Carnegie Mellon University

Course descriptions are updated at the beginning of each semester. However, for the most up-to-date course descriptions, visit the university-wide schedule of classes. Click on each course name for a brief description.

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Undergraduate Courses

03050/03051 Study Abroad

03101 Biological Sciences First Year Seminars

Various seminars are offered that introduce first-year students to current topics of modern biology. These are mini courses that meet for half a semester. Topics have included: Proteins in Disease, Genes and Diseases, Pills and Poisons, Curing Cancer, Organ Transplantation Blood Substitutes, and Prions - Mad Cows and Englishman. Courses restricted to first year students in the Mellon College of Science.

3-6 units

03115/03116 Phage Genomics Research

This course will provide an introduction to biological investigation through a research project in bacteriophage genomics. Genomics combines experimental and computational approaches for large-scale analysis of the biological information contained in DNA sequences. The ability to analyze the complete DNA of any organism has revolutionized modern genetics and is influencing many areas of biology and medicine. The most abundant biological entities are bacteriophages (viruses that infect bacteria). Their enormous diversity and number make bacteriophages important models for the study of gene structure, function and regulation, population genetics and evolution. In addition they are the source of important tools in biotechnology. The research goals of this course will be to identify new bacteriophage species and incorporate them into a comparative genomic study to better understand the genetic organization and evolution of these organisms. While accomplishing these goals students will develop an understanding of the research process, including the ability to design experiments and interpret novel data. Fall semester: Samples will be collected in the field. From these samples students will identify and purify bacteriophages. The bacteriophages will be characterized structurally by electron microscopy, and their DNA will be purified and sequenced.

6 units

COREQUISITES: 03110 , 03121 , 03151

03121 Modern Biology

This is an introductory course that provides the basis for further studies in biochemistry, cell biology, genetics and molecular biology. This course emphasizes the chemical principles underlying biological processes and cell structures as well as the analysis of genetics and heredity from a molecular perspective. This is the introductory biology course for all science and non-science majors.

9 units

03124 Modern Biology Laboratory

This laboratory is designed to introduce students to modern concepts in the biological sciences. The experiments illustrate many of the principles covered in 03-121 and 03-230. Experimentation using living organisms and/or their tissues, cells or molecules is an essential component of this course.

9 units

COREQUISITES: 03121 , 03151

03125 Evolution

Evolutionary theory is the unifying principle of biology. A good comprehension of the concepts that underlie this theory is therefore important to properly appreciate and understand any biological process. This course is designed for students intending to continue studies in biology so that they may gain an understanding of the evolutionary framework in their more advanced courses, and also non-biology majors who want to extend their knowledge of biology at an introductory level. The lectures will include (i) an examination of the history and development of evolutionary theory, (ii) consideration of some of the facts that have established the theory, (iii) an introduction to the concepts of phylogenetics, (iv) discussion of the patterns and mechanism that lead to the diversity and origins of the groups of life, (v) an introduction to genetics and population genetic theory, and (vi) discussion of and how this applies to natural selection and speciation. The course will also include some more specialist topics, including evolution of development, sexual selection, evolutionary applications to medicine and conservation biology, and genome evolution. Assessment will be based on several in-class exams and quizzes, homework assignments, a written term paper, and a final exam.

9 units

03127 How Biological Experiments Work - A Project Course

The goal of this course is to provide an understanding of the nuts and bolts of biological experimentation. We will discuss the molecular principles behind the wide variety of experiments that were used to discover how cells work. The first half of the class will be a lecture based discussion of key experimental methods used in biological research. The second half of the class will be dedicated to group projects that create story boards to explain in molecular terms how these experiments work. The story boards will be used by modelers at the Pittsburgh Supercomputing Center to generate high-end animations of these experimental processes. This will prepare students for working in research labs and biology courses beyond Modern Biology. This course is limited to first, second, and third year students.

9 units

PREREQUISITES: 03121 or 03151

03132 Basic Science to Modern Medicine

This course will focus on the genetics, cell biology, and developmental biology behind human biology and human disease, as well as the growing opportunities for novel therapeutic options that basic science delivers. This is a topics based course, with topics chosen to cover aspects of human biology and health that students are likely to encounter in their daily lives such as cancer, stem cells, genome sequencing, and the human microbiota. Students will explore these topics from both a basic science and a human health perspective.

9 units

03151 Honors Modern Biology

This course will cover in some depth, the basics of the structure and function of the major biomolecules in the cell, cellular structure and function, genetic replication, transmission and expression of biological information, and cell-cell interactions. While similar core topics will be covered in all sections of Modern Biology, this section will be offered at an accelerated pace, requiring more independent learning. The extra class time this pacing provides will allow the exploration of the molecular basis of life to help students integrate and apply the core principles of biology covered in the course. THIS SECTION IS RESERVED FOR INCOMING FIRST-YEAR MCS STUDENTS.

10 units

03161 Molecules to Mind

This course provides a depth-first approach to understanding neuroscience. We will begin with a clinical focus on neuroanatomy, introducing students to some basic neurological diagnostic techniques. We will then explore the biological basis of neuronal function and link the function of individual neurons to a broader context of neural systems. This will be done in the context of primary literature. Students who complete this course will therefore have an understanding of research methods and be prepared to evaluate scientific literature. The course will have a strong focus on the biological and cellular basis of neuronal excitability and also give students significant, in depth exposure to the function of synapses and their plasticity. Finally, the course will give students an in depth look at sensory and/or motor systems by focusing on one system in particular, rather than providing a broad overview of many different sensory and motor systems.

9 units

03201 Undergraduate Colloquium for Sophomores

The purpose of this seminar series is to update biology undergraduates about university and departmental functions, seminars, etc. that are pertinent or useful. In addition, research talks by faculty and undergraduates will be used to introduce students to the research being conducted in faculty laboratories. Additional topics may include graduate and medical school applications, career options, topics in the press, and important scientific discoveries.

1-3 units

CROSS-LISTED COURSES: 03301 , 03401

03206 Biomedical Engineering Laboratory

This laboratory course is designed to provide students with the ability to make measurements on and interpret data from living systems. The experimental modules reinforce concepts from 42-101 Introduction to Biomedical Engineering and expose students to four areas of biomedical engineering: biomedical signal and image processing, biomaterials, biomechanics, and cellular and molecular biotechnology. Several cross-cutting modules are included as well. The course includes weekly lectures to complement the experimental component. Prerequisites: 42-101 Introduction to Biomedical Engineering and 03-121 Modern Biology. Priority for enrollment will be given to students who have declared the Additional Major in Biomedical Engineering. Notes: This course number is reserved for students registered with the HPP program that, are CIT majors. If you require a biology lab for pre-health admissions requirements, please contact Dr. Conrad Zapanta and Dr. Maggie Braun (in the same email) for permission to register for 03-206 instead of 42-203. Priority for enrollment will be given to students who have declared the Additional Major in Biomedical Engineering.

9 units

PREREQUISITES: (03121 or 03151) and (42101)

CROSS-LISTED COURSES: 42203

03210 Independent Study

Students will read papers from the original literature under the direction of a faculty member. Students will be required to demonstrate mastery of the readings by discussions with the sponsoring faculty member, oral presentations, or writing of one or more papers summarizing and extending the information in the readings. If appropriate, students may write a program(s) to satisfy this last requirement. A student may take this course only once. This is a mini format course. Special permission required.

1-12 units

03220 Genetics

The mechanisms of transmission of inherited traits in viruses, bacteria, fungi, plants and animals are discussed. Molecular mechanisms of gene expression and gene regulation are analyzed. Recombinant DNA and its applications in genetic analysis, biotechnology, forensics, agriculture, medicine, and the pharmaceutical industry are presented. Special topics in human genetics are considered, such as the genetics of cancer. Principles and methods for the study of developmental genetics, population genetics and complex traits are also introduced.

9 units

PREREQUISITES: 03121 or 03151

03230 Intro to Mammalian Physiology

This course will survey the major organ systems, with an emphasis on cellular physiology and biochemistry. Current ideas of research and scientific controversy will also be presented. This course is intended to broaden students exposure to cellular processes in the context of complex organ systems.

9 units

COREQUISITES: 03121

03231 Biochemistry I

This course provides an introduction to molecules and processes found in living systems. Amino acids, sugars, lipids and nucleotides and their corresponding higher structures, the proteins, polysaccharides, membranes and nucleic acids are studied. Kinetics and mechanisms of enzymes as well as elementary metabolic cycles and the energetics of biological systems are discussed.

9 units

PREREQUISITES: 09217 (or 09219) and 03121 (or 03151)

03232 Biochemistry I

This course provides an introduction to the application of biochemistry to biotechnology. The functional properties of amino acids, nucleotides, lipids, and sugars are presented. This is followed by a discussion of the structural and thermodynamic aspects of the organization of these molecules into higher-order structures, such as proteins, nucleic acids, and membranes. The kinetics and thermodynamics of protein-ligand interactions are discussed for non-cooperative, cooperative, and allosteric binding events. The use of mechanistic and kinetic information in enzyme characterization and drug discovery are discussed. Topics pertinent to biotechnology include: antibody production and use, energy production in biochemical systems, expression of recombinant proteins, and methods of protein purification and characterization. The course is an alternate to 03-231.

9 units

PREREQUISITES: (09217 or 09219) and (09106 or 06221)

03240 Cell Biology

This course provides descriptive information and mechanistic detail concerning key cellular processes in six areas: membrane function, protein targeting, signaling, cytoskeleton, cell division, and cell interaction. An attempt is made to introduce the methodology that was used to obtain this information and to discuss how our understanding of these processes relates to the treatment of human disease.

9 units

PREREQUISITES: (03121 or 03120 or 03151) and (03232 or 03233 or 03231)

03250 Introduction to Computational Biology

This class provides a general introduction to computational tools for biology. The course is divided into two modules, which may be taken individually as courses 03-251/02-251 and 03-252/02-252. Module 1 covers computational molecular biology/genomics. It examines important sources of biological data, how they are archived and made available to researchers, and what computational tools are available to use them effectively in research. In the process, it covers basic concepts in statistics, mathematics, and computer science needed to effectively use these resources and understand their results. Specific topics covered include sequence data, searching and alignment, structural data, genome sequencing, genome analysis, genetic variation, gene and protein expression, and biological networks and pathways. Module 2 covers computational cell biology, including biological modeling and image analysis. It includes homeworks requiring use or modification of Matlab scripts. The modeling component includes computer models of population dynamics, biochemical kinetics, cell pathways, neuron behavior, and stochastic simulations. The imaging component includes basics of machine vision, morphological image analysis, image classification and image-derived models. Lectures and examinations are joint with 02-250 but recitations are separate. Recitations for this course are intended primarily for biological sciences or biomedical engineering majors at the undergraduate or graduate level who have had little or no prior experience with computer science or programming. Students may not take both 03-250/02-250 and either 03-251/02-251 or 03-252/02-252 for credit. Prerequisite: 03-121 or permission of the instructors.

12 units

PREREQUISITES: 03120 or 03151 or 03131 or 03121

03251 Introduction to Computational Molecular Biology

This class provides a general introduction to computational tools for biology with specific emphasis on molecular biology and genomics. Along with 03-252, it makes up one half of the full Introduction to Computational Biology, 03-250, although either half can be taken individually. 03-251 will examine important sources of biological data, how they are archived and made available to researchers, and what computational tools are available to use them effectively in research. In the process, it will cover basic concepts in statistics, mathematics, and computer science needed to effectively use these resources and understand their results. Specific topics to be covered include sequence data, searching and alignment, structural data, genome sequencing, genome analysis, genetic variation, gene and protein expression, and biological networks and pathways. Lectures and examinations are joint with 02-251 but recitations are separate. Recitations for this course are intended primarily for biological sciences or biomedical engineering majors at the undergraduate or graduate level who have had little or no prior experience with computer science or programming. Students may not take both 03-251/02-251 and 03-250/02-250 for credit. Prerequisite: 03-121 or permission of the instructor.

6 units

PREREQUISITES: 03121 or 03151

03252 Introduction to Computational Cell Biology

This course presents an overview of important modeling and image analysis applications of computers to solve problems in cell biology. Along with 03-251, it makes up one half of the full Introduction to Computational Biology, 03-250, although either half can be taken individually. Major topics covered are computer models of population dynamics, biochemical kinetics, cell pathways, neuron behavior, and stochastic simulations. The imaging component includes basics of machine vision, morphological image analysis, image classification and image-derived models. It includes homeworks requiring use or modification of Matlab scripts. Lectures and examinations are joint with 02-252 but recitations are separate. Recitations for this course are intended primarily for biological sciences or biomedical engineering majors at the undergraduate or graduate level who have had little or no prior experience with computer science or programming. Students may not take both 03-252/02-252 and 03-250/02-250 for credit. Prerequisite: 03-121 or permission of the instructor.

6 units

PREREQUISITES: 03121 or 03151

03260 Neurobiology of Disease

This course will explore the biological basis of several neurological and neuropsychiatric diseases, with an emphasis on medical diagnostic tools and techniques. It will include discussions of the anatomical basis of neurological diseases as well as recent research into understanding the mechanisms of disease. This course is intended to broaden students understanding of how diseases are diagnosed and studied. Students will also learn how basic neurological and psychiatric evaluations are conducted and gain proficiency in these evaluation techniques. We will begin with a discussion of clinical neuroanatomy to serve as a basis for understanding brain structures and functional alterations in a variety of developmental, degenerative, neurological, and psychiatric disorders. Specific diseases covered may vary from year to year.

9 units

03301 Undergraduate Colloquium for Juniors

The purpose of this seminar series is to update biology undergraduates about university and departmental functions, seminars, etc. that are pertinent or useful. In addition, research talks by faculty and undergraduates will be used to introduce students to the research being conducted in faculty laboratories. Additional topics may include graduate and medical school applications, career options, topics in the press, and important scientific discoveries.

1-3 units

CROSS-LISTED COURSES: 03201 , 03401

03320 Cell Biology

This course provides descriptive information and mechanistic detail concerning key cellular processes in six areas: membrane function, protein targeting, signaling, cytoskeleton, cell division, and cell interaction. An attempt is made to introduce the methodology that was used to obtain this information and to discuss how our understanding of these processes relates to the treatment of human disease.

9 units

PREREQUISITES: (03120 or 03121 or 03151) and (03232 or 03233 or 03231)

03326 Evolution of Regulatory Genomics

This course will introduce central concepts of evolutionary theory, e.g. drift, selection, phylogenetics and an introduction into how genomes are sequenced, assembled and annoted. This will require a basic undertsanding of genetics. Course topics will then unify these two areas of biology to examine process by which genomes evolve and how this in turn has lead to the diversity of animal pheonotypes. This will include discussion of how genomes control embryonic development, how gene regulation has evolved (focusing on cis regulatory evolution and non-coding RNA regulatory evolution) and the concept of gene regulatory network evolution. Concepts and specific examples will come through lectures, selected readings from advanced texts and primary literature.

4.5 units

PREREQUISITES: 03231 or 03232
COREQUISITES: 03220 , 03330

03342 Introduction to Biological Laboratory Practices

This course is designed for students in the BS in Computational Biology degree program. It is a required co-requisite for 03-343, Experimental Genetics and Molecular Biology and is designed to be an introduction to basic laboratory practices. The course will introduce biological and chemical safety training and basic laboratory practices. Techniques of solution preparation and titration, pipetting, UV/VIS spectroscopy, and quantitation of biological compounds will be covered.

1 unit

COREQUISITES: 03343

03343 Experimental Techniques in Molecular Biology

This laboratory course is designed to teach experimental methods of modern biology. Experiments in microbial genetics, molecular biology and eukaryotic genetics are performed. Emphasis is placed on understanding and applying the biological principles of each experiment. This course is designed to be taken during the junior year and is intended to prepare students for undergraduate research. Experimentation using living organisms and/or their tissues, cells or molecules is an essential component of this course.

12 units

PREREQUISITES: (03232 or 03231) and (09222 or 09208)

COREQUISITES: 03220 , 03330

3344 Experimental Biochemistry

This course is designed to be taken as a sequel to 03-343. Experiments cover a variety of methods for investigating the structure and function of biological molecules. Experimental methods with proteins, enzyme kinetics, lipids, spectroscopy, and isolation and quantization of biological molecules are covered. During several experiments, students design their own projects. Experimentation using living organisms and/or their tissues, cells or molecules is an essential component of this course.

12 units

PREREQUISITES: (03231 or 03232) and 03343

03345 Experimental Cell and Developmental Biology

This laboratory is designed to teach concepts and experimental methods in cell and developmental biology. Students work with a variety of organisms to examine how cells traverse development from rapidly dividing, undifferentiated cells, through cell commitment and the establishment of spatial and temporal patterns of gene expression, to the specific characteristics and responses of terminally differentiated cells. The course makes extensive use of video microscopy with phase contrast, DIC and fluorescence microscopes. Biochemical, immunological and molecular biological techniques are used to probe the molecules and processes of cells undergoing development. Experimentation using living organisms and/or their tissues, cells or molecules is an essential component of this course.

12 units

PREREQUISITES: (03343) and (03232 or 03231) and (03240 or 03320)

COREQUISITES: 03350 , 03362

03350 Developmental Biology

How does a complex, multicellular organism arise from a single cell? How do cells with identical genomes acquire distinctive properties? What are the medical consequences of abnormal embryonic development? How does regeneration occur? How has evolution modified developmental programs to produce different body plans? These are some of the central questions in the field of developmental biology. This course serves as an introduction to current concepts and experimental approaches in this rapidly advancing field. Topics in the course include genomics, differential gene expression, cell signaling, cell movements, tissue morphogenesis, stem cells, human development, and regeneration. The course examines the genes and signaling pathways that control development and the role that mis-regulation of these pathways plays in human disease.

9 units

PREREQUISITES: 03240 or 03320

03355 Stem Cell Engineering

This course is offered only at CMUs campus in Qatar. This course covers the progress of stem cell research and its application to tissue engineering and regenerative therapy. The students will learn about the different types of stem cells, the biochemical stimuli that are responsible for regulating stem cell differentiation and techniques involved in the culture of stem cells. This subject will also highlight the development of various biomaterials that are used as biological substitutes in regenerative therapy. Current and emergent stem cell technologies in selected applications of tissue engineering in bone, skin and vascular tissues will be emphasized. The course will be delivered through problem-based learning where students are expected to participate in discussions, perform literature search, present their findings through presentations and written reports on selected topics. The class is designed for undergraduates with a strong interest in stem cell biology and tissue engineering, and the desire to actively contribute to discussions in the class.

9 units

PREREQUISITES: 03240

03362 Cellular Neuroscience

Modern neuroscience is an interdisciplinary field that seeks to understand the function of the brain and nervous system. This course provides a comprehensive survey of cellular and molecular neuroscience ranging from molecules to simple neural circuits. Topics covered will include the properties of biological membranes, the electrical properties of neurons, neural communication and synaptic transmission, mechanisms of brain plasticity and the analysis of simple neural circuits. In addition to providing information the lectures will describe how discoveries were made and will develop students abilities to design experiments and interpret data.

9 units

PREREQUISITES: 03161 or 03320 or 03240 or 42202 or 85219

03363 Systems Neuroscience

Modern neuroscience is an interdisciplinary field that seeks to understand the function of the brain and nervous system. This course provides a comprehensive survey of systems neuroscience, a rapidly growing scientific field that seeks to link the structure and function of brain circuitry to perception and behavior. This course will explore brain systems through a combination of classical, Nobel prize-winning data and cutting edge primary literature. Topics will include sensory systems, motor function, animal behavior and human behavior in health and disease. Lectures will provide fundamental information as well as a detailed understanding of experimental designs that enabled discoveries. Finally, students will learn to interpret and critique the diverse and multimodal data that drives systems neuroscience.

9 units

PREREQUISITES: 03161 or 85219 or 42202 or 03240 or 03320

03365 Neural Correlates of Learning and Memory

This course will examine the biological substrates of learning, memory, and behavioral adaptation. The focus will be on addressing how neural circuits change during new skill acquisition and adapt to variations in the environment. An introduction to experience-dependent changes in neural structure and function, in addition to behavioral learning paradigms, will be provided. Then we will consider the ways in which specific changes in biological substrates give rise to the emergent properties that drive behavioral adaptation, followed by in depth coverage of deciphering which biological substrates constitute a lasting memory trace. Finally, the concept of age-dependent learning will be examined. Concepts and specific examples will come through reading of primary literature and selected readings from advanced texts.

9 units

PREREQUISITES: 03161 or 85219 or 03240 or 03320

03366 Biochemistry of the Brain

This course is designed to give students a comprehensive understanding of the major neurotransmitter systems in the brain. Students will explore qualitative and quantitative approaches to understanding how various neurotransmitters function as well as how they are modulated by endogenous and exogenous agents. The qualitative exploration will include basic principles of neural communication, signal transduction and second messenger systems, main classes of neurotransmitters, and the effects of medications and drugs of abuse. Quantitatively, we will explore the kinetics of neurotransmitter binding, affinity of different receptors for their neurotransmitters, and apply concepts of competitive, uncompetitive, and mixed inhibition to understanding the effects of exogenous agonists and antagonists on these receptors. Students will learn how these qualitative and quantitative biochemical processes affect the endocrine system, neuroinflammatory responses, addictive behaviors, and neurotoxic or degenerative conditions.

9 units

PREREQUISITES: 03231 or 03232

03370 Principles of Biotechnology

This course is intended to provide an introduction to a set of core areas important for understanding and managing biotechnology business. Essentially, the focus of the course will be the basics of the biotechnology entrepreneurial process and a deep background on biotechnology enabled products. The objective is to provide the background for management-level personnel to make decisions based on knowledge of contemporary biotechnologies and the legal and regulatory environment. Because it is impossible to be comprehensive with regard to all applications, the goal is to provide students with sufficient familiarity with current biotechnology and with a framework for assessing bio-related business questions that they may encounter in the future through a combination of independent research, assessment of opportunities and pitfalls, and historical comparisons. NOTE: This course CANNOT be counted towards the advanced biology electives for any major or minor in Biological Sciences.

9 units

PREREQUISITES: (03231 or 03232) and (03240 or 03320)

03380 Virology

The concepts and methods of virology are covered, with emphasis on animal viruses, within the framework of cell biology, genetics, molecular biology, immunology, pathology, and epidemiology. The strategies that a wide variety of different DNA and RNA viruses, including some new and emerging ones, use to replicate and express their genomes during infection of host cells will be examined in some detail. The effects that viruses inflict on these cells will also be examined, as will some of the host cell responses generated by such virus-cell interactions, including interferon induction, the antiviral response generated by interferon, and oncogenic transformation. In addition, anoverview of procedures used for prevention and treatment of viral diseases via vaccinesand antiviral drugs, respectively, will be presented, as will a brief discussion of viroids and prions, and the characteristics of these agents which distinguish them from viruses.

9 units

PREREQUISITES: 03240

COREQUISITES: 03330

03390 Molecular and Cellular Immunology

This course offers the student a comprehensive view of modern immunology at the molecular and cellular level. The first half of the course presents the fundamentals of immunology, beginning with innate immunity, followed by a discussion of the structure and function of important molecules in the immune system, such as antibodies, major histocompatibility antigens, complement, and the T-cell receptor. This portion of the course is concluded with a discussion of the development and function of the cellular immune response. The second half of the course is focused on applied immunology and discusses hypersensitivity, autoimmunity, immunodeficiencies, tumor immunology, infectious disease, and transplantation immunology. Presentations at the end of the course provide an opportunity for the student to explore additional topics in contemporary immunology.

9 units

PREREQUISITES: (03231 or 03232) and (03240 or 03320)

03391 Microbiology

The course provides introductory level microbial science and molecular biology that is aimed for students from all disciplines of natural science. It covers microbiology, genetics, genomics, as well as bacterial, fungal, and protozoan pathogenesis. Topics include: the human microbiome, genome sequencing, gene transfer across species, virulence, and drug resistance.

9 units

PREREQUISITES: 03231 or 03232

03401 Undergraduate Colloquium for Seniors

The purpose of this seminar series is to update biology undergraduates about university and departmental functions, seminars, etc. that are pertinent or useful. In addition, research talks by faculty and undergraduates will be used to introduce students to the research being conducted in faculty laboratories. Additional topics may include graduate and medical school applications, career options, topics in the press, and important scientific discoveries.

1-3 units

03410 Special Topics in Biological Sciences: Genome Editing Biotechnology

Special Topics in Biological Sciences. Topics will vary depending on the semester and instructor. Please read the individual section descriptions for more information. Genome Editing Biotechnology Description: This course will introduce students to the revolution in genome editing biotechnology based on the CRISPR bacterial immune system. Specific topics include CRISPR moving parts, discovery and diversity of CRISPR systems, CRISPR implementation in mammals, and other mammalian genetic engineering systems. We will view these topics in the context of human genetic diseases and the use of mouse genetics for disease research. We will consider ethical challenges including triparental embryos and CRISPR patent rights.

4.5 units

PREREQUISITES: 03121 or 03151 or 03709

03411 Topics in Research

During the year students attend and submit brief summaries of weekly seminars given by outside speakers or members of the Biology Department on current research topics in modern biology; some seminars outside of the department may be substituted.

1-2 units

03435 Cancer Biology

Cancer affects roughly 1 in 3 people worldwide, and originates from both hereditary as well as environmental causes. Its prevalence makes it practically inescapable. Its of great relevance from both scientific and sociocultural perspectives. This course aims to examine various hallmarks of the biology of cancer while exploring novel concepts that challenge our understanding of cell biology. From the perspective of a cancer cell, we will learn about basic concepts of cell division, DNA replication, cell signaling, cell cycle control, cell metabolism, the regulation of gene expression in human cells, oncogenes, tumor suppressor genes, mutations, the process of metastasis, cancer diagnosis, cancer treatments and ethical questions surrounding treating patients, the epidemiology of cancer including prevalence and historical trends in diagnosis, as well as social impacts of a cancer diagnosis. Students will also explore the primary literature and scientific review articles to better understand research and methods of investigation into the cellular and molecular processes of tumorigenesis. This course will include interactive lectures, guest speakers, and in class discussion exercises aimed at building class participation and association, as well as confidence in public speaking about the sciences. Given the well-documented link between stress and cancer, there will also be a small component aimed at making students aware of health and wellness, such as reducing stress and anxiety.

9 units

PREREQUISITES: 03330 or 03220

COREQUISITES: 03320 , 03240

03439 Introduction to Biophysics

This intermediate level course is primarily offered to Physics and Biology undergrads (junior/senior) and provides a modern view of molecular and cellular biology as seen from the perspective of physics, and quantified through the analytical tools of physics. This course will not review experimental biophysical techniques (which are covered, e.g., in 03-871). Rather, physicists will learn what sets bio apart from the remainder of the physics world and how the apparent dilemma that the existence of life represents to classical thermodynamics is reconciled. They also will learn the nomenclature used in molecular biology. In turn, biologists will obtain (a glimpse of) what quantitative tools can achieve beyond the mere collecting and archiving of facts in a universe of observations: By devising models, non-obvious quantitative predictions are derived which can be experimentally tested and may lead to threads that connect vastly different, apparently unrelated phenomena. One major goal is then to merge the two areas, physics and biology, in a unified perspective.

9 units

PREREQUISITES: 03231 or 03232

03442 Molecular Biology

The structure and expression of eukaryotic genes are discussed, focusing on model systems from a variety of organisms including yeast, flies, worms, mice, humans, and plants. Topics discussed include (1) genomics, proteomics, and functional proteomics and (2) control of gene expression at the level of transcription of mRNA from DNA, splicing of pre-mRNA, export of spliced mRNA from the nucleus to the cytoplasm, and translation of mRNA.

9 units

PREREQUISITES: 03220 or 03330

03445 Undergraduate Research

Students may investigate research problems under the supervision of members of the faculty. Permission of a faculty advisor required.

1-18 units

03451 Advanced Developmental Biology and Human Health

This course will examine current research in developmental biology, focusing on areas that have important biomedical implications. The course will examine stem cell biology, cellular reprogramming, cell signaling pathways, tissue morphogenesis, and genetic/developmental mechanisms of birth defects and human diseases. Emphasis will be placed on the critical reading of recent, original research papers and classroom discussion, with supporting lectures by faculty.

9 units

PREREQUISITES: (03240 or 03320) and (03220 or 03330)

03511 Computational Molecular Biology and Genomics

An advanced introduction to computational molecular biology, using an applied algorithms approach. The first part of the course will cover established algorithmic methods, including pairwise sequence alignment and dynamic programming, multiple sequence alignment, fast database search heuristics, hidden Markov models for molecular motifs and phylogeny reconstruction. The second part of the course will explore emerging computational problems driven by the newest genomic research. Course work includes four to six problem sets, one midterm and final exam.

9 units

PREREQUISITES: (03121 or 03151) and (15122)

03512 Computational Methods for Biological Modeling and Simulation

This course covers a variety of computational methods important for modeling and simulation of biological systems. It is intended for graduates and advanced undergraduates with either biological or computational backgrounds who are interested in developing computer models and simulations of biological systems. The course will emphasize practical algorithms and algorithm design methods drawn from various disciplines of computer science and applied mathematics that are useful in biological applications. The general topics covered will be models for optimization problems, simulation and sampling, and parameter tuning. Course work will include problems sets with significant programming components and independent or group final projects.

9 units

PREREQUISITES: (03121 or 03151) and (15122)

03534 Biological Imaging and Fluorescence Spectroscopy

This course covers principles and applications of optical methods in the study of structure and function in biological systems. Topics to be covered include: absorption and fluorescence spectroscopy; interaction of light with biological molecules, cells, and systems; design of fluorescent probes and optical biosensor molecules; genetically expressible optical probes; photochemistry; optics and image formation; transmitted-light and fluorescence microscope systems; laser-based systems; scanning microscopes; electronic detectors and cameras: image processing; multi-mode imaging systems; microscopy of living cells; and the optical detection of membrane potential, molecular assembly, transcription, enzyme activity, and the action of molecular motors. This course is particularly aimed at students in science and engineering interested in gaining in-depth knowledge of modern light microscopy.

9 units

PREREQUISITES: (03231 or 03232) and (03240 or 03320) and (21259) and (09344 or 09214)

03545 Honors Research

This semester of research consists primarily of research and preparation of an acceptable written thesis. Oral presentation and defense of the thesis research will be required. This course ordinarily will be taken in the second semester of the senior year. Permission of the research advisor required.

9 units

PREREQUISITES: 03445

Graduate Courses

03601 Computational Biology Internship

This course allows a student to gain computational biology experience in a real-world setting. Internships vary widely in scope, but common to all is the chance to practice computational biology skills acquired in the classroom. Typically, students seek and secure their own internships.

3-36 units

03620 Techniques in Electron Microscopy

This course is designed to teach basic methods in transmission electron microscopy to graduate and undergraduate students. Sophomores with an interest in electron microscopy are encouraged to enroll, and will have the option and opportunity to utilize their skills in various laboratories during their junior or senior year. The course will be offered once each year, during the spring semester. Course enrollment will be limited to 4-6 students. Preferential enrollment will be given to graduate students and undergraduate students who have demonstrated a need for this technique in their research. The class will include one hour of lecture and 4 hours of laboratory each week (some additional laboratory time outside of the scheduled laboratory time is required). Students will learn basic methods in specimen preparation for both transmission and scanning electron microscopy (fixation, embedding and ultramicrotomy, drying and metal coating) and will be trained in the operation of both the Hitachi 7100 and 2460N electron microscopes. Lectures and laboratories during the last few weeks of the semester will introduce the students to special techniques (e.g. immunoelectron microscopy , cryoultramicrotomy, freeze substitution, variable pressure SEM, etc.) and will allow them to work with samples from their own research. Experimentation using living organisms and/or their tissues, cells or molecules is an essential component of this course.

9 units

03700 MS Thesis Research

A student enrolled in this course conducts an independent investigation on a project in a faculty advisors lab. The project is selected from a major area of research study with the advice and approval of the faculty advisor. This course is required of students who are enrolled in the Master of Science program and wish to write and defend a thesis.

6-36 units

03709 Applied Cell and Molecular Biology

The purpose of this course is to review key cellular and molecular phenomenon in biological pathways with strong emphasis on latest experimental techniques used in applications including but not limited to disease diagnosis, therapeutics, large-scale genomic and proteomic analysis. Knowledge gained from this course will be both conceptual and analytical. Students will periodically write extensive research reports on select topics and give oral presentations on a select few, while critically analyzing primary literature.

12 units

03711 Computational Molecular Biology and Genomics

An advanced introduction to computational molecular biology, using an applied algorithms approach. The first part of the course will cover established algorithmic methods, including pairwise sequence alignment and dynamic programming, multiple sequence alignment, fast database search heuristics, hidden Markov models for molecular motifs and phylogeny reconstruction. The second part of the course will explore emerging computational problems driven by the newest genomic research. Course work includes four to six problem sets, one midterm and final exam.

12 units

Prerequisites: (03121 or 03151) and (15122)

03712 Computational Methods for Biological Modeling and Simulation

This course covers a variety of computational methods important for modeling and simulation of biological systems. It is intended for graduates and advanced undergraduates with either biological or computational backgrounds who are interested in developing computer models and simulations of biological systems. The course will emphasize practical algorithms and algorithm design methods drawn from various disciplines of computer science and applied mathematics that are useful in biological applications. The general topics covered will be models for optimization problems, simulation and sampling, and parameter tuning. Course work will include problems sets with significant programming components and independent or group final projects.

12 units

Prerequisites: (03121 or 03151) and (15122)

03713 Bioinformatics Data Integration Practicum

This course provides a hands-on, self-directed experience dealing with biological data and integrating it to produce software and analyses that are of use to biologists. Data are taken from a variety of sources, including academic research labs, large scale public genomics projects and data from private industry partners. Students will be given a project and asked to design a solution using a combination of existing tools and their own developed software.

6 units

03726 Evolution of Regulatory Genomics

This course in will examine the processes by which genomes evolve and how this genetic variation leads to phenotypic diversity. An introduction to gene regulation, how the genome controls development, comparisons of development and the phenotypic diversity in animals will be provided. Then we will consider ways in which genomes evolve, followed by in depth coverage of how gene regulation has evolved (focusing on cis regulatory evolution and non-coding RNA regulatory evolution). Finally the concept of gene regulatory network control of development and understanding evolution as change in these networks will be examined. Concepts and specific examples will come through reading of primary literature and selected readings from advanced texts. Grading will be based on written assignments from readings of literature, participation in class discussion, and two in class exams. The graduate level course (03-726) will in addition require a term paper based on thorough and critical reading of primary literature focused on one of the general topics presented in the course.

6 units

Corequisites: 03330 , 03220

03730 Advanced Genetics

This course considers selected current topics in genetics at an advanced level. Emphasis is on classroom discussion of research papers. Topics change yearly. Recent topics have included nucleocytoplasmic trafficking of RNA in yeast, genome imprinting in mammals, genetics of learning and memory in Drosophila, and viral genomics.

12 units

Prerequisites: (03330 or 03220) and (03742 or 03442)

03740 Advanced Biochemistry

This is a special topics course in which selected topics in biochemistry will be analyzed in depth with emphasis on class discussion of papers from the recent research literature. Topics change yearly. Recent topics have included single molecule analysis of catalysis and conformational changes; intrinsically disordered proteins; cooperative interactions of aspartate transcarbamoylase; and the mechanism of ribosomal protein synthesis.

12 units

03741 Advanced Cell Biology

This course covers fourteen topics in which significant recent advances or controversies have been reported. For each topic there is a background lecture by the instructor, student presentations of the relevant primary research articles and a general class discussion. Example topics are: extracellular matrix control of normal and cancer cell cycles, force generating mechanisms in trans-membrane protein translocation, signal transduction control of cell motility, and a molecular mechanism for membrane fusion.

12 units

Prerequisites: (03240 or 03320) and (03232 or 03231)

03742 Molecular Biology

The structure and expression of eukaryotic genes are discussed, focusing on model systems from a variety of organisms including yeast, flies, worms, mice, humans, and plants. Topics discussed include (1) genomics, proteomics, and functional proteomics and (2) control of gene expression at the level of transcription of mRNA from DNA, splicing of pre-mRNA, export of spliced mRNA from the nucleus to the cytoplasm, and translation of mRNA.

12 units

Prerequisites: 03220 or 03330

03744 Membrane Trafficking

While the focus of this course is to analyze membrane/protein traffic along both the biosynthetic and endocyctic pathways, our general goal is to teach students how to read and interpret the literature. In particular, we emphasize the conclusions and discuss their validity. The course is updated each year to include topics in which new and interesting developments have occurred. Emphasis is placed on how membrane traffic is regulated and where applicable how it is disrupted or subverted during disease processes. The course is of general interest to students, fellows, and faculty interested in cell biology, immunology, neurobiology, pharmacology and virology.

9 units

Prerequisites: 03240 or 03320

03745 Core Course in Biochemistry

This course is designed to provide first year doctoral students in the Department of Biological Sciences with a broad foundation in biochemistry and biophysical techniques. Topics include protein structure, enzymology, and methods to characterize protein structure and function. Students will be evaluated throughout the course, and with a final exam.

6 units

03746 Core Course in Cell Biology

This course is designed to provide first year doctoral students in the Department of Biological Sciences with a broad foundation in cell biology. Topics include, but are not limited to, intracellular trafficking, signal transduction, the cytoskeleton, the cell cycle, and cell-cell interactions. This is a lecture-based course and will include some discussion of the primary literature. Students will be evaluated weekly, and with a final exam. Enrollment requires instructor permission.

6 units

03747 Proposal Preparation and Peer Review

The concise and clear presentation of an experimental research plan is an essential skill for research scientists. This mini course is designed to introduce 2nd year students to the structure and preparation of a structured research proposal as well as formalize instruction in professional standards in research ethics, CV preparation, and scientific writing and data presentation. Course material is taken from actual grant proposals and previous years qualifying exam proposals, as well as primary research publications and faculty grant proposals. The course is highly interactive, and students are required to participate in review of each others work throughout the duration of the course. Coursework is expected to form the basis of the Ph.D. qualifying exam proposal in the winter of the second year.

4 units

03748 Scientific Speaking and Peer Review

Effective public presentation of scientific data is an important skill for every scientist. This interactive course will provide students with specific guidelines on organizing, preparing, and delivering an effective and engaging scientific talk. The topics covered include data organization, choice of content based on audience, PowerPoint and graphic design, charts and graphs representation, use of animation, fonts and color schemes, body language, overcoming stage-fear, and compensation for accents. The course is designed for third year graduate students. Students will present their upcoming Journal Club talk a week or two before in class, and receive formal review from a panel comprising of other students in the class, departmental multimedia designer, and the instructor. Further, each talk will be video recorded, and students will use the recording for self-critique and further input from the instructor. Each students Journal Club talk will then be recorded to provide a benchmark for the final talk incorporating the critiques provided. Students are required to participate in review of each others work throughout the duration of the course, and will therefore actively learn the elements of an effective presentation.

3 units

03750 Graduate Seminar

Each semester, all Department of Biological Sciences graduate students are required to register for and attend the weekly departmental Research Seminar (03-750; 1 unit). Graduate students are strongly urged to meet the speakers to broaden their knowledge of cutting-edge biological science, to discuss career paths and strategies and to make useful contacts; the faculty host can arrange group meetings for interested students.

1 unit

03751 Advanced Developmental Biology and Human Health

This course will examine current research in developmental biology, focusing on areas that have important biomedical implications. The course will examine stem cell biology, cellular reprogramming, cell signaling pathways, tissue morphogenesis, and genetic/developmental mechanisms of birth defects and human diseases. Emphasis will be placed on the critical reading of recent, original research papers and classroom discussion, with supporting lectures by faculty.

12 units

Prerequisites: (03240 or 03320) and (03330 or 03220)

03755 Graduate Research Seminar

Each semester, all Departmental of Biological Sciences graduate students are required to register for and attend the weekly departmental Journal Club (Graduate Research Seminar 03-755; 3 units) during which students and faculty members give 25-minute presentations. Second-year students present a research paper or topic from the literature, and more senior students present their research results; typically, graduate students give four Journal Club presentations during their time in the department. Each succeeding year those students who speak at the Departmental Retreat or who are graduating by May of their fifth year are not required to present at Journal Club that year.

3 units

03756 Graduate Independent Study

Variable units

03762 Advanced Cellular Neuroscience

This course is an introductory graduate course in cellular neuroscience. As such it will assume little or no background but will rapidly progress to discussions of papers from the primarily literature. The structure of the course will be about half lectures and half discussions of new and classic papers from the primary literature. These discussions will be substantially led by students in the course. Topics covered will include ion channels and excitability, synaptic transmission and plasticity, molecular understanding of brain disease and cell biology of neurons. Assessment will be based on class participation, including performance on in-class presentations and a writing assignment.

12 units

03763 Advanced Systems Neuroscience

This course is a graduate version of 03-363. Students will attend the same lectures as the students in 03-363, plus an additional once weekly meeting. In this meeting, topics covered in the lectures will be addressed in greater depth, often through discussions of papers from the primary literature. Students will read and be expected to have an in depth understanding of several classic papers from the literature as well as current papers that illustrate cutting edge approaches to systems neuroscience or important new concepts. Use of animals as research model systems will also be discussed. Performance in this portion of the class will be assessed by supplemental exam questions as well as by additional homework assignments.

12 units

Prerequisites: 03121 or 03151 or 03762 or 03362

03765 Advanced Neural Correlates of Learning and Memory

This course will examine the biological substrates of learning, memory, and behavioral adaptation. The focus will be on addressing how neural circuits change during new skill acquisition and adapt to variations in the environment. An introduction to experience-dependent changes in neural structure and function, in addition to behavioral learning paradigms, will be provided. Then we will consider the ways in which specific changes in biological substrates give rise to the emergent properties that drive behavioral adaptation, followed by in depth coverage of deciphering which biological substrates constitute a lasting memory trace. Finally, the concept of age-dependent learning will be examined. Concepts and specific examples will come through reading of primary literature and selected readings from advanced texts.

12 units

03770 Principles of Biotechnology

This course is intended to provide an introduction to a set of core areas important for understanding and managing biotechnology business. Essentially, the focus of the course will be the basics of the biotechnology entrepreneurial process and a deep background on biotechnology enabled products. The objective is to provide the background for management-level personnel to make decisions based on knowledge of contemporary biotechnologies and the legal and regulatory environment. Because it is impossible to be comprehensive with regard to all applications, the goal is to provide students with sufficient familiarity with current biotechnology and with a framework for assessing bio-related business questions that they may encounter in the future through a combination of independent research, assessment of opportunities and pitfalls, and historical comparisons. NOTE: This course CANNOT count towards the advanced electives required for majors or minors in Biological Sciences.

12 units

03791 Advanced Microbiology

This course will use both lectures and current research literature in the area of Microbiology and Infectious Diseases to introduce such topics as prokaryotic cytoskeletal functions, the human microbiome and its impact, metabolic engineering, transposon mutagenesis for gene function elucidation, synthetic genome construction and applications, pathogenicity islands, functional and expression-based identification of pathogenicity determinants, horizontal gene transfer, regulatory RNAs, biofilm formation quorum sensing, and antimicrobial drug development.

12 units

03871 Structural Biophysics

The physical properties of biological macromolecules and the methods used to analyze their structure and function are discussed. Topics covered include: protein architecture and folding; nucleic acid structures and energetics; structure determination by X-ray crystallography and NMR; biological spectroscopy with emphasis on absorption, fluorescence, and NMR spectroscopies; other methods to characterize proteins and protein-ligand interactions, such as mass spectrometry, calorimetry, and surface plasmon resonance. Sufficient detail is given to allow the student to critically evaluate the current literature.

12 units

Prerequisites: (03231 or 03232) and (09214 or 09345) and (21120 or 21122)

03900 Doctoral Thesis Research

Doctoral Thesis Research consists of an independent investigation on a project selected from a major area of research study with the advice and approval of the faculty advisor.

5-36 units