Undergraduate Courses

BB 356X. MOLECULAR BIOLOGY AND GENETIC ENGINEERING: APPROACHES AND APPLICATIONS

In this laboratory based course, students will learn to use current techniques in molecular and genetic engineering to address authentic research questions. Students will design and execute experiments to assess hypotheses, and evaluate data relative to those hypotheses. Specific approaches may include the generation of novel plasmids, genes, and cells, designed to specifically address contemporary problems in biology and biomedical science. In each offering, the problem addressed will be selected from and the results contribute to current faculty research initiatives. Recommended background: Working knowledge of the principles of molecular biology (BB 2950 or BB 2920 or equivalent) and cell biology (BB 2550 or equivalent), as well as relevant biology laboratory experience (BB 2901 or BB 2905).

BB 1001. INTRODUCTION TO BIOLOGY

Cat. I This course is designed for students seeking a broad overview of biologic concepts, especially at the cell and organism level. It is conducted in an active style including the use of case studies, class discussion/participation, and classroom polling systems. The major goal of this course is to help students become more informed citizens, skeptical when presented with data in the media, and knowledgeable enough to question and make informed decisions about scientific advances and science policy. It will primarily focus on current topics which may include stem cells, ethical uses of DNA, development of personalized medicine, genetic engineering, antibiotic resistance. This course is intended for non-life science majors. Recommended background: High School biology

BB 1002. ENVIRONMENTAL BIOLOGY

Cat. I This course is designed for students seeking a broad overview of ecological systems and the effect of humans on the ecosystems. It provides an introduction to natural ecosystems, population growth, and the interaction between human populations and our environment. It is conducted in an active style including the use of case studies, class discussion/participation, and classroom polling systems. The major goal of this course is to help students become more informed environmental citizens, skeptical when presented with data in the media, and knowledgeable enough to question and make informed decisions about the environment. It will primarily focus on current topics but areas of discussion likely to be covered include ecosystems, populations, biodiversity, pollution, environmental economics and climate change. This course is intended for non- life science majors. Recommended background: High School biology

BB 1025. HUMAN BIOLOGY

Cat. I This course presents students with an introduction to general concepts of human biology with particular focus on human structure and function. Concepts such as homeostasis, structure/function, and regulatory systems will be introduced. Discussion of current topics related to human health, such as personalized medicine and recent advances in cancer research and auto immune disease will be integrated throughout the course. This course is intended for BBT and other life science majors. Recommended background: a solid working knowledge of biological principles

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 1045. BIODIVERSITY

Cat. I Through lectures, readings, and discussions this course will examine the breadth, patterns, mechanisms, and conservation of biodiversity. Case studies and peer-to-peer learning will be used to examine threats to regional and global biodiversity and assess management and engineering strategies for solutions to the biodiversity crisis. Students will investigate and interpret past and contemporary research to quantify, document, and track trends in biodiversity. This course will use problem sets and assignments to explore the natural, social, and economic tradeoffs associated with threats to and conservation of biodiversity. Students will develop an area of expertise and synthesize their comprehension of topics through project work (e.g., management plan, report, presentation, citizen science). Finally, this course will provide a synthesis of the interdisciplinary nature of biodiversity conservation and how principles of conservation biology, landscape ecology, metapopulation biology, and biogeography can be applied to strategies aimed towards sustaining Earth?s biota. This course is intended for BBT and other life science majors. Recommended Background: a solid working knowledge of biological principles

BB 2002. MICROBIOLOGY

Cat. I This course will introduce the basic principles of microbiology. It 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 who seek a good general education in modern biology. Recommended background: BB 1035 (Intro to Biotech), BB 2950 (Molecular Biology), BB2550 (Cell Biology) or equivalent

BB 2003. FUNDAMENTALS OF MICROBIOLOGY

Cat. I This course will introduce the basic principles of microbiology through lectures, discussion, readings, and projects. The course will explore both the fundamental biology of microbes and the ways in which microbes influence society and the world. Topics will include the morphology, physiology, and genetics of unicellular organisms with a primary focus on bacteria. Special attention will be given to organisms known to have important roles in health, research, industry, and the environment. This course is designed for all biology majors and other students who seek a good general education in modern biology. Recommended background: A basic understanding of cell biology and elementary biochemical processes (BB 1035, BB 2550 or equivalent). Students may not receive credit for both BB 2002 and BB 2003

BB 2030. PLANT DIVERSITY

Cat. I This course focuses on general concepts as they relate to the vast array of plant species and their taxonomic links. Current uses of major plant phyla in both society and the biotechnology industry will be explored. Some emphasis will be given to economically important species chosen from agronomic and non-agronomic situations. Recommended background: a working knowledge of concepts in biodiversity (BB1045 or equivalent). Students may not receive credit for both BB 2030 and BB 1040 (no longer offered).

BB 2040. PRINCIPLES OF ECOLOGY

Cat. I This course is intended to help students understand ecological concepts at different levels of integration, from individuals to ecosystems, and the linkages among them. Students will also practice the application of qualitative and quantitative models to ecological systems and processes, as well as hypothesis generation, experimental design, and analysis and interpretation of data. In a format that includes team-based case studies, discussion and presentations, and ecological simulations, students will explore topics in both basic and applied ecology, which may include population ecology, host-parasite ecology and epidemiology, climate change, and sustainable agriculture, among others. Recommended background: a working knowledge of concepts in biodiversity (BB1045 or equivalent) and integral and differential calculus.

BB 2050. ANIMAL BEHAVIOR

Cat. I This course will provide an introduction to the scientific study of animal behavior. A combination of lecture, reading, and video will be used to illustrate how proximate and ultimate forces interact to shape animal behavior in complex and fascinating ways. Behavioral phenomena in all members of the animal kingdom will be discussed and analyzed from ecological, evolutionary, cognitive, and neurobiological perspectives to highlight how the use of an integrative approach has greatly accelerated our ability to solve complex behavioral problems. Primary scientific literature will be used to outline experimental tools and techniques used to investigate behavior in different contexts, including communication, foraging, navigation, mate choice, predation, and social behavior.

BB 2550. CELL BIOLOGY

Cat. I The goal of this course is to help students to develop a working understanding of the unifying concepts that define cell structure and function including replication, metabolism, regulation, communication and death. Applications in therapeutics, molecular medicine, and genetic engineering will be introduced. Classic and current research examples will provide practice in hypothesis generation and testing as well as making clear the importance of a working knowledge of cell biology to support advances in biotechnology and medicine. The course serves as the foundation of all fields of modern biology, and is recommended for all BBT and other life science majors. Recommended background: BB 1035 (Biotechnology) or equivalent

BB 2902. ENZYMES, PROTEINS, AND PURIFICATION

Cat. I (1/6 unit) This course gives basic practical experimental experience in enzymology, how enzymes work and how to purify them for later use. These techniques are the foundation the design and production of many therapeutic products. Examples of the types of techniques and experiences included in this course are: ? The action and optima of enzyme catalysis ? Induction of enzyme production ? Quantification and detection techniques for proteins ? Extraction and purification of protein from biological material using column chromatography ? Identification of compounds using Thin Layer Chromatography Recommended background: BB 1035 (Biotechnology)or equivalent

BB 2903. ANATOMY AND PHYSIOLOGY

Cat. I (1/6 unit) This course is an active exploration of a number of topics in anatomy and physiology through the use of simulations, measurement and hands on discovery. It will be particularly relevant to any student considering a heath related career, doing work where body structure is relevant or has interest in how body systems connect. A significant portion of this discovery will be accomplished by a hands-on dissection. Examples of the specific types of techniques and experiences included in this course are: ? Comparative and general anatomy of several organisms ? Physiology and function of body systems, processes and organs. ? Enzyme Linked Immunosorbent Assay (ELISA) ? Microscopy Recommended background: BB 1025 (Human Biology) or equivalent

BB 2904. ECOLOGY, ENVIRONMENT, AND ANIMAL BEHAVIOR

Cat. I (1/6 unit) This course examines topics in ecology and animal behavior through hands on experimentation and simulation. Activities in this course include interactions and observation of live animals as well as some outdoor activities and environmental sampling. This course will be relevant to students who have an interest in biology at more than the individual organism level as well as those with majors involving environmental and ecological concerns. Examples of the specific types of techniques and experience included in this course are: ? Observing, recording, understanding, and analyzing animal behaviors ? Handling of organisms ? Environmental and ecological assessment and sampling ? Observations of population dynamics Recommended background: BB 1045 (Biodiversity) or equivalent

BB 2915. SEARCHING FOR SOLUTIONS IN SOIL: MICROBIAL AND MOLECULAR INVESTIGATIONS

Students in this course will be part of a national student crowd sourcing initiative, developed in response to a decreasing supply of effective antibiotics and increased microbial resistance, to identify novel antibiotics produced by soil bacteria. Operating in an authentic research paradigm, students will gain skill in the process of scientific inquiry, including hypothesis generation and testing, and in common procedures of microbial culture and characterization. They will learn about and have the opportunity to use the techniques of recombinant DNA including the use of plasmids, restriction enzymes, and PCR. At the conclusion of the course students will report their findings in a poster style format and will be able to see the results of other groups around the country. Recommended background: A familiarity with current topics in biotechnology or microbiology such as those introduced in BB 1035 and BB 2003, or equivalent. Students may not receive credit for this course and either BB2901 and BB2905.

BB 2916. PHAGE HUNTERS: THE QUEST

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 3550 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 may not receive credit for both BB 291X and BB 2916

BB 2920. GENETICS

Cat. I Through interactive lectures, group problem solving, and analysis of primary scientific literature, this course will help students understand the gene concept and its application in modern biological analysis. This course will cover patterns of inheritance, the relationship between genotype and phenotype, and the transmission, coding, and expression of genetic information contained in DNA, in several model systems. Students will gain an understanding of the modern tools of genetic analysis, including gene cloning, creation of transgenic organisms, high-throughput sequencing and RNA interference. Applications of genetic analysis to current advancements in agriculture through crop improvements, and in human health, including gene therapy and personalized medicine, will be explored. Recommended background: BB 1035 (Biotechnology) or equivalent

BB 2950. MOLECULAR BIOLOGY

Cat. I Through a combination of lectures and in class discussion, students will learn and understand the essential concept of molecular biology, including the mechanisms by which information stored in nucleic acids is maintained and processed in living systems. An evolutionary framework will help illustrate how genomes are structured and how they change. Basic regulatory mechanisms of gene expression will be addressed, with emphasis in eukaryotic gene regulatory proteins. The concepts learned in this course will provide the foundation to continue exploring this rapidly expanding field. Recommended background: BB 1035 (Biotechnology) or equivalent

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 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 3040. EXPERIMENTAL DESIGN AND DATA ANALYSIS

Cat. II This applied course introduces students to the design of experiments and analysis of data. A combination of lecture, reading and discussion will be used to cover a variety of experimental situations occurring frequently in modern biology, including testing the fit of data to theoretical distributions, comparisons of groups, and regression analysis. Emphasis will be placed on the formulation of hypotheses, the design of experiments to test a formulated hypothesis, and the selection of appropriated statistical tests to perform. Readings from primary scientific literature will be used to illustrate the importance of experimental control as well as some of the most common errors made in choosing and performing statistical tests. Students will learn to use computer packages to carry out both parametric and non-parametric tests on their own experimental data. Recommended background: a solid background in a biological area at about the depth provided by any BB3000 or 4000 level course. This course will be offered in 2016-17 and alternating years thereafter. Students may not receive credit for both BB4040 and BB3040.

BB 3080. NEUROBIOLOGY

Cat. I The nervous system underlies every aspect of our behavior, including sensation, movement, emotion, and cognition. In this course, students will develop an understanding of neurobiology at several levels, from the physiology of individual neurons, through the functioning of neural circuits, and finally to the behavior of neural systems such as vision, motion, and memory. The class will be based on lectures accompanied by in-class activities, and will include weekly discussion of a paper from the scientific literature. The class will focus each year on a guiding theme, such as a particular neurotransmitter system, and will emphasize research on human neurological problems, such as schizophrenia, addiction, Alzheimer's disease, and autism. Recommended background: BB2550 (Cell Biology), and either BB2920 (Genetics) or BB2950 Molecular Biology) or equivalent Suggested additional background: BB 3101 (Anatomy & Physiology: Movement and Communication) or equivalent

BB 3101. HUMAN ANATOMY & PHYSIOLOGY: MOVEMENT AND COMMUNICATION

Cat. I The form and function of the systems that are responsible for the support, movement, internal communication, and interaction of the human body with its environment will be presented and discussed: Integumentary, Skeletal, Muscular, Nervous (including the senses), and Endocrine. Recommended background: BB 1025 and BB 2550. Suggested background: Concurrent Laboratory Module: BB 3511. Students who have received credit for BB 2130 may not take BB 3101 for credit.

BB 3102. HUMAN ANATOMY & PHYSIOLOGY: TRANSPORT AND MAINTENANCE

Cat. I The form and function of the systems of the human body that provide for the intake, distribution, and processing of nutrients, water, and oxygen, and the systems that safeguard health by elimination of wastes, regulation of metabolism, and surveillance against disease will be presented and discussed. Digestive, Respiratory, Circulatory, Lymphatic, Endocrine, Urinary, and Reproductive. Recommended Background: BB 1025 and BB 2550; CH 1010 and CH 1020. Suggested background: Concurrent Laboratory Module: BB 3514. Students who have received credit for BB 3110 may not take BB 3102 for credit.

BB 3120. PLANT PHYSIOLOGY

Cat. II This course explores the remarkable physiology of plants and emphasizes their importance in past and future life on earth. Conserved and unique aspects of plant cellular physiology will provide the foundation to understand the challenges of life on land and multicellularity. Topics such as water relations, mineral nutrition, intra- and inter-cellular transport, photosynthesis, and light responses will be discussed. Examples from the recent literature will be used to illustrate some of the key existing problems in plant physiology. Recommended background: BB 1045 (Biodiversity), BB 2550 (Cell Biology) , CH 1020 (Forces and Bonding) or equivalent This course will be offered in 2016-17 and alternating years thereafter.

BB 3140. EVOLUTION: PATTERN AND PROCESS

Cat. II In this course, students will explore the foundations of micro- and macro-evolutionary theory and will learn to apply these fundamental evolutionary principles through critical analysis of the primary scientific literature. In a course format that emphasizes team-based case studies, discussion of recent and classic papers, and computer simulation of evolutionary processes, students will explore the evolutionary foundations of a wide range of biological disciplines, and will gain experience in critical evaluation of approaches, arguments, and points of view in the field. Topics may include the history of life on Earth; biogeography and the origins of biodiversity; host-pathogen coevolution; and genomic and molecular evolution, among others. Recommended background: BB2040 (Principles of Ecology), BB2920 (Genetics), MA 1021-1022 (Calculus I and II) or equivalent. This course will be offered in 2015-16 and 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 3512. MOLECULAR GENETICS LAB

The topic of gene therapy will be used to give students experience with several fundamental skills in biotechnological research and practice: on-line information search and retrieval, computer cloning, and biological sequence analysis and manipulation. Course is entirely computer based. Recommended background: BB2901 (Molecular Biology, Microbiology and Genetics), BB2920 (Genetics), BB2950 (Cell Biology).

BB 3513. CELL CULTURE TECHNIQUES FOR ANIMAL CELLS

Cat. I (1/6 unit) Basic laboratory skills in mammalian cell culture to include cell counting, freezing and thawing cell lines, culture of suspension and attached cells. Recommended background: BB 2901, BB 2550 and knowledge of aseptic techniques. Concurrent or prior registration in BB 4008 is recommended.

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 3516. SEPARATION TECHNIQUES IN BIOTECHNOLOGY

A laboratory course in chromatographic and electrophoretic separation of proteins; chromatographic techniques will include two of the most commonly used in industry. Students will also gain experience with essential techniques in the molecular biologists tool kit: plasmid isolation, restriction digestion and electrophoretic separation of DNA. Recommended background: BB2902 (Enzymes, Proteins and Purification), BB2950 (Cell Biology), concurrent or prior registration in CH4110 (Biochem I) or equivalents

BB 3517. FERMENTATION

The experiments in this course focus on basic fermentation theory and practice, common to any bio-product production facility. Students will gain significant experience in hypothesis generation and testing as they work toward the goal of optimizing their proposed culture media. Recommended background: BB2901 (Molecular Biology, Microbiology and Genetics), BB2550 (Cell Biology)

BB 3518. MOLECULAR BIOLOGY

Laboratory investigations of select molecular characteristics of proteins and DNA; techniques include western and southern blotting. Recommended background: BB2901 (Molecular Biology, Microbiology and Genetics), BB2550 (Cell Biology), BB2950 (Molecular Biology) and CH4110 (Biochem I), concurrent or prior registration in CH4130 (Biochem III) or equivalents

BB 3519. PROTEIN PURIFICATION

This is a laboratory course focusing on the theory and practice of protein purification from a primary source. Chromatographic techniques will include two more of the most commonly used in the biotech industry. Recommended background: BB 2002 (Enzymes, Proteins and Purification) CH 4110 (Biochem I) or equivalents

BB 3521. MICROSCOPY

Cat. I (1/6 unit) Through a research-based laboratory and short lectures, students will learn the basic principles of image formation, resolution, and digital imaging. Students will develop confidence in the use of light microscopy and be able to apply different modes of microscopy to solve biological problems. This course emphasizes a quantitative approach to microscopy and digital imaging applied toward simple phenotypic analysis. Students will develop scientific writing skills and learn how to prepare professional quality images. Recommended background: a working knowledge of laboratory techniques in molecular biology, and microbiology (BB 2901 or equivalent), and concepts in cell biology (BB 2550 or equivalent). Students may not recieve credit for both BB 324X and BB 3524

BB 3524. BIOINFORMATICS LAB

Laboratory course giving students practice with some of the basic tools currently available for on-line literature searching, sequence data mining, comparison of nucleotide and/or protein sequences, and analysis of nucleotide and protein sequences. Course is entirely computer based. Recommended background: BB2901( Molecular Biology, Microbiology and Genetics), BB2920 (Genetics), BB2950 (Cell Biology), and CH4110 (Biochem I) or equivalents. Concurrent or prior registration in CH4130 is suggested. Students who have received credit for BB324X may not receive credit for BB3524.

BB 3525. PLANT PHYSIOLOGY

Cat. I (1/6 unit) Basic studies in the biochemical and physical systems plants use to sustain life; includes an introduction to plant cell culture techniques. Recommended background: BB 1045 and BB 2903. Concurrent or prior registration in BB 3120 is recommended. Students who have received credit for BB 325X may not receive credit for BB 3525.

BB 3526. PHAGE HUNTERS: THE ANALYSIS

In this computer lab students will work with phage genomic sequences obtained from novel bacteriophages isolated in BB2910, Phage Hunters: The Quest. The raw genome files will be finished and oriented; students will then search the sequence to identify and map existing genes and other genomic components (sequence annotation). Additional course goals are to do an initial comparative genomic analysis and post-annotation experimentation. The ultimate goal is to produce novel bacteriophage genome sequences that are ready to be submitted to GenBank, the US repository of DNA sequence information at the National Institute of Health. Recommended background: a working knowledge of genome structure and function (BB 2920, BB2950, or equivalent). Students planning to take this course may wish to consider enrollment in BB 2916 (Phage Hunters: The Quest) Students may not receive credit for both BB 350X and BB 3526

BB 3620. DEVELOPMENTAL BIOLOGY

Cat. II Through lecture, reading, and discussion, this course will help students understand how developmental biologists study the development of a fertilized egg into a multi-cellular animal. Beginning with the description of developmental events, the major problems of developmental biology such as determination of cell fate, differentiation, and pattern formation will be explored. Emphasis will be placed on techniques such as analysis of mutations, molecular genetics, gene transfer, and the use of model organisms. Societal implications of the ability to control the outcome of development will be discussed. Recommended background: BB 2002 (Microbiology), BB 2550 (Cell Biology), BB 2920 (Genetics) or equivalent This course will be offered in 2015-16 and alternating years thereafter.

BB 3920. IMMUNOLOGY

Cat. I Through lecture, reading, and discussion, this course will help students understand the origin of immune cells in bone marrow development, the distinction between innate and adaptive immunity, and the function of the immune system in health and disease. The mechanisms responsible for the exquisite specificity of the adaptive immune system will be described. Throughout the course, the probable paths of evolution of the immune system will be stressed. As examples of major genetic diseases of immunity, case studies will be discussed on a weekly basis. Recommended background: BB 2550 (Cell biology), BB 2920 (Genetics), CH 4110 and 4120 (Biochemistry I and II) or equivalents.

BB 4008. CELL CULTURE THEORY AND APPLICATIONS

Cat. I Using readings from the literature, students will gain insight into the current uses of cultured cells in basic research and commercial production. Class discussion will explore the benefits and limitations of cells as model systems. Class size will be limited to allow a robust exchange of ideas and information among the participants. Recommended background: A working knowledge of cell biology, genetics, basic biochemistry (BB 2550, 2920, CH 4110 and 4120 or equivalents)

BB 4010. ADVANCED MOLECULAR GENETICS

Cat. I Emphasis will be on learning the newer trends in molecular genetics and their applications in biology and medicine using a variety of model systems. Students will gain an understanding of the similarities and differences in the mechanisms of transcription and translation in prokaryotic and eukaryotic systems. Principles and technologies of "omic?level" approaches, such as genomics and proteomics, and how they are transforming our understanding of biological processes and human diseases will be discussed. Recommended background: BB 2002(Microbiology), BB 2550 (Cell Biology) and BB 2920 (Genetics) and BB 2950 (Molecular Biology) or equivalents

BB 4065. VIROLOGY

Cat. I Through lectures and discussions of current and landmark scientific research articles, this advanced-level course will help elucidate the concepts related to viral structure, function, and evolution. The course will especially focus on data analysis and critique, covering topics in pathological mechanisms of various human disorders, especially emerging diseases. Applications and implications of the use of viruses in research will be introduced and discussed. Recommended background: BB 2550 (Cell Biology) or equivalent

BB 4150. ENVIRONMENTAL CHANGE: PROBLEMS & APPROACHES

Cat. II 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 systainability. 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: BB1045 (Biodiversity), BB2040 (Principles of Ecology), ENV1100 (Intro to Environmental Studies) or equivalent. This course will be offered in 2016-17 and alternating years thereafter.

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.

BB 4550. ADVANCED CELL BIOLOGY

Cat. I Through lectures and discussions of current and landmark scientific research articles, this advanced-level course will help elucidate for the students concepts related to the molecular biology of cell function. The course will especially focus on data analysis and critique, covering topics in molecular medicine, biological mechanisms of autoimmune disorders, stem cells, gene therapy, neurotrophic factors, and Alzheimer's disease. Recommended background BB 2550 (Cell Biology) or equivalent

BB 4801. BIOINFORMATICS

Cat. II In an age when the amount of new biological data generated each year is exploding, every biologist should feel comfortable using bioinformatics tools to explore biological questions. This class will provide an understanding of how we organize, catalog, analyze, and compare biological data across whole genomes, covering a broad selection of important databases and techniques. Students will acquire a working knowledge of bioinformatics applications through hands-on use of software to ask and answer biological questions in such areas as genetic sequence and protein structure comparisons, phylogenetic tree analysis, and gene expression and biological pathway analysis. Recommended background: BB2920 (Genetics), BB2950 (Molecular Biology), and MA 2610 or 2611 (Statistics) or equivalent. This course will be offered in 2016-17, and in alternating years thereafter.

BB 4900. CAPSTONE EXPERIENCE IN BIOLOGY AND BIOTECHNOLOGY

These classes will serve as integrative experiences for students majoring in Biology & Biotechnology. 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. Prior to enrolling in the seminar, a student should have completed all of the BB course distribution requirements for BBT majors at the 1000 and 2000 level, or should seek advice from the course instructor. Topics will be announced prior to registration in the year preceding the course offering.  See complete listing of capstone courses...

BB 4900-A17. SYSTEMS BIOLOGY AND MOLECULAR ENGINEERING

Emphasis will be on analysis of biological phenomena from a systems-level perspective. Principles and technologies of “omic–level” approaches such as genomics, proteomics and metabolomics will be discussed. Case studies that address modern frontiers of systems will be discussed. Focus will be on learning about emerging technologies of molecular engineering and evaluate their role in understanding the principles of living systems and human diseases. Recommended background: BB 2950, BB2920.

BB 4900- B17. CELL MOTILITY AND NANO-MACHINES

Cell motility is important for all cells, from bacteria to neurons. The motile mechanisms of cells are diverse, but in many cases, the cellular components responsible have been conserved in evolution. Some of the key molecules for motility are 80-90% identical between animal, fungi and plants! Despite this similarity, these molecular machines are responsible for generating differences in cell shape and motility such as those between fungal hyphae, leaf cells, and neurons. How are these molecular machines organized to allow the incredible diversity of forms and behaviors of cells? How is energy converted and forces generated by machines only a few nanometers in size? What cellular assemblies and structures are responsible for muscle contraction, phagocytosis of bacteria, or metastatic behavior? In this class we will explore the recent and classic literature in this field and we will also explore the constantly expanding collection of exciting videos of cells in motion. Suggested background: BB 2550 (Cell Biology).

BB4900-C18. THE HUMAN MICROBIOME

Somewhere on the order of 10-100 trillion microbial symbiants are harbored with each of our bodies! At the genome level, humans are ~99.9% identical to one another, but can be 80-90% different in terms of their microbiome. The Human Microbiome Project, launched by the NIH, seeks to characterize microbial communities and begin to answer questions such as: is there an identifiable core of “normal” bacteria?; how does the microbiome interface with other systems such as the immune system or the central nervous system?; does intrapersonal microbial diversity change over time?;and can we identify correlations between changes in the microbiome and human health? Does the phrase “I have a gut feeling” refer to links between the microbiome and behavior? By reading the primary literature and learning about recent technologic advances in the field, we may begin to answer these and other questions. Students should have a strong foundational knowledge of cell biology, microbiology and genetics.

BB4900-D18. SYNTHETIC BIOLOGY

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. Students should have a strong foundational knowledge of cell biology, molecular biology, and genetics, as would be obtained from BB2550, BB2920, and BB2950.

Graduate Courses

BB 501. SEMINAR

(1 Credit)

BB 505. FERMENTATION BIOLOGY

(3 Credits) 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 509. SCALE UP OF BIOPROCESSING

(3 Credits) 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 (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). (Prerequisites: BB 4050/505 and BB 4060/560 as a working knowledge of the bench-scale processing will be assumed. Otherwise, instructor permission is required.)

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 551. RESEARCH INTEGRITY IN THE SCIENCES

(1 Credit) 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.

BB 552. SCIENTIFIC WRITING AND PROPOSAL DEVELOPMENT

(2 Credits) 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.

BB 553. EXPERIMENTAL DESIGN AND STATISTICS IN THE LIFE SCIENCES

(2 Credits) 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.

BB 554. JOURNAL CLUB

(1 Credit) 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.

BB 560. METHODS OF PROTEIN PURIFICATION AND DOWNSTREAM PROCESSING

(3 Credits) 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.)

BB 561. MODEL SYSTEMS: EXPERIMENTAL APPROACHES AND APPLICATIONS

(2 Credits) 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.

BB 562. CELL CYCLE REGULATION

(3 Credits) 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.

BB 565. VIROLOGY

(3 Credits) 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

(variable credit) Speciality subject courses are offered based on the expertise of the department faculty such as Stem Cell Biology.

BB 575. ADVANCED GENETICS AND CELLULAR BIOLOGY

(3 Credits) 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.

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.