing or facilitating a conference session (20% delivery limit). In addition to covering course pedagogy, the faculty member arranges for the student teacher to be evaluated by students enrolled in the course and reviews the student reports with the student teacher.
This course provides a detailed hands-on survey of state-of-the-art methods employed by the biotechnology industry for the purification of products, proteins in particular, from fermentation processes. Focus is on methods that offer the best potential for scale-up. Included is the theory of the design, as well as the operation of these methods both at the laboratory scale and scaled up. It is intended for biology, biotechnology, chemical engineering and biochemistry students. (Prerequisite: knowledge of basic biochemistry is assumed.)
The course is intended to introduce students to the use of model experimental systems in modern biological research. The course covers prokaryotic and eukaryotic systems including microbial (Escherichia coli) and single cells eukaryotes (fungi); invertebrate (Caenorhabditis elegans, Drosophila melanogaster) and vertebrate (mice, zebra fish) systems and plants (moss, algae and Arabidopsis thaliana). Use of these systems in basic and applied research will be examined. Students may receive credit for either BB 561 or a BB 570 course entitled Model Systems: Experimental Approaches and Applications but not both.
This course focuses on molecular events that regulate cell cycle transitions and their relevance to mammalian differentiated and undifferentiated cells. Topics include control of the G1/S and G2/M transitions, relationships between tumor suppressor genes such as p16, Rb, p53 or oncogenes such as cyclin D, cdc25A, MDM2 or c-myc and cell cycle control. Where appropriate, the focus is on understanding regulation of cell cycle control through transcriptional induction of gene expression, protein associations, posttranslational modifications like phosphorylation or regulation of protein stability like ubiquitin degradation. Students may receive credit for either BB 562 or a BB 570 course entitled Cell Cycle Regulation but not both.
This advanced level course uses a seminar format based on research articles to discuss current topics related to the molecular/cell biology of viral structure, function, and evolution. Particular emphasis is placed on pathological mechanisms of various human disorders, especially emerging disease, and the use of viruses in research.
Specialty subject courses are offered based on the expertise of the department faculty, example topics include: Stem Cell Biology, Cell Cycle Regulation, and Model Systems in Biology.
Topics in this course focus on the basic building blocks of life: molecules, genes and cells. The course will address areas of the organization, structure, function and analysis of the genome and of cells. (Prerequisite: A familiarity with fundamentals of recombinant DNA and molecular biological techniques as well as cell biology.)
This course will provide an overview of bioinformatics, covering a broad selection of the most important techniques used to analyze biological sequence and expression data. Students will acquire a working knowledge of bioinformatics applications through hands-on use of software to ask and answer biological questions. In addition, the course will provide students with an introduction to the theory behind some of the most important algorithms used to analyze sequence data (for example, alignment algorithms and the use of hidden Markov models). Topics covered will include protein and DNA sequence alignments, evolutionary analysis and phylogenetic trees, obtaining protein secondary structure from sequence, and analysis of gene expression including clustering methods. (Prerequisite: knowledge of genetics, molecular biology, and statistics at the undergraduate level.) Students may not receive credit for both BB 581 and BB 4801.