Biology (BIOL)

BIOL 0004 Killer Viruses: What threat do they pose in contemporary society?

The goal of this course is two fold: to provide students with an introductory, practical view of biological systems, and to enable students to evaluate the health threat of viruses as natural or terrorist-driven agents in contemporary society. We are all well aware of the recent emergence of multiple viruses as potential treats to the public health: examples include SARS-CoV-2 and other SARS, HIV, West Nile and Ebola viruses. However, still greater threats may arise by expansion of existing virus, such as smallpox and influenza that we more commonly think of as being either eradicated or harmless. Through this course we will examine the general properties of viruses, our capacity to ward-off common virus infections using the immune response, the general concept of vaccination, the emergence of new virus pathogens, and the capacity of these pathogens to spread within our population based on regional and global culture and finance.

Not Offered Every Year

1 Course Unit

BIOL 0005 The Genomic Revolution: A First Year Seminar

The goal of this course is to convey a basic understanding of human genome science and in so doing, to learn of its impact on treatment of human disease and discernment of aspects of human identity. Our current understanding of the structure and function of genes will allow a personalized treatment for many diseases, but just how such advances are applied will involve ethical as well as scientific considerations. We will discuss how the field of genetics has been changed dramatically by the ability to clone and sequence genes, and then to be further transformed by massive sequencing of whole genomes. A major part of the course will be devoted to how these advances have led to understanding and treatment of genetic disease and cancer. We will also discuss the tremendous potential (and dangers) of gene editing advances. Finally, we will explore how genomics has allowed an understanding of deep human history, as well as the ability to decipher one's more immediate ancestry. Readings will be from a number of books written for an informed general audience rather than from a textbook. The seminar should be of interest to those who would like to fulfill their Living World General Education requirement, and particularly also to those who eventually might be interested in taking courses in the Life Sciences but initially would like an introductory seminar-type approach within a focused area.

Fall

1 Course Unit

BIOL 0006 Evaluating Medical Treatment: How Do We (and the FDA) Know What Works?

The development of new medical treatments typically culminates in one or more clinical trials - experiments in which the effects of the new treatment are compared with the effects of another treatment or no treatment. A great many considerations go into the design of these medical experiments. In this seminar, we will discuss the basic structure of the clinical trial, the varying types of designs that may be used, the scientific and ethical issues that arise, and the regulatory process that ultimately determines whether medical products are effective and safe and whether they can be made available to the public.

Not Offered Every Year

1 Course Unit

BIOL 0010 Ecological Consequences of Climate Change

Students will read and discuss seminal papers on a number of major topics in the ecology of climate change and the long-term consequences of the effects of climate change on ecological systems. Some of the topics include: effects of climate change on species distributions, disruption of plant pollinator systems and the consequences for ecosystem composition and stability, changes in the distribution and epidemiology of insect-borne infectious diseases, and the consequences of sea level rise and the increased intensity and frequency of severe weather events. Other topics may be covered. Grading will be based on participation in discussions, a paper on an approved topic, and a presentation on the topic of the student's paper.

Spring

1 Course Unit

BIOL 0014 Descent with Modification: An introduction to the science of evolution

Evolution provides the unifying framework for the biological sciences and has been confirmed by a huge and diverse body of evidence. Public opinion polls show, however, that evolution continues to be socially and politically controversial in the United States. In this first-year seminar, we will explore the scientific basis for evolution by reading and discussing historical sources, a current nonspecialist text on evolution, and selected papers and articles from the scientific and popular literature. With our knowledge of evolutionary fact and theory as background, we will also discuss social and political opposition to the teaching of evolution. Grading will be based on participation in class discussions and on performance in several brief writing assignments. There is no course prerequisite, but high school introductory biology would be helpful.

Fall, even numbered years only

1 Course Unit

BIOL 0016 How to Think Like an Evolutionary Biologist

This first year seminar will provide insights to an evolutionary biologist's perspective of the living world. Readings and discussion will center around The Blind Watchmaker by Richard Dawkins and similar works. Students will write a paper on a topic of their choice after consultation with the instructor. There will be two short answer/essay exams on the assigned readings.

Spring

1 Course Unit

BIOL 1011 Humans in a Microbial World

Microbes are a fundamental part of life on this planet. This course will explore the causes and consequences of the distribution and abundance of microbes (microbial ecology) as well as microbial evolution on human health and disease risk. We will address the interplay between human society and microbial ecology and evolution in shaping disease risk and directing scientific study. This course will apply concepts from basic biology, ecology, and evolution to study infectious microbes as living creatures.

Not Offered Every Year

1 Course Unit

BIOL 1017 The Biology of Food

This course will examine the ways in which humans manipulate - and have been manipulated by - the organisms we depend on for food, with particular emphasis on the biological factors that influence this interaction. The first part of the course will cover the biology, genetics, evolution, and breeding of cultivated plants and animals; the second part will concern the ecological, economic, and political factors that influence food production.

Spring, even numbered years only

1 Course Unit

BIOL 1019 Biological Science and Public Policy

This course will examine the scientific basis of public policy decision making in areas of human health, the environment, energy, and agriculture. A general understanding of the science involved in these areas - predominantly genetics, cell biology, physiology, and ecology - will be applied to topics such as drug and herbicide resistance, endangered species, regulation of biotechnology, microbial sources of energy, control of toxic substances, and the war against cancer. No formal background in biology or policy is required. The course should be particularly useful for non-science students who would like to gain insight into areas of biology of importance to public decision making and to students of public policy who would like a better background on biological issues.

Fall

1 Course Unit

BIOL 1101 Introduction to Biology A

General principles of biology focusing on the basic chemistry of life, cell biology, molecular biology, and genetics in all types of living organisms. Particular emphasis will be given to links between the fundamental processes covered and current challenges of humankind in the areas of energy, food, and health.

Fall or Spring

1.5 Course Unit

BIOL 1102 Introduction to Biology B

General principles of biology focusing on evolution, physiology, development, and ecology in all types of living organisms.

Fall or Spring

Prerequisite: BIOL 1101

1.5 Course Unit

BIOL 1110 Introduction to Brain and Behavior

Introduction to the structure and function of the vertebrate nervous system. We begin with the cellular basis of neuronal activities, then discuss the physiological bases of motor control, sensory systems, motivated behaviors, and higher mental processes. This course is intended for students interested in the neurobiology of behavior, ranging from animal behaviors to clinical disorders.

Fall or Spring

Also Offered As: NRSC 1110, PSYC 1210

1 Course Unit

BIOL 1121 Introduction to Biology - The Molecular Biology of Life

An intensive introductory lecture course covering the cell, molecular biology, biochemistry, and the genetics of animals, bacteria, and viruses. This course is comparable to Biology 1101, but places greater emphasis on molecular mechanisms and experimental approaches. Particular attention is given to the ways in which modern cell biological and molecular genetic methods contribute to our understanding of evolutionary processes, the mechanistic basis of human disease, and recent biotechnological innovations. Students are encouraged to take BIOL 1121 and BIOL 1123 concurrently.

Fall

Prerequisite: CHEM 1011

1 Course Unit

BIOL 1123 Introductory Molecular Biology Laboratory

An intensive introductory laboratory course emphasizing how molecular biology has revolutionized our understanding of cell and organism functions. BIOL 1121 and BIOL 1123 should be taken concurrently.

Fall

Prerequisite: BIOL 1121

.5 Course Units

BIOL 1124 Introductory Organismal Biology Lab

An intensive introductory laboratory course in organismal biology.

Spring

.5 Course Units

BIOL 1380 Energy Transformations and Living Off-the-Grid

The course will examine major sources of energy on earth: sunlight, mechanical, chemical and biological, and how this energy is transformed into useful energy for humans - typically electrical energy or food. Considerable emphasis will be on forms of regenerative energy that can be used when living off-the-grid. As a case study, we will examine some approaches taken by the US military to provide energy capability for dismounted Marines operating on foot in austere environments. Faculty lectures will be supplemented by guest lectures from leaders in government and industry. No scientific knowledge is assumed beyond high school biology, chemistry and physics. Energy is necessarily a quantitative subject so students should be comfortable with quantitative approaches. A major goal of this course is for students to develop an awareness for the amounts of energy they use in their daily lives, and how they might reduce them. As an exercise, students will measure how much energy their smart phones and laptops use in a day and try to generate a comparable amount of energy through physical effort.

Fall, odd numbered years only

1 Course Unit

BIOL 1604 Humans and the Environment

Intensive exposure to current issues and solutions in contemporary human interactions with the environment. Global in scope, but focused on case histories. Emphasis on providing biological and sociological background for a given major environment-human interaction, and state-of-the-art suggested solutions.

Fall

1 Course Unit

BIOL 1605 Field Studies in Tropical Biodiversity and Conservation

We will use the Area de Conservacion Guanacaste (ACG) in Costa Rica as a living laboratory and case study in how to effectively foster community based environmental stewardship of natural ecosystems. This is an immersion course that broadly covers four major themes including: 1, biodiversity; 2, conservation philosophies and practices; 3, primary ecosystems within the Costa Rican ACG and their major species composition; and 4, fundamentals of field ecology (terrestrial and marine) including the practice and implementation of the scientific method. Students will learn how to develop and conduct research experiments via field-based activities, and will gain familiarity with a diversity of terrestrial and marine organisms including insects, endemic and invasive species of terrestrial flora and megafauna, corals, algae, invertebrates, fish, sea turtles and marine mammals. Additional topics covered will include fundamentals of oceanography, ecological and evolutionary principles as applied to ecosystem structure, function, and biodiversity, and environmental and management challenges of the Costa Rican ACG and tropical ecosystems globally.

Fall

1 Course Unit

BIOL 1999 Clinical & Translational Research

Independent study for students doing research based on data that is generated in a clinical setting. Projects must be sponsored by standing faculty of the University of Pennsylvania and co-sponsored by a faculty member in the Department of Biology. The project must be of biological interest and must use appropriate quantitative or statistical methods. A final paper is required. Apply at the Academic Office, 102 Leidy Labs.

Fall or Spring

1 Course Unit

BIOL 2001 Essentials of Cell Biology

An intermediate level exploration of cell structure and function including membrane structure, intracellular organelles, membrane trafficking, surface receptors and signal transduction, the cytoskeleton, cell motility and communication, and the cell cycle. This course is open to students in the College of Liberal and Professional Studies only.

Fall or Spring

Prerequisite: (BIOL 1101 AND BIOL 1102) OR BIOL 1121

1 Course Unit

BIOL 2010 Cell Biology

A conceptual view of cell structure and function including membrane structure, intracellular organelles, membrane trafficking, surface receptors and signal transduction, the cytoskeleton, cell motility and communication, and the cell cycle. Cell biology is a dynamic field and recent research discoveries will be included in the lectures.

Fall

Prerequisite: (BIOL 1101 AND BIOL 1102) OR BIOL 1121

1 Course Unit

BIOL 2110 Molecular and Cellular Neurobiology

Cellular physiology of neurons and excitable cells; molecular neurobiology and development. Topics include: action potential generation; synaptic transmission; molecular and physiological studies of ion channels; second messengers; simple neural circuits; synaptic plasticity; learning and memory; and neural development.

Fall

Also Offered As: NRSC 2110

Prerequisite: (BIOL 1101 AND BIOL 1102) OR BIOL 1121

1 Course Unit

BIOL 2140 Evolution of Behavior: Animal Behavior

The evolution of behavior in animals will be explored using basic genetic and evolutionary principles. Lectures will highlight behavioral principles using a wide range of animal species, both vertebrate and invertebrate. Examples of behavior include the complex economic decisions related to foraging, migratory birds using geomagnetic fields to find breeding grounds, and the decision individuals make to live in groups. Group living has led to the evolution of social behavior and much of the course will focus on group formation, cooperation among kin, mating systems, territoriality and communication.

Fall

Also Offered As: NRSC 2140, PSYC 2220

Prerequisite: BIOL 1102 OR BIOL 1121 OR PSYC 0001

1 Course Unit

BIOL 2201 Essentials of Molecular Biology and Genetics

This course will survey the discipline of molecular genetics. Mendelian and molecular genetics will be discussed as well as the use of genetic analysis to address questions in all areas of biology. The processes of DNA replication, transcription, and translation will be discussed at the molecular level. Other topics include the regulation of gene expression and genomics. This course is open to students in the College of Liberal and Professional Studies only.

Fall or Spring

Prerequisite: (BIOL 1101 AND BIOL 1102) OR BIOL 1121

1 Course Unit

BIOL 2210 Molecular Biology and Genetics

This course will survey the discipline of molecular genetics. Two broad areas will be considered 1) Molecular Biology: DNA replication, transcription, translation, regulation of gene expression in both prokaryotic and eukaryotic systems, and genomics and 2) Genetics: basic Mendelian & molecular genetics.

Fall or Spring

Prerequisite: BIOL 1101 OR BIOL 1121

1 Course Unit

BIOL 2301 Essentials of Vertebrate Physiology

A comparative and quantitative approach to the physiological function of vertebrates. Topics include muscles, nervous system, cardiovascular system, respiration, and renal function. This course is open to students in the College of Liberal and Professional Studies only.

Fall or Spring

Prerequisite: (BIOL 1101 AND BIOL 1102) OR (BIOL 1121 AND BIOL 1124)

1 Course Unit

BIOL 2310 Vertebrate Physiology

The course will focus on integrative aspects of physiological function of vertebrates. Comparative, environmental and quantitative approaches will be used. Major topics include muscle, the cardiovascular system, respiration, renal function and the nervous system.

Fall or Spring

Mutually Exclusive: BIOL 3310

Prerequisite: BIOL 1102 OR BIOL 1121 OR BIOL 1124

1 Course Unit

BIOL 2311 Human Physiology

This course examines the physiological mechanisms underlying homeostasis in humans. Integration from the cellular to organismal level as well as cooperation of multiple organ systems will be explored. Examples of pathophysiology during disease states will be discussed and highlighted. Although the focus will be on humans, we will study comparative aspects from other vertebrate and non-vertebrate organisms.

Spring

Mutually Exclusive: BIOL 3310

1 Course Unit

BIOL 2410 Evolutionary Biology

Theories and mechanisms of evolution, with emphasis on the genetic basis of evolutionary change.

Spring

Prerequisite: (BIOL 1101 AND BIOL 1102) OR BIOL 1121

1 Course Unit

BIOL 2510 Statistics for Biologists

Introductory probability theory. Principles of statistical methods. Problems of estimation and hypothesis testing in biology and related areas.

Fall

Mutually Exclusive: BIOL 4510, BIOL 5510

Prerequisite: MATH 1400

1 Course Unit

BIOL 2610 Ecology: From individuals to ecosystems

The study of living organisms in their natural environment, spanning the ecological physiology of individuals, the structure of populations, and interactions among species, including the organization of communities and ecosystem function.

Fall

Prerequisite: BIOL 1102 OR BIOL 1121

1 Course Unit

BIOL 2701 Elements of Microbiology

Microbiology plays a central role in diverse areas of human life such as infectious disease, ecology, and biotechnology. This course will cover aspects of modern microbiology with an emphasis on prokaryotic organisms. The topics will include basic aspects of microbial diversity, genetics, and pathogenesis as well as examples of applied microbiology. This course is open to students in the College of Liberal and Professional Studies only.

Fall or Spring

Prerequisite: (BIOL 1101 OR BIOL 1121) AND (BIOL 2201 OR BIOL 2210)

1 Course Unit

BIOL 2801 Essentials of Biochemistry

Intermediate level course covering principles of modern biochemistry. Topics include protein structure, protein purification and characterization, proteomics, enzyme kinetics and mechanisms, membrane structure and function, metabolism, and cellular energy transduction. Emphasis will be on biochemical problem solving, experimental design, and application of quantitative methods in a biological and clinical context. This course is open to students in the College of Liberal and Professional Studies only.

Fall or Spring

Prerequisite: ((BIOL 1101 AND BIOL 1102) OR BIOL 1121) AND CHEM 2410

1 Course Unit

BIOL 2810 Biochemistry

BIOL 204 examines the basic principles of protein structure, protein purification and characterization, proteomics, enzyme kinetics and mechanism, membrane structure and function, metabolism, and cellular energy transduction. The primary objective is to provide life scientists with an appreciation of basic principles of modern biochemistry, and of how the current conceptual and technical framework arose. Emphasis is placed on the experimental approaches and reasoning behind the dissection and reconstitution of these processes in a biological and, in some cases, clinical context. Discussions directed at biochemical problem solving, experimental design and the application of quantitative methods are integral to the course.

Spring

Prerequisite: ((BIOL 1101 AND BIOL 1102) OR BIOL 1121) AND CHEM 2410

1 Course Unit

BIOL 3004 Infectious Disease Biology

This course focuses on selected topics concerning infectious agents, the diseases they cause in humans, and the social and scientific challenges they pose. The first section addresses the principles of epidemiology and microbial pathogenesis, as well as pathophysiology of infectious diseases. In the second section, tools and techniques of diagnosis, tracking, and control of infectious diseases will be discussed. To develop a broad understanding of the many different aspects of infectious processes, selected viral, fungal, protozoan, and helminthic pathogens and related infectious diseases will be presented. This course is open to students in the College of Liberal and Professional Studies only.

Spring

Prerequisite: (BIOL 2201 OR BIOL 2210) AND BIOL 2701 AND BIOL 4004

1 Course Unit

BIOL 3006 Histology

This course is designed to introduce the undergraduate student to the structure of tissues at the cellular level and to the way in which those tissues are assembled into organs. This knowledge of structure will be the basis for discussion of tissue and organ function. This course is open to students in the College of Liberal and Professional Studies only.

Fall or Spring

Prerequisite: ((BIOL 1101 AND BIOL 1102) OR BIOL 1121) AND (BIOL 2001 OR BIOL 2010)

1 Course Unit

BIOL 3008 Immunology in Action

A foundational understanding of the immune response is central to our ability to address challenges in treating and preventing disease as scientists and to understand advances as citizens. The study of immunology can be daunting, in part because our response is complex and integrates many systems, and in part because the vocabulary that has developed around this discipline is dense with abbreviations and acronyms. In this class, we will work together to demystify the immune system by considering responses in context - for example, by considering how vaccines exploit the ability of the immune system to generate memories, analyzing the design of a CAR-T cell to understand how it can be used to attack tumors, evaluating the remarkable history and current promise of monoclonal antibodies in treatment of inflammatory diseases, and more. The course, which will consist of a combination of weekly interactive synchronous sessions and asynchronous assignments, should provide you with tools to critically evaluate information about advances - and a foundation that will allow you to contribute to new discoveries in this fascinating, dynamic field.

Spring

1 Course Unit

BIOL 3054 Developmental Biology

A view of how an animal embryo is specified to develop and differentiate into a wide spectrum of cell types, and how the spatial patterns and axes of embyros are determined. The course will focus on genetic and molecular approaches, but will also cover the comparative anatomy of developing embryos to the extent necessary to understand the conserved aspects of embryonic patterning. Special emphasis will be placed on organisms with particular advantages for the study of embryonic development: e.g., mouse, frog, zebrafish, and Drosophila. The first half of the course will cover cell fate restrictions, cloning animals using nuclear transfer, stem cell biology, formation of the embryonic axes in vertebrates and Drosophila, and patterning of the neural tube and mesodermal tissues. The second half of the course will focus on emerging ideas and findings in the field, with emphasis on analysis of original literature.

Spring

Prerequisite: BIOL 2010 OR BIOL 2210

1 Course Unit

BIOL 3310 Principles of Human Physiology

Our focus will be on human physiology and we will cover most of the major organ systems in some depth. We seek to understand physiological phenomena using physical and chemical principles where possible. Basic cell and molecular biology, (bio)chemistry, physics and mathematics are prerequisites for the course, although we will quickly review the required background material when needed. Much of the motivation for the study of physiology is to understand disease, which in turn allows us to better appreciate normal physiology. We will discuss disease throughout the class. In physiology, structure often implies function, and we will thus also cover a fair amount of anatomy and histology.

Fall

Mutually Exclusive: BIOL 2310, BIOL 2311

Prerequisite: BIOL 1102 OR BIOL 1121

1 Course Unit

BIOL 3313 Essentials of Pathophysiology

This course is a study of homeostatic changes that occur with disease, and the implications of those changes in the progression and treatment of disease at molecular and cellular levels. Generalized mechanisms of disease as well as diseases of individual organ systems will be examined, with a view to understanding homeostatic compensations that occur as a result of altered function.

Spring

1 Course Unit

BIOL 3430 Comparative Vertebrate Anatomy and Evolution

This course will survey the phylogeny and anatomy of vertebrate organisms from a comparative evolutionary perspective. The lecture will concentrate on the history, diversity, structure and function of vertebrates. A companion lab course, BIOL 3431, is available for those students interested in a more complete understanding of vertebrate anatomy.

Spring

Prerequisite: BIOL 1102 OR BIOL 1121

1 Course Unit

BIOL 3431 Comparative Vertebrate Anatomy Lab

Laboratory portion of BIOL 3430 Comparative Vertebrate Anatomy and Evolution. Students will learn comparative anatomy through dissection of representative vertebrates. Students taking the lab must have credit or register for the lecture course, BIOL 3430.

Spring

Prerequisite: BIOL 3430

0.5 Course Units

BIOL 3625 Marine Biology

An introduction to marine biology and oceanography. Topics will include chemical and physical oceanography, a survey of form, function and phylogeny of algae, invertebrates and vertebrates, and an examination of ecological and evolutionary principles as applied to marine organisms and ecosystems.

Fall

Prerequisite: BIOL 1102 OR BIOL 1121

1 Course Unit

BIOL 3710 Microbial Diversity and Pathogenesis

Microbiology plays a central role in diverse areas of human life such as infectious disease, ecology, and biotechnology. This course will cover aspects of modern microbiology with an emphasis on prokaryotic organisms. The topics will include basic aspects of microbial diversity, genetics, virology, and pathogenesis as well as examples of applied microbiology.

Spring

Prerequisite: ((BIOL 1101 AND BIOL 1102) OR BIOL 1121) AND BIOL 2210

1 Course Unit

BIOL 3711 Microbial Diversity and Pathogenesis Lab

The importance of microbiology in complex issues, such as the impact of the microbiome in human health or as alternative energy sources, is being appreciated more and more each day. This upper level laboratory course provides students with a robust technical skill set while also giving them an opportunity to participate in an authentic research project that may lead to novel discoveries. Students will generate research questions, formulate hypotheses, design experiments, analyze data, and present their research findings to the class. In each project, students will use the cutting edge approach of metagenomics to evaluate the microbial diversity of their environment via Next Generation Sequencing. Students will also examine the function of microbial species within their communities. Potential projects include the isolation of novel antibiotic producers and the antibiotic they produce, designing and optimizing microbial fuel cells that can be used to generate electricity, or isolating antibiotic resistant bacteria and attempting novel approaches to inhibit or prevent their growth.

Spring

Prerequisite: BIOL 3710

1 Course Unit

BIOL 3999 Independent Study

Laboratory research with a faculty member in the Department of Biology. Research may also be conducted elsewhere on campus but co-sponsored by a faculty member in Biology. A final paper is required. Apply at the Biology Academic Office, 102 Leidy Labs.

Fall or Spring

1 Course Unit

BIOL 4004 Immunobiology

Early development of microbiology, pathology, and immunobiology; molecular and cellular bases of immune phenomena including: immunity to pathogens, immune diseases, autoimmunity, and hypersensitivity. This course is open to students in the College of Liberal and Professional Studies only.

Fall or Spring

Prerequisite: (BIOL 2001 OR BIOL 2010) AND (BIOL 2201 OR BIOL 2210)

1 Course Unit

BIOL 4007 Cancer Cell Biology

This course will focus on the molecular mechanisms by which fundamental cellular processes are disrupted in the development of cancer.

Fall

Prerequisite: BIOL 2010 AND 2210

1 Course Unit

BIOL 4010 Advanced Cell Biology

This course is designed for beginning graduate students and advanced undergraduates with a particular enthusiasm for cell biology. Biology 4010 does not attempt to cover all aspects of cell biology, and is therefore not appropriate for students seeking a lecture course which provides a comprehensive survey of the field. Rather, the primary objective of this course is to teach those students considering a career in the biomedical sciences how to read, discuss, and question original research papers effectively. Intensive classroom discussions focus on the experimental methods used, results obtained, interpretation of these results in the context of cell structure and function, and implications for further studies.

Fall

Also Offered As: CAMB 4800

Prerequisite: BIOL 2001 OR BIOL 2010

1 Course Unit

BIOL 4015 First Line of Defense: The Role of Innate Immunity in Disease

All organisms, from bacteria to humans, rely on innate, non-specific defense systems to protect against infection and mediate damage. Even in organisms that can generate highly specific and efficient adaptive responses, such as humans, defects in innate immune system components can be fatal. In this course, we will examine the cellular and molecular mechanisms of the components of the innate immune system through discussion of primary literature. We will explore how the innate immune system influences the course of infections and cancer, as well as autoinflammatory disorders that lead to host tissue damage. Though our focus will be on mammalian immunity, we will also explore the evolutionary development of innate immunity through comparison of systems in different organisms.

Fall

Prerequisite: BIOL 2010

1 Course Unit

BIOL 4016 Molecular Mechanisms of Infectious Disease Biology

This course is designed for advanced undergraduates and beginning graduate students with a particular interest in infectious disease biology. Note that this course is not a comprehensive survey of the field and is not appropriate for students seeking a lecture course on disease. The primary objective of this course is to teach students considering a career in the biomedical sciences how to read, discuss, and question research papers effectively. Intensive classroom discussions focus on the experimental methods used, results obtained, interpretation of these results in the context of pathogen interactions with host cells and organisms, and implications for basic research and therapeutic development.

Spring

Prerequisite: BIOL 2010

1 Course Unit

BIOL 4018 Cell Communication and Disease

Effective coordination between cells through cell communication and signaling enables multicellular organisms to develop and survive. Conversely, aberrations in these pathways are at the heart of a wide variety of human diseases. In this seminar course, we will discuss the molecular and cellular mechanisms of cell communication using a series of human diseases as a framework. The course will introduce postbac and advanced undergraduate students to the fundamental principles of cell signaling and will explore current questions of interest to the field. The synergistic nature of research directed at understanding basic cell biology, development and physiology with research aimed at elucidation and control of specific human ailments will be emphasized. The course will be comprised of a combination of introductory lectures and extensive discussion of primary literature. Students are expected to have a basic knowledge of cell biology, biochemistry and cell structure. BIOL 2201 and BIOL 2801 are recommended pre-requisites.

Fall

1 Course Unit

BIOL 4022 Cell Signaling

The evolution of multicellularity required that cells be able to both send and receive signals from their neighbors. The development of organs and differentiation of cells and tissues requires reliable and continuous communication between cells. Consequences of inappropriate or anomalous signaling include development abnormalities and cancer. This class will examine mechanisms of cell-to-cell signaling between cells in plants and animals with an emphasis on the cell biology of development.

Fall

Prerequisite: BIOL 2010

1 Course Unit

BIOL 4024 Cell Motility and the Cytoskeleton

Cytoskeleton and cell motility plays a crucial role in many aspects of normal and pathological physiology of individual cells, tissues, and whole organisms, including morphogenesis, immune response, wound healing, oncogenesis, and infection. This course will cover current topics in cell biology with emphasis on cytoskeleton and cell motility and their roles in these processes. Lectures, student presentations, and discussions in the class will be based on primary scientific literature.

Fall

Prerequisite: BIOL 2010

1 Course Unit

BIOL 4026 Chromosomes and the Cell Cycle

Life depends on the propagation of genetic material from one generation to the next through cycles of genome replication and cell division. The genome is copied by the parent, and one exact copy is inherited by each daughter cell. We will treat chromosomes as discrete entities, rather than collections of genes, that are replicated and divided with high fidelity to ensure that the genome remains stable over many generations. By reading selected primary literature covering several decades, we will build an understanding of the cell cycle by focusing on chromosomes and the associated molecular machinery. We will explore mechanisms that underlie replication and division, particularly control mechanisms that maintain genome integrity and are critical to prevent disease. The goal of the course is to develop a picture of the cell cycle by examining some of the key experiments and insights that have led to our current understanding.

Spring

Also Offered As: CAMB 4860

Mutually Exclusive: BIOL 5026

Prerequisite: BIOL 2010

1 Course Unit

BIOL 4048 Principles of Drug Action

Principles of Drug Action covers the concepts of pharmacological sciences as they relate to biochemistry, cell biology, and drug therapy. The intent of the course is to provide a solid grounding in targets of drug action, dose-response relationships, pharmacodynamics, and pharmacokinetics. The grounding is achieved by a discussion of these concepts explicitly and, through selected examples, implicitly. The first part of the course covers each of the concepts. Emphasis is placed on the integration with principles of cell biology and biochemistry. The second part of the course covers selected therapeutic applications. The applications chosen fall within four areas: cardiovascular, brain and behavior, antipyretic and anti-inflammatory, and antimicrobial. They are used to recapitulate important concepts and provide insight into the interplay between pharmacology and human physiology. The applications and the areas they represent are by no means comprehensive, but students will be able to pursue additional interests through papers.

Fall

Prerequisite: BIOL 2010

1 Course Unit

BIOL 4077 The Science and Art of Biotechnology

Biotechnology transforms basic biological research into pharmaceutical therapies. This course will examine some explanations for American biotechnology vitality by studying case histories in which fundamental, biological observations were subsequently developed, successfully and unsuccessfully, for therapeutic applications. Along the way, we will also seek to understand the interactions among academic research institutions, biotechnology companies, large pharmaceutical companies, the Food and Drug Administration, financial institutions, venture groups, and the Patent and Trademark Office. Classes will be highly interactive. Students will present case histories in a critical fashion. Ultimately, students will conduct mock negotiations focused on university technology transfers, clinical trial design, financing, and intellectual property.

Fall

Prerequisite: BIOL 2810 OR BIOL 2010 OR BIOL 2210

1 Course Unit

BIOL 4110 Neural Systems and Behavior

This course will investigate neural processing at the systems level. Principles of how brains encode information will be explored in both sensory (e.g. visual, auditory, olfactory, etc.) and motor systems. Neural encoding strategies will be discussed in relation to the specific behavioral needs of the animal. Examples will be drawn from a variety of different model systems.

Spring

Also Offered As: NRSC 4110, PSYC 3220

Prerequisite: BIOL 2110

1 Course Unit

BIOL 4116 Neural Circuits for Survival

A fundamental goal of neuroscience is to understand how neural circuits in the brain function to influence behavior. The aim of this course is to highlight the neural basis of behavior and discuss modern approaches and novel methods to study the neuronal control of classically studied aspects of behavior. Through a combination of discussions, student presentations, and interactive lectures, we will explore the neural systems that regulate the interactions an animal has with the external world. We will explore sensory systems (such as vision, taste, and olfaction), motor systems, and survival behaviors (such as feeding, drinking, mating, and aggression). The course evaluation will be based largely on written work, participation, and presentations.

Spring

Prerequisite: BIOL 2110

1 Course Unit

BIOL 4119 Biological Basis of Animal Diversity

Animals display extraordinary diversity in their morphology, physiology, and behavior. Traditionally, these topics have been mostly studied from an ecological perspective. This course will focus on recent advances and discoveries that address the underlying biological mechanisms of animal diversity. Specific topics will include the genetic, molecular, and developmental basis of animal morphological diversity, and genetic, molecular, and neural basis of animal behavioral diversity. Students will gain an understanding of how animal diversity is encoded at the different levels of biological organization. The course will be comprised of lectures to introduce topics, discussion of primary literature, and in-class activities.

Spring

1 Course Unit

BIOL 4142 Neurobiology of Learning and Memory

This course focuses on the current state of our knowledge about the neurobiological basis of learning and memory. A combination of lectures and student seminars will explore the molecular and cellular basis of learning in invertebrates and vertebrates from a behavioral and neural perspective.

Fall

Also Offered As: NRSC 4442, PSYC 3301

1 Course Unit

BIOL 4210 Molecular Genetics

A detailed analysis of gene structure and expression in both prokaryotic and eukaryotic organisms. Rapid advances in DNA technology and genomics will be emphasized. The application of these advances to the molecular genetic analysis of development, cell function and disease will be discussed.

Fall

Prerequisite: BIOL 2210

1 Course Unit

BIOL 4231 Genome Science and Genomic Medicine

This course will be a focused study of genomes, genomic techniques, and how these approaches are and will be used in diagnosing and treating human disease. Topics will include genome sequencing, analysis of sequences and microarrays, and new techniques including high-throughput sequencing and reverse genetic analysis with a focus on genome-wide mutant collections.

Spring

Also Offered As: CAMB 4310

Mutually Exclusive: BIOL 5231

Prerequisite: BIOL 2210

1 Course Unit

BIOL 4233 The Genetics of Adaptation: How sex, conflict, and pathogens shape modern genomes

In this course we explore the genetic basis of adaptation. We will investigate the forces that drive adaptation (e.g., environmental stress, pathogens, conflict, sex), the genetic mechanisms of adaptation (protein sequence changes, expression divergence, gene duplication, etc.), and the consequences of adaptation for contemporary cellular functions, developmental processes, and ecological interactions. The class meetings will be structured around both lectures and student-led discussions of the primary literature.

Spring

Mutually Exclusive: BIOL 5233

Prerequisite: BIOL 2210 OR BIOL 2410

1 Course Unit

BIOL 4234 Epigenetics

This course investigates epigenetic phenomena: heritable alternate states of gene activity that do not result from an alteration in nucleotide composition (mutations). Epigenetic mechanisms regulate genome accessibility and cell differentiation. They play a key role in normal development and in oncogenesis. For example both mammalian X-chromosome inactivation and nuclear transfer (cloning) are subject to epigenetic regulation. Amongst the epigenetic mechanisms we will discuss in this course are chromatin organization, histone modification, DNA methylation and non-coding RNAs. The course is geared toward advanced undergraduate and beginning graduate students and is a combination of lectures, student presentations and research presentations by guest speakers. Students will work with the current scientific literature.

Spring

Also Offered As: CAMB 4830

Mutually Exclusive: BIOL 5234

Prerequisite: BIOL 2210

1 Course Unit

BIOL 4235 The RNA World: A functional and computational analysis

A focused study of genomic, biochemical, cellular, and molecular aspects of RNA. Topics of study will include RNA structure, RNA processing and turnover, splicing, ribozymes and riboswitches, RNA editing and modification, RNA interference, endogenous eukaryotic RNA silencing pathways, small RNA biology, computational methodologies for studying RNA biology, and RNA viruses. Lectures, students presentations, and discussions will be based on readings from the primary literature.

Spring, odd numbered years only

Also Offered As: CAMB 4850

Prerequisite: BIOL 2210

1 Course Unit

BIOL 4244 Epigenetics of Human Health and Disease

Epigenetic alterations encompass heritable, non-genetic changes to chromatin (the polymer of DNA plus histone proteins) that influence cellular and organismal processes. This course will examine epigenetic mechanisms in directing development from the earliest stages of growth, and in maintaining normal cellular homeostasis during life. We will also explore how diverse epigenetic processes are at the heart of numerous human disease states. We will review topics ranging from an historical perspective of the discovery of epigenetic mechanisms to the use of modern technology and drug development to target epigenetic mechanisms to increase healthy lifespan and combat human disease. The course will involve a combination of didactic lectures, primary scientific literature and research lectures, and student-led presentations.

Spring, even numbered years only

Also Offered As: CAMB 4930, GCB 4930

Prerequisite: BIOL 2210

1 Course Unit

BIOL 4266 Molecular Genetics of Neurological Disease

This course will focus on the molecular basis of neurological diseases, exploring in detail key papers that cover topics including defining the disease genes, development of animal models that provide mechanistic insight, and seminal findings that reveal molecular understanding. Diseases covered will include neurological diseases of great focus today such as Alzheimer's, Fragile-X and autism, dementia, motor neuron degeneration, and microsatellite repeat expansion disorders. The course will provide a perspective from initial molecular determination through current status. Students will gain an understanding of how the molecular basis of a disease is discovered (from classical genetics to modern genomics) and how such diseases can be modeled in simple genetic systems for mechanistic insight. The course will be comprised of lectures with detailed analysis of primary literature and in-class activities. Grading will be based on class participation, exams, and written papers.

Fall

Also Offered As: NRSC 4266

Prerequisite: BIOL 2210

1 Course Unit

BIOL 4310 Molecular Physiology

This course is designed for advanced undergraduate and graduate students who are interested in molecular physiology of sensory signal transduction. The major topics to cover will be signal transduction mechanisms used by membrane ion channels and receptors that detect the sensory stimuli (light, sound, temperature and taste, for example) and transmit the signals to the nervous system. Modern molecular/structural techniques (patch clamp, protein crystallization, molecular genetics, expression cloning and protein purification) will be introduced along with each topic. References will be primary research articles. Students will critically evaluate research discoveries by reading and presenting one to two original research papers. Each student is required to write a 10-page research proposal and to critique proposals written by fellow students.

Fall

Prerequisite: (BIOL 1101 AND BIOL 1102) OR BIOL 1121

1 Course Unit

BIOL 4313 Energy Transformations and Living off-the-Grid

The course will examine major sources of energy on earth: sunlight, mechanical, chemical and biological, and how this energy is transformed into useful energy for humans -- typically electrical energy, heat, mechanical power or food. Considerable emphasis will be on forms of regenerative energy that can be used when living off-the-grid. As a case study, we will examine some approaches taken by the US military to provide energy capability for dismounted Marines operating on foot in austere environments. Faculty lectures will be supplemented by guest lectures from leaders in various areas of science. A major goal of the course is for students to develop an awareness of the amounts of energy they use in their daily lives, and how they might reduce them. As an exercise, students will measure how much energy their smart phones and laptops use in a day and try to generate a comparable amount of energy through physical effort. The course will include lectures, discussion, guest expert lectures, and laboratory measurements.

Spring, even numbered years only

1 Course Unit

BIOL 4314 Molecular Evolution of Physiological Functions

This course is designed for students who are interested in understanding how physiological functions are achieved. Taking advantage of the recent explosion in genetic data and high-resolution protein structure analysis across organisms, the course focuses on the evolution of physiological functions at the genetic, structural, circuit and organismal levels. Examples include the co-evolution of toxins and toxin resistance between hunter and prey, the evolution of substance transport across cell membranes, intracellular signaling cascades, intercellular communication, distributed and centralized nervous systems, neural circuits controlling physiological functions such as feeding, locomotion and visual information processing. Students are expected to learn 1) basic physiological processes, their origin and adaptation, 2) modern genetic, structural and physiological techniques, 3) to critically evaluate research findings, 4) to present scientific papers, and 5) to write a research report.

Fall

Prerequisite: NRSC 1110 OR BIOL 2310 OR BIOL 2210 OR BIOL 2110

1 Course Unit

BIOL 4318 Systems Biology: Integrative physiology and biomechanics of the muscular system

The course will focus on muscle function from the level of molecules to whole animal locomotion. At each level of organization, muscle function will be explored from mechanical and energetic viewpoints. The course will include lectures, demonstrations, and several guest expert lectures. Students will also be introduced to realistic musculo-skeletal modelling and forward dynamic simulations to explore integrated function.

Spring

Prerequisite: BIOL 2310 OR BIOL 2110

1 Course Unit

BIOL 4410 Advanced Evolution

Mechanisms of evolution at the genetic and populational levels. Empirical and theoretical approaches to natural selection, population structure, gene flow, and quantitative genetics will be emphasized.

Fall, odd numbered years only

Prerequisite: BIOL 2410

1 Course Unit

BIOL 4411 Evolutionary Ecology

This course will focus on topics at the intersection of evolutionary biology and ecology, including the evolution of cooperation and conflict from genes to societies to ecological communities, life history evolution, and the evolution of interspecific interactions and ecological communities. The course will use a combination of lectures and discussion of readings from the primary literature.

Spring

Prerequisite: BIOL 2410 OR BIOL 2140 OR BIOL 2610

1 Course Unit

BIOL 4430 Evolution and Ecology of Infectious Diseases

This course will focus on fundamental topics related to the ecological and evolutionary processes driving the transmission of pathogenic microbes among hosts including life-history strategies; evolution of pathogenic traits; the impacts of temporal, spatial and host-trait heterogeneity; and factors causing the emergence of an infectious pathogen. Examples will be drawn from human, wildlife, and plant pathogens to illustrate these ecological and evolutionary topics. Students will learn to develop and apply current ecological and evolutionary theory to infectious microbe research and gain practical experience accessing, interpreting and synthesizing the peer-reviewed scientific literature through a combination of popular and scientific readings, discussion, and lecture.

Fall

Mutually Exclusive: BIOL 5430

Prerequisite: BIOL 2410 OR BIOL 2610

1 Course Unit

BIOL 4450 Macroevolution

Macroevolution, or evolution above the population level and on long timescales,as a field addresses fundamental questions about the origins of life, past and present.These include but are not limited to: How are highly dissimilar speciesrelated? Why are animals on distant continents so similar? How and when did major groups, like birds or mammals, originate? What drives evolutionary arms races? Why are there so many more species of beetle than crocodile? Why are there more species in the tropics than the arctic? Did dinosaursprevent the diversification of mammals? Why do some animals survive mass extinction? How can invasive species spread so rapidly? Students will learn importantconcepts underlying our understanding of modern biodiversity and the fossil record, as well as how to use different methods and lines of evidence, including evolutionary trees (phylogeny), fossil databases, past climate and global events,mathematical modeling, and even modern genomics, to answer fundamental questions about the evolution of life.

Spring, odd numbered years only

Also Offered As: EESC 4550

1 Course Unit

BIOL 4511 Biological Data Analysis

This course focuses on the underlying principles, implementation, and interpretation of statistical methods commonly used in biology. Lectures will incorporate exercises that implement these analyses in the open source software R, as well as exercises in data visualization. We will draw on examples from ecology, evolution, genetics, and genomics.

Spring, even numbered years only

1 Course Unit

BIOL 4517 Theoretical Population Biology

Introduction to basic theoretical tools to study the evolutionary and ecological dynamics of populations. Topics to be discussed include: basic population dynamics and population genetics theory, evolutionary game theory/adaptive dynamics, social evolution (kin selection/multilevel selection), life-history evolution, and stochastic models. Other topics may be added based on the specific interests of students in the class.

Spring

Prerequisite: BIOL 2410 AND MATH 1400

1 Course Unit

BIOL 4536 Introduction to Computational Biology & Biological Modeling

The goal of this course is to develop a deeper understanding of techniques and concepts used in Computational Biology. The course will strive to focus on a small set of approaches to gain both theoretical and practical understanding of the methods. We will aim to cover practical issues such as programming and the use of programs, as well as theoretical issues such as algorithm design, statistical data analysis, theory of algorithms and statistics. This course WILL NOT provide a broad survey of the field nor teach specific tools but focus on a deep understanding of a small set of topics. We will discuss string algorithms, hidden markov models, dimension reduction, and machine learning (or phylogeny estimation) for biomedical problems.

Fall

Also Offered As: CIS 4360

Mutually Exclusive: BIOL 5535

Prerequisite: MATH 1400 AND (BIOL 2510 OR BIOL 5510)

1 Course Unit

BIOL 4600 Field Botany

This course focuses on teaching students the Pennsylvania flora, both native and naturalized. Through weekly field trips, students will gain an appreciation for the diversity of plant species and plant communities in PA, and observe and discuss ecological and historical forces that influence plant species occurrences and plant communities. The ability to quickly and accurately identify plants in the field, through both sight identification and the use of a dichotomous key, is the major thrust of this course. Students will also learn how to appropriately collect plant materials for further study/identification in the laboratory and for archiving in an herbarium collection.

Fall

Mutually Exclusive: BIOL 5600

Prerequisite: (BIOL 1101 AND BIOL 1102) OR BIOL 1124

1 Course Unit

BIOL 4612 Animal Physiological and Population Ecology

This course explores the interactions of environmental variables, such as temperature, with the physiology of vertebrate animals and the mechanistic links of those interactions with population dynamics.

Spring, odd numbered years only

Prerequisite: BIOL 2610

1 Course Unit

BIOL 4615 Freshwater Ecology

Survey of the physical, chemical and biological properties of freshwater ecosystems, both riverine and lentic, natural and polluted.

Spring

Also Offered As: ENVS 2390

Prerequisite: BIOL 1101 OR BIOL 1121

1 Course Unit

BIOL 4616 Field Studies in Aquatic Microbial Ecology

This is a field and laboratory-based course that involves students in hands-on research methods in aquatic microbial ecology. Students will gain familiarity with experimental design, field measurements of environmental parameters (physical, chemical, and biological), sample collection techniques, and laboratory analyses required to assess the activity, health, and community composition of aquatic microbial ecosystems in an urban environment. We will compare and contrast various watersheds in and around the greater Philadelphia area, and students will design and conduct original independent research as a final course project. Enrollment preference given to students who have completed BIOL 240.

Spring

Prerequisite: BIOL 1101 OR BIOL 1121

1 Course Unit

BIOL 4623 Plant Ecology

The course consists of both lecture material and hands on research involving questions in plant population or community ecology. Quantitative information from published studies will be discussed and students, working in teams, will summarize and analyze data from class experiments.

Not Offered Every Year

1 Course Unit

BIOL 4669 Plant Physiology Through Space and Time

This course is a lab/lecture/seminar hybrid that will meet once per week for three hours. Each session will consist of mini-lecture/lab, paper discussions/lab, or solely lab efforts. All reading assignments will be available on Canvas (no textbook fees). We will exam various aspects of photosynthesis, water relations and nutrient acquisition in the context of the evolutionary progression of higher plants. With each subject, we will consider, measure, and in some cases model whole-plant physiology while examining sub-cellular-level controls and ecosystem-to-global-level consequences. This course is designed to give molecular biologists through earth-system scientists the tools to measure and understand whole-plant physiological responses to molecular manipulation and environmental variability. All students will learn to appreciate the context of their work on both micro and macro scales.

Spring

Prerequisite: BIOL 2610

1 Course Unit

BIOL 4701 Prokaryotic Microbiology: A Pragmatic View

This interactive course is intended for a small group of students aspiring to pursue research in microbiology, preferably using prokaryotes. Students will study selected papers and will attend the Prokaryotic Microbiology Seminars on Fridays. Specific problems of importance to a given field at a particular time will be critically analyzed and discussed: How were cutting edge techniques of the time used to address these problems? How would the same problems be approached using current techniques? The emphasis of the course will be on learning to become a thoughtful experimentalist rather than acquiring the hottest emerging knowledge.

Spring

1 Course Unit

BIOL 4710 Topics in Prokaryotic Biology: From Molecules to Microbiomes

This course will cover research articles from both the classic and contemporary literature on the genetics, cell biology, and physiology of prokaryotes. The material will focus on a small number of subjects in depth, with an emphasis on how the field has arrived at its current state of knowledge and on exciting new research directions. Possible topics include: stress responses, cell signaling, subcellular organization, bacteriophages, microbial communities, and host-microbe interactions.

Spring, odd numbered years only

Prerequisite: BIOL 2210 OR BIOL 3710

1 Course Unit

BIOL 4825 Biochemistry and Molecular Genetics Superlab

Intensive laboratory class where open-ended, interesting biological problems are explored using modern lab techniques. Topics may include protein structure/function studies; genetic screens, genomics and gene expression studies; proteomics and protein purification techniques; and molecular cloning and DNA manipulation. The course emphasizes developing scientific communication and independent research skills. Course topics reflect the interests of individual Biology faculty members. This course is recommended for students considering independent research.

Fall or Spring

Mutually Exclusive: BIOL 5825

Prerequisite: BIOL 2810 OR BIOL 2010 OR BIOL 2210

1 Course Unit

BIOL 4999 Advanced Independent Study

A second semester of independent study, in most cases extending the research undertaken for the BIOL 3999. Apply at the Biology Academic Office, 102 Leidy Labs.

Fall or Spring

1 Course Unit

BIOL 5022 Cell Signaling

The evolution of multicellularity required that cells be able to both send and receive signals from their neighbors. The development of organs and differentiation of cells and tissues requires reliable and continuous communication between cells. Consequences of inappropriate or anomalous signaling include development abnormalities and cancer. This class will examine mechanisms of cell-to-cell signaling between cells in plants and animals with an emphasis on the cell biology of development.

Fall

Prerequisite: BIOL 2010

1 Course Unit

BIOL 5026 Chromosomes and the Cell Cycle

Life depends on the propagation of genetic material from one generation to the next through cycles of genome replication and cell division. The genome is copied by the parent, and one exact copy is inherited by each daughter cell. We will treat chromosomes as discrete entities, rather than collections of genes, that are replicated and divided with high fidelity to ensure that the genome remains stable over many generations. By reading selected primary literature covering several decades, we will build an understanding of the cell cycle by focusing on chromosomes and the associated molecular machinery. We will explore mechanisms that underlie replication and division, particularly control mechanisms that maintain genome integrity and are critical to prevent disease. The goal of the course is to develop a picture of the cell cycle by examining some of the key experiments and insights that have led to our current understanding.

Spring

Mutually Exclusive: BIOL 4026

1 Course Unit

BIOL 5210 Molecular Biology and Genetics

This course will survey the discipline of molecular genetics. Two broad areas will be considered 1) Molecular Biology: DNA replication, transcription, translation, regulation of gene expression in both prokaryotic and eukaryotic systems, and genomics and 2) Genetics: basic Mendelian & molecular genetics.

Fall or Spring

Prerequisite: BIOL 1101 OR BIOL 1121

1 Course Unit

BIOL 5220 Human Evolutionary Genomics

Advanced seminar on current topics in human genomics and human evolution. Topics include the methods used for mapping and sequencing genomes; phylogenetic and population genetic analysis; and detecting variation in the human genome. This course is designed for graduate students but advanced undergraduates with a strong background in genetics are also welcome.

Spring, odd numbered years only

Also Offered As: CAMB 5220

1 Course Unit

BIOL 5231 Genome Science and Genomic Medicine

This course will be a focused study of genomes, genomic techniques, and how these approaches are and will be used in diagnosing and treating human disease. Topics will include genome sequencing, analysis of sequences and microarrays, and new techniques including high-throughput sequencing and reverse genetic analysis with a focus on genome-wide mutant collections.

Spring

Mutually Exclusive: BIOL 4231

1 Course Unit

BIOL 5233 The Genetics of Adaptation: How sex, conflict, and pathogens shape modern genomes

In this course we explore the genetic basis of adaptation. We will investigate the forces that drive adaptation (e.g., environmental stress, pathogens, conflict, sex), the genetic mechanisms of adaptation (protein sequence changes, expression divergence, gene duplication, etc.), and the consequences of adaptation for contemporary cellular functions, developmental processes, and ecological interactions. The class meetings will be structured around both lectures and student-led discussions of the primary literature.

Spring

Mutually Exclusive: BIOL 4233

1 Course Unit

BIOL 5234 Epigenetics

This course investigates epigenetic phenomena: heritable alternate states of gene activity that do not result from an alteration in nucleotide composition (mutations). Epigenetic mechanisms regulate genome accessibility and cell differentiation. They play a key role in normal development and in oncogenesis. For example both mammalian X-chromosome inactivation and nuclear transfer (cloning) are subject to epigenetic regulation. Amongst the epigenetic mechanisms we will discuss in this course are chromatin organization, histone modification, DNA methylation and non-coding RNAs. The course is geared toward advanced undergraduate and beginning graduate students and is a combination of lectures, student presentations and research presentations by guest speakers. Students will work with the current scientific literature.

Spring

Mutually Exclusive: BIOL 4234

1 Course Unit

BIOL 5240 Genetic Analysis

The logic and methodology of genetic analysis in plants and animals. This lecture course will focus on the use of mutations to study gene function and higher order biological processes, methods for reporting and manipulating gene expression, and analysis of the genetic basis of natural variation.

Not Offered Every Year

Prerequisite: BIOL 2210

1 Course Unit

BIOL 5430 Evolution and Ecology of Infectious Diseases

This course will focus on fundamental topics related to the ecological and evolutionary processes driving the transmission of pathogenic microbes among hosts including life-history strategies; evolution of pathogenic traits; the impacts of temporal, spatial and host-trait heterogeneity; and factors causing the emergence of an infectious pathogen. Examples will be drawn from human, wildlife, and plant pathogens to illustrate these ecological and evolutionary topics. Students will learn to develop and apply current ecological and evolutionary theory to infectious microbe research and gain practical experience accessing, interpreting and synthesizing the peer-reviewed scientific literature through a combination of popular and scientific readings, discussion, and lecture.

Fall

Mutually Exclusive: BIOL 4430

Prerequisite: BIOL 2410 OR BIOL 2610

1 Course Unit

BIOL 5510 Statistics for Biologists

Introductory probability theory. Principles of statistical methods. Problems of estimation and hypothesis testing in biology and related areas.

Fall

Mutually Exclusive: BIOL 2510, BIOL 4510

Prerequisite: MATH 1400

1 Course Unit

BIOL 5535 Introduction to Computational Biology & Biological Modeling

The goal of this course is to develop a deeper understanding of techniques and concepts used in Computational Biology. The course will strive to focus on a small set of approaches to gain both theoretical and practical understanding of the methods. We will aim to cover practical issues such as programming and the use of programs, as well as theoretical issues such as algorithm design, statistical data analysis, theory of algorithms and statistics. This course WILL NOT provide a broad survey of the field nor teach specific tools but focus on a deep understanding of a small set of topics. We will discuss string algorithms, hidden markov models, dimension reduction, and machine learning (or phylogeny estimation) for biomedical problems.

Fall

Mutually Exclusive: BIOL 4536

Prerequisite: MATH 1400 AND (BIOL 2510 OR BIOL 5510)

1 Course Unit

BIOL 5536 Fundamentals of Computational Biology

Introductory computational biology course designed for both biology students and computer science, engineering students. The course will cover fundamentals of algorithms, statistics, and mathematics as applied to biological problems. In particular, emphasis will be given to biological problem modeling and understanding the algorithms and mathematical procedures at the "pencil and paper" level. That is, practical implementation of the algorithms is not taught but principles of the algorithms are covered using small sized examples. Topics to be covered are: genome annotation and string algorithms, pattern search and statistical learning, molecular evolution and phylogenetics, functional genomics and systems level analysis.

Fall

Also Offered As: CIS 5360, GCB 5360

Prerequisite: ((BIOL 1101 AND BIOL 1102) OR BIOL 1121) AND STAT 111 AND STAT 112

1 Course Unit

BIOL 5568 Mathematical Modeling in Physiology and Cell Biology

Mathematical modeling is increasingly becoming a standard technique in physiology and cell biology. In this class, we will cover some classical models in physiology and cell biology. Half of the course will be devoted to electrophysiology (Hodgkin-Huxley model, action potential propagation and related topics), which has arguably been the most successful area of application of mathematical techniques to biology. We will then consider models of molecular motors and muscle mechanics, of pattern formation and cell polarization.

Not Offered Every Year

Also Offered As: AMCS 5681

1 Course Unit

BIOL 5571 Topics in Computational Biology

Course for graduate students planning research in computational biology and genomics. Assigned readings will cover algorithms and data analysis techniques in computational biology. The course will include presentations and discussion of research problems involving computational analysis and there. Active group participation is required. Topics could include string algorithms, probability theory, multivariate statistics, molecular evolution, Markov Models, phylogenetic trees, and machine learning.

Not Offered Every Year

1 Course Unit

BIOL 5600 Field Botany

This course focuses on teaching students the Pennsylvania flora, both native and naturalized. Through weekly field trips, students will gain an appreciation for the diversity of plant species and plant communities in PA, and observe and discuss ecological and historical forces that influence plant species occurrences and plant communities. The ability to quickly and accurately identify plants in the field, through both sight identification and the use of a dichotomous key, is the major thrust of this course. Students will also learn how to appropriately collect plant materials for further study/identification in the laboratory and for archiving in an herbarium collection.

Mutually Exclusive: BIOL 4600

Prerequisite: ((BIOL 1101 AND BIOL 1102) OR BIOL 1124)

1 Course Unit

BIOL 5710 Microbial Diversity and Pathogenesis

Microbiology plays a central role in diverse areas of human life such as infectious disease, ecology, and biotechnology. This course will cover aspects of modern microbiology with an emphasis on prokaryotic organisms. The topics will include basic aspects of microbial diversity, genetics, virology, and pathogenesis as well as examples of applied microbiology.

Spring

Prerequisite: BIOL 2210

1 Course Unit

BIOL 5711 Microbial Diversity and Pathogenesis Lab

The importance of microbiology in complex issues, such as the impact of the microbiome in human health or as alternative energy sources, is being appreciated more and more each day. This upper level laboratory course provides students with a robust technical skill set while also giving them an opportunity to participate in an authentic research project that may lead to novel discoveries. Students will generate research questions, formulate hypotheses, design experiments, analyze data, and present their research findings to the class. In each project, students will use the cutting edge approach of metagenomics to evaluate the microbial diversity of their environment via Next Generation Sequencing. Students will also examine the function of microbial species within their communities. Potential projects include the isolation of novel antibiotic producers and the antibiotic they produce, designing and optimizing microbial fuel cells that can be used to generate electricity, or isolating antibiotic resistant bacteria and attempting novel approaches to inhibit or prevent their growth.

Spring

1 Course Unit

BIOL 5825 Biochemistry and Molecular Genetics Superlab

Intensive laboratory class where open-ended, interesting biological problems are explored using modern lab techniques. Topics may include protein structure/function studies; genetic screens, genomics and gene expression studies; proteomics and protein purification techniques; and molecular cloning and DNA manipulation. The course emphasizes developing scientific communication and independent research skills. Course topics reflect the interests of individual Biology faculty members. This course is recommended for students considering independent research.

Mutually Exclusive: BIOL 4825

Prerequisite: BIOL 2810 OR BIOL 2010 OR BIOL 2210

1 Course Unit

BIOL 5860 Mathematical Modeling in Biology

This course will cover various mathematical models and tools that are used to study modern biological problems. Mathematical models may be drawn from cell biology, physiology, population genetics, or ecology. Tools in dynamical systems or stochastic processes will be introduced as necessary. No prior knowledge of biology is needed to take this course, but some familiarity with differential equations and probability will be assumed.

Fall

Also Offered As: MATH 5861

1 Course Unit

BIOL 5999 Master's Independent Study

Laboratory research for the Master's of Science in Biology submatriculation program. Apply at the Academic Office, 102 Leidy Labs.

Fall or Spring

0.5-2 Course Units

BIOL 6010 Communication for Biologists

Basic science writing and presentation skills for PhD students in Biology. Designed for second year graduate students preparing for qualifying exams. In the first half of the course, students will produce weekly writing assignments and critique writing submitted by others. In the second half, students will learn techniques for effective research presentations in both seminar style environments and chalk-talk settings.

Spring

1 Course Unit

BIOL 7000 Advanced Topics in Current Biological Research

Integrative seminar on current biological research for first-year PhD students.

Fall

1 Course Unit

BIOL 9999 Independent Study and Research

Advanced laboratory reserach with a member of the Biology Graduate Group.

Fall or Spring

0.5-4 Course Units