Biophysics

BIOL W1015x Molecular Biology and Evolution for Nonscientists Not offered in 2013-2014. Lecture and recitation. Normally may not be taken for credit by any student who has previously completed any biology course numbered 2000 or above. Want to learn enough to understand the Tuesday Science Times? Be able to explain cloning to your friends? This is the course for you. What molecular biologists know, how they figured it out, and what they are likely to try next. How molecular biology and evolutionary theory influence each other. Experiments leading to current knowledge in molecular biology and evolution are discussed in detail and analyzed quantitatively. Science requirement: Partial Fulfillment. Website: http://www.columbia.edu/cu/biology/courses/c1015/index.html

BIOL W1130y Genes and Development 3 pts.Not offered in 2013-2014. Prerequisites: Introductory biology course at Columbia, AP Biology, or permission of the instructor. This course covers selected topics in genetics and development, with special emphasis on issues that are relevant to contemporary society. Lectures and readings will provide students with the scientific knowledge to understand how genes regulate development, and how alterations in genes lead to abnormal development and disease. Interspersed workshops will allow students to research and discuss the ethical and societal impact of specific topics (e.g. in vitro fertilization, steroid use, and stem cell therapy).

BIOL C2005x Introductory Biology I: Biochemistry, Genetics & Molecular Biology 4 pts. Prerequisites: One year of college chemistry, or a strong high school chemistry background. Lecture and recitation. Recommended as the introductory biology course for biology and related majors, and for premedical students. Fundamental principles of biochemistry, molecular biology, and genetics. Website: http://www.columbia.edu/cu/biology/courses/c2005/index.html

BIOL C2006y Introductory Biology II: Cell Biology, Development & Physiology 4 pts. Prerequisites: EEEB W2001 or BIOL C2005, or the instructor's permission. Lecture and recitation. Recommended second term of biology for majors in biology and related majors, and for premedical students. Cellular biology and development; physiology of cells and organisms. Website: http://www.columbia.edu/cu/biology/courses/c2006/

BIOL F2401x Contemporary Biology I: Biochemistry, Genetics & Molecular Biology 3 pts. Prerequisites: A course in college chemistry or the written permission of either the instructor or the premedical adviser. Recommended as the introductory biology course for science majors who have completed a year of college chemistry and premedical students. The fundamental principles of biochemistry, molecular biology, and genetics. Website: http://www.columbia.edu/cu/biology/courses/c2005/index.html

BIOL F2402y Contemporary Biology II: Cell Biology, Development & Physiology 3 pts. Prerequisites: A course in college chemistry and Biology C2005 or F2401 or the written permission of either the instructor or the premedical adviser. Same lectures as Biology C2006, but recitation is optional. For a detailed description of the differences between the two courses, see the course web site or http://www.columbia.edu/cu/biology/ug/advice/faqs/gs.html. Cellular biology and development; physiology of cells and organisms. Website: http://www.columbia.edu/cu/biology/courses/c2006/

BIOL W2501x or y Contemporary Biology Laboratory 3 pts. Corequisites: Strongly recommended prerequisite or corequisite: BIOL C2005 or F2401. Experiments focus on genetics and molecular biology, with an emphasis on data analysis and experimental techniques. The class also includes a study of mammalian anatomy and histology. Each section is limited to 28 students. Lab Fee $150.

BIOL C2908x First-Year Seminar in Modern Biology 1 pt. If you are interested in doing biology-related research at Columbia University this is the course for you. Each week a different Columbia University professor's discusses their biology-related research giving you an idea of what kind of research is happening at Columbia. Come ask questions and find out how the body works, the latest therapies for disease and maybe even find a lab to do research in. http://www.columbia.edu/cu/biology/courses/c2908/index.html

BIOL W3002 Introduction to Animal Structure and Function 6 pts.Not offered in 2013-2014. Prerequisites: one year each of biology and college physics. Laboratory fee: $150. Both laboratory sessions are required. Introduction to animal form and function, using the vertebrates as examples, with emphasis on the comparative and evolutionary approaches. Interrelationship between the form-function complex with emphasis on the skeletal-muscular systems, and the organismal-environmental interactions; different morphological solutions to the same environmental problem. Laboratories include dissection of vertebrate structure and the analysis of its function. Registration for one of the two lab sections (BIOL W3012) is required. Lab Required.

BIOL W3004 Neurobiology I: Cellular and Molecular Neurobiology 4 pts. Prerequisites: one year of biology; a course in physics is highly recommended. Lecture and recitation. This is an advanced course intended for majors providing an in depth survey of the cellular and molecular aspects of nerve cell function. Topics include the cell biology and biochemistry of neurons, ionic and molecular basis of electrical signals, synaptic transmission and its modulation, function of sensory receptors. Although not required, it is intended to be followed by Neurobiology II (see below). The recitation meets once per week in smaller groups and emphasizes readings from the primary literature. Discussion Section Required.

BIOL W3005 Neurobiology II: Development & Systems 4 pts. Prerequisites: Biology W3004, one year of biology or instructor's permission. This course is the "capstone" course for the Neurobiology and Behavior undergraduate major at Columbia University and will be taught by the faculty of the Kavli Institute of Brain Science (http://www.kavli.columbia.edu/). It is designed for advanced undergraduate and graduate students. Knowledge of Cellular Neuroscience (how an action potential is generated and how a synapse works) will be assumed. It is strongly recommended that students take w3004 Neurobiology 1: Molecular and Cellular Neuroscience, or a similar course, before enrolling in w3005. Students unsure about their backgrounds should check a representative syllabus of w3004 on the w3004 website (http://www.columbia.edu/cu/biology/courses/w3004/). Website for w3005: http://www.columbia.edu/cu/biology/courses/w3005/index.html

BIOL W3006 Physiology 3 pts. Prerequisites: Biol C2005 & C2006 or F2401 & F2402, or the instructor's permission. Major physiological systems of vertebrates (circulatory, digestive, hormonal, etc.) with emphasis on cellular and molecular mechanisms and regulation. Readings include research articles from the scientific literature.

BIOL W3008 The Cellular Physiology of Disease 3 pts.Not offered in 2013-2014. Prerequisites: One 3000 level course in Cell Biology or Biochemistry or the instructor's permission. This course will present a quantitative description of the cellular physiology of excitable cells (mostly nerve and muscle). While the course will focus on examining basic mechanisms in cell physiology, there will be a thread of discussion of disease mechanisms throughout. The end of each lecture will include a discussion of the molecular mechanisms of selected diseases that relate to the topics covered in the lecture. The course will consist of two lectures per week. This course will be of interest to advanced (3000-4000 level)undergraduates that aim to pursue careers in medicine as well as those that will pursue careers in biomedical research. This course will also be of interest to graduate students desiring an introduction to the cellular physiology of nerve and muscle.

BIOL W3022 Developmental Biology 3 pts. Prerequisites: BIOL C2005-C2006 or equivalent Come discover how the union of egg and sperm triggers the complex cellular interactions that specify the diverse variety of cells present in multicellular organisms. Cellular and molecular aspects of sex determination, gametogenesis, genomic imprinting, X-chromosome inactivation, telomerase as the biological clock, stem cells, cloning, the pill and cell interactions will be explored, with an emphasis on humans. Original research articles will be discussed to further examine current research in developmental biology. BIOL W3022_001_2007_1">

BIOL W3031 Genetics 3 pts. Prerequisites: BIOL C2005-C2006 or the equivalent. Students may receive credit for W3031 or C3032, but not both due to overlap in course content. General course in genetics and genomics dealing with principles of gene structure, function, regulation and transmission. Historical development, experimental basis of current knowledge, and roles of model organisms are stressed. Includes a thorough understanding of disease gene discovery, and an introduction to topics in developmental, cancer and population genetics.

BIOL W3034 Biotechnology 3 pts. Prerequisites: genetics or molecular biology. For upper-level undergraduates. The course covers techniques currently used to explore and manipulate gene function and their applications in medicine and the environment. Part I covers key laboratory manipulations, including DNA cloning, gene characterization, association of genes with disease, and methods for studying gene regulation and activities of gene products. Part II also covers commercial applications, and includes animal cell culture, production of recombinant proteins, novel diagnostics, high throughput screening, and environmental biosensors.

BIOL W3040 Lab in Molecular Biology 3 pts. Prerequisites: 1 year of biology (C2005-C2006) and Contemporary Biology Laboratory (c2501). This lab will explore various molecular biology techniques frequently utilized in modern molecular biology laboratories. The lab will consist of three modules: 1. Molecular verification of genetically modified organisms (GMOs), 2. Site-directed mutagenesis and 3. PCR isolation, cloning and analysis of the GAPDH gene. The maximum number of participants is 12. (Lab Fee: $150).

BIOL W3041 Cell Biology 3 pts. Prerequisites: one year of biology, normally BIOL C2005-C2006, or the equivalent. Corequisites: Biochemistry. Introduction to cell biology stressing the architecture of the cell as it relates to cellular function, physiology, biochemistry, and disease, as well as some detailed discussions of the experiments that have informed our current views of the cell.

BIOL W3050 Project Laboratory In Protein Biochemistry 5 pts.Not offered in 2013-2014. Prerequisites: One year of biology (C2005-C2006) plus 1 upper-level course recommended.Enrollment is not restricted as long as total is no more than 14. Seniors will be given preference in the unlikely event that restriction is necessary. Students with specific questions should e-mail the instructor (jfh21@columbia.edu). This course provides an intensive introduction to professional biomedical laboratory research. Students conduct a portion of an ongoing biochemical research project and write-up their results in a format suitable for publication in a peer-reviewed scientific research journal. Techniques in molecular biology and protein biochemistry are used to address a problem in mechanistic biochemistry or molecular pharmacology. Students are exposed to the full spectrum of techniques used in contemporary protein biochemistry including molecular sequence analysis of genomic databases, molecular cloning and manipulation of recombinant DNA, protein expression in E. coli, protein purification, and biophysical characterization (typically including crystallization for x-ray structure determination). The couse emphasizes the use of critical thinking skills in scientific research while giving students the opportunity to apply the basic knowlegde learned in a wide variety of biology and chemistry lecture courses to a real research project. Examples of past projects can be found on the course website: https://www1.columbia.edu/sec/cu/biology/courses/w3050/class/index.html (cunix account required to login). Biol W3050 will not be offered in the 2011-2012 academic year. An alternate Project Lab WILL be offered in the 2011-2012 academic year: Biol W3058 Project Lab in Microbiology.

BIOL C3052 Project Laboratory in Molecular Genetics 5 pts. Prerequisites: one year of introductory biology and the instructor's permission. Enrollment limited to approximately 12. Fee: $150. Project laboratory on the manipulation of nucleic acids in prokaryotes, including DNA isolation, restriction mapping, and transformation. The first part of the laboratory involves learning of techniques to be used subsequently in independent research projects suggested by the professor.

BIOL W3058 Project Laboratory in Microbiology 5 pts. Prerequisites: 1 year of Intro Bio. An introductory biology or chemistry lab is recommended. Bacteria are not just unicellular germs. This lab course will broaden your awareness of the amazing world of microbiology and the diverse capabilities of microbes. The focus will be on bacterial multicellularity, pigment production, and intercellular signaling. Pigment-producing bacteria will be isolated from the wild (i.e. Morningside Campus or your skin), and characterized using standard genetic genetic tools (PCR, DNA gel electrophoresis, transformation, screen) and microbiology techniques (isolation of bacteria and growth of bacterial colonies, media preparation, enrichment techniques for pigments). These techniques will also be applied in the study of bacterial multicellularity and signaling in the standard lab strain Pseudomonas aeruginosa. Lab fee: $150

BIOL W3073 Cellular and Molecular Immunology 3 pts. Prerequisites: Two semesters of a rigorous, molecularly-oriented introductory biology course (such as C2005 and C2006), or the instructor's permission. This course will cover the basic concepts underlying the mechanisms of innate and adaptive immunity, as well as key experimental methods currently used in the field. To keep it real, the course will include clinical correlates in such areas as infectious diseases, autoimmune diseases, cancer and transplantation. Taking this course won't turn you into an immunologist, but it may make you want to become one, as was the case for several students last year. After taking the course, you should be able to read the literature intelligently in this rapidly advancing field.

BIOL W3190 Stem Cells: Biology, Ethics and Applications 3 pts. Prerequisites: Introductory Biology (BIOL W2005, W2006) plus one semester of Biology at the 3000 level or above; otherwise permission should be sought from the instructor (contact ddk1@columbia.edu). Dramatic advances in Stem Cell biology have created new possibilities for medical research and treatment. Realization of potential benefits requires continued scientific advances but also negotiation of the regulatory terrain and ethical considerations that determine what types of research and applications can and should be advanced. This course addresses the major breakthroughs and possibilities for both pluripotent stem cells (Embryonic Stem Cells and induced Pluripotent Stem Cells) and adult tissue-specific stem cells, including ethical and regulatory perspectives. Several classes will be predominantly lecture style while others will be largely discussion of ethics, medical applications or research papers. In addition the course features two public lectures concerning cutting edge stem cell research, an invited expert on regulatory affairs and a visit to the New York Stem Cell Foundation Laboratory. The course can be used as an elective for majors in Biology, Biochemistry, Biophysics or Neuroscience and Behavior.

HPSC W3201 Philosophy and History of Evolutionary Biology 4 pts. Prerequisites: the instructor's permission. This course does not carry credit as a biology course. Explores the philosophical basis and historical development of evolutionary biology as a means of inquiry into causation, explanation, and testing in biology, and the implications for human understanding. Topics include Darwinian evolutionary theory, problems of creationism, theories of inheritance, Mendelism and natural selection, species concepts, adaptation and macroevolution, and the rise of the synthetic theory of evolution, both nomological and historical.

BIOL W3208 Introduction to Evolutionary Biology 3 pts. Recommended preparation: an introductory course in college biology. Introduction to principles of general evolutionary theory, both nomological and historical; causes and processes of evolution; phylogenetic evolution; species concept and speciation; adaptation and macroevolution; concepts of phylogeny and classification.

BIOL W3310 Virology 3 pts. Prerequisites: Two semesters of a rigorous, molecularly-oriented introductory biology course (such as C2005), or the instructor's permission. The course will emphasize the common reactions that must be completed by all viruses for successful reproduction within a host cell and survival and spread within a host population. The molecular basis of alternative reproductive cycles, the interactions of viruses with host organisms, and how these lead to disease are presented with examples drawn from a set of representative animal and human viruses, although selected bacterial viruses will be discussed.

BIOL W3500 Independent Research 3-4 pts. Prerequisites: Concurrent with registering for this course, a student must register with the department, provide a written invitation from a mentor and submit a research proposal; details of this procedure are available on the Internet at http://www.columbia.edu/cu/biology/courses/w3500/index.htm Corequisites: BIOL W3600 required in the spring for students who have not previously taken W3500. Up to 4 points of letter-grade credit may be used toward the major. Fee: $150. Independent study, faculty-supervised laboratory projects in contemporary biology. A paper summarizing results of the work is required by the last day of finals for a letter grade; no late papers will be accepted.

BIOC C3501 Biochemistry: Structure and Metabolism 4 pts. Prerequisites: BIOL W2001 or C2005 and one year of organic chemistry. Lecture and recitation. Students wishing to cover the full range of modern biochemistry should take both BIOC C3501 and C3512. C3501 covers subject matters in modern biochemistry, including chemical biology and structural biology, discussing the structure and function of both proteins and small molecules in biological systems.Proteins are the primary class of biological macromolecules and serve to carry out most cellular functions. Small organic molecules function in energy production and creating building blocks for the components of cells and can also be used to perturb the functions of proteins directly. The first half of the course covers protein structure, enzyme kinetics and enzyme mechanism. The second half of the course explores how small molecules are used endogenously by living systems in metabolic and catabolic pathways; this part of the course focuses on mechanistic organic chemistry involved in metabolic pathways.

BIOC C3512 Molecular Biology 3 pts. Prerequisites: One year of biology. Recommended but not required: BIOC C3501. This is a lecture course designed for advanced undergraduates and graduate students. The focus is on understanding at the molecular level how genetic information is stored within the cell and how it is regulated. Topics covered include genome organization, DNA replication, transcription, RNA processing and translation. This course will also emphasize the critical analysis of the scientific literature and help students understand how to identify important biological problems and how to address them experimentally.

BIOL W3600 Biological Research Skills 1 pt. Corequisites: BIOL C3500. This is a companion course to BIOL C3500 Independent Research. Students will present their research plans and results in order to gain experience in communicating about science and to get feedback (from the instructor and other students) to improve their presentation and research skills. This is a pass/fail course.

BIOL W3700 Independent Clinical Research 2-4 pts. Prerequisites: Concurrent with registering for this course, a student must register with the department, provide a written invitation from a mentor and submit a research proposal. BIOL 3700 will provide an opportunity for students interested in independent research work in a hospital or hospice setting. In these settings, where patients and their needs Are paramount, and where IRB rules and basic medical ethics make "Wet-lab biology research" inappropriate, undergraduate may well find a way nevertheless, to assist and participate in ongoing clinical research. Such students, once they have identified a mentor willing to provide support, participation, and advising, may apply to the faculty member in charge of the course for 2-4 points/semester in BIOL W3700. This course will closely follow procedures already in place for BIOL 3500, but will ask potential mentors to provide evidence that students will gain hands-on experience in a clinical setting, while participating in a hospital- or hospice-based research agenda. A paper summarizing results of the work is required by the last day of finals for a letter grade; no late papers will be accepted.

BIOL C3799 Molecular Biology of Cancer 3 pts. Prerequisites: three terms of biology (genetics and cell biology recommended). Lecture and discussion. For upper-level undergraduates. Readings tracing the discovery of the role of DNA tumor viruses in cancerous transformation are discussed. Oncogenes and tumor suppressors are analyzed with respect to their function in normal cell cycle, growth control and human cancers.

BIOL W3990 Readings in Cell Biology 4 pts. Prerequisites: Cell Biology (3041/4041) and the permission of the instructor. The class size is strictly limited to 24 students. This is an advanced cell biology course that uses detailed discussion of the primary literature to understand fundamental cellular processes. The focus is on dissecting research papers to gain insight into the rationale behind specific experimental approaches, understand how experiments are performed and critically analyze the data and interpretations. We will start with an introduction to critical thinking and experimental design and then probe four sequential papers from a prominent research lab that all investigate the same biological process. In this way, students gain an understanding of the creative nature of laboratory research and see how a research project develop and diversifies. Course requirements: Students must read assigned sections of each paper prior to class and be prepared to discuss the experimental approaches, outcomes and interpretations. Students will participate in group discussions, small group activities and must present findings to the class. Assessment will be based on periodic assignments, a midterm take-home exam, a final exam and a folio that students will maintain to track their own progress and document their findings. Participation in class discussions will also contribute to the final grade.

BIOL W3995 Topics In Biology- Neuroscience and The Law 1 pt. Prerequisites: At least one advanced course in neurophysiology. No background in law is needed. Neuroscience and The Law - J. Meszaros, 1 credit. This course discusses the human behaviors that are subject to the law, and examines the neurobiological understanding of those behaviors. Closeness of fit between legal notions of human behavior will be compared with knowledge of neurobiology -- especially in the understanding of anxiety, drug addiction, and adolescence. Each week, a different type of behavior or class of individuals will be discussed. Readings will be split between primary literature in neuroscience and scholarly articles in law.

BIOL W3995 (Section 1) Topics in Biology: Crossroads in Bioethics 2 pts. Prerequisites: At least one lower-level full year course in biology. A background in history or philosophy is recommended Crossroads in Bioethics. J. Loike, 1 credit. This course examines both the underlying scientific principles of biotechnologies and the ethical controversies brought about by recent advances in biology and medicine. This course is designed to engage students in difficult dialogues around the scientific, social, legal, and bioethical issues related to emerging areas of biotechnology and medicine. Topics include human stem cell research, human cloning, genetically modified organisms, reproductive medicine (IVF and pre-implantation genetic diagnosis), neuroethics, and the impact of genetics on medicine. This discussion-based course is designed is to provide students with a comprehensive understanding of the interrelationship between biomedical technologies and bioethics.

BIOL W3995y (Section 3) Topics in Biology: Intro to Clinical Research in Emergency Medicine 1-2 pts. This course is designed to introduce students who are interested in medical careers to the goals, nomenclature, principles, and practical reality of clinical research, with an emphasis on the emergency department (ED) setting. The course focuses on terminology, data collection techniques, research design, and basic biostatistics. Understanding research and clinical emergency medicine as an avenue to understanding clinical studies and their implications will be emphasized. Group exercises will include design and implementation of two factitious hypothetical studies where funding, time scale, and resource availability will be considered. A mid-term examination will concentrate on terminology, data collection techniques, and a final examination will focus on research design. Basic didactic biostatistics material will be taught primarily for purposes of familiarization and interpretation of research and will be aimed at the non-mathematician (no math or statistics pre-requisites). There will be an option for a 1-point or 2-point version of the course when registering. The 1-point course will include didactic material and one lecture per week, and will not include ED time. The 2-point course (limited to 40 students per semester) in which students will act as research assistants will require inclusion in the Academic Associates research assistant program at St. Luke's/Roosevelt Hospital ED or in the Sinai Associates Program at Mt Sinai School of Medicine ED. This includes two 4-hour shifts per week of ED time in which students will learn how to assist in the execution of clinical research including performing consents, data collection, and database interaction (for further details regarding the Academic Associate program, see the web site (http://www.columbia.edu/cu/aap/). ED time will be arranged to fit in and around the student's academic schedule as needed. Additionally, three to five evening practical sessions will cover ongoing individual ED projects in depth, and students will be shown and instructed on basic procedural skills in emergency medicine (lumbar puncture, endotracheal intubation, etc.) as well as shown dynamic and static invasive imaging including ultrasound, CT scans, and others. The 2-point course is recommended for those students looking to gain clinical research experience and hands on ED time with physicians in the clinical setting.

BIOL W4001x Advanced Genetic Analysis 3 pts. Prerequisites: For undergrads:Introductory Genetics (W3031)and permission of the instructor. This seminar course provides a detailed presentation of areas in classical and molecular genetics for advanced undergraduates and beginning graduate students. Topics include transmission genetics, gain and loss of function mutations, genetic redundancy, suppressors, enhancers, epistasis, expression patterns, using transposons, and genome analysis. The course is a mixture of lectures, student presentations, seminar discussions, and readings from the original literature. Undergraduates wishing to take the course need to have taken Genetics W3031 or its equivalent and received the instructor's permission. Enrollment is limited to 25 students.

BIOL W4011 Circuits in the Brain 3 pts. This course is an advanced seminar that will review current knowledge about the computations carried out by circuits present in the CNS. The class will run as a seminar discussion, where it is assumed that every student will have studied the reading material ahead of time and will be knowledgeable enough to explain it. W3004 and W3005 are ideal background for the course. To maintain a small class size and ensure the participation of all students in all the discussions, only 25 students will be admitted. Graduate students are welcome but undergraduate students in their final year majoring in Neuroscience and Behavior will have preference. Auditors will not be accepted. Instructor permission is necessary for registration. For grading, a short (maximum 5 page) essay on any of the topics discussed in the course is due on the last day of class and will be used for the final grade, together with evaluation of class participation.

BIOL G4013x Advanced Seminar in Neurobiology: Developmental Wiring of Neural Systems 3 pts. Prerequisites: one year of introductory biology and W3004/W4004 "Cellular and Molecular Neurobiology" (or equivalent). Students will read and discuss classical as well as contemporary research papers on membrane excitability, ion channels and transporters, synaptic transmission and plasticity, and sensory receptors. Focus will be on intellectual creativity, conceptual breakthroughs and technical advances. A key goal of this course is to help students become a critical reader and thinker. Graduate students in all disciplines are welcome. Advanced undergraduate students can enroll with the instructor's permission.

BIOL G4035y Seminar in Epigenetics 3 pts.Not offered in 2013-2014. Prerequisites: Genetics (3032/4032) or Molecular Biology (3512/4512), and the permission of the instructor. This is a combined lecture/seminar course designed for advanced undergraduates and graduate students. The focus is on understanding the mechanisms underlying epigenetic phenomena: the heritable inheritance of genetic states without change in DNA sequence. Epigenetic mechanisms play important roles during normal animal development and oncogenesis. It is an area under intensive scientific investigation and the course will focus on recent advances in understanding these phenomena. In each class, students will present and discuss in detail recent papers and background material concerning each individual topic, followed by an introductory lecture on the following week's topic. This course will emphasize critical analysis of the scientific literature and help students understand how to identify important biological problems and how to address them experimentally.

BIOL G4044 Advanced Topics in Cell Biology 3 pts.Not offered in 2013-2014. Prerequisites: Enrollment in the Biological Sciences Ph.D. Program, one of the other biomedical Ph.D. programs, or permission of the instructor. Generally students with a solid background in biology (four or more courses) are accepted. Advanced Topics in Cell Biology is a graduate course, primarily enrolling Ph.D. students, but also enrolling advanced M.A. students and undergraduates with consent of one of the instructors. This year's offering will concentrate on the basic cell biology of signal transduction and its readouts within the cytoskeleton and its activities inside the cell. Students will read the literature and give presentations. Topics include the pathways by which cells respond to extracellular signals such as growth factors and cell-cell contact, and the mechanisms by which extracellular signals are translated into alterations in the cell cycle, morphology, differentiation state, and motility of the responding cells.

BIOL W4070 The Biology and Physics of Single Molecules 3 pts. Prerequisites: calculus, chemistry, physics, 1 year biology, or instructors' permission This course will examine the fundamental mechanisms underlying the behavior of biological molecules, at the single molecule level. The course will cover the methods used to track single molecules: optical tweezers, single molecule AFM, Magnetic tweezers, Optical techniques and Fluorescence energy transfer (FRET) probes. The course will cover the mechanism of action of mechanical motors such as myosin dyneyin, kinesin. It will cover the action of DNA binding enzymes such as topoisomerases, helicases, etc. We will also discuss the function of large motors such as the ATP Synthase and the bacterial AAA ATPases. We will discuss the mechanical properties of DNA, RNA, and proteins. The course will consist mainly of reviewing classical experiments in each category, and developing the background physical theories to promote a deep understanding of biological mechanisms at the mesoscopic level.

BIOL G4075 Biology at Physical Extremes 3 pts. Prerequisites: One year each of biology and physics, or permission from the instructor. This is a combined lecture/seminar course designed for graduate students and advanced undergraduates. The course will cover a series of cases where biological systems take advantage of physical phenomena in counter intuitive and surprising ways to accomplish their functions. In each of these cases, we will discuss different physical mechanisms at work. We will limit our discussions to simple, qualitative arguments. We will also discuss experimental methods enabling the study of these biological systems. Overall, the course will expose students to a wide range of physical concepts involved in biological processes.

BIOL W4077 Survey in Molecular and Cellular Biology: Cellular Stress Responses 3 pts. Prerequisites: One year of introductory biology and at least one semester of additional biology courses, recommended: BIOL W3041 Cell Biology, BIOL C3512 Molecular Biology This is an advanced molecular and cellular biology course geared to upper level undergraduates and graduate students. The topic of this year will be cellular stress responses. We will read and analyze a series of reviews on this topic ranging from the stress of DNA damage on cells to metabolic stress to the stress of aging. We will also read key research articles on these topics. The signaling pathways, mechanisms, targets and biological relevance will be reviewed. An emphasis will be made on understanding how important discoveries were made. Students will develop their own review articles on related subjects and present multiple research proposals.

BIOL G4095 Chemical Genomics 2 pts. Prerequisites: One year of college-level biology and one year of organic chemistry, or the instructor's permission. Advanced undergraduate students are encouraged to enroll, and they will be given extra assistance in preparing the research proposal (no prior experience in writing proposals is needed). For 2011-2011 See equivalent: CHEM W4312 Chemical Biology. In this course, we will cover subject matter in chemical biology and genomics. We will discuss approaches for discovering and optimizing chemical tools for measuring and perturbing biological systems. Topics covered will include high-throughput assay development, chemical and genomic screening, chemical library creation, high-throughput chemistry, affinity purification of target proteins and target validation, protein microarrays and the druggable genome. The course is intended to provide a foundation needed for advanced chemical biology and genomic research, i.e. the creation and use of chemical and genomic probes of biological processes. The course will be of interest to students at the interface between chemistry and biology, and students interested in medicine, academic chemical biology and drug discovery efforts.

BIOT W4200 Biopharmaceutical Development & Regulation 3 pts. The program aims to provide current life sciences students with an understanding of what drives the regulatory strategies that surround the development decision making process, and how the regulatory professional may best contribute to the goals of product development and approval. To effect this we will examine operational, strategic and commercial aspects of the regulatory approval process for new drug, biologic and biotechnology products both in the United States and worldwide. The topics are designed to provide a chronological review of the requirements needed to obtain marketing approval. Regulatory strategic, operational, and marketing considerations will be addressed throughout the course. We will examine and analyze the regulatory process as a product candidates are advanced from Research and Development, through pre-clinical and clinical testing, to marketing approval, product launch and the post-marketing phase. The goal of this course is to introduce and familiarize students with the terminology, timelines and actual steps followed by Regulatory Affairs professionals employed in the pharmaceutical or biotechnology industry. Worked examples will be explored to illustrate complex topics and illustrate interpretation of regulations.

BIOT W4201 Seminar in Biotechnology Development and Regulation 3 pts. Prerequisites: BIOT W4200 This course will provide a practical definition of the current role of the Regulatory Professional in pharmaceutical development, approval and post-approval actions. This will be illustrated by exploration, and interactive discussion of regulatory history, its evolution, current standards and associated processes. The course will seek to clarify the role of Regulatory in development and lifecycle opportunities, demonstrating the value Regulatory adds by participation on research, development and commercial teams. The course will utilize weekly case studies and guest lecturers to provide color to current topical events related to the areas.

BIOL G4260 Proteomics Laboratory 3 pts. Prerequisites: Instructor's permission Starting with fall 2009, this course will now be offered only in the fall semester.

Open to students in M.A. in Biotechnology Program (points can be counted against laboratory requirement for that program), Ph.D. and advanced undergraduate students with background in genetics or molecular biology. Students should be comfortable with basic biotechnology laboratory techniques as well as being interested in doing computational work in a Windows environment. This course deals with the proteome: the expressed protein complement of a cell, matrix, tissue, organ or organism. The study of the proteome (proteomics) is broadly applicable to life sciences research, and is increasing important in academic, government and industrial research through extension of the impact of advances in genomics. These techniques are being applied to basic research, exploratory studies of cancer and other diseases, drug discovery and many other topics. Techniques of protein extraction, two-dimensional gel electrophoresis and mass spectrometry will be covered. Emphasis will be on mastery of practical techniques of MALDI-TOF mass spectrometry and database searching for identification of proteins separated by gel electrophoresis as well as background tutorials and exercises covering other techniques used in descriptive and comparative proteomics. Lab Fee: $150.

BIOL W4300 Drugs and Disease 3 pts. Prerequisites: Four semesters of biology with a firm foundation in molecular and cellular biology. Introduces students to the current understanding of human diseases, novel therapeutic approaches and drug development process. Selected topics will be covered in order to give students a feeling of the field of biotechnology in health science. This course also aims to strengthen students' skills in literature comprehension and critical thinking. Website: http://www.columbia.edu/cu/biology/courses/w4300/

BIOL G4305 Seminar in Biotechnology 3 pts. Prerequisites: W4300 or instructor's permission. A weekly seminar and discussion course focusing on the most recent development in biotechnology. Professionals of the pharmaceutical, biotechnology and related industries will be invited to present and lead discussions.

This a Chemistry course offered jointly by Chemistry and Biological Sciences, listed as CHEM W4312.

BIOL W4312y Chemical Biology 4 pts. Prerequisites: Elementary organic chemistry CHEM C3443, CHEM C3444. Recommended preparation elementary physical chemistry and biochemistry CHEM C3079 CHEM C3080. Development and application of chemical methods for understanding the molecular mechanisms of cellular processes. Review of the biosynthesis, chemical synthesis, and structure and function of proteins and nucleic acids. Application of chemical methods--including structural biology, enzymology, chemical genetics, and the synthesis of modified biological molecules--to the study of cellular processes--including transcription, translation, and signal transduction.

BIOL W4400 Computational Genomics 4 pts. Prerequisites: Permission needed from instructor This course will meet as a seminar once weekly and will give a "hands on" introduction to genomics research. I will introduce the computational tools and statistical concepts needed to analyze and interpret next generation sequencing data (primarily RNA-seq). The course will cover machine-learning approaches to model and mine biological data. The course will survey current topics in systems biology including gene expression, transcriptional regulation, epigenomics, ribosome profiling, enhancer localization, and genome conformation. The course will include a reading of primary literature and a genomics research project.

BIOL W4510y Molecular Systems Biology 4 pts. Prerequisites: One year of Biology, Chemistry, and Physics. Courses taken at CU are recommended, but AP courses may be sufficient with permission from the instructors. This course will provide students with a quantitative understanding of the ways in which molecular interactions between nucleotides and proteins give rise to the behavior of gene regulatory networks. The key high-throughput genomics technologies for probing the cell at different levels using microarrays and next-generation sequencing will be discussed. Strategies for interpreting and integrating these data using statistics, biophysics and genetics will be introduced. In computer exercises, student will learn the basics of the R language, and use it to perform analyses of genomics data sets. No prior computer programming experience is assumed. This highly interdisciplinary course is intended for advanced undergraduates as well as beginning graduate students in Biology, Chemistry, Physics, Engineering, and Computer Science. (Offered in previous years as CHBC W4510)

BIOL G4700 Seminar in Stem Cell Biology 3 pts.Not offered in 2013-2014. Alternating weeks of high-level research seminars from guest speakers and class discussions will cover selected topics at the forefront of stem cell biology research in a course designed for PhD and advanced Masters' students. Grading based on class participation, written assignments every other week and a term paper with an original synthesis of ideas or a research proposal.

BIOL G6002x (Section 2) Grad Core II: Protein Thermodynamics 2 pts. This course presents a rigorous introduction to solution thermodynamics and applies it to understanding the structural and functional features of proteins. After exploring the conceptual origins of thermodynamic theory, the standard equations describing solution equilibria are derived and applied to analyzing biochemical reactions, with a focus on those involved in protein folding and allosteric communication. The semester culminates with exploration of the energetic factors controlling the formation of protein secondary structures and the role of entropy-enthalpy compensation in determining the complex temperature-dependent thermodynamic properties of aqueous solutions. The course emphasizes both qualitative understanding of the thermodynamic forces controlling the evolution and function of living organisms as well as practical application of thermodynamic methods and structural insight in laboratory research. Tutorials cover the use of curve-fitting techniques to analyze biochemical equilibria as well as the use of molecular visualization software to understand protein structure and function. Open to PhD candidates in the biomedical and chemical sciences and to other qualified graduate, undergraduate, and continuing education students with permission of the instructor. Course start date: Monday October 26, 2011. This is a half semester, 2 point course.