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Department of Biological Sciences Courses

Note on Course Numbers

Each Carnegie Mellon course number begins with a two-digit prefix which designates the department offering the course (76-xxx courses are offered by the Department of English, etc.). Although each department maintains its own course numbering practices, typically the first digit after the prefix indicates the class level: xx-1xx courses are freshmen-level, xx-2xx courses are sophomore level, etc. xx-6xx courses may be either undergraduate senior-level or graduate-level, depending on the department. xx-7xx courses and higher are graduate-level. Please consult the Schedule of Classes each semester for course offerings and for any necessary pre-requisites or co-requisites.

03-050 Study Abroad
Fall
03-051 Study Abroad
Spring
03-101 Biological Sciences First Year Seminars
Fall
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.
03-115 Phage Genomics Research
Fall: 6 units
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.
Corequisites: 03-110 and 03-121 and 03-151
03-116 Phage Genomics Research
Spring: 6 units
Spring Semester: The DNA sequences will be analyzed with bioinformatic tools and compared with those of phages isolated at other locations to identify genes, their organization, the differences that may characterize different phage groups, and how these have arisen during evolution.
Prerequisite: 03-115
03-121 Modern Biology
All Semesters: 9 units
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.
03-124 Modern Biology Laboratory
Fall and Spring: 9 units
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.
Corequisite: 03-121
03-125 Evolution
Fall: 9 units
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.
Prerequisite: 03-121
03-126 Cellular Response to the Environment
Fall: 4 units
This laboratory course provides a multifaceted view of the cell, with the opportunity for new discovery, through microscopic imaging of a cell’s response to environmental changes. We will identify yeast gene products that undergo changes in expression or subcellular localization after simple environmental perturbations or drug treatments. Students will be trained in basic molecular biological methods, including recombinant DNA manipulation, and basics of functional genomic resources. Enrollment is limited to first-year students in MCS. Special permission required.
Corequisite: 03-121
03-127 How Biological Experiments Work - A Project Course
Spring: 9 units
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 year students in MCS.
Prerequisite: 03-121
03-131 Genes Drugs & Diseases
Fall: 9 units
The central goals of this course are to explore the genetic basis of diseases and to explain the molecular basis of action for various drugs used to treat diseases. The first part of the course provides the student with sufficient background to understand the biological basis of drug action with emphasis on retroviral inhibitors. The usefulness of genetic engineering in the production of proteins for drug discovery is then explored. This is followed by an overview of DNA replication, transcription, and protein synthesis, with an emphasis on the inhibitory action of antibiotics on prokaryotic processes. The fundamental properties of carbohydrates, lipids, and membranes are discussed at a level to develop an understanding of penicillin and the treatment of elevated cholesterol levels. Signaling processes in eukaryotic cells is discussed with reference to cancer treatment and pain management. The treatment of disease using antibody, and the treatment of inappropriate immune responses (allergy) is also discussed. The course ends with a discussion of inheritance and genetic deficiencies that give rise to disease.

Course Website: http://www.andrew.cmu.edu/user/rule/03_131/
03-132 Basic Science to Modern Medicine
Fall: 9 units
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.
03-151 Honors Modern Biology
Fall: 10 units
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.
03-161 Molecules to Mind
Spring: 9 units
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.
03-201 Undergraduate Colloquium for Sophomores
Fall
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.
03-202 Undergraduate Colloquium for Sophomores
Spring
03-206 Biomedical Engineering Laboratory
Fall and Spring: 9 units
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.
Prerequisites: 03-121 and 42-101
03-210 Independent Study
Fall and Spring
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.
03-230 Intro to Mammalian Physiology
Spring: 9 units
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.
Corequisite: 03-121
03-231 Biochemistry I
Fall: 9 units
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.
Prerequisite: 03-121
Corequisite: 09-217
03-232 Biochemistry I
Spring: 9 units
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.
Prerequisites: 09-217 or 09-219
Corequisites: 06-221 or 09-106
03-240 Cell Biology
Spring: 9 units
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.
Prerequisites: (03-120 or 03-121) and (03-231 or 03-232 or 03-233).
03-250 Introduction to Computational Biology
Spring: 12 units
This is a 12-unit class intended to provide 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 visions, morphological image analysis, image classification and image-derived models. This course is 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. Prerequisites: 03-121 or permission of the instructors
Prerequisites: 03-120 or 03-121 or 03-131
03-251 Introduction to Computational Molecular Biology
Spring: 6 units
This 6-unit mini class intended to provide 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. This course is 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 03-250/42-334 and either 03-251 or 03-252 for credit. Prerequisites: 03-121 or permission of the instructors
Prerequisite: 03-121
03-252 Introduction to Computational Cell Biology
Spring: 6 units
This course presents an overview of important modeling and image analysis applications of computers to solve problems in biology. It is intended for students without computer programming experience. Major topics covered are biological imaging (digital image processing, morphological image analysis, image databases, image classification and image-derived models) and biological modeling and simulation (including computer models of population dynamics, biochemical kinetics, neuron behavior, cell pathways, and the cell cycle). Required recitations and homeworks consist of exercises making use of web site, software packages and simple Matlab scripts for these applications. Course grade is based on recitation participation, homework assignments based on the exercises, and mid-term and final exams. Note that this course is the second half of 03-250 (Introduction to Computational Biology) and that credit may not be given for both 03-250/02-250 and 03-252/02-252. Prerequisites: 03-121 or permission of instructor.
Prerequisite: 03-121
03-260 Neurobiology of Disease
Fall: 9 units
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.
Prerequisites: 03-121 or 85-219
03-301 Undergraduate Colloquium for Juniors
Fall
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.
03-302 Undergraduate Colloquium for Juniors
Spring
03-326 Evolution of Regulatory Genomics
Fall: 4.5 units
This course 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.
Prerequisite: 03-231
Corequisite: 03-330
03-327 Phylogenetics
Fall: 9 units
An advanced introduction to theory and practice of phylogenetic analysis (evolutionary tree reconstruction), with a focus on molecular evolution. Basic concepts will be introduced in the context of a historical survey of phylogeny reconstruction. A comprehensive introduction to phylogenetic methods will be presented, including data selection, multiple sequence alignment, character state data versus distance matrices, sequence evolution models, and the four major approaches to phylogeny reconstruction: Parsimony, Distance matrix, Maximum likelihood, and Bayesian analysis. Sources of error and methods for assessing the reliability of phylogenetic inference will be discussed. We will cover additional topics as time allows, such as phylogenetic hypothesis testing, genome scale approaches, the interface between phylogenetics and population genetics, gene tree reconciliation, horizontal gene transfer, and phylogenetic networks.
Prerequisites: 03-231 or 03-232 or 03-250
03-330 Genetics
Fall: 9 units
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.
Prerequisites: 03-231 or 03-232
03-342 Introduction to Biological Laboratory Practices
Fall: 1 unit
This course is designed for students in the BS in Computational Biology degree program. It will be taught as a first mini as 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.
Corequisite: 03-343
03-343 Experimental Techniques in Molecular Biology
Fall: 12 units
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.
Prerequisites: (03-231 or 03-232) and 09-222
Corequisite: 03-330
03-344 Experimental Biochemistry
Spring: 12 units
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.
Prerequisites: 03-343 and (03-231 or 03-232).
03-345 Experimental Cell and Developmental Biology
Spring: 12 units
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.
Prerequisites: 03-343 and (03-231 or 03-232) and 03-240 and 03-330
Corequisite: 03-350
03-346 Experimental Neuroscience
Intermittent: 12 units
This laboratory is designed to teach concepts and experimental methods in neurobiology. Students work with a variety of organisms to study the anatomy, function, and development of the nervous system. Immunological, molecular, biochemical, and ballistic labeling techniques are used to examine the gene expression and structure in the mature and developing nervous system. Students study the function of neurons through neurophysiological techniques in invertebrates and computer simulation. This course makes extensive use of video microscopy and phase contrast, DIC, and fluorescence microscopes.
03-350 Developmental Biology
Spring: 9 units
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.
Prerequisite: 03-240
03-362 Cellular Neuroscience
Fall and Spring: 9 units
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.
Prerequisite: 03-121
03-363 Systems Neuroscience
Spring: 9 units
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.
Prerequisites: 03-121 or 03-362 or 03-762 or 15-386 or 85-219
03-364 Developmental Neuroscience
Fall: 9 units
This course examines the principles that govern the developmental assembly of a complex nervous system. Topics range from the earliest steps of induction of neural tissue and birth of neurons to the plasticity within developing circuits and the development of behavior. By the end of this course students should be able to describe the major steps in neural development and to interpret key experiments using vertebrate and invertebrate models have helped to elucidate these steps. This course is taught on the University of Pittsburgh campus by faculty from Carnegie Mellon and Pitt.
Prerequisites: 03-240 or 03-362 or 03-363
03-365 Neural Correlates of Learning and Memory
Spring: 9 units
Will be updated in F14.
03-370 Principles of Biotechnology
Spring: 9 units
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.
Prerequisites: (03-231 or 03-232) and 03-240
03-390 Molecular and Cellular Immunology
Spring: 9 units
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.
Prerequisites: (03-231 or 03-232) and 03-240
03-391 Microbiology
Spring: 9 units
The course provides introductory level molecular biology that is aimed for students from all disciplines of natural science. It covers microbiology, genetics, genomics and virology, as well as related biophysics of RNA and DNA packaging, protein self-assembly and molecular motors. We also review the latest biophysical methods with a focus on single molecule techniques that have revolutionized the biological sciences.
Prerequisites: 03-231 or 03-232
03-392 Microbiology Laboratory
Spring: 6 units
This is an upper level biology course for students who have taken or are currently taking the Microbiology course and are interested in laboratory experience in microbiology. It is designed with the recommendations of the American Society for Microbiology for a student laboratory course in mind in order to introduce the student to a broad spectrum of techniques in microbiology. You will learn the skills needed to perform experiments that help to differentiate various types of microbes, examine antimicrobial and antibiotic sensitivity and resistance, and begin to explore microbial diversity. Finally, you will develop an understanding of the theory behind the techniques you use and will be given the opportunity to further develop your skills in the process of experimental design.
Corequisite: 03-391
03-401 Undergraduate Colloquium for Seniors
Fall
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.
03-402 Undergraduate Colloquium for Seniors
Spring
03-411 Topics in Research
Fall
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.
03-412 Topics in Research
Spring
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.
03-439 Introduction to Biophysics
Fall: 9 units
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.
Prerequisites: 03-231 or 03-232
Course Website: http://www.cmu.edu/smsl/teaching/IntroBioPhys.html
03-442 Molecular Biology
Fall: 9 units
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.
Prerequisite: 03-330
03-445 Undergraduate Research
Fall and Spring
Students may investigate research problems under the supervision of members of the faculty. Permission of a faculty advisor required.
03-511 Computational Molecular Biology and Genomics
Fall: 9 units
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.
Prerequisites: 03-121 and 15-122
Course Website: http://www.cs.cmu.edu/~durand/03-711/
03-512 Computational Methods for Biological Modeling and Simulation
Fall: 9 units
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.
Prerequisites: 03-121 and 15-122
03-534 Biological Imaging and Fluorescence Spectroscopy
Spring: 9 units
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.
Prerequisites: (03-231 or 03-232) and 03-240 and 21-259 and (09-214 or 09-344).
03-545 Honors Research
Spring
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.
Prerequisite: 03-445
03-601 Computational Biology Internship
All Semesters
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.
03-620 Techniques in Electron Microscopy
Spring: 9 units
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. Special permission is required.
03-700 MS Thesis Research
All Semesters
A student enrolled in this course conducts an independent investigation on a project in a faculty advisor's 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.
03-709 Applied Cell and Molecular Biology
Fall: 12 units
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.
03-710 Computational Biology
Spring: 12 units
This course covers a range of applications of computers to solve problems in biology and medicine. Specific topics covered are computational molecular biology (analysis of protein and nucleic acid sequences), biological modeling and simulation (including computer models of neuron behavior, biochemical kinetics, and simulation of mutation), and biological imaging. Course work will include use of software packages for these applications, reading of scientific papers, and programming assignments. Students may use one of the following courses for credit, 03-310, 03-311, 03-510 or 03-710.
Prerequisites: 03-121 and (15-200 or 15-211).
03-711 Computational Molecular Biology and Genomics
Fall: 12 units
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.
Prerequisites: 03-121 and 15-122
Course Website: http://www-2.cs.cmu.edu/~durand/03-711/
03-712 Computational Methods for Biological Modeling and Simulation
Spring: 12 units
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.
Prerequisites: 03-121 and 15-122
03-713 Bioinformatics Data Integration Practicum
Spring: 6 units
03-726 Evolution of Regulatory Genomics
Fall: 6 units
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.
Corequisite: 03-330
03-727 Phylogenetics
Fall: 12 units
An advanced introduction to theory and practice of phylogenetic analysis (evolutionary tree reconstruction), with a focus on molecular evolution. Basic concepts will be introduced in the context of a historical survey of phylogeny reconstruction. A comprehensive introduction to phylogenetic methods will be presented, including data selection, multiple sequence alignment, character state data versus distance matrices, sequence evolution models, and the four major approaches to phylogeny reconstruction: Parsimony, Distance matrix, Maximum likelihood, and Bayesian analysis. Sources of error and methods for assessing the reliability of phylogenetic inference will be discussed. We will cover additional topics as time allows, such as phylogenetic hypothesis testing, genome scale approaches, the interface between phylogenetics and population genetics, gene tree reconciliation, horizontal gene transfer, and phylogenetic networks. Course work will include readings from textbooks and seminal articles from the primary literature, problem sets, a final exam and possibly in class exams. Students in 03-727 will also carry out a major data analysis project, intended to familiarize the student with the practical application of principles taught in class. A short paper summarizing the results of this project will be required.
03-730 Advanced Genetics
Spring: 12 units
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.
Prerequisites: 03-330 and (03-442 or 03-742).
03-740 Advanced Biochemistry
Spring: 12 units
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.
03-741 Advanced Cell Biology
Spring: 12 units
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.
Prerequisites: 03-240 and (03-231 or 03-232).
03-742 Molecular Biology
Fall: 12 units
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.
Prerequisite: 03-330
03-744 Membrane Trafficking
Spring: 9 units
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.
Prerequisite: 03-240
03-745 Core Course in Biochemistry
Fall: 6 units
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.
03-746 Core Course in Cell Biology
Fall: 6 units
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.
03-747 Proposal Preparation and Peer Review
Fall: 4 units
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.
03-750 Graduate Seminar
Fall and Spring: 1 unit
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.

Course Website: http://www.cmu.edu/bio/seminars_events/seminar/index.html
03-751 Advanced Developmental Biology
Fall: 12 units
This course examines current topics in developmental biology at an advanced level. The course is team-taught by faculty from Carnegie Mellon University, the University of Pittsburgh Department of Biological Sciences, and the University of Pittsburgh Medical School. Each year several areas of current research are examined. Previous topics have included pattern formation, molecular signaling pathways, morphogen gradients, cell movements, and stem cells. Emphasis is on critical reading of original research papers and classroom discussion, with supporting lectures by faculty.
Prerequisite: 03-350
03-755 Graduate Research Seminar
Fall and Spring: 3 units
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.

Course Website: http://www.cmu.edu/bio/seminars_events/journal_club/index.html
03-761 Neural Plasticity
Spring: 9 units
Neural plasticity underlies the capacity of the central nervous system to encode new information, develop new abilities and adapt to the environment. Plasticity is required for learning and is modulated during development and by disorders of the brain. Recent advances in experimental methodology have led to new insights on the biological mechanisms underlying neural plasticity. The topics if the papers chosen for review will center on recent experimental and theoretical studies of topics such as synaptic plasticity, developmental and activity dependent changes in sensory and motor maps.
Prerequisite: 03-360.
03-762 Advanced Cellular Neuroscience
Spring: 12 units
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.
03-763 Advanced Systems Neuroscience
Fall: 12 units
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.
Prerequisites: 03-121 or 03-362 or 03-762
03-770 Principles of Biotechnology
Spring: 12 units
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.
03-791 Advanced Microbiology
Spring: 12 units
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.
03-871 Structural Biophysics
Fall: 12 units
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.
Prerequisites: (03-231 or 03-232) and (09-214 or 09-345) and (21-120 or 21-122).
03-900 Doctoral Thesis Research
All Semesters
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.
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