ORIENTATION OF COURSES IN DIFFERENT SEMESTERS FOR M. SC. IN NEUROSCIENCE

Detailed Syllabus for Two-year M. Sc. Programme in Neuroscience

First Semester

NS C11: Biomolecules

NS C12: Cell Biology

Evolution of cells (from prokaryotes to eukaryotes; from single cells to multicultural organisms), Cell-structure and function. Internal Organization of the cell: Membrane structure – Lipid Bilayer, membrane protein; Membrane transport of small molecules and the electrical properties of membrane; Principles of membrane transport, carrier protein and active membrane transport, ion channel and the electrical properties of membranes; Intracellular compartments & protein sorting; Intracellular vesicular traffic; Energy conversion and Mitochondria; Cell communication - General principles of cell communication signaling through G-protein linked cell surface receptor. Shape and structure of protein and protein function. Cytoskeleton - Self assembly & dynamic structure of cytoskeletal filaments, regulation of cytoskeletal filaments, Molecular motor, Cytoskeleton and cell behaviour. Cell Cycle and programmed cell death. Components of cell cycle control system, intracellular control of cell cycle events; Apoptosis, extracellular control of cell division, cell growth and apoptosis. Cell  Division - Mitosis and Meiosis, Genetic diversity). Concept of extracellular matrix and adhesion molecules. The cytoskeleton, myofibrils and their function in cell shape. Isolating cells and growing them; fractionation of cell, Methods of studying the cell surface, re-constitutional studies; fluorescence assisted methods e.g. flow cytometry.

NS C13: Molecular Biology

Gross anatomy of adult brain, organisation of the nervous system, subdivision of the nervous system, concept of CNS, ANS & PNS, meninges. The scalp, skull, menenges and cerebrosponial fluid, anatomy of the pituitary (normal & enlarged), vertebral column, cutaneus nerve, supply/ of head and neck limb and trunk. Brain, spinal cord, cranial nerve, spinal nerve, autonomic nervous system.

Practicals: Gross examination, dissected Brain and its different parts (human & animal), histology of animal brain

NS C15: Neurophysiology                                           

Neurotropisms, histogenesis, degeneration, regeneration and repair; excitability of nerve, nature, functions, physiology, pathology and pharmacology; nervous conduction, propagation and transmission, synaptic and ephaptic reflexes; Pain-analgesis, headache, referred pain, and management; Muscle tone, reflex regulation of posture, locomotion, gait; Intrinsic and extrinsic mechanism of reflexes at different levels; Vestibular apparatus, balance, orientation in space, motion sickness; Circulation of the brain disorders and ischaemia of the brain, blood-brain barrier; Conditioned reflex, Split brain, operant and instrumental conditioning; Integrative functions of thalamus, alpha rhythm, biofeed-back; Cerebellum. Neurons and excitable cells, molecular neurobiology and development, action potential generation, synaptic transmission.

Practical: Animal preparations: Spinal, Cerveau-Isole, Decerebrate, Thalamic, Mesencephalic, Mid-Collicular and Neuronally isolated Cortex preparations. Stereotaxic preparations: Ablation, Lesioning (Surgical, Electrolytic and Chemical); to study the electrical or chemical stimulation of the brain and its different parts. Electrphysiological studies of the brain in animals; EEG, EKG, EMG and ENG studies in mammals including evoked potentials, Reflexes of the Human Body and Psychophysiological experiments, Polygraphic studies; Human studies including B. P., Respiratory, Postural and Vestibular Reflexes.

Bioenergetics: Laws of thermodynamics, extensive and intensive variables; mathematical description of a system with two or more variables, exact and partial differential; first law of thermodynamics, isothermal process, entropy and second law of thermodynamics, reversible and irreversible process, free energy and chemical potential; Gibb’s free energy; Application of thermodynamics in biological systems, high-energy biomolecules; mitochondrial oxidative phosphorylation.
Techniques and Instrumentation: Principles and application following spectroscopy in biological systems: Absorption Spectroscopy (UV-visible), Fluorescence and Phosphorescence, Circular Dichroism (CD), Infrared spectroscopy (IR), Resonance Raman spectroscopy; Electron spin resonance (ESR), Liquid Scintillation counter; pH meter; Ultracentrifuges, Optical microscopes, optical microscopy; phase, ultraviolet and interference microscope- their basic principles; optical systems and ray diagrams- their applications in cell biology; fluorescence microscope; microspectrophotometry of cells and tissues, fluorescence activated cell sorter (FACS). Electron microscopy: theory of magnetic and electrostatic lenses and their focal length; construction of electron microscope; limiting resolution and useful magnification; contrast formation; shadowing and staining technique; scanning electron microscopy; specimen preparation techniques; application of electron microscopy in cell and molecular biology; embedding and section cutting.

NS S12: Enzymes and Reaction Kinetics

Definition of enzymes; active site, substrate, coenzyme, cofactor and different kinds of enzyme inhibitors; enzyme kinetics, two substrate kinetics, three substrate kinetics, deviation from linear kinetics; ligand binding studies; rapid kinetics; association and dissociation constants; use of isotopes in enzyme kinetics mechanism analysis; effect of pH, temperature and isotopically labeled substrates on enzyme activity; allosteric model of enzyme regulation; substrate induced conformational change in enzyme.

Second Semester

Practicals: Neurochemical studies: TLC, Silica gel chromatography, etc. Analysis of neurotransmitters by fluorometry, HPLC.

Evolution of human brain and development, cellular and molecular mechanisms of the organogenesis of the central nervous system. Development of the cerebral cortex and cortical neural networks. Embryology of spinal cord, Neurulation, spinal nerve. Neurogenesis, neuronal migration and cortical differentiation, development of neuron and glia. Developmental disorders - Congenital anomalies of brain, spinal cord, errors in development of pituitary body. Neuro-endocrinology of hypothalamus, neuroendocrinol and neurochemical mechanisms.

NS C24: Neuroimmunology

Basic Immunology - Immunoglobins, organization and expressions of Ig genes; B cell maturation, activation and differentiation; MHC/ HLA; antigen processing and presentation; T-cells, T-cell receptors, T-cell maturation, activation and differentiation; cytokines; cell mediated and humoral effector responses, auto immunity, immunodeficiency diseases, transplantation immunology, cancer and immune system. Monoclonal and polyclonal antibodies, monoclonal antibody technique.
Cellular immunology, Neural cell immunology, Microglia (antigen presentation), Neuro-immunomodulation — Neuro-immunology, Neurodiversity. Immune Diversity: Lymphocytes that respond to individual antigens, immunoglobulin genes, diversity of germline information, T-cell receptors, somatic mutations and diversity, immunogenetics. Relation between neuroendocrine system and immune system, feed back regulation of neuroendocrine – immune network. Stem cell differentiation – embryonic/fetal/adult cell transplantation

NS S22: Genetics & Molecular Diagnostics

Basic genetics - Mode of Inheritence - Concept in Mendelian inheritance - locus, alleles, homozygous, heterozygous, dominant, recessive, X-linked, X-inactivation, Genetic variation – polymorphism and mutation: Inherited variation and polymorphism at the DNA level, molecular basis of mutation and their detection. Genetic Diseases - A brief overview on chromosomal abnormalities, single gene disorder, multifactorial diseases, Molecular approaches to characterize genetic diseases - Genome mapping, Functional and positional cloning, Positional-candidate approach to detect the genes responsible for diseases caused by single gene mutation. Gene Expression, Basic Molecular Biology techniques to assess gene expression.
Molecular techniques - manipulating proteins, DNA, RNA – Cell culture, fractionation of cell, DNA-isolation, cloning and sequencing, analysis of protein structure and function, studying gene expression & function, visualizing cells, molecules in cells.
Molecular diagnostics - Gene function evaluation and mutation detections using techniques, such as, DNA microarray, knock out in mice, transgenic mice, Southern blot, northern blots, DNA sequencing, RFLPs, single nucleotide polymorphisms, methods for identification of mutations. PCR based diagnostics, DNA fingerprinting, DNA chip.

Practicals: DNA isolation, restriction enzyme digestion, gel electrophoresis, etc. Techniques for mutation detection: Genomic DNA preparation; Polymerase chain reaction (PCR); Analysis of PCR products by polyacrylamide gel electrophoresis; SSCP analysis, Analysis of DNA sequencing data by BLAST and primer designing for PCR.

Third Semester

Cellular neurobiology of clinical entitles —molecular neuropathology, Basic organization of nervous system, nerve nets, interneurons, Morphological and molecular organization of the neuron and glial tissues. Molecular and physiological studies of ion channels, second messengers, simple neural circuits, synaptic plasticity. The structure and function of vertebrate nervous system, the physiological bases of motor control, sensory activity, perception, drive, and higher mental processes. The behavioral and motivational mechanism of the brain – The limbic system and the hypothalamus, Sensory receptors, neuronal circuits for processing Information, Neural control of emotion, aggression, Mood Disorders, cellular basis of learning and memory

Practicals: Behavioural studies: Neuropharmacology of emotion, Analgesics, Anaesthesia, Reflexes, experimental Epilepsy, Startle Reflexes. Study of the electrical or chemical stimulation of the brain and its different parts.

NS C32: Genomics and Neurogenetics

Introduction to genomics and first generation sequencing strategies; Overview of new sequencing strategies; Study of variants: SNP in genomics; Study of gene expression: Microarray miRNA in Genomics. Genetic and physical maps, physical mapping and map-based cloning, choice of mapping population, simple sequence repeat loci, southern and fluorescence in situ hybridization for genome analysis, chromosome microdisection, molecular markers in genome analysis; RAPD and AFLP analysis, molecular markers linked to disease resistant genes, application of RFLP in forensic, disease prognosis, genetic counseling, pedigree, varietal etc. Genome sequencing: genome sizes, organelle genomes, genomic libraries, YAC, BAC libraries, strategies for genome sequencing, packaging, transfection and recovery of clones, application of sequence information for identification of defective genes.  Pharmacogenetics, genetics of globin triplet repeat disorders, cancer genetics; immunogenetics; mapping of human genome; somatic cell genetics; DNA polymorphism in mapping; structure and function; biochemical genetics; polygenic inheritance.
Pharmacogenomics: Effects of drugs in individual and susceptibility; Acetylation polymorphisms, Succinyl choline sensitivity and G6PD deficiency. Human genome and its impact on medicine-Genome mapping and sequencing, implications of human genome sequence information, molecular medicine, pharmacogenomics and personalized medicine, Databases for disease and mutation information.
History and development of Human genetics- hereditary traits, genetics and disease; Organization of the Human genome; Repetitive DNA in human genome; Methods of’ genetic study in man Pedigree analysis, Chromosomal analysis; Biochemical analysis; Somatic cell genetics; Human Genome Project;
Neurogenetic diseases - Autosomal (recessive and dominant) and X-linked neurological diseases – Neurodegenerative diseases, unstable mutation (repeat expansion) causing spinocerebellar ataxias, Huntington’s disease, Myotonic dystrophy, Friedreich’s ataxia, Fragile-X syndrome, etc., and molecular pathology. Metabolic defects causing neurological diseases (Tay-Sach’s, Gaucher’s diseases, etc). Genetics of Migraine, Epilepsy and other neurological diseases of complex inheritance - Complex genetic diseases, gene environment interactions, various loci identified, approach to identify the genetic contributors.

NS C33: Proteomics

Introduction and techniques applicable to macromolecule / proteomics: Standard technologies to identify and characterize protein-protein interactions, Biophysical approaches, computation and functional approach, Characterization of the proteome by ORF analysis, Gene disruption Knockouts; study of gene interaction by yeast two-hybrid system, Study of developmental regulation by using DNA chips. Physical techniques (absorption and fluorescence spectroscopy, IR, NMR techniques); Chromatography: TLC, GLC, HPLC, FPLC, gel filtration, ion-exchange and affinity chromatography; CD, ORD, X-Ray Diffraction and crystallography and its application in protein structure determination, 2D gel electrophoresis. Mass spectroscopy, basic principle, MALDI-TOF, ESI; 2-D Gel electrophoresis, Nuclear magnetic resonance spectroscopy (NMR), basic principles, chemical shift, spin-spin interaction, NOE, 2D-NMR , NOESY,COSEY. X-ray Crystallography: Principle of X-ray diffraction, scattering vector, structure factor, phase problem, reciprocal lattice and Ewald sphere, Miller indices, Zone axes, crystal lattice, Lane Equations, Bragg’s law, special properties of protein crystals, model building, refinement and R-factor.
Microscopy: Bright field, fluorescence, phase contrast, electron microscopy; UV, visible, and infra-red absorption spectrophotometer and their working - principles; microspectrophotometry of cells and tissues; Fluorescence activator cell sorter (FACS); Patch Clamp, MRI, Mass spectrometry.

Practical: Gel Filtration, Protein analysis by 1-D and 2-D GEL and protein expression analysis

NS C34: Animal Biotechnology

Computer applications: Basics of Computer applications-introduction to structural organization and types of digital computers, operating systems, word processing, Computer programs in the analysis of statistical methods and preparation of graphs. Application of Programs to solve - Algebric and matrix equations - Differential equations -Dynamical systems Models – Linear Regression, Handling Files - Containing Numerical and /orcharacter data -Files from sequence and structural data banks.
Bio-informatics: Applications and Prospects, Genome and protein information resources, sequence analysis, multiple sequence alignment, homology and analogy, pattern recognition, analysis package. DNA, RNA, Protein sequence analysis, DNA Translation, identifying ORF, restriction sites, finding SNPs, Primer design, Predicting elements of DNA RNA structure, Using BLAST to compares Protein and DNA sequences, finding protein structures, multiple sequence alignment, internet resources for geneticists, Human genetic variations – database and concepts, in silico computational techniques for gene functions.
Neuroinformatics: Elements of Neural network and computation, complexcity and learning. Non-linear elements and networks, linear and polynomial threshold elements, network capacity, learning theory, the sample complexcity of learning, perception training, learning complexcity, the intractability of learning, model selection. Brain as electrical machine.

NS S32: Evolution Biology and Biodiversity

Origin of life (include in aspects of periodic environment and molecular evolution); concepts of evolution, Theories of organic evolution; mechanisms of speciation; Hardy-Weinberg genetic equilibrium; genetic polymorphisms and selection; origin and evolution of economically important microbes; interactions between environment and biota, types of ecosystems, population ecology and biological control; community structure and organization, concept of habitat and ecological niches, limiting factor, energy flow, food chain, food web and tropic levels, ecological pyramids and recycling, biotic community- concept, structure, dominance, fluctuation and succession; ecosystem dynamics and management, stability and complexity of ecosystems, speciation and extinctions, environmental impact assessment; principles of conservation; conservation strategies; sustainable development.

Fourth Semester 

NS C41: Cognitive Function

Mechanism in Learning & Memory; limbic system the centre of emotion. Function of the Brain in Communication – Language input and output, function of the corpus callosum and anterior commissure to transfer thoughts, memories, training and others. Thoughts, consiousness and memory (short and long term). Basal ganglia and cognitive function. Biology and biochemistry of depression.

Definition of Psychology, application of Psychology, methods in Psychology, Principles of Learning, Behaviour, memory, thinking and language, emotion and stress, social perceptions, influences and relationships, attitudes, Psychological assessment and testing, Abnormal Psychology, Therapy for Psychological distress.  

Epilepsies and Convulsive diseases, Cerebrovascular diseases Dementia Parkinson's Disease, Torsion dystonia, Progressive Supranuclear Palsy (PSP).
Motor neuron Diseases [Amyotropic Lateral Sclerosis (ALS)], Lower Motor Neuron Disorder - Kennedy's Disease, others; Upper Motor Neuron Disorder - Primary Lateral Sclerosis, Familial Spastic Paraplegia; Ataxia: (Frederich's Ataxia, others); Demyelinating Diseases: (Multiple Sclerosis, Other Demyelinating Diseases, Encephalomyelities); Viral diseases - Encephalitis etc., Prions (Proteinaceous infectious particles) – Transmissible Neurodegenerative diseases; Nutritional and Metabolic Diseases: Neurocutaneous Syndromes, Developmental Disorders.
Clinical Neurology –Epidemiology, Anatomical Diagnosis, Pathological diagnosis, Symptoms of neurological diseases, examination of Nervous system,
Neuroimaging- Neuroradiology: CT, MRI, Mylography; Interventional Radiology - PET (Positron Emission Tomography) – CVA, Epilepsy etc., Single - Photon Emission Computed Tomography, MR Spectroscopy, Magnetic Source imaging.

NS C44: Neuro-environmental Biology

NS C45: Seminar

Students will have to submit a paper, 4-5 pages long, on any topics on neuroscience based on literature search and will present in front of a panel of internal and external examiners. Evaluation will be based on both the paper write-up and presentation.
                         
NS S41: Gene therapy and Bioethics

Focusing on emerging infections, viral classifications, transmissions and preventions, viral pathogenesis, mechanisms of viral induced cancer and viral evolution, developmental biology of virally induced birth defects, factors in pathogenesis and transmission of prions. Cell mediated and Gene therapy as a novel form of drug delivery, vectors, cell types. Responses to viral infections; slow and persistent infections, anti viral agents, interferons, equipments and materials for animal cell culture technology.  Primary and established cell line cultures. Introduction to the balanced salt solution and the simple growth medium.  Brief discussion on the chemical, physical and metabolic functions of different constituents of culture medium.  Serum and protein free defined media and their applications. Measurements of viability and cytotoxicity. Biology and characterization of the culture cells, measuring parameters of growth. Basic techniques of mammalian cell culture in vitro; desegregation of tissue and primary culture, maintenance of cell culture, cell separation.  Scaling up of animal cell culture.  Cell synchronization.  Cell cloning and micromanipulation. Cell transformation. Application of animal cell culture.  Stem cell culture, embryonic stem cells and their applications. Cell culture based vaccines, somatic cell genetics, organ and histotypic cultures.
Bioethics, Biosafety, Intellectual property right: patents, Biohazards, human safety, environmental and ecological hazards.

NS S42: Summer Project

A project performance report based on the summer research training in a reputed laboratory of excellence will have to be submitted. A presentation of the accomplishments will be required before a panel of experts. Evaluation will be based on both the project report and presentation.

NS S43: Grand viva

Students will be evaluated on all the topics discussed in the two years programme by a panel of experts.