Biology and Biotechnology

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. This will not fulfill a major distribution requirement for BBT majors.

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. This will not fulfill a major distribution requirement for BBT majors.

Life scientists are generating huge amounts of data on many different scales, from DNA and protein sequence, to information on biological systems such as protein interaction networks, brain circuitry, and ecosystems. Analyzing these kinds of data requires quantitative knowledge and approaches using computer science and mathematics. In this project-based course, students will use case studies to learn about both important biological problems and the computational tools and algorithms used to study them. Students will study a sampling of topics in the field; recent topics included complex disease genetics, HIV evolution, antibiotic resistance, and animal migration behavior. In addition, students will hear from several guest speakers about their interdisciplinary research. Computational tools explored will include both freely-available tools to analyze sequences and build phylogenetic trees (e.g. BLAST, MUSCLE, MEGA) as well as guided programming using languages such as Python, R, and Netlogo. Students may not receive credit for both BCB / BB 100X and BCB / BB 1003. BBT majors may count this course as fulfilling part of their quantitative science and engineering requirement, but not as part of their BB 1000 level course requirement.

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 autoimmune disease will be integrated throughout the course. This course is intended for BBT and other life science majors.

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.

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.

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.

This course focuses on general biological 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. Students may not receive credit for both BB 2030 and BB 1040.

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.

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.

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.

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

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 health 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

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

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. Students may not receive credit for this course and either BB 2901 and BB 2905.

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.

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.

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.

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.

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. This course will be offered in 2022-23, and in alternating years thereafter.

In this course, students will learn and apply advanced cellular and molecular biology concepts to understand causes and consequences of cancer cell transformation. Through an integration of primary literature and lecture material students will explore how research into basic mechanisms of cancer biology is used to identify therapeutic targets, and inform drug design. This course will cover discussion of the hallmarks of cancer including the deregulation of cell growth, cell death, and metabolism; corruption of genome stability, evasion of immune response, and metastatic potential.

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. Students may not receive credit for both BB 4080 and BB 3080.

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. Students who have received credit for BB 2130 may not take BB 3101 for credit.

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. Students who have received credit for BB 3110 may not take BB 3102 for credit.

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. This course will be offered in 2021-22, and in alternating years thereafter. Some sections of this course may be offered as Writing Intensive (WI).

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. This course will be offered in 2021-22, and in alternating years thereafter.

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.

Basic laboratory skills in mammalian cell culture to include cell counting, freezing and thawing cell lines, culture of suspension and attached cells.

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. 

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.

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.

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 the light microscope 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. Student will develop scientific writing skills and learn how to prepare professional quality images. Some sections of this course may be offered as Writing Intensive (WI).

Basic studies in the biochemical and physical systems plants use to sustain life; includes an introduction to plant cell culture techniques. Concurrent or prior registration in BB 3120 is recommended. Students who have received credit for BB 325X may not receive credit for BB 3525. Some sections of this course may be offered as Writing Intensive (WI).

In this computer lab students will work with phage genomic sequences obtained from novel bacteriophages isolated in BB 2910, 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. 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

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. Students may not receive credit for both BB 356X and BB 3527.

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.

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.

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. This course will be offered in 2021-22, and in alternating years thereafter.

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.

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 spectro-fluorimetry, and real-time quantitative PCR. Methods of data analysis, common statistical approaches and technical writing will be emphasized throughout the course.

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.

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.

In an age when the amount of new biological data generated each year is exploding, it has become essential to use 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. In addition, the course will provide students with an introduction to some of the theory underlying the software (for example, how alignments are made and scored). This course will be offered in 2022-23, and in alternating years thereafter.

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.

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.