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Biology

Year:

2020-21

104 Food, Fiber, and Pharmaceuticals

It is perhaps impossible to experience a day without plants. From the air we breathe, the bed we sleep in, the soap we wash with and clothes we put on, to the foods we consume and the medicines we take, we are very much dependent upon plants and their products. Through a combination of lecture, discussion, and observation, we will explore how, why, and when plants became vital to people and their societies. Several economically important plant groups will be studied, including those that provide food and beverages, medicines and narcotics, spices, perfumes, fuels, and fiber. What are the characteristics of these groups enabling their exploitation, and what is the history of these associations? How and when were plants domesticated and what are the consequences of large-scale agriculture? What impacts do human population growth and habitat destruction have on the ways that people interact with plants now and in the future? Finally, we will explore the role of technology in efforts to both improve and synthesize plant products. Three classroom hours per week.

This course will be conducted in-person. Online components are available, as needed, supported by appropriate technology.  Options for online-only participation will be available for those students unable to participate in person.

Limited to 18 students. This course is for non-majors. Students majoring in Biology will be admitted only with consent of the instructor. Omitted 2020-21. Senior Lecturer Levin.

2020-21: Not offered
Other years: Offered in Spring 2013, Fall 2013, Fall 2015, Fall 2016, Fall 2017, Spring 2020

110 Contagion

This course explores the biological mechanisms underlying infectious disease, as well as the challenges associated with fighting their emergence and spread. We will begin by learning about diseases of global health importance, such as HIV/AIDS and cholera, to introduce strategies that pathogens have evolved that ensure their persistence. We will investigate their fundamental biology, and interpret patterns of evolutionary divergence that aid in understanding patterns of transmission. We will study treatments and prevention measures, but we will also see that this knowledge must be integrated with awareness of complex ecological and societal issues to inform and implement solutions.  As we consider these questions, we will focus much of our attention on the COVID-19 pandemic, caused by the SARS-CoV-2 virus, in order to critically examine what we know about the virus, its emergence, disease susceptibility and symptoms, as well as treatments and preventative measures. Discussions will focus upon the many perspectives from which infectious diseases are encountered, drawing on resources from the literature on microbiology, policy, and ethics, as well as personal accounts, current news stories, and readings from Spillover by David Quammen, as well as other popular science books. Three hours of lecture and discussion per week.  This course is for non-science majors and will not count toward the Biology major.
Limited to 20 students. Spring 2021. Professor Purdy.

Learning approach:  Hyflex. This course will be conducted in a hybrid format, with on-line and in-person components as needed, supported by appropriate technology.  Options for online-only participation will be available for those students unable to participate in person.

2020-21: Offered in Spring 2021
Other years: Offered in Spring 2013, Spring 2014, Fall 2017

181 Adaptation and the Organism

An introduction to the evolution, ecology, and behavior of organisms and how these relate to the diversity of life. Following a discussion of the core components of evolutionary theory, we'll examine how evolutionary processes have shaped morphological, anatomical, physiological, and behavioral adaptations in organisms that solve many of life's problems, ranging from how to find or acquire food and avoid being eaten, to how to attract and locate mates, and how to optimize reproduction throughout a lifetime. We'll relate and compare characteristics of animals, plants, fungi, protists, and bacteria, examining how and why these organisms have arrived at various solutions to life's problems. Laboratory exercises will complement lectures and will involve field experiments on natural selection and laboratory studies of vertebrates, invertebrates and plants. Four classroom hours and three laboratory hours per week.

This course will be conducted in a hybrid format, with both in-person and on-line components as needed, supported by appropriate technology. Options for online-only participation will be available for those students unable to participate in person. Students enrolling in this course should register for ONE of the four “LEC" sections and ONE of the five "LAB" sections.

Fall semester. Professors Clotfelter and Miller; Lab Coordinator Kristensen.

Please note that the same textbook is used for both BIOL 181 and BIOL 191.

2020-21: Offered in Fall 2020
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, Spring 2018, Fall 2018, Fall 2019, Fall 2020

191 Molecules, Genes and Cells

An introduction to the molecular and cellular processes common to life with an emphasis on control of energy and information flow. Central themes include metabolism, macromolecular function, and the genetic basis of cellular function. We examine how membranes work to establish the internal composition of cells; how the structure of proteins including enzymes affects protein function; how energy is captured, stored and utilized by cells; and how cells communicate, move and divide. We explore inheritance patterns and underlying molecular mechanisms of genetics, the central dogma of information transfer from DNA replication to protein synthesis, and recombinant DNA methods and medical applications. Laboratories include genetic analyses, enzyme reaction kinetics, membrane transport, and genomic analysis. Two hours of lecture, two hours of team-based learning, and three laboratory hours per week.

Requisite: Prior completion of, or concurrent registration in, CHEM 161 or CHEM 165. Limited to 96 students. Fall semester: Professors Purdy and Kim, Lab Coordinator Emerson. Spring semester: Professors Goutte and Wu Orr, Lab Coordinator Emerson. 

In Fall 2020, Biol-191 will be conducted entirely online. Lectures will be held asynchronously and/or synchronously and recorded. Discussion sections and laboratories will be held synchronously, but for students in need of other arrangements due to their time zone or other considerations, alternative group meetings times and/or asynchronous options will be made available. For students on campus, optional in-person gatherings of small groups will be facilitated to promote discussion of course material, while students preferring online modes of learning will be encouraged to gather through online platforms

Please note that the same textbook is used for both BIOL 181 and BIOL 191.

2020-21: Offered in Fall 2020, Spring 2021
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2013, Fall 2014, Fall 2015, Fall 2016, Fall 2017, Fall 2018, Spring 2019, Fall 2019, Spring 2020, Fall 2020

201 Disease Ecology

Advances in organismal biology hinge upon an understanding of natural history and are enhanced by quantitative observation, hypothesis formation, and experimentation with systems that occur in nature. In this course, we will apply these principles specifically to the study of infectious diseases in natural populations. With a combination of lecture, discussion, and field-based activities, the course will focus on deriving important questions and the variety of approaches to address them. While covering the fundamentals of disease ecology, the applicability of the field-based approaches to other areas of organismal biology will be emphasized as a foundation for further studies. Three classroom hours and three laboratory/fieldwork hours per week.
Hyflex. Disease Ecology will have in-person sessions for students able to attend and material provided remotely for those who need it.  This includes lecture and lab material.  There will be live Zoom lectures for the remote students, which will also be recorded and available on demand.  To the extent possible, the lab component will include hands-on activities and field studies, in combination with data analysis and mathematical models.

Requisite: BIOL 181. Limited to 16 students. Fall Semester. Professor Hood.

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2019, Fall 2020

214 Neurobiology

(Offered as BIOL 214 and NEUR 214) An introduction to the structure and function of the nervous system, this course explores the basic functions of neurons and synapses as well as neural mechanisms of sensation at molecular, cellular, circuit and system levels. Basic topics in neurobiology and neurophysiology will be covered with emphasis on neuroscience history and understanding how neuroscientists approach the study of the nervous system. Three class hours per week.

Requisite: BIOL 191. Limited to 45 students. Fall semester. Professor Roche.

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2007, Fall 2008, Spring 2010, Fall 2012, Fall 2013, Fall 2016, Fall 2017, Fall 2018, Fall 2019, Fall 2020

221 Developmental Biology

How can a single cell, the fertilized egg, give rise to all the specialized cells of an adult? What gives rise to biological form? What is the molecular logic of the pathways that progressively refine cellular identities? How do cells "talk" to one another so as to coordinate their behaviors as embryos develop form and function? How can parts of an organism be regenerated with only the appropriate regions remade, structured identically to the missing ones? How does a stem cell differ from a non-stem cell? How can genetically identical organisms be cloned? This course will offer an integrative study of the development of animals, leading to the formulation of the principles of development, including an introduction to experimental embryology and developmental physiology, anatomy, genetics and "evo-devo." Laboratory work explores embryonic development and regeneration in amphibians, sea urchins, nematodes, flatworms, fruit flies, fish, and chickens. Three classroom hours plus three hours of laboratory per week.
Requisite: BIOL 191. Not open to first-year students. Limited to 16 students. Fall Semester. Professor Ragkousi.

This course will be conducted in-person. On-line components are available, as needed, supported by appropriate technology.  Options for online-only participation will be available for those students unable to participate in person.

 

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2007, Spring 2009, Spring 2010, Fall 2011, Fall 2014, Spring 2016, Fall 2018, Fall 2019, Fall 2020

230 Ecology

(Offered as BIOL 230 and ENST 210) A study of the relationships of plants and animals (including humans) to each other and to their environment. We'll start by considering the decisions an individual makes in its daily life concerning its use of resources, such as what to eat and where to live, and whether to defend such resources. We'll then move on to populations of individuals, and investigate species population growth, limits to population growth, and why some species are so successful as to become pests whereas others are on the road to extinction. The next level will address communities, and how interactions among populations, such as competition, predation, parasitism, and mutualism, affect the organization and diversity of species within communities. The final stage of the course will focus on ecosystems, and the effects of humans and other organisms on population, community, and global stability. Three hours of lecture per week.

Requisite: BIOL 181 or ENST 120 or equivalent. Limited to 40 students. Fall Semester. Professor Temeles.

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Spring 2012, Fall 2012, Fall 2013, Fall 2014, Fall 2015, Fall 2016, Fall 2017, Fall 2018, Spring 2019, Spring 2020, Fall 2020

250 Being Human in STEM

(Offered as BIO 250, CHEM 250, LLAS 250 and SOCI 250) This is an interactive course that combines academic inquiry and community engagement to investigate identity, inequality and representation within Science Technology Engineering and Mathematics (STEM) fields--at Amherst and beyond. We begin the course by grounding our understanding of the STEM experience at Amherst in national and global contexts. We will survey the interdisciplinary literature on the ways in which identity - race, gender, class, ability, sexuality- and geographic context shape STEM persistence and belonging. We will bring this literature into conversation with our own Amherst experiences. These challenging conversations require vulnerability, openness and the ability to tolerate discomfort. We will work from day one to build a brave space whose foundation is trust, accountability and growth. Students will design group projects that apply themes from the literature and our seminar discussions to develop resources and engage the STEM community, whether at the college, local, or national level. Course work includes critical reading and discussion, reflective writing, and collaborative work culminating in community engagement projects which students will share with the campus and the broader public. The class will meet synchronously most days for the remote January term and will also involve asynchronous small group work.

Open to sophomores, juniors and seniors. This course will be taught in two sections, each taught by a partnering of a scientist and a humanist/social scientist. Each section will be limited to 18 students due to the remote format and the discussion- and project-based nature of the class.

January Term. Professors Jaswal, Corañez Bolton, Schmalzbauer and Trapani.

2020-21: Offered in January 2021
Other years: Offered in Spring 2020, January 2021

260 Animal Physiology

This course will examine the function of tissues, organs, and organ systems, with an emphasis on the relationship between structure and function. Building outward from the level of the cell, we will study bodily processes including respiration, circulation, digestion and excretion. In addition, the course will address how different organisms regulate these complex processes and how ion and fluid balance is maintained. We will also study the nervous system in the context of sensory systems, focusing on how external stimuli are transformed into meaningful neuronal signals and processed by the brain. Weekly discussions will include readings from primary literature. Four classroom hours per week.

Requisite: BIOL 191 and either BIOL 181 or NEUR 226. Limited to 18 students. Spring semester. Professor Trapani.

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2011, Spring 2013, Spring 2017

264 Form and Function

(Offered as BIOL 264 and PHYS 264) Functional morphology is the study of how organisms work. It integrates anatomy and biomechanics in an ecological and evolutionary framework. The course begins with basic principles of evolutionary theory and biomechanics, before turning to the fundamental importance of body size and metabolism in governing nearly all aspects of animal biology. We then focus on locomotion (running, jumping, swimming, gliding, and flying) using examples of both living and extinct animals. We will also discuss morphological adaptations underlying unusual movements such as climbing walls, hovering in midair, and walking on water. Finally, we touch on examples of human innovation inspired by animal morphology. The course uses a combination of lectures and discussions of articles from the primary literature. Three hours of lecture/discussion per week.

Requisite: Students registering for BIOL 264 must have taken BIOL 181. Students registering for PHYS 264 must have taken PHYS 116 or PHYS 123. Not open to first-year students. Limited to 24 students. Omitted 2020-21. Professors Clotfelter and Loinaz.

2020-21: Not offered
Other years: Offered in Spring 2017, Spring 2020

265 Form and Function w/Lab

(Offered as BIOL 265 and PHYS 265) Functional morphology is the study of relationships between the anatomy and the ecology and behavior of organisms. The course begins by focusing on the fundamental importance of body size and metabolism in governing nearly all aspects of animal biology. We then study the biomechanics of running, jumping, swimming, gliding, and flying, using examples of both living and extinct animals. We will also learn about morphological adaptations underlying unusual movements such as climbing walls, hovering in midair, and walking on water. Finally, we touch on examples of human innovation inspired by animal morphology. The course uses a combination of lectures and discussions of articles from the primary literature. Laboratories focus primarily on comparative anatomy and analyzing animal performance. Three hours of lecture/discussion and three hours of laboratory per week.

Requisite: BIOL 181. Not open to first-year students. Limited to 16 students. Omitted 2020-21. Professors Clotfelter and Loinaz.

2020-21: Not offered
Other years: Offered in Spring 2017, Spring 2020

270 Microbiology

Microbes inhabit the world's oceans, deserts, lakes, soils, and atmosphere, and play a vital role in the Earth's biogeochemical cycles. As humans, we harbor a diverse microbial flora estimated to outnumber our own human cells. During this course, we will explore this microbial world by investigating the structure, physiology, genetics, and evolution of microorganisms with a focus on bacteria, but including discussions of archaea, viruses, and microbial eukaryotes. The goal of the course is to gain an understanding of the unique properties of microbes that enable their persistence and diversification. We will also pay special attention to microbial interactions with eukaryotic organisms, by studying both host and microbe contributions to virulence, mutualism, and symbiotic relationships. Three hours of lecture and one hour of discussion per week.

Requisite: BIOL 191. Recommended: BIOL 181. Limited to 15 students. Not open to first-year students. Omitted 2020-21. Professor Purdy.

2020-21: Not offered
Other years: Offered in Fall 2012, Fall 2013, Spring 2015, Spring 2017, Spring 2018, Spring 2019

271 Microbiology with Lab

Microbes inhabit the world's oceans, deserts, lakes, soils, and atmosphere, and play a vital role in the Earth's biogeochemical cycles. As humans, we harbor a diverse microbial flora estimated to outnumber our own human cells. During this course, we will explore this microbial world by investigating the structure, physiology, genetics, and evolution of microorganisms with a focus on bacteria, but including discussions of archaea, viruses, and microbial eukaryotes. The goal of the course is to gain an understanding of the unique properties of microbes that enable their persistence and diversification. We will also pay special attention to microbial interactions with eukaryotic organisms by studying both host and microbe contributions to virulence, mutualism, and symbiotic relationships. Laboratory exercises will include explorations of microbial functions and diversity in a variety of contexts using both classical and molecular approaches. Three hours of lecture, three hours of laboratory and one hour of discussion per week.

Requisite: BIOL 191. Recommended: BIOL 181. Limited to 15 students. Not open to first-year students. Omitted 2020-21. Professor Purdy.

2020-21: Not offered
Other years: Offered in Fall 2012, Fall 2013, Spring 2015, Spring 2017, Spring 2018, Spring 2019

275H Evolutionary Ecology Laboratory

This laboratory explores how underlying evolutionary changes in the morphology, physiology or behavior of organisms is associated with ecological interactions within or between species.  By employing artificial selection, students will determine whether genetic variation associated with herbivore defense exists.  This experiment will be coupled with ecological investigations to explore the potential of herbivory to drive evolutionary change.  Further, using the model system Daphnia, students will have the opportunity to engage in a self-directed, in-depth investigation of selection on morphological and life history traits across varying environmental conditions.  Throughout the course, students will engage with the scientific literature, and develop their skills in identifying relevant and important questions, experimental design and hypothesis formulation, data analysis and scientific communication.  Three hours of laboratory each week.

Requisite: Prior completion of or concurrent registration in either BIOL-230 or BIOL-320. Limited to 16 students. Professors Miller and Temeles and Lab Instructor Kristensen.Spring semester.

2020-21: Offered in Spring 2021

280 Animal Behavior

Shaped by millions of years of evolution, animals have evolved myriad abilities to respond to their environment, their potential predators and prey, and members of their own species. This course examines animal behavior from both a mechanistic and a functional perspective. Drawing upon examples from a diverse range of taxa, and using articles from the primary scientific literature, we will discuss topics such as behavioral endocrinology, sexual selection and mating systems, animal communication, and kinship and cooperation. Four classroom hours per week.

Requisite: BIOL 181. Limited to 20 students. Spring. Professor Clotfelter.

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Fall 2011, Fall 2013, Spring 2015, Fall 2015, Fall 2016, Fall 2017, Spring 2019, Fall 2019

281 Animal Behavior with Lab

Shaped by millions of years of evolution, animals have evolved myriad abilities to respond to their environment, their potential predators and prey, and members of their own species. This course examines animal behavior from both a mechanistic and a functional perspective. Drawing upon examples from a diverse range of taxa, and using articles from the primary scientific literature, we will discuss topics such as behavioral endocrinology, sexual selection and mating systems, animal communication, and kinship and cooperation. Four classroom hours and three laboratory hours per week; the laboratory projects will require additional time outside of class.

Requisite: BIOL 181. Limited to 15 students per lab section. Omitted 2020-21. Professor Clotfelter.

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Fall 2011, Fall 2013, Spring 2015, Fall 2015, Fall 2016, Fall 2017, Spring 2019, Fall 2019

291 Cell Structure and Function

(Offered as BIOL 291 and BCBP 291) An analysis of the structure and function of eukaryotic cells. Topics to be discussed include the cell surface and membranes, cytoskeletal elements and motility, cytoplasmic organelles and bioenergetics, the interphase nucleus and chromosomes, mitosis, meiosis, and cell cycle regulation. There will be four classroom hours  consisting of  both lectures and problem-solving sessions, and three hours of laboratory per week. The course  will be taught in-person, or on-line as needed. 

Requisite: BIOL 191, CHEM151/155, and CHEM161/165. Limited to 16 students. Spring semester. Professor Edwards.

2020-21: Offered in Spring 2021
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, Spring 2018, Spring 2019, Spring 2020

301 Molecular Neurobiology

(Offered as BIOL 301 and NEUR 301) An analysis of the molecules and molecular mechanisms underlying nervous system function, development, and disease. We will explore the proteins that contribute to the unique structure and function of neurons, including an in-depth analysis of synaptic communication and the molecular processes that modify synapses. We will also study the molecular mechanisms that control brain development, from neurogenesis, neurite growth, and synaptogenesis to cell death and degeneration. In addition to analyzing neural function, throughout the course we will also study nervous system dysfunction resulting when such molecular mechanisms fail, leading to neurodevelopmental and neurodegenerative disease. Readings from primary literature will emphasize current molecular techniques utilized in the study of the nervous system. Four classroom hours and three hours of laboratory per week.

Requisite: BIOL 191 and CHEM 161/CHEM 165. Limited to 16 students. Spring semester. Professor Sally Kim

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2010, Fall 2011, Fall 2014, Fall 2015, Fall 2016, Spring 2020

310 Structural Biology

(Offered as BIOL 310 and BCBP 310) Have you ever wondered how scientists determine the three dimensional structure of proteins? Or what can be learned about the function of a protein from its structure? This course will concentrate on the structure of proteins at the atomic level. It will include an introduction to methods of structure determination, to structural bioinformatics, and to the visualization and representation of structural data. These tools will be used to study the relationship between function and specific structures (such as membrane, nucleic acid binding, regulatory, structural, or metabolic proteins). These proteins will provide the framework for the discussion of such concepts as domains, motifs, molecular motion, and structural homology, as well as for addressing how specific biological questions are answered at the atomic level. Two 80-minute classroom hours per week plus one hour discussion.

Requisite: BIOL 191 and CHEM 151 or 155, and CHEM 161; CHEM 221 would be helpful but is not required. Limited to 18 students. Omitted 2020-21.

2020-21: Not offered
Other years: Offered in Fall 2007, Fall 2012, Spring 2017, Spring 2020

320 Evolutionary Biology

Evolution is a powerful and central theme that unifies the life sciences. In this course, emphasis is placed on microevolutionary mechanisms of change, and their connection to large-scale macroevolutionary patterns and diversity. Through lectures and readings from the primary literature, we will study genetic drift and gene flow, natural selection and adaptation, molecular evolution, speciation, the evolution of sex and sexual selection, life history evolution, and inference and interpretation of evolutionary relationships. Three hours of lecture and one hour of discussion each week.

Requisite: BIOL 181; BIOL 191 recommended. Not open to first-year students. Spring semester. Professor Miller

This course will be conducted in-person. Online components are available, as needed, supported by appropriate technology. Options for online-only participation will be available for those students unable to participate in person.

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017, Spring 2019, Spring 2020

321 Evolutionary Biology with Lab

Evolution is a powerful and central theme that unifies the life sciences. In this course, emphasis is placed on microevolutionary mechanisms of change, and their connection to large-scale macroevolutionary patterns and diversity. Through lectures and readings from the primary literature, we will study genetic drift and gene flow, natural selection and adaptation, molecular evolution, speciation, the evolution of sex and sexual selection, life history evolution, and inference and interpretation of evolutionary relationships. The laboratory investigates evolutionary processes using computer simulations, artificial selection experiments, and a semester-long project that characterizes phenotypic breeding relationships among individuals and integrates these results with analyses of molecular sequence variation for genes contributing to mating recognition. Three hours of lecture, one hour of discussion and four hours of laboratory work each week.

Requisite: BIOL 181 and BIOL 191. Limited to 16 students. Not open to first-year students. Omitted 2020-21. Professor Miller.

2020-21: Not offered
Other years: Offered in Fall 2007, Fall 2008, Spring 2010, Fall 2011, Fall 2012, Spring 2016, Spring 2017, Spring 2019

330 Biochemical Principles of Life at the Molecular Level

(Offered as CHEM 330 and BIOL 330) What are the molecular underpinnings of processes central to life? We will explore the chemical and structural properties of biological molecules and learn the logic used by the cell to build complex structures from a few basic raw materials. Some of these complex structures have evolved to catalyze chemical reactions with an enormous degree of selectivity and specificity, and we seek to discover these enzymatic strategies. We will consider the detailed balance sheet that shows how living things harvest energy from their environment to fuel metabolic processes and to reproduce and grow. Examples of the exquisite control that permits a cell to be responsive and adapt its responses based on input from the environment will be considered. We will also consider some of the means by which cells respond to change and to stress. A student may not receive credit for both CHEM 330 and BCBP/BIOL/CHEM 331.

Requisite: BIOL 191 and CHEM  221. Limited to 40 students with 20 students per discussion section.

Spring semester. Professors Bishop and Jeong.

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2011, Fall 2012, Fall 2013, Fall 2014, Fall 2015, Fall 2016, Fall 2017, Fall 2018, Spring 2020

331 Biochemistry

(Offered as BIOL 331, BCBP 331, and CHEM 331) Structure and function of biologically important molecules and their role(s) in life processes. Protein conformation, enzymatic mechanisms and selected metabolic pathways will be analyzed. Additional topics may include: nucleic acid conformation, DNA/protein interactions, signal transduction and transport phenomena. Four classroom hours and four hours of laboratory work per week. Offered jointly by the Departments of Biology and Chemistry. A student may not receive credit for both BCBP/BIOL/CHEM 331 and CHEM 330.

Requisite: CHEM 231 and BIOL 191; or consent of the instructor. (CHEM 231 may be taken either as a prerequisite or as a co-requisite.) Limited to 30 students. Fall semester. Professors Bishop and Wu Orr. 

2020-21: Offered in Fall 2020
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, Spring 2018, Spring 2019, Fall 2019, Fall 2020

340 Cell and Molecular Disease Mechanisms

This is an advanced cell/molecular biology course that will introduce students to translational research, which seeks to bridge our knowledge of disease mechanisms to the development of therapeutic strategies. We will investigate the cellular and molecular pathophysiology of  HIV/AIDS, Glioblastoma Multiforme, and Diabetes. Students will engage with scientific literature with a focus on recent innovations in cellular and molecular techniques. We will explore how these techniques provide insight into disease mechanisms and drive therapeutic innovation. There will be two eighty-minute discussions per week, and occasional guest lectures from subject matter experts. This course will be conducted in-person. On-line components are available, as needed, supported by appropriate technology.  Options for online-only participation will be available for those students unable to participate in person.

Requisite: BIOL 191, and at least one additional Biology, Neuroscience, Biochemistry, or Chemistry course at the 200 level or above, or by special permission of the instructor. Limited to 18 students. Fall semester. Professor Edwards.

 

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2020

350 Neurophysiology

(Offered as BIOL 350 and NEUR 350) This course will provide a deeper understanding of the physiological properties of the nervous system. We will address the mechanisms underlying electrical activity in neurons, as well as examine the physiology of synapses; the transduction and integration of sensory information; the function of nerve circuits; the trophic and plastic properties of neurons; and the relationship between neuronal activity and behavior. Laboratories will apply electrophysiological methods to examine neuronal activity and will include experimental design as well as analysis and presentation of collected data. Throughout the course, we will focus on past and current neurophysiology research and how it contributes to the field of neuroscience. Three classroom lecture hours, plus a fourth discussion hour to be used for group work, paper presentations, and review sessions.

Requisites: BIOL 191 and CHEM 151; PHYS 117 or 124 is recommended. Limited to 12 students. Open to juniors and seniors. Omitted 2020-21. Professor Trapani.

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2007, Fall 2008, Spring 2010, Fall 2012, Fall 2013, Fall 2016, Fall 2017, Fall 2018, Fall 2019, Fall 2020

351 Neurophysiology with Lab

(Offered as BIOL 351 and NEUR 351) This laboratory course will provide a deeper understanding of the physiological properties of the nervous system. We will address the mechanisms underlying electrical activity in neurons, as well as examine the physiology of synapses; the transduction and integration of sensory information; the function of nerve circuits; the trophic and plastic properties of neurons; and the relationship between neuronal activity and behavior. Laboratories will apply electrophysiological methods to examine neuronal activity and will include experimental design as well as analysis and presentation of collected data. Throughout the course, we will focus on past and current neurophysiology research and how it contributes to the field of neuroscience. Lecture meetings will be combined with BIOL 350 students for three classroom hours plus a fourth hour to be used for group work, paper presentations, and review sessions. Three hours of laboratory work per week.

Requisites: BIOL 191 and CHEM 151; PHYS 117 or 124 is recommended. Limited to one lab section with 18 students. Open to juniors and seniors. Omitted 2020-21. Professor Trapani.

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2007, Fall 2008, Spring 2010, Fall 2012, Fall 2013, Fall 2016, Fall 2017, Fall 2018, Fall 2019, Fall 2020

370 Molecular Genetics

(Offered as BIOL 370 and BCBP 370) A study of the molecular mechanisms underlying the transmission and expression of genes. DNA replication and recombination, RNA synthesis and processing, and protein synthesis and modification will be examined. Both prokaryotic and eukaryotic systems will be analyzed, with an emphasis upon the regulation of gene expression. Application of modern molecular methods to biomedical and agricultural problems will also be considered. Four classroom hours per week.

Requisite: BIOL 191 or equivalent. Limited to 15 students. Not open to first-year students. Omitted 2020-21. Professor Jeong.

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016, Fall 2017, Fall 2018, Fall 2019, Spring 2020, Fall 2020

371 Molecular Genetics W/Lab

(Offered as BIOL 371 and BCBP 371) A study of the molecular mechanisms underlying the transmission and expression of genes. DNA replication and recombination, RNA synthesis and processing, and protein synthesis and modification will be examined. Both prokaryotic and eukaryotic systems will be analyzed, with an emphasis upon the regulation of gene expression. Application of modern molecular methods to biomedical and agricultural problems will also be considered. The laboratory component will focus upon recombinant DNA methodology. Four classroom hours and four hours of laboratory per week.

This course will be conducted in a hybrid format, with both in-person and on-line components as needed, supported by appropriate technology.  Options for online-only participation will be available for those students unable to participate in person.

Requisite: BIOL 191 or equivalent. Limited to 30 students. Not open to first-year students. Fall semester.  Professors Jeong and Lee.

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016, Fall 2017, Fall 2018, Fall 2019, Spring 2020, Fall 2020

372 Immunology

The vertebrate immune response is a consequence of the developmentally programmed or antigen-triggered interaction of a complex network of cell types. These interactions, controlled by regulatory cells and molecules, often result in the production of highly specific cellular or molecular effectors of immune responses. This course will present the principles underlying immune responses and introduce the literature and methodology of immunological research. Critical and detailed review of cases from clinical immunology will also be employed to illustrate the recent impact of immunotherapies on the treatment of cancer. In addition to classroom presentations, one-on-one tutorials will be used for a detailed exploration of significant papers taken from the research literature of immunology. The class will meet twice per week and will also include periodic individual tutorials by appointment.

Requisite: BIOL 191 and at least one more advanced BIOL course or its equivalent incorporating cell and or molecular biology. Limited to 20 students. Omitted 2020-21. Professor Emeritus Goldsby.

2020-21: Not offered
Other years: Offered in Fall 2011, Spring 2014, Fall 2017, Fall 2019

376 Epigenetics

Genes can undergo heritable modifications that alter gene expression without altering genetic information. Such modifications are known as epigenetic modifications, and are heritable through cell division (mitotic inheritance) or from parents to progeny (meiotic inheritance). Epigenetic modifications can be influenced by multiple biological and environmental factors, thus providing an added layer to the relationship between genotype and phenotype. Understanding how this layer of regulation works is becoming an important aspect of molecular genetics. In this course, we will cover basic concepts in epigenetics and discuss various epigenetic processes such as DNA methylation, chromatin remodeling, gene imprinting, post-translational histone modification, epigenomics, environmental epigenetics and the relationship between epigenetic modification and human health. Three hours of lecture per week plus one fourth hour per week.

Requisite: BIOL 191. Limited to 30 students. Omitted 2020-21. Visiting Assistant Professor Lee.

2020-21: Not offered
Other years: Offered in Spring 2019

380 Genome Biology

A study of the architecture and interactions of genetic systems. Advances in genomics are providing insights into a variety of important issues, from the structural limits of DNA-based inheritance to the discovery of novel infectious and genetic diseases. We will address how heritable information is organized in different groups of organisms. We will also cover a major challenge of this emerging field—the application of vast amounts of genetic data to understanding genomic integrity and regulation. We will critically assess the genome as a "cooperative assemblage of genetic elements" and conclude by discussing the consequences of genomic structure for shaping species traits and long-term evolutionary potential. Three hours of lecture per week.
Requisite: BIOL 181 and 191. This course is designed as an overflow class for those who cannot take BIOL 381 and the combined enrollment for these courses will be 30 students. Spring Semester. Professor Hood.

Genome Biology will have in-person sessions for students able to attend and material provided remotely for those who need it.  This includes lecture, and lab material in the case of BIOL 381.  There will be live Zoom lectures for the remote students, which will also be recorded and available on demand.  To the extent possible, the lab component will include hands-on activities, in combination with data analysis and mathematical models.

 

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Spring 2012, Spring 2013, Spring 2014, Spring 2017, Spring 2018, Spring 2020

381 Genome Biology with Lab

A study of the architecture and interactions of genetic systems. Advances in genomics are providing insights into a variety of important issues, from the structural limits of DNA-based inheritance to the discovery of novel infectious and genetic diseases. We will address how heritable information is organized in different groups of organisms. We will also cover a major challenge of this emerging field—the application of vast amounts of genetic data to understanding genomic integrity and regulation. We will critically assess the genome as a "cooperative assemblage of genetic elements" and conclude by discussing the consequences of genomic structure for shaping species traits and long-term evolutionary potential. Three hours of lecture, and three hours of laboratory per week. Lab activities will require work outside of the scheduled meeting times.

Requisite: BIOL 181 and 191. Limited to 18 students.Spring Semester. Professor Hood.

Genome Biology will have in-person sessions for students able to attend and material provided remotely for those who need it.  This includes lecture, and lab material in the case of BIOL 381.  There will be live Zoom lectures for the remote students, which will also be recorded and available on demand.  To the extent possible, the lab component will include hands-on activities, in combination with data analysis and mathematical models.

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Spring 2012, Spring 2013, Spring 2014, Spring 2017, Spring 2018, Spring 2020

400 Molecular and Cellular Biophysics

(Offered as PHYS 400, BIOL 400, BCBP 400, and CHEM 400) How do the physical laws that dominate our lives change at the small length and energy scales of individual molecules? What design principles break down at the sub-cellular level and what new chemistry and physics becomes important? We will answer these questions by looking at bio-molecules, cellular substructures, and control mechanisms that work effectively in the microscopic world. How can we understand both the static and dynamic shape of proteins using the laws of thermodynamics and kinetics? How has the basic understanding of the smallest molecular motor in the world, ATP synthase, changed our understanding of friction and torque? We will explore new technologies, such as atomic force and single molecule microscopy that have allowed research into these areas. This course will address topics in each of the three major divisions of Biophysics: bio-molecular structure, biophysical techniques, and biological mechanisms.

For Spring 2021: This course will be a hybrid model using both asynchronous and synchronous group work.  The course will meet in-person as health and safety considerations permit.

Requisite: CHEM 161/165, PHYS 116/123, PHYS 117/124, BIOL 191 or evidence of equivalent coverage in pre-collegiate courses. Spring semester. Professors Jaswal and Loinaz. 

2020-21: Offered in Spring 2021
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017, Spring 2018, Spring 2019, Spring 2020,

411 Seminar in Synapses: Synaptic Development and Plasticity

Plastic changes to synapses are thought to underlie many higher order functions of the brain in both the developing and adult nervous system. Knowledge of the underlying molecular mechanisms of synaptic plasticity is critical to understanding the complex functions of the brain to which these changes contribute. This seminar course will primarily focus on the most well-studied example of synaptic plasticity, synaptic modifications in a region of the brain called the hippocampus. These changes are thought to underlie our ability to learn and remember. We will look at the experimental attempts to understand these processes, explore the most recent advances in synaptic development and function, and relate this information to prior studies of synaptic modulation and pathologies associated with altered synaptic function. Students will utilize critical analysis of primary literature in order to gain a broad understanding of the historical underpinnings of the field as well as the most recent advances.  Students will analyze and discuss primary research papers, covering topics that include invertebrate memory models, long-term potentiation in the mammalian hippocampus, developmental plasticity, and synaptic tagging.

Requisites: BIOL/NEUR-214 required, and either BIOL/NEUR-301 or BIOL/NEUR-351 are recommended, Limited to 18 students. Spring. Professor Roche.

2020-21: Offered in Spring 2021

430 Seminar in Behavioral Ecology

This course will explore the relationship between an animal's behavior and its social and ecological context. The topic for 2018 will be the evolution of sexual dimorphism in animals. Sexual dimorphism is widespread in animals, yet its causes remain controversial and have generated much debate. In this seminar, we will examine a variety of sexual dimorphisms in different groups of animals and consider hypotheses for how these sexual dimorphisms may have evolved. We will then consider how these hypotheses are tested in an attempt to identify the best approaches to studying the evolution of sexual dimorphism. Then we will look at evidence that either supports or refutes various hypothesized mechanisms for the evolution of sexual dimorphisms in different animal groups. Finally, we will consider whether some mechanisms for the evolution of sexual dimorphism are more convincing among certain kinds of organisms than others. Three hours per week.

Requisite: One or more courses from BIOL 181, BIOL 230, BIOL 280, BIOL 281, BIOL 320, BIOL 321 or consent of the instructor. Not open to first-year students or to students who have taken the seminar in previous years. Limited to 15 students. Omitted 2020-21. Professor Temeles.

2020-21: Not offered
Other years: Offered in Spring 2010, Spring 2012, Fall 2013, Fall 2018, Fall 2019

434 Seminar in Ecology: Plant-animal Interactions

Most animals on Earth obtain their energy from green plants, and, thus, it is not surprising that interactions between plants and animals have played a prominent role in our current understanding of how ecological processes such as predation, parasitism, and mutualism shape evolutionary patterns in plants and animals. The main topics that we will discuss in this seminar include pollination, fruit and seed dispersal, deception, herbivory, and phytocarnivory, considering both ecological and evolutionary perspectives. We will also examine the biodiversity consequences of the loss of these associations via human-induced environmental change. Class readings emphasize the relevant primary literature. Students will have the opportunity to lead discussion and present independent literature research in both oral and written format. Three classroom hours per week.

Requisite: One of the following Biology courses: BIOL 201, 211, 230, 280/1, 320/1, or consent of the instructor. Limited to 15 students. Not open to first-year students. Spring Semester. Professor Temeles.

2020-21: Offered in Spring 2021
Other years: Offered in Fall 2007, Fall 2009, Fall 2011, Spring 2013, Fall 2014, Spring 2016, Spring 2019, Spring 2020

440 Seminar in Conservation Biology

(Offered as BIOL 440 and ENST 441) Conservation biology is a highly interdisciplinary field, requiring careful consideration of biological, economic, and sociological issues. Solutions to biodiversity conservation and environmental challenges are even more complex. Yet, conservation is a topic of timely importance in order to safeguard biological diversity. Utilizing close reading and discussion of articles from the primary literature, the course will explore key topics including overexploitation (including connections between the wildlife trade and emergent diseases such as COVID-19), habitat fragmentation, climate change, restoration, protected areas, payments for ecosystem services, as well as how to determine appropriate conservation priorities. Three classroom hours per week.

This course will be conducted in a hybrid format, with both in-person and online components as needed, supported by appropriate technology.  Options for online-only participation will be available for those students unable to participate in person.

Requisite: BIOL 230/ENST 210 or BIOL 320, or consent of the instructor. Not open to first-year students. Limited to 14 students. Fall Semester. Senior Lecturer Levin.

2020-21: Offered in Fall 2020
Other years: Offered in Spring 2012, Fall 2013, Fall 2015, Fall 2016, Spring 2018, Fall 2019, Fall 2020

450 Seminar in Physiology: Classic Papers in Neurophysiology

(Offered as BIOL 450 and NEUR 450) Concentrating on reading and interpreting primary research, this course will focus on classic and soon-to-be classic neurophysiology papers. We will discuss the seminal experiments performed in the 1950s that led to our understanding of action potentials; experiments in the 1960s and 1970s that unlocked how synapses function; and more recent research that combines electrophysiology with optical methods and genetic techniques to investigate the role of many of the molecular components predicted by the work from the earlier decades. Assignments will include written reviews of literature as well as oral presentations.

Requisite: PHYS 117 or PHYS 124 and one of NEUR 226, BIOL 260, BIOL 351, or consent of the instructor. Limited to 18 students. Not open to first-year students. Omitted 2020-21. Professor Trapani.

2020-21: Not offered
Other years: Offered in Spring 2013, Spring 2017, Spring 2019

454 Seminar in Tropical Biology

Most biodiversity on our planet can be found in tropical latitudes. Tropical rainforests, for example, which account for less than 10% of the Earth’s surface, may contain 50-75% of all plant and animal species. In this course we will examine some of the myriad biotic interactions that occur in the tropics using an ecological, evolutionary, and behavioral approach. The course is divided into two main components: a two-week interterm field course and an advanced seminar. During the field course students will be immersed in the tropical forests of Costa Rica, with a focus on organismal identification and comparisons between three sites (lowland Caribbean rainforest, cloud forest, and coastal dry forest). While in Costa Rica, we will utilize the expertise of local specialists to learn more about taxonomic groups that are particularly significant in the tropics, such as bats, frogs, and epiphytic plants. Back on campus, students will analyze tree diversity data collected in the field, as well as focus on a specific topic within tropical biology, around which students will design experimental research that will be presented in an NSF-style grant proposal. Three hours per week.

Requisite: BIOL 181. Recommended: one or more of the following courses: BIOL 230/ENST 210, BIOL 201, BIOL 280/281, BIOL 320/321. Not open to first-year students. Limited to 12 students. Admission with consent of the instructor. Omitted 2020-21. Professor Clotfelter and Senior Lecturer Levin.

2020-21: Not offered
Other years: Offered in Spring 2014, Spring 2015, Spring 2017, Spring 2019

457 Seminar in Developmental Genetics

This seminar will focus on understanding germ cells. Although germ cells do not contribute to the form or function of an individual, they have the important role of providing the continuity of life between generations. In many animals, they are among the first cells to be differentiated from others during embryonic development. Elaborate mechanisms ensure that the genetic information in these reproductive cells is protected and packaged in unique ways to be used in the next generation. We will explore primary literature readings that probe the specialized development and genetic regulation of germ cells in model systems such as mice, flies, and nematodes. Classic developmental genetic approaches as well as more modern molecular genetic methods will be discussed as ways of understanding these extraordinary cells. Students will use oral and written formats to present paper reviews and analyses. Three classroom hours a week.

Requisite: One of the following: BIOL 221, BIOL 241, BIOL 291, BIOL 370, BIOL 371 or consent of the instructor. Limited to 15 students. Omitted 2020-21. Professor Goutte.

2020-21: Not offered
Other years: Offered in Fall 2018, Spring 2020

460 Seminar in Cell and Organism Formation in the Light of Evolution

This course will investigate how evolution has shaped the specialization of cells and the development of organisms we encounter today. We read and interpret primary research with the goal to identify the conserved and diverse underlying principles of organization inside various cell types and among cells during tissue formation and organism development. We will focus on the concept of the "cell type," and its establishment and plasticity during development and evolution. We will also discuss current research on cell and tissue biogenesis in the lab, including its limitations and potential for therapy. Students will use oral and written formats to present and discuss papers. Three classroom hours per week.
This course will be conducted in-person. Online components are available, as needed, supported by appropriate technology.  Options for online-only participation will be available for those students unable to participate in person.

Limited to 18 students. Spring semester. Assistant Professor Ragkousi. 

2020-21: Offered in Spring 2021

490, 290, 290H, 490H Special Topics

Independent reading or research course. A full course. Does not normally count toward the major.

Fall and spring semesters. The Department.

2020-21: Offered in Fall 2020, Spring 2021
Other years: Offered in Fall 2011, Spring 2012, Fall 2012, Spring 2013, Fall 2013, Spring 2014, Fall 2014, Spring 2015, Fall 2015, Spring 2016, Fall 2016, Spring 2017, Fall 2017, Spring 2018, Fall 2018, Spring 2019, Fall 2019, Spring 2020, Fall 2020

498, 499D Senior Departmental Honors

Honors students take three courses of thesis research, usually, but not always, with the double course load in the spring (499D). The work consists of seminar programs, individual research projects, and preparation of a thesis on the research project.

Open to seniors. Fall semester. The Department.

2020-21: Offered in Fall 2020
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2013, Fall 2014, Fall 2015, Fall 2016, Fall 2017, Fall 2018, Fall 2019, Fall 2020