Molecular Biology
- CHM 542/MOL 542: Principles of Macromolecular Structure: Protein Folding, Structure and DesignThis course will be taught from the scientific literature. We will begin the semester with several classic papers on protein folding. As the semester progresses, we will read about protein structure, stability, and folding pathways. The latter part of the semester will focus on recent papers describing new research aimed toward the construction of novel proteins from "scratch." These papers will cover topics ranging from evolution in vitro to computational and rational design. The course will end by discussing the possibility of creating artificial proteomes in the laboratory, and further steps toward synthetic biology.
- ISC 233/CHM 233/COS 233/MOL 233/PHY 233: An Integrated, Quantitative Introduction to the Natural Sciences IIAn integrated, mathematically and computationally sophisticated introduction to physics and chemistry, drawing on examples from biological systems. This year long, four course sequence is a multidisciplinary course taught across multiple departments with the following faculty: T. Gregor, J. Shaevitz (PHY); O. Troyanskaya (COS); J. Akey (EEB); E. Wieschaus, M. Wuhr (MOL); B. Bratton, J. Gadd, A. Mayer, Q. Wang (LSI). Five hours of lecture, one experimental lab, one three-hour precept.
- ISC 234/CHM 234/COS 234/MOL 234/PHY 234: An Integrated, Quantitative Introduction to the Natural Sciences IIAn integrated, mathematically and computationally sophisticated introduction to physics and chemistry, drawing on examples from biological systems. This year long, four course sequence is a multi-disciplinary course taught across multiple departments with the following faculty: T. Gregor, J. Shaevitz (PHY); O. Troyanskaya (COS); J. Akey (EEB); E. Wieschaus, M. Wuhr (MOL); B. Bratton, J. Gadd, A. Mayer, Q. Wang (LSI). Five hours of lecture, one three-hour lab, one three-hour precept.
- ISC 326/EEB 326/MOL 326/GHP 326: Human Genomics: The Past, Present and Future of the Human GenomeThe completion of the human genome and the continuing effort to sequence tens of thousands of human genomes is yielding unprecedented insights into human biology and the evolutionary history of our species. We will review the key advances enabling researchers to decipher the structure and function of the human genome as well as the genetic basis of variation among individuals and populations. Topics include the evolutionary origins and current structure of human populations, methods for detecting genomic features, cancer genomics and mapping the genes and variants underlying population-specific adaptations and disease susceptibility.
- MAT 586/APC 511/MOL 511/QCB 513: Computational Methods in Cryo-Electron MicroscopyThis course focuses on computational methods in cryo-EM, including three-dimensional ab-initio modelling, structure refinement, resolving structural variability of heterogeneous populations, particle picking, model validation, and resolution determination. Special emphasis is given to methods that play a significant role in many other data science applications. These comprise of key elements of statistical inference, image processing, and linear and non-linear dimensionality reduction. The software packages RELION and ASPIRE are routinely used for class demonstration on both simulated and publicly available experimental datasets.
- MOL 101/STC 101: From DNA to Human ComplexityThis lecture course will acquaint non-biology majors with the theory and practice of modern molecular biology focusing on topics of current interest to society. The course will cover basic molecular biology topics such as information storage and readout by DNA, RNA and proteins. The course will address how recent scientific advances influence issues relevant to humanity including stem cells and CRISPR; the human microbiome and bacterial pathogens; and how the human genome can be used to understand the evolution of modern humans.
- MOL 214/EEB 214/CBE 214: Introduction to Cellular and Molecular BiologyImportant concepts and elements of molecular biology, biochemistry, genetics, and cell biology, are examined in an experimental context. This course fulfills the basic biology requirement for students majoring in the biological sciences and satisfies the basic biology requirement for entrance into medical school and most other health professions schools.
- MOL 250/GHP 360: Food, Drugs and SocietyThe current environment in the US for the use and abuse of foods and drugs will be examined from a scientific fact-based perspective. Historical, economic, marketing, political, and public health drivers will be considered. Specific topics include government dietary recommendations (food politics), dietary supplements (from Vitamins to herbal extracts), pharmacology and ethical drug development (sulfa drugs, NSAIDS, etc), addiction and substance abuse (alcohol, nicotine, stimulants, opioids, etc), Alzheimer's disease and the problem of long-term care in an aging population, and Psychedelic drug use and abuse (psilocybin, mescaline, LSD, etc).
- MOL 290: Quantitative Methods in Cell and Molecular BiologyModern biology research increasingly relies on quantitative tools to make precise measurements of cell state. This course will provide an introduction to the experimental techniques and computational methods that enable the quantitative study of biological systems. We will start with an intro to programming using Python and we will employ the learned skills to analyze proteomics and sequencing data for studying gene networks within and across species, modeling biochemical reactions to study the dynamics of gene and protein networks, and extracting information about the spatial organization of biological systems using fluorescence imaging.
- MOL 340: Molecular and Cellular ImmunologyA broad survey of the field of immunology and the mammalian immune system. The cellular and molecular basis of innate and acquired immunity will be discussed in detail. The course will provide frequent examples drawn from human biology in health and disease.
- MOL 342: GeneticsBasic principles of genetics illustrated with examples from prokaryote and eukaryote organisms. Classical genetic techniques as well as molecular and genomic approaches will be discussed. The evolving concept of the gene, of genetic interactions and gene networks, as well as chromosome mechanics will be the focus of the course. Selected topics will include gene regulation, cancer genetics, the human biome, imprinting, and stem cells.
- MOL 348: Cell and Developmental BiologyThe course will investigate the roles that gene regulation, cell-cell communication, cell adhesion, cell motility, signal transduction and intracellular trafficking play in the commitment, differentiation and assembly of cells into specialized tissues. The mechanisms that underlie development of multicellular organisms, from C. elegans to humans, will be examined using biochemical, genetic and cell biological approaches. In-class problem solving, group work, and active learning approaches will be used to emphasize key concepts and analyze experimental data.
- MOL 423/GHP 423: Molecular Basis of CancerWe will explore the molecular events leading to the onset and progression of human cancer. We will review the central genetic and biochemical elements that make up the cell cycle, followed by a survey of the signal transduction pathways and checkpoints that regulate it. We will discuss oncogenes, tumor suppressor and mutator genes that act in these pathways and review the role of viral oncogenes and their action on cells. We will investigate the role of cancer stem cells and the interaction between tumor and the host environment. We will explore specific clinical case studies in light of the molecular events underlying different cancers.
- MOL 431: Regulatory Mechanisms in DevelopmentHow do organisms ensure that genes are expressed at the right time and place as they develop from a single egg cell into a multicellular animal? In this seminar style course, we will explore some of the diverse mechanisms that control gene expression, including those involved in transcriptional regulation, epigenetic silencing, translational regulation and cell-cell signaling. By reading and critically evaluating the primary literature, we will explore many of the crucial molecular biology, cell biology and genetics techniques that have helped illuminate the gene regulatory mechanisms that are essential for animal development.
- MOL 433/CBE 434/GHP 433: BiotechnologyThis course will consider the principles, development, outcomes and future directions of therapeutic applications of biotechnology, with particular emphasis on the interplay between basic research and clinical experience. Topics to be discussed include production of hormones and other therapeutic proteins, gene therapy, gene editing, oncolytic viruses, and stem cells. Reading will be from the primary literature.
- MOL 460/STC 460/GHP 460: Diseases in Children: Causes, Costs, and ChoicesWithin a broad context of historical, social, and ethical concerns, a survey of normal childhood development and selected disorders from the perspectives of the physician, the biologist, and the bioethicist. There is an emphasis on the complex relationship between genetic and acquired causes of disease, the environment, medical practice, social conditions, and cultural values. The course features visits from children with some of the conditions discussed, site visits, and readings from the original medical, scientific, and bioethical literature.
- MOL 518: Quantitative Methods in Cell and Molecular BiologyModern biology research increasingly relies on quantitative tools to make precise measurements of cell state. This course provides an introduction to the experimental techniques and computational methods that enable the quantitative study of biological systems. We start with an intro to programming using Python and we employ the learned skills to analyze proteomics and sequencing data for studying gene networks within and across species, modeling biochemical reactions to study the dynamics of gene and protein networks, and extracting information about the spatial organization of biological systems using fluorescence imaging.
- MOL 523: Molecular Basis of CancerWe explore the molecular events leading to the onset and progression of human cancer. We review the central genetic and biochemical elements that make up the cell cycle, followed by a survey of the signal transduction pathways and checkpoints that regulate it. We discuss oncogenes, tumor suppressor and mutator genes that act in these pathways and review the role of viral oncogenes and their action on cells. We investigate the role of cancer stem cells and the interaction between tumor and the host environment. We explore specific clinical case studies in light of the molecular events underlying different cancers.
- MOL 541: Research Projects in Molecular Biology (Laboratory Rotations)Students perform research in the laboratories of potential faculty advisors.
- MOL 561: Scientific Integrity in the Practice of Molecular BiologySatisfies the NIH mandate for training in the ethical practice of science. The course is discussion-based, and uses readings, videos, case studies and guest participants to examine basic ethical and regulatory requirements for the responsible conduct of research. Topics include: the nature of - and response to - research misconduct; collaborative research; protection of human and animal subjects; conflicts of interest and commitment; authorship, publication and peer review; mentorship; societal impacts of scientific research; diversity and inclusion in scientific research; and contemporary ethical issues in biomedical research.
- NEU 502A/MOL 502A/PSY 502A: Systems and Cognitive NeuroscienceA survey of modern neuroscience that covers experimental and theoretical approaches to understanding how the brain works. This semester builds on 501, focusing on how the circuits and systems of the brain give rise to cognition. The course covers the neural mechanisms responsible for vision, long-term memory, sleep, motor control, habits, decision making, attention, working memory, and cognitive control. How these functions are disrupted in neurodegenerative and neuropsychiatric disorders are also covered. This is the second term of a double-credit core lecture course required of all Neuroscience Ph.D. students.
- NEU 502B/MOL 502B: From Molecules to Systems to BehaviorThis lab course introduces students to the variety of experimental and computational techniques and concepts used in modern cognitive neuroscience. Topics include functional magnetic resonance imaging, scalp electrophysiological recording, and computational modeling. In-lab lectures provide students with the background necessary to understand the scientific content of the labs, but the emphasis is on the labs themselves, including student-designed experiments using these techniques. This is the second term of a double-credit core lab course required of all Neuroscience Ph.D. students.
- QCB 490/MOL 490: Molecular Mechanisms of Longevity: The Genetics, Genomics, and Cell Biology of AgingAging is a fascinating biological phenomenon because it seems inevitable, yet recent research suggests that longevity can be manipulated through genetics and environment. Moreover, aging is the major risk factor for a host of chronic and neurological diseases; thus, understanding the molecular regulation of aging will be critical in addressing these health issues in the future. We will explore the current state of the field, including genetic discoveries of longevity mutants, cell biological and metabolic characterization of aging animals, and genomic and computational analyses used to uncover molecular mechanisms that control longevity.