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Theoretical   550 marks Semester I Course ID Course Name Marks C 1.1 Biomolecules: structure and function 50 C 1.2 Metabolism &     Bioenergetics 50 C 1.3 Nutritional Biochemistry   50 C 1.4 Enzymology 25 Total 150 Semester II Course ID Course Name Marks C 2.1 Microbiology 25 C 2.2 Plant Biochemistry 25 C 2.3 Methods in Biology (I )   25 C 2.4 Cell Biology(I)     25 C 2.5 Molecular Biology(I)   25 C2.6 Neurobiochemistry    25 Total 150 Semester III Course ID Course Name Marks C 3.1 Genetics 25 C 3.2 Genomics & Proteomics 25 C 3.3 Cell Biology(II) 25 C 3.4 Molecular Biology(II)   25 C 3.5 Systems Biology Bioinformatics & Biostatistics 25 Total 125 Semester IV Course ID Course Name Marks C 4.1 Immunology  25 C 4.2 Methods in Biology (II)  50 C 4.3 Metabolic disorders and Clinical biochemistry    25 Optional Courses: Any One 1x25 O 4.1 Molecular Recognition in Biology 25 O 4.2 Biochemical toxicology 25 O 4.3 Neuropharmacology 25 O 4.4 Structural Biology 25 O 4.5 Microbial Ecology and Pathogenesis 25 O 4.6 Nanobiotechnology 25 Total 125 Practical   450 marks Semester I Course ID Course Name Marks P 1.1 Biophysical methods 50 P 1.2 Enzymology.   25 P 1.3 Food analysis   25 Total 100 Semester II Course ID Course Name Marks P 2.1 Microbiology 50 P 2.2 Protein purification 25 P 2.3 Methods in Biology 25 Total 100 Semester III Course ID Course Name Marks P 3.1 Molecular Biology 50 P 3.2 Systems Biology and Bioinformatics 25 P 3.3 Project presentation 50 Total 125 Semester IV Course ID Course Name Marks P 4.1 Immunotechniques 25 P 4.2 Analytical Biochemistry 25 P 4.3 Grand Viva     25 P 4.4 Critical Reading  25 Optional Courses: Any One 1x25 OP 4.1 Molecular Recognition in Biology 25 OP 4.2 Biochemical toxicology 25 OP 4.3 Structural Biology 25 OP 4.4 Microbial Ecology and Pathogenesis 25 OP 4.5 Nanobiotechnology 25 OP 4.6 Neurobiochemistry and NeuroPharmacology 25 Total 125

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Marks distribution in Semesters

	Semester 1	Semester 2	Semester 3	Semester 4
Theory	150	150	125	125
Practical	100	100	125	125
Total	250	250	250	250

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C 1.1 Biomolecules:

 

DNA—structure of double helix---physical and chemical properties—DNA supercoiling—triplex DNA—left handed Z-DNA, miscellaneous alternative conformations of DNA like parallel stranded DNA, slipped and mispaired DNA—organisation of DNA into chromosomes .

 RNA- The "RNA world" hypothesis , secondary structure tertiary structure,  Folding and assembly principles of RNA . ribozymes catalytic site generation,  Guided tours through rRNA, tRNA, and  mRNA

 Protein structure— amino acids, primary, secondary, tertiary, quaternary structures, supersecondary structure, domains, motifs—hemoglobin , myoglobin--- protein folding, molten globule structure—chaperone.

 Lipid/membranes - Diversity of membrane lipids: membrane structure, membrane bends rafts,  membrane Proteins:  hydropathy profiles, sequence motifs, topology grammar; their interactions with lipid bilayer; Bundles and Barrels: a-helical membrane proteins; ß-barrelsporins:  Membrane Proteins as Enzymes, transporters and Receptors.

 Stereochemistry of Biomolecules---D-L, R-S configuration of enantiomers, Pro R, Pro S   ligands of   prochiral molecules, re, si faces of C=C and C=O functions

Stereochemical aspects of some biochemical reactions of biosynthesis of glucose, fructose, sucrose, serine from glycine, D aminoacid oxidase, glycolic acid oxidase etc

 Phi-Psi plot - Biomolecular Interactions-- Visualization of Biomolecules  

Recommended Books

1.DNA Structure and Function---Richard Sinden ( Academic Press)

2.Biochemistry—Voet and Voet

3.Understanding DNA—Calladine C.R, Drew H R et al (Academic Press)

4.Genes—Benjamine Lewin

5. Van Holde  - Physical Biochemistry

6. RNA world - Raymond F. Gesteland, Thomas R. Cech, John F. Atkins

7. Creighton 2nd ed. Proteins: Structures and Molecular Properties

8. Branden and Tooze, Introduction to Protein Structure

 

Weblinks

http://www.wiley.com/legacy/college/boyer/0470003790/structure/dna/dna_intro.htm

http://www.fhcrc.org/science/labs/stoddard/Conj544/conj544.html

http://blanco.biomol.uci.edu/Bilayer_Struc.html

http://en.wikipedia.org/wiki/Ramachandran_plot

http://cnx.org/content/m11612/latest/

http://www.chromatin.us/chrom.html

C1.2 Metabolism & Bioenergetics

 Concept of metabolism. Nutritional importance, digestion, absorption, transport, mechanism of activation of digestive enzymes.

 Carbohydrate Metabolism : Carbohydrates Source – Chemistry, Digestion, Absorption, Intestinal transport. Intra Cellular metabolism of glucose – glycolysis, HMP Shunt, Citric acid cycle; Glycogenolysis,Glycogen synthesis, metabolism of sugar other than glucose. Regulation of blood glucose level.Gluconeogenesis, biosynthesis of disaccharides, glycoproteins, the glyoxalate cycle. Metabolic regulation.

 Amino acid Metabolism : Dynamic Equilibrium of body protein, Nutritional and Metabolic importance of amino acids,General catabolism of amino acids, Metabolism of a few individual amino acids, one carbon fragment metabolism amino acid as biosynthetic precursors. Urea, Metabolic diseases.

 Lipid metabolism-Concept of metabolism, nutritional importance, absorption, transport, biosynthesis and catabolism of simple and complex lipids. Metabolic regulation. Lipoproteins, lipid storage and transport. Cholesterol metabolism and regulation. Abnormal metabolism of lipids.                                 

Nucleotides metabolism-Biosynthesis degradation of purines and Pyrimidines and their nucleotides, their interconversion & regulation. Salvage pathways. Regulation of biosynthesis of deoxyribonucleotides from ribonucleotides, abnormal metabolism of purines ans pyrimidines .

Basic Thermodynamic Principles – Free energy Concept – Eh & pH – Nonequilibrium Thermodynamics – Model for Chemiosmotic Coupling – Electron Transport Chain and F1-Fo ATPase

 Recommended Books

 Lehninger Principles of Biochemistry

Stryer  Biochemistry

Voet & Voet Fundamentals of Biochemistry: Life at the Molecular Level

Van Holde Kensal E van Holde, Curtis Johnson, and Pui Shing Ho - Principles of Physical Biochemistry (2nd Edition)

 

Web Links

http://memo.cgu.edu.tw/chia-chu/I.html

http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=71291&ZOOM=2

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1147494

http://ull.chemistry.uakron.edu/genobc/Chapter_24/

C1.3 Nutritional Biochemistry

Transport of nutrients, study of active and passive transport mechanisms, the glucose transporter as unique family of proteins, the role of specialized heavy metal ATP ases as transporter, energy requirements, BMR, SDA, RQ , quantitative problems, the effect of physical activity on energy consumption. N-balance, estimation of protein quality, protein score, assessment of protein status, protein calorie, malnutrition states, deficiency of amino acids and their effects on the developing offspring, specificity of amino acids in several physiological processes e.g., suppression of pain., stimulation of appetite, the role of metals and non-metals in nutritional biochemistry, with emphasis on the interaction with enzymes, proteins and nucleic acids, nutraceuticals, food toxins.

Analysis of food including genomic analysis for GM food - The genomics of protein nutrition- high protein and restricted protein diets- The genomics of leptin mediated responses-obesity and its regulation- The dietary influence of food and the influence of genes on diet-nutrigenomics and nutrigenetics- Nutraceuticals and their appraisal in terms of gene expression and metabolite formation.

 

Recommended Book(s)

Tom Brody - Nutritional Biochemistry

 Web links

http://en.wikipedia.org/wiki/Nutrition

http://www.answers.com/topic/nutritional-biochemistry

http://www.who.int/nutrition/topics/dietnutrition_and_chronicdiseases/en/

 

C1.4 Enzymology

 Nomenclature and classification, general properties, coenzyme and their function, factors influencing enzyme reaction kinetic properties, Michaelis constant inhibition,  purification, methods for determining activities of some important enzymes, isoenzyme, mechanism of enzyme action, two substrate reaction mechanism, regulation of enzyme activity, allostericity and feed back inhibition, Steady state kinetics immobilized enzyme and its kinetics.

 Recommended Books

Schimmel, Paul R.- Fundamentals of Enzymology

 

Web Links

http://www.expasy.org/enzyme/

http://www.brenda-enzymes.info/

http://www.biochemweb.org/enzymes.shtml

C2.1 Microbiology

 Experiment of Miller  - Structural organization of microbes, Cytoplasmic Membrane, Structures involved in attachment, Pili and Fimbrae, Chemotaxis and quorum sensing - Microbial Physiology- Microbial Nutrition, Classification of Microorganisms, Methods for studying microorganisms- Microbial Fermentation and Production of small and Macro molecules -Growth of bacteria in liquid medium, growth kinetics, growth on solid medium, differential media, selective media, synthetic media-Stains and Staining (No. of Lectures-Control of microorganisms by physical agents-Control of microorganisms by chemical agents-Antibiotics and other chemotherapeutic agents-Resistance to antimicrobial drugs.

 

Recommended Book

1. Microbiology Principles and Explorations by Jacquelyn G. Black –John Wiley and Sons Inc.
2. Microbiology by L. M. Prescott, J.P. Harley and D.A. Klein—WCB McGraw-Hill
3. Principles of Microbiology by Ronald M. Atlas----TATA McGraw-Hill
4. Fundamental Principles of Bacteriology by A.J. Salle-- TATA McGraw-Hill
5. Microbiology by Pelzer and Cheng- TATA McGraw-Hill
6. Microbiology by B.D. Davis-HIE publication.

Weblink

http://www.biosci.ohio-state.edu/~mgonzalez/Micro521.html

C2.2 Plant Biochemistry

Phytohormones.  Structure ..Function..Mode of action

Cell Wall primary cell wall secondary cell wall  composition and architecture cell wall degradation -Synthesis of cellulose and its regulation-bioengineering cellulose synthesis Synthesis of lignin and its regulation- bioengineering lignin production

Pectin production and breakdown in plants- genomics and control .Use of plant materials for generating value added products-bioconversions

Photosynthesis . Photosystems. Mechanism of solar energy harvest. Z scheme establishment. Mechanism of excess energy dissipation.  Chemiosmotic theory/ATP generation. 2C, 3C, 6C photosynthate synthesis and distribution.  Evolution of photosynthesis. 

Nitrogen fixation..Basic chemistry of nitrogen reduction. Asymbiotic nitrogen fixation by prokaryotes vs  Symbiotic nitrogen fixation by flowering plants.  Exchange of photosynthates and aminoacides between the plant and the symbiont. Evolution of nitrogen fixation.

Recommended Books

1. Biochemistry & Molecular Biology of Plants by Bob Buchanan, Wilhelm Gruissem, Russell                  Jones

2. Plant Physiology, TAIZ & ZEIGER

3. Plant Growth regulators – J. Hart & R. Holy
 

Web Links

http://www.plant-hormones.info/

http://www.ccrc.uga.edu/~mao/intro/ouline.htm

http://photoscience.la.asu.edu/photosyn/education/learn.html

http://www2.toulouse.inra.fr/centre/lbmrpm/eng/symbiose.htm

 

2.3       Methods in Biology (I)

Spectroscopy – Basics of Absorption and Emission Spectroscopy – Light Scattering Principles, FRET , Principles of Stopped Flow , Circular Dichroism , X ray crystallography – Basic Principles – Protein Databank ( PDB) -NMR – Basic Principles and applications – Structure of small molecules and proteins.

 

Recommended books

Biophysical Chemistry -  Alan Cooper

Physical Biochemistry - Van Holde

Physical Biochemistry - David Freifelder

 

Web Links

http://en.wikipedia.org/wiki/Fluorescence_spectroscopy

http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13310,00.html

http://www.800mainstreet.com/elsp/Elsp.html

http://www.800mainstreet.com/irsp/eir.html

http://www.newark.rutgers.edu/chemistry/grad/chem585/lecture1.html

http://chemistry.library.wisc.edu/subject-guides/x-ray-crystallography.html

http://www.biology-online.org/biology-forum/about11635.html

http://www.cis.rit.edu/htbooks/nmr/inside.htm

http://www.rcsb.org/pdb/home/home.do

C 2.4 Cell Biology I:                                                             

 Cytoskeleton: Cytoskeleton and Microtubule structure and function, Dynamic instability, Motor proteins, Dynein, Kinesin, Drugs affecting microtubule structure.

ECM: Extracellular matrix, Basement membranes, Proteoglycans, collagen, Integrins, Fibronectin, Cell migration, Gap junction.

Signal transduction: Study of EGF & TGF beta receptors-structure and function, genomic regulation and relation to clinical disorders including cancer.

Endocrines, Paracrines, Autocrines; Hormones, Neuro-transmitters, Growth factors

Signaling via intracellular receptors e.g. steroid and steroid-like ligands

Signaling via cell surface receptors like GPCR, RTK, Jak-STAT; NF-kB mediated pathways

 

Recommended books

 Molecular Cell Biology by Harvey Lodish, Arnold Berk, Paul Matsudaira, and Chris A. Kaiser

Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, and Martin Raff

Cell Signaling. ed. J.T.Hancock.

 

 

Web links

http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Cell_Signaling/Scientific_Resources/Pathway_Slides_Charts.html

http://www.signaling-gateway.org

http://www.cytoskeleton.com/InfoR.htm

http://biology.designerz.com/cell-biology-cytoskeleton.php

 

2.5: Molecular Biology I:

A.  Replication : Fundamentals of replication. Models, Enzymology and Mechanism.  Fidelity of replication. (10 lectures)

B. Transcription: Fundamentals of transcription. Prokaryotic model : lac, trp and ara operons. (5 lectures)

C. Translation: Genetic code, Codon-anticodon interaction, Fundamentals of translation: Cap dependent and Cap independent. (10 lectures)

Recommended books

 

Molecular Biology of the Gene by James D. Watson , Tania A. Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Losick

Fundamentals of Biochemistry: Life at the Molecular Level   by Voet & Voet

Genes by Benjamine Lewin

Biochemistry by Stryer

 

Web links

http://www.fhsu.edu/chemistry/twiese/664/replication.pdf

http://wps.prenhall.com/esm_madigan_brockbio_10/0,6207,374303-,00.html

http://www.mun.ca/biochem/courses/3107/Lectures/Topics/

 2.6  Neuro Biochemistry

 Organization of nervous system-CNS, ANS & PNS, meninges, Blood Brain Barrier, cerebrospinal fluid– composition, function and circulation, Neuron & its cell biology, glial cells, Biochemical composition of brain tissue. Carbohydrate, lipid metabolism of brain, transports of amino acids in brain, Synapse- Synaptogenesis, myelination, synaptic function, biochemistry of developing and aging brain, Neural signaling, channels pumps and transporters, Neurotransmitters, Neuromediators, Neuromodulators and synaptic transmission; Neurotransmitter receptors, neuroplasticity and their molecular aspects.

Recommended Books

Handbook of Neurochemistry and Molecular Neurobiology: Neurotransmitter Systems: Sylvester E. Vizi, Abel Lajtha

Handbook of Neurochemistry and Molecular Neurobiology: Brain Energetics. Integration of Molecular and Cellular Processes Gary E. Gibson, Gerry A. Dienel, Abel Lajtha

Neurobiology: Gordon M. Shepherd

Principles of Neural Science:  Eric R. Kandel, James H. Schwartz and Thomas M. Jessell.

Fundamental Neuroscience: Zigmond, M.J., Bloom, F.E., Landis, S.C., Roberts, J.L. & Squire, L.R. Academic Press, San Diego

Neurophysiology: RHS Carpenter

Human Physiology: C. C. Chatterjee

Neurobiology. Eds. V.Torre and F. Conti.

Neuchemistry Fundamentals and concepts. Ed. F. Hucho.

Advances of Neurochemistry. Eds.B.W.Agranoff and M.H.Aprison.

 

 

Recommended Link

 http://www.esnips.com/_t_/neurobiology?q=neurobiology

 

3.1 Genetics

 

Microbial genetics  and Virology: Conjugation- mapping of bacterial chromosomes, Transformation : plasmid, Generalized and specialized transduction. Bacterophage and Viruses. (15 lectures)

Transmission genetics:  Mendelian inheritance pedigree analysis, sex-linked single gene inheritance Linkage and epistasis Non mendelian inheritance (10 lectures)

 

Recommended books

 

Essentials of Genetics by William S. Klug , Michael R. Cummings

Genetics by Monroe W Strickberger

Genetics: Analysis and Principles by Robert J. Brooker

Introduction to Genetic Analysis by Anthony J.F. Griffiths, Susan R. Wessler, Richard C. Lewontin, and Sean B. Carroll

Medical Genetics  by Lynn B. Jorde, John C. Carey, Michael J. Bamshad, and Raymond L. White

 

Web links

http://plato.stanford.edu/entries/population-genetics/

http://www.ndsu.edu/instruct/mcclean/plsc431/431g.htm

http://www.sci.sdsu.edu/~smaloy/Glossary/

3.2 Genomics and Proteomics

Genome projects : Creating the sequence map of a genome. Making sense of DNA sequence. DNA sequence variation and SNP, Application of SNP-technology-mapping genes underlying monogenic and multigenic disorder.  Comparative genomics, transcriptomics, and Functional Genomics. Gross chromosome abnormalities and Cytogenetics. Population genetics and Cancer genetics.Proteomics: Mass spectroscopy, basic principle, MALDI-TOF, ESI; 2-D Gel electrophoresis, DIGE, PF-2D, SELDI-TOF. Softwares for analysis of proteomic data.

 Recommended books

Human Molecular Genetics by Tom Strachan and Andrew P. Read

Genomes 3 by T A Brown

Principles of Genome Analysis and Genomics by Sandy B. Primrose and Richard Twyman

 

Web links

www.genome.gov/18016863

www.uic.edu/classes/bms/bms655/lesson13.html

http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/

http://www.expasy.ch/

3.3 Cell Biology(II)  

 

Cell cycle :   Biochemical and genetic evidences that form  a framework for  cell cycle regulation. Highlighting the reversible phosphorylation mediated regulatory steps, and the steps involving  proteolysis.  Concepts and examples of several checkpoints. Disorders of cell cycle.  Cancer and Apoptosis

 Intracellular Protein transport to Nucleus, Mitochondria/ Chloroplast peroxisome. Vesicular trafficking of protein to Golgi, plasmamembrane, lysosome/endosome and secretory vesicles.

 

Recommended books

Molecular Cell Biology by Harvey Lodish, Arnold Berk, Paul Matsudaira, and Chris A. Kaiser

Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, and Martin Raff

 Web links

http://nobelprize.org/nobel_prizes/medicine/laureates/2001/illpres/index.html

http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/cellcycle/cellcycl1.htm

http://www.unom.ac.in/gcl-opac/lifemcb.html

 

  3.4 : Molecular Biology II:

A Recombination:  Mechanism of recombination- homologous recombination, gene conversion.(5 lectures)

B. Mutation and  Repair :  Mutagenesis, Ames test, Repair mechanisms (5 lectures)

C. Gene expression : RNA polymerase and transcription factors. post-transcriptional processing, Splicing, RNA transport and turn-over,  (5 lectures)

D. Epigenetics: Karyotyping.. Nucleosome and chromatin structure.. histone modifications chromatin remodeling Gene silencing Chromatin boundaries and insulators. DNA methylation and Genomic imprinting (10 lectures)

 

Recommended books

Molecular Cell Biology by Harvey Lodish, Arnold Berk, Paul Matsudaira, and Chris A. Kaiser

Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, and Martin Raff

Chromatin and Gene Regulation: Molecular Mechanisms in Epigenetics by B. M. Turner

Molecular Biology of the Gene by James D. Watson , Tania A. Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Losick

 

Web links

 

http://www.biochemweb.org/genes.shtml

 

 

 C 3.5  Systems Biology Bioinformatics & Biostatistics

 Statistics - Probability, hypothesis testing, confidence intervals, t-tests, analysis of variance, regression analysis, power and sample size, and simulations.

 Bioinformatics - Statistical behavior of  Sequence – BLOSUM  & PAM matrix

Introduction to Biological Databases- Sequence Databases - Motifs and Domains - Pathway Databases - Structural Databases -  Blast Search - Secondary structure prediction –

 Systems Biology - Graphs and networks in Systems Biology – Phylogeny  Understanding Dymamics and Function of Cellular Networks Example problems - SBML ( System biology markup language)- Gepasy - Cell Designer Oscillations in Biology . Comparing delayed negative feedback oscillators to those with interlinked positive and negative feedback- changing the amplitude and frequency of oscillations demonstration using circadian oscillator.

Recommended books

An Introduction to Systems Biology – Design Principles and Biological Circuits

-Uri Alon

Foundations of Systems Systems Biology – Kitano ( Edited)

 

Web Links

http://en.wikipedia.org/wiki/Systems_biology

http://www.ploscompbiol.org/home.action

http://www.ncbi.nlm.nih.gov/pubmed/

http://expasy.org/

http://www.rcsb.org/pdb/home/home.do

http://bioinformatics.fccc.edu/cgi-bin/bitool_pagemaker.pl

 C4.1   Immunology

 Introduction: overview of the Immune system. Cells and organs of Immune system. Innate immunity and Adaptive immunity, Antigens.  Immunoglobulins, Immunoglobin genes, generation of diversity, B cell maturation, activation and differentiation.       Antigen-Antibody interactions..Major histocompatibility complex, Antigen processing and presentation. T cell maturation, activation and differentiation, TCR gene rearrangement, T cell cytotoxicity.Cell-mediated effectors function, Cytokines, Immunological tolerance. Complement, regulation of complement activation pathways,.Hypersensitivity reactions. Autoimmunity, Immunodeficiency. Immune response during bacterial (tuberculosis), parasitic (malaria) and viral (HIV) infections. Vaccines..Cancer and immune system, Cancer Immunotherapy.                     

 

Recommended Books                    

Immunology - Kuby

Immunology by I. Roitt, J. Brostoff, and David Mole (4^th Ed.).

                     

Web links

http://www.immunologylink.com/

 

C4.2    Methods in Biology (II)

Recombinant DNA technology

Restriction endonucleases, restriction mapping , electrophoresis and documentation.           Vectors  Plasmid, phage and cosmid vectors, prokaryotic versus eukaryotic expression vectors, shuttle vectors, Yeast vectors, BAC vectors.  PCR and its various applications, Cloning strategies, transformation, transfection, genomic and cDNA library, selectable marker and reporter genes, recombinant selection and screening, Gateway cloning Expression of gene of interest (GOI) in prokaryotes and eukaryotes, transient expression versus transgenics., Complementarity and hybridization techniques:  Southern , Northern, Microarray,  etc DNA Sequencing, Site directed mutagenesis

http://www.bioteach.ubc.ca/TeachingResources/Applications/GMOpkgJKloseGLampard2.swf               http://biology.kenyon.edu/courses/biol114/Chap08/Chapter_08a.html
http://www.sci-ed-ga.org/modules/dna/index.html
http://biowww.net/methods/browse-14.html    
http://www.protocol-online.org/prot/Molecular_Biology/DNA/Mutagenesis/

 

Cell Biology

Animal cell culture :  Primary and established cell line cultures, cell culture media: Balanced salt solutions, simple growth media, role of CO2, serum and supplements, serum free defined media, measurement of viability and cytotoxicity, basic techniques of mammalian cell culture in vitro, maintenance of cell culture, cell separation, scaling-up of animal cell culture, cell synchronization, application of animal cell culture.  Production of monoclonal antibodies.

Plant cell culture : Basic difference between animal and plant cell culture. Primary versus transformed cell cultures. Micropropagation. Generation of conditionally sensitive mutants. FACS  Principle of cell separation Tools for discovering  interacting proteins : Phage display, Yeast two hybrid, coimmunoprecipitation  Microscopy. Fluoresecence microscopy: Live cell imaging versus fixed tissue imaging. Tools for observing subcellular organization, Localisation of expression of GOI, FISH,  Ultrastructure analysis by  SEM and TEM and AFM Radiolabelling. Strategies for labeling of biomolecules. Pulse labeling applications. safety measures

http://www.wormbook.org/chapters/www_intromethodscellbiology/intromethodscellbiology.html

http://www.cellbio.com/protocols.html

http://biowww.net/browse-2.html

Chromatography  

HPLC, FPLC, GLC, TLC, Electrophoresis

http://elchem.kaist.ac.kr/vt/chem-ed/sep/chromato.htm

 O4.1 Molecular Recognition in Biology

 Molecular basis of  recognition of the physical world, odor, taste, light, etc

(7 transmembrane receptors)

Molecular basis of pathogen associated molecular pattern recognition (Toll receptors)

Molecular basis of Cell-cell recognition in fate determination in Developmental Biology (Notch delta signaling)

 

Suggested reading

 

1. Seven transmembrane receptors: something old, something new.

Acta Physiol (Oxf). 2007 May;190(1):9-19.

2. Structural diversity of G protein-coupled receptors and significance for drug discovery.

Nat Rev Drug Discov. 2008 Apr;7(4):339-57.

3. Signaling mechanisms of GPCR ligands.

Curr Opin Drug Discov Devel. 2008 Mar;11(2):196-202.

4. Pharmacology under the microscope: the use of fluorescence correlation spectroscopy to determine the properties of ligand-receptor complexes.

Trends Pharmacol Sci. 2007 Dec;28(12):637-45.

5. Plants and animals: a different taste for microbes?

Curr Opin Plant Biol. 2005 Aug;8(4):353-60.

6. Recognition of bacterial products by toll-like receptors.

Chem Immunol Allergy. 2005;86:99-119.

7. Pattern-recognition receptors in plant innate immunity.

Curr Opin Immunol. 2008 Feb;20(1):10-6.

8. PAMP recognition and the plant-pathogen arms race.

Bioessays. 2006 Sep;28(9):880-9..

9. Notch signaling--constantly on the move.

Traffic. 2007 Aug;8(8):959-69. Epub 2007 Jun 5

10. Regulation of vascular morphogenesis by Notch signaling.

Genes Dev. 2007 Oct 15;21(20):2511-24.

11. Crossing paths with Notch in the hyper-network.

Curr Opin Cell Biol. 2007 Apr;19(2):166-75. Epub 2007 Feb 20

12. The segmentation clock in mice: interaction between the Wnt and Notch signalling pathways.

J Theor Biol. 2007 Sep 7;248(1):37-47. Epub 2007 May 22

O4.2 Biochemical Toxicology

Predictive toxicology- ADMET concepts- Databases for Toxicology-Use of tools for in silico toxicology-Prediction of genotoxicity and teratogenic potential- molecular markers and their use- high throughput screens including biosensors-construction of tailored biosensors-Toxicity of nano-particles-Photo-toxicity and toxic oxygen species-Xenobiotic metabolism and its relation to toxicology

Recommended Books

Molecular aspects of toxicology: Hathway D.E.

Cassaret and Doull’s Toxicology: Ed. C.D.Klaassen

http://www.in-silico.de/

O 4.3  Neuropharmacology

CNS active drugs-classification & their mode of action-  neurotoxicity. Pharmacology of neurotransmitters receptors, neurotransporters. cognative behaviour, pain, emotion, sex etc. and brain function, pharmacology of mental disorder. Pharmacology of neuroendocrine and age related disorders, neuro-immune pharmacology and molecular neurobiology.

 Recommended Books

Handbook of Neurochemistry and Molecular Neurobiology: Degenerative Diseases of the Nervous System:  Abel Lajtha, Moussa B.H. Youdin, Peter Riederer, Sylvia A. Mandel, Leontino Battistin

Handbook of Neurochemistry and Molecular Neurobiology: Amino Acids and Peptides in the Nervous System (Handbook of Neurochemistry and Molecular Neurobiology) Simo Oja, Arne Schousboe, Pirjo Saransaari, Abel Lajtha

Molecular Basis of Neuropharmacology: A Foundation for Clinical Neuroscience by Eric J. Nestler, Steven E. Hyman, and Robert C. Malenka

Frontiers in Clinical Neuroscience: Neurodegeneration and Neuroprotection (Advances in Experimental Medicine and Biology) :Laszlo Vecsei

O 4.4 Structural Biology

Biocalorimetry and basic concepts of thermodynamics-.Experimental tools of structural Biology—NMR, Xray Crystallography , Mass Spectra, and other spectroscopic techniques-Basic concepts of non covalent interaction-Protein engineering, folding—thermodynamics and kinetics-protein-DNA interaction, proteins in disease-DNA structure—bending and cruciform 

Reference 

Protein structure—Creighton

Biophysical Chemistry--Friefelder

O4.5    Microbial ecology and pathogenesis

Microbial flora of the human host, Epidemiology of infectious diseases, epidemiological markers, role of the host in infectious diseases, airborne, waterborne, food borne and  Arthropod-borne transmission,  Cholera, pathogenesis and epidemiology of cholera, virulence factors, transcriptional regulation of virulence genes, pathogenecity island,  treatment and prevention. whooping cough, causative agent, stages of the disease, virulence factors, regulation of virulence genes, treatment and prevention. Dysentery: Shigella species, Virulence factors, HUS, regulation of virulence genes, treatment and prevention. Life cycle and pathogenesis of E. histolytica.  E. coli, gastrointestinal infections, serotypes and virotypes, mechanism of pathogenesis, urinary tract infection, community and hospital acquired infections, virulence factors, organization and regulation of virulence genes, treatment and prevention. Yersinia infection: food and waterborne infections, Arthropod-borne infection (plague), virulence mechanism, treatment and prevention. Salmonella infection, virulence mechanisms, treatment and prevention. Campylobacteriasis, Gastric and Duodenal ulcers, H. pylori infection, virulence mechanism, detection, treatment and prevention.  Host microbes interaction, Life cycle and pathogenesis of Trypanosoma spp.

Recommended Books

Concept of Habitat and Niche, Species interaction: Symbiosis, Ecosystem structure: function, Energy flow and mineral cycling, Carbon cycle, nitrogen cycle, phosphorous cycle. Biodiversity: status, monitoring and documentation. Nitrogen fixation, Nif genetics. Diptheria, Botulinum, Tetanus toxin – structure – function, Malaria, Kalaazar, Tuberculosis, Metagenomics and Biodiversity.

Medical Microbiology: A Guide to Microbial Infections: Pathogenesis, Immunity, Laboratory Diagnosis and Control by C. F. Corke, Richard Slack, John Peutherer, Slack Richard C. B., John F. Peutherer. Elsevier Health Sciences.Pub. Date: October 2002.

Foodborne Microbial Pathogens: Mechanisms and Pathogenesis by Arun K. Bhunia. Springer; 1 edition (December 12, 2007).

Microbial Ecology: Fundamentals and Applications by Ronald M. Atlas (Author), Richard Bartha (Author) Benjamin Cummings; 4 edition (December 21, 1997).

Microbial Ecology: An Evolutionary Approach by J Vaun McArthur Academic Press; 1 edition (February 1, 2006)

Chapman, J.L. and Reiss, M.J. Ecology- Principles and Applications. Cambridge Univ. Press.           

Microbiology by M. J. Pelczer et al., Tata McGraw Hill.

O 4.6 Nanobiotechnology 

Shift of properties from bulk to nanoscale – Synthetic and evolved nano objects –Characterization Techniques – Plasmonics – Atomic force Techniques –Dimensional diversity of Nanoparticles – Quantum Dots and their use in Bioimaging -  Nanoparticles as Drug delivery agents and  Nanomedicine applications–  Nanotoxicology

Recommended Books

Nanobiotechnology: concepts, applications and perspectives/ Niemeyer Christof M, Editor ; Mirkin Chad A  ,Editor

Nanotechnology and nanoelectronics: materials, devices, measurements, techniques -Fahrner W. R  ,Editor

Nanotubes and nanofibers- Gogotsi Yury  ,Editor

Nanoparticle technology handbook-Hosokawa M ;  Nogi K; Naito M; Yokoyama T (Editor)

Nanostructures: theory and modeling-Delerue C   ; Lannoo M 

Micromachines as tools for nanotechnology-Fujita H  ,Editor

Nanotechnology-Timp Gregory  ,Editor

Nanotechnology and nanoelectronics: materials, devices, measurements, techniques-Fahrner W. R  ,Editor

Nanotechnology: principles and practices-Kulkarni Sulabha  K

 

Links

http://nanosurface.blogspot.com/

http://pubs.acs.org/journals/nalefd/

http://en.wikipedia.org/wiki/Nanotoxicology

http://www.infinitesima.com/downloads/pdf/APL_paper.pdf

http://www.mobot.org/jwcross/spm/

http://ajrccm.atsjournals.org/cgi/reprint/172/12/1487

http://sjay.myweb.uga.edu/intro.html