20.219 Selected Topics in Toxicology ( , , , ) Prereq: Permission of Instructor Units arranged Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects. Staff
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20.309J Instrumentation and Measurement for Biological Systems ( , ) (Same subject as 2.673J , 6.122J , MAS.402J ) (Subject meets with 20.409 ) Prereq: Biology (GIR) , Physics II (GIR) , 6.00 , 18.03 ; 2.001 , 20.310 , or 6.02 ; or permission of instructor; Coreq: 20.330 Units: 3-6-3 Lecture: TR12 ( 4-237 ) Lab: TBA Recitation: F12 ( 4-231 , 4-153 ) Sensing and measurement aimed at quantitative molecular/cell/tissue analysis in terms of genetic, biochemical, and biophysical properties. Methods include light and fluorescence microscopies, electronic circuits, and electro-mechanical probes (atomic force microscopy, optical traps, MEMS devices). Application of statistics, probability, signal and noise analysis, and Fourier techniques to experimental data. Final design project emphasizes utilization of principles underlying biological instrumentation. Preference to juniors and seniors. Fall: S. Manalis, P. T. So, S. Wasserman Spring: E. Boyden, S. Wasserman, M. F. Yanik
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20.310J Molecular, Cellular, and Tissue Biomechanics ( ) (Same subject as 2.797J , 3.053J , 6.024J ) Prereq: 2.370 or 2.772J ; 18.03 or 3.016 ; Biology (GIR) Units: 4-0-8 Develops and applies scaling laws and the methods of continuum mechanics to biomechanical phenomena over a range of length scales. Topics include structure of tissues and the molecular basis for macroscopic properties; chemical and electrical effects on mechanical behavior; cell mechanics, motility and adhesion; biomembranes; biomolecular mechanics and molecular motors. Experimental methods for probing structures at the tissue, cellular, and molecular levels. R. D. Kamm
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20.320 Analysis of Biomolecular & Cellular Systems ( ) Prereq: 20.110 , 18.03 , 6.00 ; Coreq: 5.07 Units: 4-0-8 Lecture: TR9.30-11 ( 56-114 ) +final Analysis of molecular and cellular processes across a hierarchy of scales, including genetic, molecular, cellular, and cell population levels. Topics include gene sequence analysis, molecular modeling, metabolic and gene regulation networks, signal transduction pathways and cell populations in tissues. Emphasis on experimental methods, quantitative analysis, and computational modeling. F. White, E. Fraenkel
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20.330J Fields, Forces and Flows in Biological Systems ( ) (Same subject as 2.793J , 6.023J ) Prereq: 2.005 , 6.021 , 20.320 or permission of instructor Units: 4-0-8 Introduction to electric fields, fluid flows, transport phenomena and their application to biological systems. Flux and continuity laws, Maxwell's equations, electro-quasistatics, electro-chemical-mechanical driving forces, conservation of mass and momentum, Navier-Stokes flows, and electrokinetics. Applications include biomolecular transport in tissues, electrophoresis, and microfluidics. J. Han, L. Griffith
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20.340J Materials for Biomedical Applications ( ) (Same subject as 3.051J ) (Subject meets with 3.962J , 20.462J ) Prereq: Chemistry (GIR) , Biology (GIR) , 3.034 , 3.012 or 3.046 ; or permission of instructor Units: 3-0-9 Introduction to the interactions between cells and surfaces of biomaterials. Surface chemistry and physics of selected metals, polymers, and ceramics. Surface characterization methodology. Modification of biomaterials surfaces. Quantitative assays of cell behavior in culture. Biosensors and microarrays. Bulk properties of implants. Acute and chronic response to implanted biomaterials. Topics in biomimetics, drug delivery, and tissue engineering. D. Irvine
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20.342 Molecular Structure of Biological Materials ( ) (Subject meets with 20.442 ) Prereq: 5.07 or 7.05 ; permission of instructor Units: 3-0-9 Lecture: TR1-2.30 ( 56-154 ) Basic molecular structural principles of biological materials. Molecular structures of various materials of biological origin, including collagen, silk, bone, protein adhesives, GFP, self-assembling peptides. Molecular design of new biological materials for nanotechnology, biocomputing and regenerative medicine. Graduate students are expected to complete additional coursework. S. Zhang
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20.360J Tissue Engineering for Analysis, Prevention, and Treatment of Human Disease ( ) (Same subject as 10.499J ) Prereq: 5.07 or 7.05 ; 7.03 ; 18.03 ; 20.110 or 5.60 Units: 3-0-6 Analysis of fundamental processes in tissue engineering with an emphasis on use of comparative animal models and in vitro tissue engineered models to understand human disease and develop therapies for human disease and for regenerating human tissues and organs. using representative examples of metabolic tissue (e.g., liver) and connective tissue (e.g., bone). Design principles and engineering approaches (e.g., use of synthetic materials) for controlling receptor-mediated processes such as cell migration, growth, and differentiation. Mass transfer limitations in design of devices for cell encapsulation and in scaffold-guided regeneration. Guided organization of multicellular structures. Current clinical prospects. Staff
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20.361J Molecular and Engineering Aspects of Biotechnology ( ) (Same subject as 7.37J , 10.441J ) Prereq: 20.110J , 2.005 , 3.012 , or 5.60 ; 7.06 ; or permission of instructor Units: 4-0-8 Biological and bioengineering principles underlying the development and use of recombinant proteins as therapeutic drugs; fundamentals of therapeutic protein action, including cell-cell and cell-matrix interactions and intracellular signaling pathways; classes of protein therapeutics; post-translational processing and secretion of proteins; gene cloning and expression in mammalian cells; physiology of cell growth and in vitro cultivation; site-specific mutation of proteins; protein pharmacology and delivery. H. Lodish, L. G. Griffith
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20.370J Cellular Biophysics ( ) (Same subject as 2.791J , 6.021J ) (Subject meets with 2.794J , 6.521J , 20.470J , HST.541J ) Prereq: Physics II (GIR) ; 18.03 ; 2.005 , 6.002 , 6.003 , 6.071 , 10.301 , or permission of instructor Units: 5-2-5 Lecture: MWF10 ( 4-231 ) Lab: TBA Recitation: TR10 ( 36-713 ) or TR11 ( 36-713 ) +final Integrated overview of the biophysics of cells from prokaryotes to neurons, with a focus on mass transport and electrical signal generation across cell membrane. First half of course focuses on mass transport through membranes: diffusion, osmosis, chemically mediated, and active transport. Second half focuses on electrical properties of cells: ion transport to action potentials in electrically excitable cells. Electrical properties interpreted via kinetic and molecular properties of single voltage-gated ion channels. Laboratory and computer exercises illustrate the concepts. Provides instruction in written and oral communication. Students taking graduate version complete different assignments. Preference to juniors and seniors. D. M. Freeman, J. Han, J. Voldman
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20.371J Quantitative Systems Physiology ( ) (Same subject as 2.792J , 6.022J , HST.542J ) (Subject meets with 2.796J , 6.522J , 20.471J ) Prereq: Physics II (GIR) , 18.03 , or permission of instructor Units: 4-2-6 Application of the principles of energy and mass flow to major human organ systems. Mechanisms of regulation and homeostasis. Anatomical, physiological and pathophysiological features of the cardiovascular, respiratory and renal systems. Systems, features and devices that are most illuminated by the methods of physical sciences. Laboratory work includes some animal studies. R. G. Mark, C. M. Stultz
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20.380 Biological Engineering Design ( ) Prereq: 7.06 , 20.309 , 20.330 Units: 5-0-7 Illustrates how knowledge and principles of biology, biochemistry, and engineering are integrated to create new products for societal benefit. Uses case-study format to examine recently developed products of pharmaceutical and biotechnology industries: how a product evolves from initial idea, through patents, testing, evaluation, production, and marketing. Emphasizes scientific and engineering principles, as well as the responsibility scientists, engineers, and business executives have for the consequences of their technology. Instruction and practice in written and oral communication provided. Enrollment limited; preference to Course 20 undergraduates. J. M. Essigmann, D. J. Irvine
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20.385 Advanced Topics in Synthetic Biology (New) ( ) Prereq: Permission of instructor Units: 3-3-3 Provides an in-depth understanding of the state of research in synthetic biology. Critical evaluation of primary research literature covering a range of approaches to the design, modeling and programming of cellular behaviors. Focuses on developing the skills needed to read, present and discuss primary research literature, and to manage and lead small teams. Students mentor a small undergraduate team of 20.020 students. Open to advanced students with appropriate background in biology. N. Kuldell
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20.390 Foundations of Computational and Systems Biology ( ) (Subject meets with 7.36 , 7.91J , 20.490J ) Prereq: 7.05 or 5.07 ; or Biology (GIR) and 6.001 ; or permission of instructor Units: 3-0-9 URL: http://web.mit.edu/7.91/ Introduction to computational biology emphasizing the fundamentals of nucleic acid and protein sequence and structural analysis, as well as the analysis of complex biological systems. Principles and methods used for sequence alignment, motif finding, expression array analysis, structural modeling, structure prediction and network modeling. Techniques include dynamic programming, Markov models, clustering techniques, and energy minimization approaches. Exposure to currently emerging research areas. Designed for advanced undergraduates and graduate students with strong backgrounds in either molecular biology or computer science. Some foundational material covering basic programming skills, probability and statistics is provided for students with non-quantitative backgrounds. C. Burge, A. Keating, E. Fraenkel
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20.400J Perspectives in Biological Engineering ( ) (Same subject as 7.548J ) Prereq: Permission of instructor Units: 4-0-8 An in-depth presentation of how engineering and biological approaches can be combined to solve problems in science and technology, emphasizing integration of biological information and methodologies with engineering analysis, synthesis, and design. Emphasis on molecular mechanisms underlying cellular processes, including signal transduction, gene expression networks, and functional responses. Enrollment restricted to Biological Engineering and Biology graduate students. F. White, E. Fraenkel
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20.409 Biological Engineering II: Instrumentation and Measurement ( , ) (Subject meets with 2.673J , 6.122J , 20.309J , MAS.402J ) Prereq: 18.03 Units: 2-7-3 Lecture: TR12 ( 4-237 ) Lab: TBA Recitation: F12 ( 4-231 , 4-153 ) Sensing and measurement aimed at quantitative molecular/cell/tissue analysis in terms of genetic, biochemical, and biophysical properties. Methods include light and fluorescence microscopies, and electro-mechanical probes (atomic force microscopy, laser and magnetic traps, MEMS devices). Application of statistics, probability and noise analysis to experimental data. Enrollment limited to 5 graduate students. S. Manalis, P. T. So, S. Wasserman
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20.410J Molecular, Cellular, and Tissue Biomechanics ( ) (Same subject as 2.798J , 3.971J , 6.524J , 10.537J ) Prereq: Biology (GIR) ; 2.002 , 2.006 , 6.013 , 10.301 , or 10.302 Units: 3-0-9 Develops and applies scaling laws and the methods of continuum mechanics to biomechanical phenomena over a range of length scales. Topics include structure of tissues and the molecular basis for macroscopic properties; chemical and electrical effects on mechanical behavior; cell mechanics, motility and adhesion; biomembranes; biomolecular mechanics and molecular motors. Experimental methods for probing structures at the tissue, cellular, and molecular levels. A. J. Grodzinsky, M. Bathe
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20.411J Cell-Matrix Mechanics ( ) (Same subject as 2.785J , 3.97J , HST.523J ) Prereq: 2.005 or 5.60 ; Biology (GIR) ; Chemistry (GIR) Units: 3-0-9 Mechanical forces play a decisive role during development of tissues and organs, during remodeling following injury as well as in normal function. A stress field influences cell function primarily through deformation of the extracellular matrix to which cells are attached. Deformed cells express different biosynthetic activity relative to undeformed cells. The unit cell process paradigm combined with topics in connective tissue mechanics form the basis for discussions of several topics from cell biology, physiology, and medicine. I. V. Yannas, M. Spector
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20.420J Biomolecular Kinetics and Cellular Dynamics ( ) (Same subject as 10.538J ) Prereq: 7.05 , 7.06 , 18.03 Units: 3-0-9 Lecture: TR10-11.30 ( 56-614 ) +final Fundamental analysis of biological rate processes using approaches from biomolecular reaction kinetics and dynamical systems engineering. Topics include binding and hybridization interactions, enzyme reactions, metabolic cycles, gene regulation, receptor/ligand trafficking systems, intra- and intercellular signaling, and cell population dynamics. K. D. Wittrup, B. Tidor
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20.430J Fields, Forces, and Flows in Biological Systems ( ) (Same subject as 2.795J , 6.561J , 10.539J , HST.544J ) Prereq: 6.013 , 2.005 , 10.302 , or permission of instructor Units: 3-0-9 URL: http://web.mit.edu/beh.430/www/ Lecture: MW1-2.30 ( 32-141 ) +final Molecular diffusion, diffusion-reaction, conduction, convection in biological systems; fields in heterogeneous media; electrical double layers; Maxwell stress tensor, electrical forces in physiological systems. Fluid and solid continua: equations of motion useful for porous, hydrated biological tissues. Case studies of membrane transport, electrode interfaces, electrical, mechanical, and chemical transduction in tissues, convective-diffusion/reaction, electrophoretic, electroosmotic flows in tissues/MEMs, and ECG. Electromechanical and physicochemical interactions in cells and biomaterials; musculoskeletal, cardiovascular, and other biological and clinical examples. A. J. Grodzinsky, D. Lauffenburger
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20.440 Analysis of Biological Networks ( ) Prereq: Permission of Instructor Units: 4-0-8 Analyzes complex biological processes from the molecular, cellular, extracellular, and organ levels of hierarchy. Emphasis placed on the basic biochemical and biophysical principles that govern these processes. Examples of processes to be studied include chemotaxis, the fixation of nitrogen into organic biological molecules, growth factor and hormone mediated signaling cascades, and signaling cascades leading to cell death in response to DNA damage. In each case, the availability of a resource, or the presence of a stimulus, results in some biochemical pathways being turned on while others are turned off. Examines the dynamic aspects of these processes and details how biochemical mechanistic themes impinge on molecular-cellular-tissue-organ level functions. Chemical and quantitative view of the interplay of multiple pathways as biological networks. Preparation of a unique grant application in an area of biological networks. R. Sasisekharan, P. C. Dedon, B. Engelward, J. Essigman
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20.441J Biomaterials: Tissue Interactions ( ) (Same subject as 2.79J, 3.96J , HST.522J ) Prereq: Chemistry (GIR) ; 2.005 or 5.60 ; Biology (GIR) Units: 3-0-9 Lecture: TR2.30-4 ( 4-231 ) Principles of materials science and cell biology underlying the design of medical implants, artificial organs, and matrices for tissue engineering. Methods for biomaterials surface characterization and analysis of protein adsorption on biomaterials. Molecular and cellular interactions with biomaterials are analyzed in terms of unit cell processes, such as matrix synthesis, degradation, and contraction. Mechanisms underlying wound healing and tissue remodeling following implantation in various organs. Tissue and organ regeneration. Design of implants and prostheses based on control of biomaterials-tissue interactions. Comparative analysis of intact, biodegradable, and bioreplaceable implants by reference to case studies. Criteria for restoration of physiological function for tissues and organs. I. V. Yannas, M. Spector
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20.442 Molecular Structure of Biological Materials ( ) (Subject meets with 20.342 ) Prereq: 5.07 or 7.05 ; permission of instructor Units: 3-0-9 Lecture: TR1-2.30 ( 56-154 ) Graduate students are expected to complete additional coursework. Basic molecular structural principles of biological materials. Molecular structures of various materials of biological origin, including collagen, silk, bone, protein adhesives, GFP, self-assembling peptides. Molecular design of new biological materials for nanotechnology, biocomputing and regenerative medicine. Graduate students are expected to complete additional coursework. S. Zhang
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20.445J Methods and Problems in Microbiology ( ) (Same subject as 1.86J , 7.492J ) Prereq: Permission of instructor or Coreq: 7.493 Units: 3-0-9 [P/D/F] Lecture: W EVE (5-8.30 PM) ( 56-202 ) Students will read and discuss primary literature covering key areas of microbial research with emphasis on methods and approaches used to understand and manipulate microbes. Limited to students in the microbiology program. L. Samson, M. Polz
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20.446J Microbial Genetics and Evolution ( ) (Same subject as 1.87J , 7.493J ) Prereq: 7.03 , 7.05 , 7.28 or permission of instructor Units: 4-0-8 Lecture: TR1-3 ( 66-160 ) Covers aspects of microbial genetic and genomic analyses, central dogma, horizontal gene transfer, and evolution. A. D. Grossman, E. Alm
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