Biology & Biotechnology
Undergraduate Courses
BB 1035. Introduction to Biotechnology
Cat. I
This course will cover topics including genes-to-proteins, cell cycle, genomics, synthetic and systems biology, stem cells and regenerative medicine, cellular signaling, personalized medicine, and the production of therapeutic biologics. Through lectures, discussion and project work, students will gain an understanding of the function of biological systems at the molecular and cellular level and explore their application through genetic and cellular engineering to biotechnology. Projects will be designed to facilitate students’ understanding of the links between biological systems, biotechnology applications and their impact on society. This course is intended for BBT and other life science majors.
Recommended background: a solid working knowledge of biological principles
BB 1035. Biotechnology
Cat I (offered at least 1x per Year). Through lectures, discussion and project work, students will gain an understanding of the function of biological systems at the molecular and cellular level. This course will explore topics such as genes-to-proteins, cell cycle regulation, genomics, and cell signaling as foundational concepts in genetic and cellular engineering, synthetic biology, stem cell generation, regenerative and personalized medicine and the production of therapeutic biologies. Projects will be designed to facilitate students understanding of the links between biological systems and biotechnology applications, including their impact on society. This course is intended for BBT and other life science majors.
BB 2917. Hunting for Phage
Cat I (offered at least 1x per Year). Students in this course will become part of a national crowd sourcing initiative to isolate and identify novel bacteriophage. Students will design experiments to initially isolate phage (bacterial viruses) from environmental samples they have collected, then characterize and determine their DNA sequence. The DNA sequences will be used in the follow-on bioinformatics course BB 3526 Phage Hunters: The Analysis. Students in this course will make significant contributions to the field of genomics while gaining skill in the process of scientific inquiry, including hypothesis generation and testing, and practice in common microbiologic techniques. Students enrolled in this course may wish to consider enrollment in BB 3526 (Phage Hunters: The Analysis). Students that have already received course credit for BB 29IX or BB 2916 may not also receive credit for BB 2917.
BB 2917. HUNTING FOR PHAGE
Cat. I Students in this course will become part of a national crowd sourcing initiative to isolate and identify novel bacteriophage. Students will design experiments to initially isolate phage (bacterial viruses) from environmental samples they have collected, then characterize and determine their DNA sequence. The DNA sequences will be used in the follow-on bioinformatics course BB 3526 Phage Hunters: The Analysis. Students in this course will make significant contributions to the field of genomics while gaining skill in the process of scientific inquiry, including hypothesis generation and testing, and practice in common microbiologic techniques. Recommended background: A working knowledge of biotechnology or microbiology (BB 1035 or BB 2003, or equivalent). Students enrolled in this course may wish to consider enrollment in BB 3526 (Phage Hunters: The Analysis). Students that have already received course credit for BB 291X or BB 2916 may not also receive credit for BB 2917.
BB 3003. MEDICAL MICROBIOLOGY: PLAGUES OF THE MODERN WORLD
Cat. I
Using a case study approach, this course will focus on molecular mechanisms of pathogenesis of a wide range of infectious diseases and host-pathogen interactions including a survey of human immunobiology. Students will gain an understanding of microbes that are of medical relevance including bacteria, viruses, fungi, and protozoans, enabling them to make informed decisions about appropriate medical interventions. Students will be able to evaluate how their day-to-day choices impact public health as well as alter microbial communities. This interactive course is designed for all biology and biochemistry majors as well as other students with the recommended background who have an interest in the pathogenesis of disease.
Recommended background: a working knowledge of concepts in biotechnology,
molecular biology and microbiology (BB 1035, BB 2950, and BB 2003 or
equivalent)
Students may not receive credit for both BB 2002 (Microbiology: Plagues of the Modern World) and BB3003
BB 3003. Medical Microbiology: Plagues of the Modern World, a Case Study Approach
Cat I (offered at least 1x per Year). Using a case study approach, this course will focus on molecular mechanisms of pathogenesis of a wide range of infectious diseases and host-pathogen interactions including a survey of human immunobiology. Students will gain an understanding of microbes that are of medical relevance including bacteria, viruses, fungi, and protozoans, enabling them to make informed decisions about appropriate medical interventions. Students will be able to evaluate how their day-to-day choices impact public health as well as alter microbial communities. This interactive course is designed for all biology and biochemistry majors as well as other students with the recommended background who have an interest in the pathogenesis of disease. Students may not receive credit for both BB 2002 Microbiology: Plagues of the Modern World and BB 3003.
BB 3010. SIMULATION IN BIOLOGY
Cat. II
Computer simulations are becoming increasingly important in understanding and predicting the behavior of a wide variety of biological systems, ranging from metastasis of cancer cells, to spread of disease in an epidemic, to management of natural resources such as fisheries and forests. In this course, students will
learn to use a graphical programming language to simulate biological systems. Most of the classroom time will be spent working individually or in groups, first learning the language, and then programming simulation projects. We will also discuss several papers on biological simulations from the primary scientific literature. In constructing and comparing their simulations, students will demonstrate for themselves how relatively simple behavioral rules followed by individual molecules, cells, or organisms can result in complex system behaviors.
Recommended background: Students taking this course must have a solid background in a biological area they would like to simulate, at about the depth provided by a BB 3000 level class. No programming experience is assumed.
This course will offered in 2016-17, and in alternating years thereafter.
BB 3511. NERVE AND MUSCLE PHYSIOLOGY
Exercises in this course focus on computer and wet laboratory studies of nerve and muscle structure and function. Students will gain experience in hypothesis generation and testing, and will have extensive experience using an interactive biomedical/physiological data acquisition and analysis system.
Recommended background: BB 2903 (Anatomy & Physiology), concurrent or prior registration in BB 3101 (Human Anatomy & Physiology: Movement and Communication) or equivalents
BB 3514. CIRCULATORY AND RESPIRATORY PHYSIOLOGY
Exercises in this course focus on wet laboratory and computer studies of circulatory and respiratory system structure, function and physiology. Students will gain experience in hypothesis generation and testing, and will be introduced to an interactive biomedical/physiological data acquisition and analysis system.
Recommended background: BB 2903 (Anatomy & Physiology), concurrent or prior registration in BB 3102 (Human Anatomy & Physiology: Transport and Maintenance) or equivalents
BB 3515. Physiologic Systems Laboratory
Cat I (offered at least 1x per Year). Exercises in this course focus on computer and wet laboratory studies of nervous, musculoskeletal, circulatory and respiratory system structure, function, and physiology. Students will gain experience in hypothesis generation and testing and will be introduced to an interactive biomedical/physiological data acquisition and analysis system.
BB 3530. Immunotherapies: The Next Generation of Pharmaceuticals
Cat I (offered at least 1x per Year). While the production of monoclonal antibodies has been around since the 1970s, their clinical use as human therapeutics represents an increasingly popular and promising application. Beginning with a hybridoma cell line and using a discovery based approach, students in this course will explore the processes involved in the production and purification of monoclonal antibodies. Using cells in culture to produce the antibody, students will explore the efficacy and cost of a purification scheme involving separation techniques such as ion exchange and affinity chromatography to produce a purified product. Purification will be assessed using typical analytical techniques such as spectroscopy, electrophoresis and immunological based methods.
BB 3570. Cell Culture Models for Tissue Regeneration
Cat I (offered at least 1x per Year). This course is an intensive hands-on laboratory that explores mammalian cells as building blocks of complex tissues in vitro. In addition to learning standard cell culture skills, students will have the opportunity to examine cell survival, proliferation, differentiation, and function under different culture conditions. The course culminates with design and development of a cell-based system for an application in regenerative medicine (e.g., wound healing and fibrosis). Students will synthesize and present their work in the form of a research manuscript.
BB 357X. CELL CULTURE MODELS FOR TISSUE REGENERATION
Cat I (1/3 unit)
This course is an intensive hands-on laboratory that explores mammalian cells as building blocks of complex tissues in vitro. In addition to learning standard cell culture skills, students will have the opportunity to examine cell survival, proliferation, differentiation and function under different culture conditions. The course culminates with design and development of a cell-based system for an application in regenerative medicine (e.g., wound healing and fibrosis). Students will synthesize and present their work in the form of a research manuscript.
Recommended background: a working knowledge of the principles of cell biology (BB 2550 or equivalent) and molecular biology and/or genetics (BB 2920 or 2950 or equivalent) as well as foundational lab experience such as that offered in the BB 2900 lab sequence.
Some sections of this course may be offered as Writing Intensive (WI)
BB 4170. EXPERIMENTAL GENETIC ENGINEERING
Cat. I
This laboratory course focuses on modern DNA technologies and general applications of gene manipulation. Topics include gene amplification and recombination, promoter and plasmid engineering, gene expression and analysis, model systems, CRISPR, genomics and transgenics. Experiments in this course are integrated into an overall genetic engineering project throughout the term that will involve techniques such as electrophoresis, quantitative spectrofluorimetry, and real-time quantitative PCR. Methods of data analysis, common statistical approaches and technical writing will be emphasized throughout the course.
Recommended background: Knowledge of organic chemistry fundamentals as well as biochemical concepts including DNA replication and recombination, RNA synthesis and protein synthesis. Familiarity with cellular architecture is also recommended. See CH 2310, BB 2550, BB 4010 and CH 4110 or equivalent.
BB 4190. REGULATION OF GENE EXPRESSION
Cat. I
Through lectures, problem sets, reading and discussion, and presentations this course will help elucidate for students the processes that allow regulated gene expression, mechanisms used in each type of regulation, and methods and techniques used for investigation of regulatory mechanisms. Readings from the current original research literature will explore the growing use of model systems and "omics" level approaches to enhance our ever expanding understanding of the gene regulatory mechanisms. The development of cell based therapeutics and genetic engineering as they relate to gene regulation will be introduced.
Recommended background Topics in Biochemistry I, II and III (CH 4110, 4120, 4130) and Advanced Molecular Genetics (BB 4010) or the equivalents.
BB4260. SYNTHETIC BIOLOGY
Cat. II
Do we yet have the technology to engineer life? Can we control gene expression to create organisms that function in useful ways? Do we understand the tenets of genetic regulation as well as we think we do? These important questions and more are investigated by the emerging field of Synthetic Biology. In this course, students will explore this exciting new realm of biology through in-depth analysis and discussion of primary literature. Topics to be covered include the design and construction of synthetic gene circuits, synthesis of new genes and genomes, logic gate regulation of gene expression, and the latest applications of synthetic biology to advances in medicine, information processing, and the environment.
Recommended background: Students should have a strong foundational knowledge of cell biology, molecular biology, and genetics, as would be obtained from BB2550, BB2920, and BB2950. This course will be offered in 2022-23, and in alternating years thereafter.
BB 4260. Synthetic Biology
Cat II (offered at least every other Year). Do we yet have the technology to engineer life? Can we control gene expression to create organisms that function in useful ways? Do we understand the tenets of genetic regulation as well as we think we do? These important questions and more are investigated by the emerging field of Synthetic Biology. In this course, students will explore this exciting new realm of biology through in-depth analysis and discussion of primary literature. Topics to be covered include the design and construction of synthetic gene circuits, synthesis of new genes and genomes, logic gate regulation of gene expression, and the latest applications of synthetic biology to advances in medicine, information processing, and the environment. This course will be offered in 2022-23, and in alternating years thereafter.
BB 4801. BIOINFORMATICS
Cat. II
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.
Recommended background: BB 2920, BB 2950, and MA 2610 or 2611.
This is being offered in 2012-13 and in alternating years thereafter.
ISU BB. Special Topics
Cat I (offered at least 1x per Year). Experimental courses, special conferences and seminars are offered by advance arrangement only. The lab activities in these courses will provide foundational skills needed for the study of living organisms and systems at the molecular, organismal and environmental level. In these labs students will begin building the skills to carry into more advanced labs, their MQPs and professional careers. In particular students will gain experience with scientific procedures and techniques, technical equipment, teamwork, laboratory safety, hypothesis generation and testing, scientific data analysis (including statistics), oral and written scientific communication and skills common to all areas of biology.
Graduate Courses
BB 501. Seminar
This course will help students develop scientific communication skills through their attendance and participation in weekly research seminars. Research talks will include both external guest speakers and graduate students from the Biology and Biotechnology department, giving students an opportunity to learn by example while also honing their data presentation and communication skills through practice. Students will receive feedback from an audience of their peers and departmental faculty. Talks given by guest speakers will be paired with informal meetings between the guest and students to promote networking and broaden the students exposure to the greater scientific community.
BB 504. Molecular Biology of the Cell
This course will facilitate a students functional knowledge of living cells from a biological, biochemical and technological perspective. Topics covered will include the structure, organization, growth, regulation, movements, and interaction of cells, as well as details of cellular metabolism and molecular biology. Emphasis will be placed on visualizing cellular architecture, describing the structure of DNA, describing the fate of various cellular RNAs, articulating information flow in cells, and describing protein outcomes. This course is intended to achieve a homogenous level of student understanding and can be used as a foundation course for the program. This course is designed to familiarize students with basic concepts of molecular biology including structure, organization, growth, regulation, movements, and interactions within a cell. Details of metabolism and molecular biology will be covered through projects and study of the primary literature to achieve a homogenous level of student understanding and rigor. Weekly online assessments are designed to ensure understanding. Note: Students may not receive credit for BB 504 and BB 570-196.
BB 505. Fermentation Biology
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.
BB 508. Animal Cell Culture
Animal cell culture technology is about maintaining cells in vitro under controlled conditions. In recent decades this technology has advanced significantly, and animal cells are used in variety of application both in research and product development. The students in this course will be exposed to the different methodologies utilized to grow cells and how this technology is becoming critical in production of many of the health care products used to control human diseases. The course is covers four general skills (1) Basic techniques for culturing and sub-culturing animal cells and growth parameters, (2) Quality control of a cell culture laboratory/How to control contamination, (3) Primary cell culture and development of cell lines, and (4) Scale-up of cell culture from a T-Flask to a bioreactor. Note: Students may not receive credit for BB 508 and BB 570-198
BB 509. Scale Up of Bioprocessing
Strategies for optimization of bioprocesses for scale-up applications will be explored. In addition to the theory of scaling up unit operations in bioprocessing, students will scale up a bench-scale bioprocess (3 liters), including fermenta- tion and downstream processing to 33 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).
BB 515. ENVIRONMENTAL CHANGE: PROBLEMS & APPROACHES
(3 Credits)
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.
BB 515. Environmental Change: Problems and Approaches
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.
BB 551. Research Integrity in the Sciences
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 BB551 or a BB570 course entitled Research Integrity in the Sciences but not both.
BB 552. Scientific Writing and Proposal Development
This course will cover key elements to writing successful grant proposals including identification and justification of a research question, experimental approaches, and experimental system selection. Emphasis will be placed on how significance, innovation, rigor and reproducibility of prior and proposed work help shape the broader research question being addressed and the specific aims proposed. Students will be expected to develop an NIH F31 style proposal based within the life sciences and outside their dissertation field. Interactive peer feedback will complement guidance obtained from the instructors and the students own research advisor and is a critical part of this course. Students are expected to complete this course in their second year of their thesis research, prior to their Qualifying Exam. Students may receive credit for either BB552 or a BB570 course entitled Scientific Writing and Proposal Development but not both.
BB 553. Experimental Design and Statistics in the Life Sciences
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 BB553 or a BB570 course entitled Experimental Design and Statistics in the Life Sciences but not both.
BB 554. Journal Club
This primary literature and discussion based course is designed to help graduate students further their scientific reading and interpretation skills. Topics covered typically reflect the expertise or interest of the instructor and students. Students will read, discuss, and present on the research questions, results, and interpretation of published research papers of the chosen topic. Through discussion of the strengths, limitations and controls for experimental approaches described in the selected manuscripts students will gain critical evaluation and experimental design skills that will translate to their own research projects.
BB 556. Mentored Teaching Experience
This course is arranged with an individual faculty member within the students 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.
BB 560. Methods of Protein Purification and Downstream Processing
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.
BB 561. Model Systems: Experimental Approaches and Applications
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 Arahidopsis thaliana). Use of these systems in basic and applied research will be examined. Students may receive credit for either BB561 or a BB570 course entitled Model Systems: Experimental Approaches and Applications but not both.
BB 562. Cell Cycle Regulation
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 Gl/S and G2/M transitions, relationships between tumor suppressor genes such as pi6, 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 BB562 or a BB570 course entitled Cell Cycle Regulation but not both.
BB 565. Virology
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.
BB 570. Special Topics
This course will engage students at an advanced level in the exploration of special topics that reflect the expertise of the department faculty. Course offerings change regularly, and past iterations have included both literature-based courses such as Medical and Applied Immunology and Biostatistics and skills-based courses such as Genetic Engineering and Synthetic Biology and Practical Process Control. NOTE: Students may earn credit for multiple offerings of this course provided each offering bear distinct course descriptions and course content.'
BB 581. BIOINFORMATICS
(3 Credits)
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.
BB 590. Capstone Experience in Biology and Biotechnology
These classes will serve as integrative experiences for graduate students who are early in their doctoral training. The course will help students integrate concepts from other courses in the curriculum, practice skills of critical analysis, and evaluate and communicate scientific information effectively. The specific theme of each offering will center around a current topic of biological interest, and may include such areas as genomics, cancer, environmental problems, and synthetic biology. Topics will be announced prior to registration in the year preceding the course offering. NOTE: Students may not earn credit for both BB 4900 and BB 590 that bear the same section number and course description.
BB 599. Master's Thesis
A Masters thesis in Biology and Biotechnology consists of a research and development project worth a minimum of 9 graduate credit hours advised by a faculty member in the BB Program. The student must satisfactorily complete a written dissertation, public presentation, and private defense with thesis committee.
BB 699. Ph.D. Dissertation
A Ph.D. thesis in Biology and Biotechnology consists of a research and development project worth a minimum of 30 graduate credit hours advised by a faculty member affiliated with the BB Program. Students must pass a qualifying exam before the student can register for Ph.D. thesis credits. The student must satisfactorily complete a written dissertation, defend in a public presentation and private defense with thesis committee.