Courses Information

Aug 2010

Introduction to Laboratory Practices (Required)
Biophysical Chemistry
Biophysics
Developmental Biology
Bioinformatics
Pre-calculus and Differential Calculus
Basic Statistics
Molecular Biology
Scientific Writing (Required)

Winter 2010

Benny Shilo Developmental Biology Course

Jan 2011

Polymers and Membranes
Bioanalytics
Cell Biology
Evolutionary Biology
Clinical Biology
Mathematics: Matrix Algebra part I
Mathematics: Matrix Algebra part II
Mathematics: Calculus
Randomness in Biology
Molecular Genetics
Problem Solving in Genetics - Cancelled
Genes, Circuits, and Behaviour
Neuroscience

Summer 2011

Global Change and the Biosphere

Aug Term

Introduction to Laboratory Practices [2010 Aug Term]

Instructors: SP Koushka, D Nair, MM Panicker

Credits: 0 (Required)
Duration: Aug 3, 2010 – Aug 20, 2010
Schedule: TWRF 4:00PM – 7:00PM, Teaching Lab

Outline: Introduction to basic laboratory practices and techniques. Lab safety and etiquette. Maintaining lab notebooks.

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Biophysical Chemistry [2010 Aug Term]

Instructors: MK Mathew, JB Udgaonkar

Credits: 3 (Basic)
Duration: Aug 23, 2010 – Dec 20, 2010
Schedule: MWF 9:00AM – 10:30AM, LH2

Outline: Structural organization of proteins, nucleic acids and membranes. Thermodynamics: the laws; biochemical thermodynamics; statistical thermodynamics; stabilizing interactions in biomolecules; thermodynamics of ion, electron and solute transport; association between molecules. Macromolecular dynamics: fluorescence methods; hydrogen exchange; biomolecular motors; kinetics; enzyme catalysis; mass spectrometry of biomolecules.

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Biophysics [2010 Aug Term]

Instructor: S Ramaswamy (IISc), Sandeep Krishna and others

Credits: 2 (Advanced)
Duration: Aug 2010 – Nov 2010
Schedule: TBA
Venue: IISc

Outline: Advanced topics in biophysics

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Developmental Biology [2010 Aug Term]

Instructors: K VijayRaghavan, M Inamdar (JNCASR)

Credits: 3 (Basic)
Duration: Sep 13, 2010 – Dec 30, 2010
Schedule: MWF 11:30AM – 1:00PM, LH2

Outline: The course will aim to understand cell- fate specification and morphogenesis in animal and plant development from a mechanistic perspective. The latter means that there will be a attempt to develop a molecular- and cellular-understanding as opposed to a descriptive one.

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Bioinformatics [2010 Aug Term]

Instructor: R Sowdhamini

Credits: 3 (Basic)
Duration: Aug 31 2010 –
Schedule: TR 10:30AM – 12:30PM, LH2

Outline: Protein sequence databases; alignment of protein sequences; clustering and phylogeny; secondary structure predictions (including membrane proteins and HMM models); protein structural hierarchy; protein folds, fold prediction; structural and functional Genomics; energy minimization; homology and fragment-based modeling; protein-ligand and protein-protein interactions; docking, molecular dynamics.

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Mathematics: Pre-calculus and differential calculus [2010 Aug Term]

Instructor: E Lebow

Credits: 3 (Basic)
Duration: Sep 10, 2010 – Nov 26, 2010
Schedule: WF 2:00PM – 3:30PM, LH2

Outline: Pre-calculus and differential calculus. Graphs and functions. Linear functions, power functions, polynomials, exponentials, logarithms. Graphical methods: scaling, inverse functions. Limits, derivatives. Graphical, physical, and algebraic meaning of derivatives. Maxima and minima; inflections. Basic calculus rules: product rule; chain rule. The integral. Differential equations.

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Introduction to Experimental Statistics [2010 Aug Term]

Instructor: Vasanth Kumar

Credits: 3 (Basic)
Duration: Sep 1, 2010 – Dec 15, 2010
Schedule: MT 2:00PM – 4:00PM, LH3; W 3:30PM – 4:30PM, LH3

Outline: Sampling, estimation, standard error. Introduction to test of hypotheses. Simple linear regression and correlation. Analysis of variance (one-way ANOVA). Two-way ANOVA with and without interaction. Principles of experimental designs. Basic expeirmental designs – completely randomized design, randomized blocks design, latin square design. Factorial experiments – two factor and three factor.

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Molecular Biology [2010 Aug Term]

Instructor: DT Nair

Credits: 3 (Basic)
Duration: Sep 2, 2010 – Nov 30, 2010
Schedule: TR 9:15AM – 10:30AM, S-11(First Floor Seminar Hall)

Outline: A molecular and mechanistic perspective of basic biological processes involving DNA will be presented. For each process, the biochemistry and structure of one or a few critical proteins will be discussed (example: RNA Polymerase in transcription). The processes discussed will include: replication, transcription, RNA splicing, translation, recombination, gene regulation and DNA repair.

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Scientific Writing [2010 Aug Term]

Instructor: G Hyde

Credits: 0 (Required)
Duration: Sep 2010 – Dec 2010
Schedule:

Outline: An eight week course that aims to upgrade your scientific writing skills. Clear and logical prose. Text composition. Argument maps. Extracting arguments from a text.

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Winter

Benny Shilo Bangalore Developmental Biology Course

Instructors: Benny Shilo, Talila Volk, Eyal Scheitjer, K. VijayRaghavan, Veronica Rodrigues, and others.

Credits: 2 (Advanced)
Duration: Dec 26, 2010 – Jan 10, 2011.
Schedule: TBA

The course will cover signaling mechanisms during development of the nervous system, mesoderm and epidermis. Drosophila, C.elegans, zebrafish and mouse will be the model organisms covered. The course will involve, teaching and research lectures as well as tutorials and paper discussions. There will also be a few experimental classes.

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Jan Term

Polymers and Membranes: Physical Principles and Biological Applications [2011 Jan Term]

Instructors: Srikanth Sastry (JNCASR) and Madan Rao
Credits: 3 (Advanced)

Duration: Jan 11, 2011 - Apr 15, 2011
Schedule: TR 11:00AM - 12:30PM, JNCASR Lecture Hall
Outline: The course will cover physical principles of polymers and membranes,along with a discussion of applications of these principles to polymeric and membrane assemblies in biological systems. The topics covered are: Polymers -- ideal polymer chain, polymers in solution, monomer-monomer and monomer-solvent interactions, coil-globule transition, semi-flexible polymers, worm-like chain model, heteropolymers, polyelectrolytes, biopolymers, dynamics, rheology. Membranes -- self assembly and phase transitions in membranes, equilibrium shapes of membranes, thermal fluctuations, multicomponent membranes, hydrodynamics of membranes, membrane-substrate interactions, membrane-protein interactions, active membranes. Prerequisites: Exposure to graduate Statistical Mechanics and Mathematical Methods is highly desirable for students taking this course. However, the course lectures and tutorials will attempt to be self-contained, and therefore students without this background are also encouraged to attend.

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Biomolecular Spectroscopy and Bioanalytical Chemistry [2011 Jan Term]

Instructors: M Puranik, D Schwudke

Credits: 3 (Basic)
Duration: TBA
Schedule: TBA

Outline: The course will cover theoretical aspects and applications of modern techniques in spectroscopy and bioanalytical chemistry. It will start with a set of preparatory lectures on fundamental concepts necessary to understand the more advanced material that will follow. Evaluation will be based on two comprehensive exams and the presentation of a paper from current literature by each student. The papers will use methods that have been taught during the course to study a biological problem. The class will meet two times a week.

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Cell Biology [2011 Jan Term]

Instructors: S Mayor and others

Credits: 3 (Basic); 2 (Advanced)
Duration: Feb 2011 – Apr 2011
Schedule:

Outline: Cellular organization. Intracellular traffic. Motors and the cytoskeleton. Cell signalling. Chromatin structure. Organellar biogenesis. Cell cycle. Apoptosis.

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Evolutionary Biology [2011 Jan Term]

Instructor: U Ramakrishnan

Credits: 3 (Basic)
Duration: Jan 28 -
Schedule: Lecture: MT 2pm-3pm, LH2; Discussion: F 10am-12pm, LH2

Outline: Biological diversity Evidence for evolution through the fossil record. Macroevolution. Evolution above the species level. Adaptation and the adaptationist approach to studying behaviour ecology and life-history. Evolution and variation across space. Micro evolutionary processes. The theory of natural selection. Evolution of phenotypic variation and the relevance of evolution and its study in human society. Species co-evolution, evolution and development. Genome evolution.

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Clinical Biology [2011 Jan Term]

Instructor: Sudhir Krishna

Credits: 2 (Advanced)
Duration: TBA
Schedule: TBA

Outline: A 2-week hands-on course: Leukemia as a system to familiarize basic scientists with research issues in the context of disease biology, covering the study of genetics and molecular biology, cytogenetics, hematological lineage analysis, drug discovery and related structural biology.

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Mathematics: Matrix Algebra part I [2011 Jan Term]

Instructor: E Lebow

Credits: 1 (Basic)
Duration: Jan 11, 2011 – Feb 10, 2011
Schedule: TR 9:15AM – 10:45AM, LH2
[Offered to both M.Sc.-Wildlife students and regular NCBS students.]
Outline: Matrices and matrix multiplication. Inverses and systems of linear equations. Vector geometry. Determinants. Eigenvalues and eigenvectors.

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Mathematics: Matrix Algebra part II [2011 Jan Term]

Instructor: E Lebow

Credits: 1 (Basic)
Duration: Feb 15, 2011 – Mar 10, 2011
Schedule: TR 9:15AM – 10:45AM, LH2
Outline: Matrices and linear transformations. Linear regression. Diagonalization. Basis and dimension.

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Mathematics: Calculus [2011 Jan Term]

Instructor: E Lebow

Credits: 2 (Basic)
Duration: Mar 2, 2011 – Apr 15, 2011
Schedule: WF 2:15PM – 4:30PM, LH2 [but first class meeting in LH3]
[Offered primarily to M.Sc.-Wildlife students, with limited space for regular NCBS students.]
Outline: Graphs and functions. Linear functions, power functions, polynomials, exponentials, logarithms. Limits, derivatives. Maxima and minima. Basic calculus rules; product rule; chain rule. The integral. Differential equations.

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Mathematics: Randomness in biology [2011 Jan Term]

Instructor: M Thattai

Credits: 2 (Advanced)
Duration: Feb 15, 2011 – Apr 28, 2011
Schedule: TR 1:30PM – 2:30PM, LH2

Outline: Random numbers; probability distributions; Examples of stochastic processes: radioactive decay, Brownian motion; Markov chains; stochastic chemical reactions; Master equation; solution by generating functions; Fokker-Planck and Langevin descriptions; first-passage times in bistable systems; noise in gene networks. Prerequisites: Differential calculus and some linear algebra.

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Molecular Genetics [2011 Jan Term]

Instructors: U VijayRaghavan, K Muniappa, U Nath, S Koushika
Credits: 3 (Basic)
Duration: Jan 2011 – Apr 2011
Schedule: TBA

Outline: Students who are interested in applying genetic techniques to their work will learn how genetic analyses contribute to understanding complex biological processes. The logic and techniques of genetic analysis; epistasis; suppressor; genetic interaction networks; reverse genetics; genomics. Illustration of the application of genetic analysis of specific pathways in model organisms: C. elegans, Drosophila, Yeast, bacteriophage and plants. Illustrative examples: RNA splicing in yeast, flower development in Arabidopsis, synapse formation in C. elegans.

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Problem Solving in Genetics [2011 Jan Term] - Cancelled

Genes Circuits and Behaviour [2011 Jan Term]

Instructors: Gaiti Hasan, Ralph Greenspan (UCSD), Ann-Shyn Chiang (NHTU Taiwan), Nick Spitzer (UCSD)

Credits: 2 (Advanced)
Duration: Feb 7, 2010 – Feb 17, 2010
Schedule:

Outline: A 10 day intensive course. Genetic studies of behavior. Circuits orchestrating innate behaviors. Drosophila: circadian rhythms; sleep and arousal; natural variation; selection and evolution; learning and memory. Vertebrate/invertebrate commonalities. Vertebrate CNS: excitability; neuronal proliferation and migration; role of activity in differentiation of axons and dendrites. The mouse model: behavioral analysis; models of human diseases; selective breeding. Forward genetics, reverse genetics, transgenic and knockout mice.

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Basic Neuroscience [2011 Jan Term]

Instructors: US Bhalla, S Chattarji, S Sane, Vatsala Thirumalai

Credits: 3 (Basic)
Duration: TBA
Schedule: TBA

Outline: Neuro basic course will consist of 4 modules of around 6 lectures each, plus a couple of labs on electrical models of cells. Each lecture will be around 90 minutes. Two lectures a week, and there will also be a TA-led tutorial session each week.
Module 1: Upi: Cellular biophysics.
Neurons as electrical entities. Passive properties and cable theory. Active properties and Hodgkin-Huxley equations.

Module 2: Shona: Synaptic transmission in invertebrate and vertebrate nervous systems;
Synaptic plasticity in the mammalian brain;
Basic concepts in neuroanatomy

Module 3: Vatsala: Small circuits and neuromodulators

Module 4: Sanjay: Comparative neurobiology and ethology

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Summer

Global Change and the Biosphere [2011 Summer]

Credits: 2 (Advanced)
Instructor: Jayashree Ratnam and others
Duration: Jun 15, 2011 – July 22, 2011
Schedule: MWF, 2:00 PM - 4:00 PM, LH2

Outline: Global change defined, Changes in global temperatures, precipitation, atmospheric CO2, N and P depositions, Drivers of change, Linkages between changes and global biogeochemical cycles of carbon, water, nitrogen and phosphorus, linkages between changes and shifts in ecosystem structure, function and services with a special focus on the terrestrial biosphere.

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