Syllabus for
Master of Science (Biotechnology)
Academic Year  (2017)

Continous Internal Assessment - 50% 

It includes various components like semiar, assignments, miniprojects, tests, review of research articles and midsemester examnination.

End Semester Examination - 50 % 

It includes two sections:

Section A- Answer any eight questions out of 10. ( each question carries 5 marks)

Section B - Answer any Six questions out of 8. (each question carries 10 marks each)

Microbes play a very significant role in the lives of higher organisms. The paper surveys the features of microbes like bacteria, viruses, fungi, algae and protozoa in order to make the students understand their biology so as to manipulate them. This course fulfils the basic knowledge in microbiology for those students who wish to pursue career in allied health fields and other technical programs.

 This course will make the students adept in the structure and functions of these microbes which in turn will give them confidence to work using these organisms. The students will become competent for jobs in dairy, pharmaceutical, industrial and clinical research.

History of Microbiology, Microscopy – Light, Phase contrast, Fluorescence & Electron microscopy – TEM and SEM, Physical and Chemical control of microorganisms, Classification and nomenclature of microorganisms, Bergey’s manual, Staining techniques - Gram’s, acid fast, capsular, flagellar and endospore staining. Microbial Taxonomy: Pure culture techniques (Streaking, spread plate, pour plate, serial dilution), Identification of microorganisms – Morphological, Biochemical, serological and molecular techniques.

Bacterial cell structure, classification based on shape and arrangement of cells, Cellwall, flagella, pili and capsule – structure & functions, endospore formation, Features of mycoplasma, Rickettsia, Prions and diseases caused. Biofilms and its significance.

Growth curve, factors affecting growth, Quorum sensing and its significance, Nutritional classification, Microbial associations (Parasitism, Saprophytism, Mutualism and Symbiosis, Commensalism, endozoic microbes). Antibiotic – types and mechanism of action, Stress physiology: effect of oxygen toxicity, pH, osmotic pressure, heat shock on bacteria, HSPs, Adaptations, uses and examples of thermophiles, halophiles, alkaliphiles,acidophiles, psychrophiles and cryophiles, their uses – adaptations & significance in biotechnology.  Nitrogen fixation mechanisms and genes involved.

Viruses – Structure and classification based on shape and nucleic acid, Plant viruses – symptoms, transmission and control strategies of TMV, CaMV, Animal viruses - DNA viruses: Hepatitis B virus. RNA viruses:HIV, bacteriophages-. Lifecycle of Lambda phage. Evolution and mutation of viruses.Cultivation and assay of viruses: Cultivation of viruses in embryonated eggs, experimental animals and cell cultures.

Fungi:- Structural features, Ainsworth’s system of classification, salient features of division–Mastigomycotina, Zygomycotina, Ascomycotina, Basidiomycotina and Deuteromycotina, parasitism, predation, mutualism and symbiosis with plants and animals,reproduction of fungi, fungi as food, as plant pathogens, control measures of fungi, Mycorrhizae- ecto and endomycorrhizae, significance, Algae:- Salient features, classification (Fritsch’s) and reproduction,measurement of algal growth, strain selection and large scale cultivation, Symbiotic algae, use as biofuel.

Major Bacterial diseases – Typhoid, Tetanus, Tuberculosis, Pneumonia and Cholera, Viral diseases - Dengue, Chikungunya, Rabies. Emerging viruses – H1N1, Ebola, Zika. Major parasitic diseases –Malaria, Amoebiasis, Giardiasis- pathogen, lifecycle and treatment measures. Etiology, symptoms and control measures of some plant diseases - Bacterial blight of rice, Late blight of potato, Coconut Root wilt, Ginger Soft Rot, Downy Mildew of Grapes, Rust of Wheat, Red Rot of Sugarcane.

Concepts of pathogenesis, virulence and epidemiology, Disease classification - Epidemic, endemic and pandemics, CDC and its role, normal human microflora, gut microbiota and its relevance. Diagnosis and control of infections, biomedical waste management, nosocomial infections, Drug resistance in bacteria – causes and consequences, super bugs.

Microbes in food manufacture (Yeast, Lactobacillus etc), food spoilage (Brucella, Bacillus, Clostridium, Escherichia etc, mycotoxins - aflatoxins, ochratoxins, ergot alkaloids), agriculture (Rhizobium, Trichoderma etc), environmental management, Biodegradation of Xenobiotics - hydrocarbons, pesticides and plastics, Bioleaching of Copper, Iron , Uranium, Gold.

The paper is intended to develop understanding and provide scientific basis of the inanimate molecules that constitute living organisms. It also gives a thorough knowledge about the structure and function of biological macromolecules (proteins, carbohydrates, lipids, and nucleic acids), and the metabolic and bioenergetic pathways within the cell. Students learn to interpret and solve clinical problems.

Forces and interactions of biomolecules; chemical bonds – Covalent and Ionic bond (bond energy), Stabilizing interactions (Van der Waals, electrostatic, hydrogen bonding, hydrophobic interaction.), high energy molecules in living system (ATP, ADP, NAD, NADH, NADPH, FAD, FADH₂), Laws of thermodynamics, Concept of free energy, enthalpy, entropy, Coupled reactions, group transfer, biological energy transducers, redox potential.Buffers and Solutions: Concept of pH, pKa, titration curve, acids, bases and buffers, Henderson-Hasselbalch Equation, biological buffer solutions.Principles of thermodynamics; Kinetics, dissociation and association constants; energy rich bonds and weak interactions; Bioenergetics.

Classification, structure and Properties of mono, oligo and polysaccharides. Chirality and optical activity, stereoisomerism, cyclic structure of monosaccharide, (pyranoses and furanoses) , structures of glucose. Absolute and relative configuration (D & L and R & S nomenclature). Disaccharides-structures of Maltose, Lactose, Sucrose, Trehalose, Raffinose. Polysaccharides. Structure and properties of homo and hetero polysaccharides. Storage polysaccharides. (Starch, Glycogen, cellulose, hemicellulose, and chitin) Derived sugars- Sugar acids (Aldonic, Aldaric and Saccharic acids), amino sugars. Derivatives of carbohydrates (Glycosaminoglycans, glycolipids, Proteoglycan and glycoproteins).

Carbohydrate metabolism:Glycogenolysis, Glycogenesis, Glycolysis- Energetics and Regulation, Fermentation reactions (Lactic acid and alcoholic fermentation), Gluconeogenesis, Reciprocal regulation of Glycolysis and Gluconeogenesis, Citric acid cycle- Energetics and regulation, Glyoxylate cycle. Pentose phosphate pathway.

Amino acids: Structure, properties, classification and functions, reactions of amino acids, modifications of amino acids in proteins, non-protein amino acids,.

Proteins- peptide bond, psi and phi angle, Ramachandran's plot,Structural organizations of proteins (primary, secondary, tertiary and quarternary, Domains, Motifs & Folds), conformational analysis. Structure and functional classification of proteins. Structure- function relationship. Thermodynamics of protein folding, chaperones and chaperonins, Stability of Protein Structures, examples of  specific proteins; Keratin, Silk fibroin, collagen triple helix and hemoglobin; Denaturation and renaturation of proteins; neurotransmitters, Peptide hormones .

Amino acid and Protein metabolism: Transamination, Deamination, Decarboxylation, basic glutamine and glutamic acid pathways, urea cycle and its regulation, formation of uric acid.

Enzyme nomenclature and classification, Isolation of enzymes. Extraction of soluble and membrane bound enzymes: Purification of enzymes-Criteria for purification; Assay of enzymes. Factors affecting enzyme activity, Isozymes, Coenzymes and cofactor, Metalloenzymes, membrane bound enzymes, Multienzyme complexes, Synthetic enzymes, Ribozymes. Mechanism of enzyme action, Active site and Specificity of enzyme. Theories on enzyme substrate complex. Free energy of enzyme reactions. Steady state kinetics. Michaelis-Menton, Lineweaver–Burk, Edde-Hofstee and Hanes-Woolf equations. Pre-steady state kinetics. Fast kinetics to elucidate the intermediates and rate limiting steps.

Enzyme inhibition: types of inhibitors; Mechanism of enzyme inhibition –competitive, non – competitive, uncompetitive, mixed and irreversible inhibition. Allosteric regulation in metabolic pathways. Applications of enzymes, enzyme engineering (Protein engineering). Immobilization of enzymes and their application.

Classification- Structure, properties, reactions and biological functions of lipids. Phospholipids, Sphingo and glyco lipids, Steroids-cholesterol-bile salts, steroid hormones,Cerebrosides, lipoamino acids, lipoproteins, lipopolysaccharides, eicosanoids (Prostaglandins, leucotrienes and thromboxane).Role of lipids in biomembranes

Metabolism of Lipids: Biosynthesis of saturated and unsaturated fatty acids and cholesterol. Beta oxidation of Fatty acids: activation, transport to mitochondria, metabolic pathway. Oxidation of saturated and unsaturated fatty acids. Alpha and omega oxidation, metabolic disorders (Triglyceridemia, NaymanSacchs Disease).

Structure and properties- Bases, Nucleosides, Nucleotides, Polynucleotides.

Nucleic acid metabolism: Biosynthesis and regulation of purines and pyrimidines, Denovo and Salvage pathways, biodegradation of purines and pyrimidines.

Vitamins: Classification, Chemistry and Biological Functions, Fat and water soluble vitamins. Role in metabolism, Vitamins as co-enzymes. Metabolic Disorders –A, B, C, D, K.

Hormones:Autocrine, paracrine and endocrine action. Endocrine glands, Classification of hormones, basic mechanism of hormone action, importance of TSH,T3,T4, Estrogen, Testosterone, HCG, FSH, LH, Prolactin, Progesteron, adrenaline, insulin and glucagon. Hormone imbalance and disorders: hypothyroidism, hyperthyroidism, Polycystic Ovarian Disorder PCOD), Insulin Dependent Diabetes.

Plant Growth regulators: Biosynthesis, Physiological role and mechanism of action of plant growth hormones (Auxins, Gibberellins, Cytokinins, Ethylene, abscisic acid, Brassinosteroids), receptors and signal transduction (salicylic acid and jasmonic acid pathways).

Electron transport chain, Electron transfer reactions in mitochondria, Electron carriers, Ubiquinone, Cytochromes, Iron sulfur centers, Methods to determine sequence of electron carriers, Fractionation of Multi enzyme complexes I, II, III, IV of Mitochondria and their inhibitors, Oxidative phosphorylation, ATP synthesis, Chemiosmotic model, Proton gradient, Structure of ATP synthetase, Mechanism of ATP synthesis, Brown fat, Regulation of Oxidative phosphorylation.

Nelson, D. C. and Cox, M.M., Lehninger Principles of Biochemistry, 5th Edition, W. H. Freeman, 2010.

Voet D., Voet J.G, Biochemistry 4th Edition., John Wiley and Sons, 2011.

Elliott, W.H., Elliott, D.C. Biochemistry and Molecular Biology 3^rd Indian edition, Pub. Oxford.

Mathews, Van Holde and Ahern, Biochemistry by 3^rd edition, Pub Pearson education

Berg J.M., Tymoczko J.L. and Stryer L., Biochemistry. 7th edition, W.H. Freeman and Co. New York, 2011.

Kuchel, P.W., Ralston Schaums, G.B. Outlines of Biochemistry 2^nd edition Pub: Tata.

Devlin, T.M. (1997). Biochemistry with clinical correlations, Wiley-Liss Inc. NY

Zubey, G.L. Parson, W.W., Vance, D.E. (1994). Principles of Biochemistry WmC Brown publishers. Oxford.

Edwards and Hassall. Biochemistry and Physiology of the cell 2^ndEdn. McGraw Hill Co. UK. Ltd.

This paper has been designed in a standard manner to impart knowledge of the cell and its various attributes among the post graduate students. The topics included in this paper gives not only the basic idea about the subject but also provides in-depth knowledge. Students get an idea about the cellular structures, as well as how these structures are helpful for the cell to communicate with its environment and transduction of various signals, whether intracellular or extra-cellular. Furthermore, students also learn the mechanism of mitotic and meiotic cell division as well as how the cell cycle is regulated. The course structure also fulfils the important criteria regarding the preparation of students for the competitive examinations, for e.g. National Eligibility Test (NET), conducted by Council of Scientific and Industrial Research (CSIR), as well as various other entrance examinations for pursuing doctoral research.

Students can apply their knowledge of cell biology in not only performing research at post graduate level, but also in the doctoral level. The advanced studies are being conducted in all the topics that have been included in the paper, for e.g. cellular communication, signal transduction, cell cycle etc.

Introduction: Discovery of cells, basic properties and classes of cells. Study of cells: Microscopy: Brief overview of Light microscopy, phase contrast microscopy, electron microscopy, Confocal Microscopes, Scanning probe microscope, micrometry. Purification of cells and their parts: cells separation and culture, flow cytometry, fractionation of cell contents.

Structure: History of studies on plasma membrane structure, Singer-Nicolson Model, Chemical composition of plasma membrane: lipids, proteins and carbohydrates; Dynamic nature of plasma membrane: role of lipids in membrane fluidity, diffusion of proteins, restrictions of lipids and proteins mobility: fluorescence recovery after photobleaching (FRAP), single-particle tracking, membrane domains and cell polarity.

Functions: Movement of substance across the membrane: Energetics of movement of solute, partition coefficient, Simple diffusion: mechanism, ion channels and types (voltage, ligand and mechano-gated ion channels), Facilitated diffusion (Glucose transport, GLUT proteins) and active transport (structure and working of F0-F1 ATPase, Na+/K+ ATPase, Ca2+ ATPase, P and V-type ATPases, H+/K+ ATPase, ABC transporters); Cotransport(Uniport, Symport and Antiport); Membrane potentials and Nerve impulse: resting potential, action potential and its propagation as an impulse.

Cell wall: Primary wall, middle lamella and secondary wall; Lysosomes: structure and functions, autophagy; Endoplasmic reticulum: structure and functions of smooth endoplasmic reticulum and rough endoplasmic reticulum; Golgi complex: structure and function and movement of materials through golgi apparatus. Structure and function of mitochondria: Structure of mitochondria: mitochondrial membranes, mitochondrial matrix; Structure and function of chloroplast: basic structure, photosynthetic units and reaction centers; Functions: photosynthetic pigments and absorption of light, photophosphorylation; carbon dioxide fixation: synthesis of carbohydrates in C3, C4 and CAM plants.

Principles and importance; Whole mount preparation; Types of microscopic slides; Types of microtome; Process: Killing and fixing, Types fixation & fixatives, Dehydration, Microtome sectioning, Stains and staining, Mounting and mountants; Histochemical techniques for starch, protein, lipid and lignin; Specimen preparation for electron microscopy: Material collection, fixing, dehydration, embedding, sectioning and staining.

Study of cytoskeleton:  Live cell fluorescence imaging, in vitro and in vivo single molecule assays; Microtubules: Structure, microtubule associated proteins, properties of microtubules with reference to the structures and functions of cilia and flagella; Intermediate filaments: structure and function; Microfilaments: basic Structure and function with reference to myosin.

Extra cellular matrix; Communication between cells and extracellular materials: roles of integrins, focal adhesions and hemidesmosomes; Communication between cells and other cells: roles of selectins, immunoglobulin superfamily, cadherins, adherens junctions and desmosomes; Tight Junctions; Gap Junctions; Plasmodesmata

Signaling mediated by G-protein coupled receptors, second messengers, enzyme tyrosine kinase, steroid receptors, role of calcium and NO as intracellular messenger, signaling via extrinsic and intrinsic pathways of apoptosis, two-component signaling in plants and bacteria; Quorum sensing.

Phases and progression of cell cycle; Control of cell cycle: Major events, cyclin dependent protein kinases (Cdks), suppression of Cdk by Cdk-Inhibirotry Proteins (CdI), dependence of Cdks on transcriptional regulation, biochemical switches in cell cycle, mitogen stimulated cell division: G1-Cdk and G1/S Cdk activities; Apoptosis: role of Caspases, Extrinsic and Intrinsic pathways, roles of Bcl2 and IAPs in apoptosis, inhibition of apoptosis by extracellular factors; Necrosis.

Cancer: Benign and Malignant tumors, metastasis, oncogenes (retinoblastoma) and tumor suppressor genes (p53).

G. Karp, Cell and Molecular Biology: Concepts and Experiments, 6^th ed. USA: Wiley and Sons, 2009.

G. M. Cooper and H. E. Robert, The Cell: A Molecular Approach, 6^th ed. USA: S Sinauer Associates Inc., 2013.

B. J. Alberts, B. Alexander, and L. Julian, Molecular Biology of the Cell, 5^th ed.  New York: Garland Science, 2008.

P. S. Verma and V.K. Agarwal, Cell Biology, Genetics, Molecular Biology, Evolution and Ecology, New Delhi: S. Chand and Co. Pvt. Ltd., 2010.

A. Paul, Text Book of Cell and Molecular Biology, 3rd ed. India: Books and Allied (P) Ltd;, 2011.

The chapters on genetics make them appreciate the flow of inherited characters from one generation to the other and study about the interaction of different genes in different organisms. The students will also gain knowledge related to quantitative, population and evolutionary genetics, in addition to microbial genetics.

The students can apply their knowledge of genetics to selected examples of mutations as exemplified in many diseases and various chromosomal abberation related syndromes.

Transmission genetics, Molecular genetics and Population genetics (brief introduction). Mendelism – basic principles (brief study). Extensions of Mendelism, penetrance and expressivity of genes. Nonmendelian inheritance – cytoplasmic inheritance.

Sex Chromosomes and sex determination in animals and plants; Dosage Compensation of X-Linked Genes: Hyperactivation of X-linked genes in maleDrosophila, Inactivation of X-linked genes in female mammals

Linkage and Crossing over - Stern’s hypothesis, Creighton and McClintock’s experiments, single cross over, multiple cross over, two-point cross, three-point cross, map distances, gene order, interference and co-efficient of coincidence. Haploid mapping (Neurospora), Mapping in bacteria and bacteriophages.

Pedigree analysis, determination of human genetic diseases by pedigree analysis, genetic mapping in human pedigrees.

Polygenic inheritance, Statistics of Quantitative Genetics: Frequency distributions, the mean and the modal class, the variance and the standard deviation, Analysis of quantitative traits: -The multiple factor hypothesis, Partitioning the phenotypic variance; QTL, effect of environmental factors and artificial selection on polygenicinheritance.

(a) Gene pool, allele and genotype frequency. Hardy-Weinberg law and its applications, estimation of allele and genotype frequency of dominant genes, codominant genes, sex-linked genes and multiple alleles. Genetic equilibrium, genetic polymorphism.

(b) Factors that alter allelic frequencies; (i) mutation (ii) genetic drift - bottle neck effect and founder effect (iii) migration (iv) selection (v) nonrandom mating, inbreeding coefficient.

Emergence of evolutionary theory; Genetic Variation in Natural Populations: variation in phenotypes, variation in chromosome structure; Molecular Evolution: Molecules As “Documents of EvolutionaryHistory”, Molecular Phylogenies, Rates of Molecular Evolution, the Molecular Clock, Variation in the Evolution of Protein Sequences, Variation in the Evolution of DNA Sequences, The Neutral Theory of Molecular Evolution, Mutation And GeneticDrift, Molecular Evolution and Phenotypic Evolution. Species concept; subspecies, sibling species, semi species, demes. Types of speciation - Phyletic speciation and True speciation. Mechanism of speciation - Genetic divergences and isolating mechanisms. Patterns of speciation - allopatric, sympatric, quantum and parapatric speciation, Convergent evolution; sexual selection; co-evolution; Human Evolution: Humans and the Great Apes, Human Evolution in the Fossil Record, DNA Sequence Variation and Human Origins

Fundamentals of Bacterial and Viral Genetics, Bacterial and Bacteriophage Evolution, Genetic Transformation, Conjugation and the Escherichia coli Paradigm, Plasmids and Conjugation Systems Other than F, Plasmid Molecular Biology, Genetics of Temperate Bacteriophages, T4 Bacteriophage as a Model Genetic System, Genetics of Other Intemperate Bacteriophages

1.      Benjamin Lewin (2000). Genes VII. Oxford university press.

2.      Gardner E J, Simmons M J, Snustad D P (1991). Principles of Genetics (III Edn). John Wiley and Sons Inc.

3.      Snustad D P, Simmons M J (2000). Principles of Genetics (III Edn). John Wiley and Sons.

4.      Strickberger (2005). Genetics (III Edn). Prentice Hall of India Pvt. Ltd.

5.      William S Klug, Michael R Cummings (1994). Concepts of Genetics. Prentice Hall.

1.      Robert J Brooker (2009). Genetics: Analysis and principles (III Edn). McGraw Hill.

2.      Daniel L Hartl, Elizabeth W Jones (2009). Genetics: Analysis of genes and genomes (VII Edn). Jones and Bartlett publishers.

3.      D Peter Snustad, Michael J Simmons (2010). Principles of genetics (V Edn). John Wiley and Sons.

4.      George Ledyard Stebbins (1971). Process of Organic evolution.

5.      Roderic D M Page, Edward C Holmes (1998). Molecular Evolution: A phylogenetic approach.

6.      Blackwell Science Ltd.

7.      MaxtoshiNei, Sudhir Kumar (2000). Molecular Evolution and phylogenetics. Oxford University Press.

8.      Katy Human (2006). Biological evolution: An anthology of current thought. The Rosen publishing group, Inc.

9.      Monroe W Strickberger (1990). Evolution. Jones and Bartlett publishers.

10.  E d w a r d A . B i r g e, Bacterial and Bacteriophage Genetics, 5^th Ed. Springer

To understand what is meant by concentration, by volume, and by amount, and their interrelationships

Make the students able to convert multiples of one unit to another

To make the students understand that there is a physical limit to the volume of a solution you can pipette, determined by your equipment

Fractions, Decimals and Percentages, Amounts, Volumes and Concentrations, Scientific Notation, Conversion of Units.

Solving Equations and Evaluating Expressions, Logarithms, Straight-Line and Non-Straight-Line Graphs, Rate of Change

Microbes play a very significant role in the lives of higher organisms. The paper surveys the features of microbes like bacteria, viruses, fungi, algae and protozoa in order to make the students understand their biology so as to manipulate them. This course fulfils the basic knowledge in microbiology for those students who wish to pursue career in allied health fields and other technical programs. 

1.      Safety rules, instrumentation and media preparation-- Nutrient agar, Potato dextrose Agar, differential media etc.

2.      Staining techniques: Simple, Differential:acid-fast, endospore, capsule, cell wall, cytoplasmic inclusion, vital stains: flagella, spore and nuclear staining.

3.      Collection and processing of clinical samples for microbiological examination

4.      Antimicrobial susceptibility tests- a. Kirby-Bauer disc diffusion test and Dilution sensitivity test-MIC and MBC against Yeast and other fungi.

5.      Mutagenesis- By physical and Chemical agents

6.      Production and separation of aflatoxin using paper chromatography.

7.      Determination of Growth of bacteria, yeast and algae – Growth curve and generation time.

8.      Isolation and culture of Rhizobium and production of biofertilizer

9.      Biochemical tests Catalase, oxidase, IMViC, motility, gelatine test, urease, coagulase, nitrate reduction, acid and gas from glucose, chitin, starch.

10.  Isolation of fungi from soil: Dilution plate method, Warcup method, stamping method.

11.  Plaque assay.

12.  Screening for antibiotic producing microbes (antibacterial, antifungal)

13.   Visit to microbiology R & D lab.

1.            Laboratory safety guidelines

2.            Preparation of buffers applying HH equation

3.            Validation of Beer-Lambert’s Law (colorimetery and spectrophotometer)

4.            Qualitative and Quantitative analysis of carbohydrates

5.            Analysis of Amino Acids and Sugars (TLC and Colorimetric)

6.            Isolation and quantification of protein (Folin Lowry/BCA, Bradford).

7.            Purification of protein by affinity chromatography

8.            Determination of isoelectric pH of proteins / amino acids

9.            Determination of specific activity, Km & Vmax, Optimum pH, Temperature of Amylase/Alkaline phosphatase /protease/cellulase

10.        Isolation, qualitative and quantitative analysis of fatty acids and lipids.

11.        Acid values Iodine number & Saponification values of fats

12.        Estimation of Ascorbic acid in citrus using 2, 6 dichlorophenol Indophenol.

13.        Simple assays for vitamins and hormones

14.        Bilirubin, Cholesterol, inorganic phosphate, creatinine, urea and uric acid estimation 

S Sadasivam and A. Manickam, Biochemical Methods, 2^nd ed. New Delhi: New Age International Publishers Ltd., 1996

The paper imparts practical knowledge on the biology of cells and also on the basic experiments in biochemistry. It deals with detailed microscopic studies of basic cell multiplication processes like mitosis and meiosis. Microscopy techniques are given utmost importance.  

1. Workout problems related to linkage, crossing over and gene mapping, human pedigree analysis.

2. Workout problems in population genetics - gene and genotype frequency, Hardy Wienberg equilibrium.

3. Genetic Studies in Drosophila melanogaster.

1. Isolation of chloroplasts and determination of chlorophyll content.

2. Comparing the effect of some physical and chemical factors on the efficiency of photosynthetic electron transport.

3. To study the effect of inhibitors and uncouplers on the activity of succinic dehydrogenase, a marker enzyme of mitochondria.

4. In situ visualization of microfilaments and microtubules by fluorescent labeling.

5. In silico analysis (sequence comparison) of mitochondrial and chloroplast genes for identification of the loci for interspecific discrimination.

6.      Microscopy: Bright field, phase contrast and fluorescence.

7.      Permanent slide preparation.

8.      Cell fractionation: Differential and density gradient centrifugation.

9.      Analysis of subcellular fractions.

10.  Succinate dehydrogenase activity in mitochondria.

11.  Permeability of artificial and natural membrane.

12.  Spectrophotometric analysis of membrane stability in beet root cells

13.  Study of metaphasic chromosome in onion root tip.

14.  Study of meiotic stages in the onion flower bud.

15.  Preparation of human chromosomes by culturing of lymphocytes.

16.  C-banding, G-banding and karyotyping of human chromosomes.

17.  Micrometry: determination of size of onion cells.

18.  Study of plasmolysis and deplasmolysis.

19.  Counting cells by hemocytometer.

20.  Buccal smearing for identification of Barr Body.

This module aims to provide students with an in-depth understanding of the basic concepts of molecular biology. The structural and functional aspects of basic biomolecules such as DNA, RNA and protein and the mechanisms of DNA replication, transcription, translation and gene regulation will be dealt with. The course facilitates the students to have a strong understanding of the molecular basis of life and the underlying genetic principles.

Nucleic Acids: - DNA and RNA as genetic material and the proof (Griffith Experiment, Avery-McCarthy-McCleod Experiment, Hershey Chase Experiment, Biochemical evidences, Experiments using HRV and TMV)

Watson and Crick model of DNA (Structure of Bases, Nuceosides and nucleotides, Chargaff Rule, Watson and Crick base pairing, Hoogsteen base pairing, physical measurements of DNA, antiparallel nature), Different forms for DNA (A, B and Z), chemical and spectroscopic properties of DNA (Effect of temperature:- denaturation and renaturation kinetics, Absorption of UV light, density gradient centrifugation, intercalating agents, effects of Acid and Alkali on DNA, solubility of DNA), DNA supercoiling (negative and positive super coiling), Topoisomerase (Types and mechanisms). Hypothesis on DNA replication, Proof for Semi conservative model of replication of DNA (Meselson and Stahl Experiment, Thymidine incorporation Assay), Polarity of DNA replication, Prokaryotic DNA Replication Machinery: Gyrase, helicase, DNA polymerases (types, functions, properties) Origin of replication of DNA, Primer, Growing Fork, Mechanism of DNA replication (initiation, elongation (lagging and leading strand synthesis) and termination. Eukaryotic DNA replication – Multiple origins of replication, Enzymes and proteins involved in replication, End replication problem and its solution (Telomere and telomerases and its significance in replication and involvement in cancer and aging). Models of DNA replication: Theta model and Rolling circle model, D-loop method. Inhibitors of DNA replication 

Mutation: Definition and Types (Point mutation: Substitution, Addition, Deletion; Frame-shift Mutation, Missense and nonsense mutation, forward and reverse mutation, suppression mutation. Somatic and germ line mutation, Transition and transversion, Neutral nonsynonymous and synonymous mutation, lethal mutation) causes of mutation: Spontaneous (Wooble base pairing, addition and deletion by DNA looping out, spontaneous chemical changes: oxidative damage, alkylation and deamination) and Induced mutations (UV, base analogues, alkylating, Hydroxylating and deaminating agents.

Photoreactivation, Mismatch repair, excision repair (BER and NER), SOS repair and recombination repair, Homologous and non-homologous; Site specific recombination; Chi sequences in prokaryotes; Gene targeting; Gene disruption; FLP/FRT and Cre/Lox recombination

Organization of genomes in prokaryotes and eukaryotes- concept of Gene, structure of genes, Monocistronic and polycistronic genes, C value paradox, Gene organization and expression in mitochondria and choloroplast, functions, significance, role in evolutionary studies. Transposable elements – classes, transposons in bacteria, maize and drosophila, retrotransposons, LINEs and SINEs, transposons and mutations. 

Structure and functions of mRNA, tRNA, rRNA, snRNA, miRNA, hnRNA and siRNA, Ribozymes, RNA polymerases, Transcription – initiation (Structure of promoter, initiation factors, mechanism of initiation), elongation (factors and mechanism) and termination (mechanism and types of termination: rho dependent and rho independent), transcription factors and its importance, Post transcriptional modifications of eukaryotic mRNA- polyA tailing, Differential Polyadenylation, splicing, capping. 

Properties of Genetic code and Wobble hypothesis. Mechanism of translation in prokaryotes and eukaryotes (activation and attachment of amino acid to tRNA, initiation, elongation and termination of polypeptide chain), role of Ribosomes in Protein synthesis, post translational modifications of proteins- (glycosylation, protein folding, acetylation, phosphorylation), polysomes, protein stability, Protein transport and regulation(Hydrolytic enzymes of lysosome).

Operon concept and its advantages, anabolic (trp operon) and catabolic operon (lac operon), Regulation of Gene expression in Eukaryotes– Britten Davidson model, Zinc finger as DNA Binding domain, Zinc finger is present in steroid hormone receptors, superfamily of ligand responsive transcription factors for thyroid hormones, genes active are DNase I sensitive, HMG proteins and chromatin configuration, activators, enhancers, silencers, DNAlooping in transcriptional regulation, RNA interference, DNA (methylation) Ubiquitination, and Histone (acetylation) modifications, Genes that regulate embryogenesis in C. elegans, gene silencing, RNA silenceing.

The objective of the course is to impart in depth knowledge about the concepts in genetic engineering - enzymes, biology of cloning vehicles, vector and host considerations, gene libraries, analysis and expression of the cloned gene in host cell and understand ethical issues and biosafety regulations. It gives emphasis to practical applications of genetic engineering tools in academic and industrial research. At the end of the course the student will have detailed knowledge of recombinant DNA technology essential for taking up projects in the field of Biotechnology.

Introduction to rDNA technology, DNA modifying enzymes and its functions (DNA Polymerases, Klenow fragment, Ligase, S1 Nuclease, Mung Bean nuclease, Alkaline Phosphatase, Terminal Transferase, Polynucleotide kinases, Polynucleotide phosphorylase, Calf intestinal alkaline Phosphatases, Shrimp Alkaline Phosphatases, RNase A, RNase H, DNase 1, DNase II, Exonuclease III, Reverse Transcriptase) Restriction modification system, Restriction enzymes – function, classification (Based on recognition and restriction sequence:-type I, II and III; based on buffer salt concentration: - low, medium and high; based on pattern of restriction:-sticky (5’ and 3’) and blunt end cutters, Plasmids (Types, copy number, properties, origin of replication and incompatibility group, plasmid amplification), bacteriophages eg. λ (Life cycle, genome organization, feasibility as a cloning vehicle), Types of Cloning Vectors (structure and general features of General Purpose cloning vectors, Expression vectors, Promotor probe Vectors, shuttle vectors), Examples of cloning vectors (pBR322, pUC series of vectors, λ insertional and replacement vectors), derivatives of phages and plasmids (cosmids, phagemids, phasmids) cloning vectors for large DNA fragments and genomic DNA library YACs, PACs and BACs. Host and vector consideration, Host Organisms and its genotypes- JM 109 & DH5α, Selectable and scorable markers, reporter genes, prokaryotic and eukaryotic markers (lacZ, CAT, Gus, GFP,cre-loxP system, sac B system, npt II gene, luciferase gene, dhfr gene, herbicide resistance gene)

General strategies for isolation of genomic and plasmid DNA, RNA, strategies for isolation of gene of interest (restriction digestion, PCR), Creation of r-DNA (Restriction Digestion, modification of vector and insert, linker, adaptors, homopolymer tailing, ligation), PCR Cloning, Construction of genomic and cDNA libraries (Selection of vectors and Complexity of library), Methods of gene transfer- Calcium chloride mediated, Electroporation, Biolistic gun, lipofection and microinjection. In vitro packaging.

Blotting techniques- Southern, Northern and Western, Differential display. Gene sequencing- Chemical, enzymatic, pyrosequencing, next generation sequencing, Immunological screening and colony and plaque hybridization, dot blot hybridization, chromosome walking, FISH, RACE, Chromosome walking.

Protein production by foreign DNA in the host bacteria E. coli, Factors influencing expression, properties of expression vector, examples of expression vectors, tags for purification of expressed proteins, FLAG expression vector system, cloning in pET vectors, eukaryotic vectors- Baculovirus based vectors, mammalian viral vectors., expression Host, Modification and folding of protein in-vitro, genome editing, CRISPR/Cas9 and Targeted Genome Editing, 

RNA interference and gene silencing, Transgenic organisms, Advantages and disadvantages of Genetically Modified Organisms, Transgenic animal- Gene therapy. The Use of Transgenic animals in areas other than recombinant protein production. Transgenic plants- applications, special emphasis to pharmaceutical products. Engineered Nutritional Changes- golden rice, Engineered herbicide resistance, Engineered pesticide resistance. Production of recombinant proteins (Insulin), recombinant vaccines (Hepatitis B), Hormones (Human growth hormone). Genome projects and its Applications. International treaties/agreements in biosafety, public perception on rDNA technology, IPR related to rDNA technology. 

E. L. Winnacker, From Genes to Clones Introduction to Gene Technology,New Delhi, India: Panima Publishing Corporation, 2003.

T. A. Brown, Gene Cloning and DNA Analysis-An Introduction. 5th ed. UK: Wiley Blackwell Publishers. 2006.

B. R. Glick. J. J. Pasternak and C. L. Patten. Molecular Biotechnology: Principles and application of recombinant DNA. 4th ed. Washington D. C: American Society for Microbiology Press, 2010.

 S. B. Primrose, R. M. Twyman and R. W. Old, Principles of Gene Manipulation, 6th ed. USA: Wiley-Blackwell, 2001

K. Wilson and J. Walker, Principles and Techniques of Biochemistry and Molecular Biology, 7th ed. New York: Cambridge University Press, 2010.

 J.  W.  Dale, M. von Schantz and N. Plant, From Genes to Genomes: Concepts and Applications of DNA Technology, USA: John Wiley & Sons Inc., 2012.

Analytical tools are becoming very important tools in different fields of Biology. The paper deals with the principle, instrumentation and uses of such tools.  This course fulfils the basic knowledge in analytical techniques for those students who wish to pursue career in allied health fields and other technical programs.

This course will make the students adept in the working of analytical instruments. They also become confident to use bioinformatics softwares and work with different databases for applications in upcoming fields of biology, which in turn make them competent for jobs in clinical and medical data analysis labs.

Concept of pH, Henderson Hesselbach equation. Importance of buffers in living systems – bicarbonate buffer, phosphate buffer. Breaking of cells by chemical and physical methods, ultrasonication, pressure cell disintegrators, detection of cell-free and cell-bound proteins.Extractions: Preparation of extracts for biochemical investigations, methods of extraction of phytochemicals (Maceration, Soxhlet, Microwave assisted, Ultrasonic, Pressurized liquid extraction)type and choice of solvents.

Centrifugation: Principle of centrifugation, the Swedberg equation, types of centrifuges and rotors. Density gradient centrifugation, Cesium chloride and sucrose density gradients; examples of separations, analytical ultracentrifuges. Ultra-filtration -Principle, instrumentation and application. Dialysis-principle and uses. Precipitation- methods and applications. Flow Cytometry; Principle and uses.

Chromatography- principle, types (Column, Ion exchange, Gel permeation, Affinity), Gas chromatography, HPLC, HPTLC

Electrophoresis - buffers, agarose gel electrophoresis, native and SDS -PAGE, Isoelectric focusing, Zymogram, 2 D gel electrophoresis, DGGE, PFGE, Protein staining, trouble shooting, 

Protein purification methods, salt fractionation, salting in and salting out, methods of crystallizing proteins

Spectroscopy: Absorption and emission spectra. Electromagnetic radiation. Fluorescence and phosphorescence, Beer- Lambert’s law, principle, operation and applications of Colorimeter, Spectrophotometer, Concept of Stoke’s shift- hypochromicity, hyperchromicity, fluorimeter, flame photometer, Atomic absorption spectrophotometer. IR, Mass spectroscopy and NMR, ICP-MS, GC-MS, LC-MS, X ray crystallography.

Radioactive isotope, Radioactivity and units of radioactivity (Curie, Rutherford and Becquerel).GM and Scintillation counters. radioactive decay, Radiocarbon dating, autoradiography, use of radioisotope tracer techniques in disease diagnosis, PET scan for tumor detection, Radioimmunoassay, ELISA, Western Blot, Nanoparticles – synthesis and uses, application of nanotechnology in disease diagnosis and treatment, Microarrays.

Introduction and application of bioinformatics. Definition and types, Nucleotide sequence database - brief note on EMBL, NCBI and DDBJ. Protein structure database [PDB]. Sequence alignment: pair wise and multiple alignments [Definition, applications, BLAST and FASTA, Clustal W, PAM and BLOSUM matrices].  ORF. Structure prediction, and molecular visualization – use of Rasmol, PDB, ExPASY and KEGG. Online tools – SDSC Biology workbench.

Genomics: Definition. Types [Structural, functional and comparative genomics].    Pharmacogenomics: Definition and its benefits in the health care sector. Genome projects- Human, Rice, Arabidopsis, Tomato, Hemophilusinfluenzae, Proteomics, Transcriptomics and Metabolomics – current status and potential applications in agriculture and medicine. Systems Biology- concept and applications.

Molecular phylogeny and phylogenetic trees, tools for phylogeny analysis, Computer aided drug design. Docking Studies - Target Selection, Active site analysis, Ligand preparation and conformational analysis, Rigid and flexible docking, Structure based design of lead compounds and Library docking.

T. Attwood and P. Smith. Introduction to Bioinformatics, USA: Pearson Education, 2007.

Brown TA. Genome III. Garland Science Publ.2007

Azuaje F &Dopazo J. Data Analysis and Visualization in Genomics and Proteomics. John Wiley & Sons.2005

K. Wilson and J. Walker,Principles and Techniques of Biochemistry and Molecular Biology, 7th ed.New York: Cambridge University Press, 2010.

S. B. Primrose and R. Twyman R. Principles of Gene Manipulation and Genomics. USA: John Wiley and Sons, 2013.

Gibson G & Muse SV. 2004. A Primer of Genome Science. Sinauer

Associates.

W. Taylor and D. Higgins. Bioinformatics: Sequence, Structure and Databanks: A    Practical Approach, Oxford, 2000.

Jollès P &Jörnvall H. 2000. Proteomics in Functional Genomics: Protein

Structure Analysis.

Campbell AM &Heyer L. 2004. Discovery Genomics, Proteomics and Bioinformatics. Pearson Education.

Students will be informed of various aspects of research such as formulation, designing, scientific documentation and communication, as well as, ethics involved. Students will also be informed about the plagiarism. They will also gain knowledge about the involvement of statistics in reserch.

Need for research, stages of research; Basic concepts of research -Meaning, Objectives, Motivation and Approaches. Types of Research (Descriptive/Analytical, Applied/ Fundamental, Quantitative/Qualitative, Conceptual/ Empirical); Research formulation -Observation and Facts, Prediction and explanation, Induction, Deduction; Defining and formulating the research problem, Selecting the problem and necessity of defining the problem; Literature review -Importance of literature reviewing in defining a problem, Critical literature review, Identifying gap areas from literature review; Hypothesis -Null and alternate hypothesis and testing of hypothesis -Theory, Principle, Law and Canon.

Research Design -Basic principles, Meaning, Need and features of good design, Important concepts; Types of research designs; Development of a research plan -Exploration, Description, Diagnosis, Experimentation, determining experimental and sample designs; Data collection techniques, Case-Control Studies, Cohort Studies.

Workbook maintenance, Project proposal writing, Research report writing (Thesis and dissertations, Research articles, Oral communications); Presentation techniques - Assignment, Seminar, Debate, Workshop, Colloquium, Conference.

Sources of Information -Primary and secondary sources; Library - books, Journals: Indexing journals, abstracting journals, research journals, review journals, e-journals. Impact factor of journals, NCBI-Pub Med.; periodicals, reference sources, abstracting and indexing sources, Reviews, Treatise, Monographs, Patents. Internet -Search engines and software, Online libraries, e-Books, e-Encyclopedia, TED Talk, Institutional Websites; Intellectual Property Rights - Copy right, Designs, Patents, Trademarks, plagiarism, Geographical indications; Safety and precaution - ISO standards for safety, Lab protocols, Lab animal use, care and welfare, animal houses, radiation hazards; Extension: Lab to Field, Extension communication, Extension tools; Bioethics: Laws in India, Working with man and animals, Consent, Animal Ethical Committees and Constitution.

The scope of biostatistics; Classification of study design, Observationalstudies and Experimental studies (uncontrolled studies, trials with external controls, crossoverstudies, trials with self-controls, trials with independent concurrent controls); Exploration and presentation of data: Scales of measurement, Tables, Graphs,Histograms, Box and Whisker plots, Frequency polygon, Scatter Plots, Principle component analysis.

Definition, mutually exclusive events and addition rule, independent events andmultiplication rule. Sampling: Reasons for sampling, methods of sampling, SRS, Systematic, Stratified, Cluster, NPS. Probability distribution: Binomial, Poisson, Gaussian,Standard normal distribution. Drawing inferences from data: Tests of significance: Statistical inference – estimation - testing of hypothesis - t-test, Chi square test (goodness of fit,independence or association, detection of linkages), Z-test, Confidence intervals,Confidence limits, Hypothesis tests, Types of errors, P-values.

Decision about single mean (normal population andnon-normal population), decision about single group, decision about paired groups, decisionabout two independent groups, equality of population variances, computer-aided illustrationfor comparison of means; Comparing three or more means: ANOVA – one way, two way, A-priori comparison,Posterior or Post Hoc comparison. Statistical methods for multiple variables: Multiple regression, predicting with more than 1 variable, Statistical test for regression coefficient, Role of R and R2 in multiple regression, Confounding variable (ANACOVA), Predicting categorical outcomes – logistic regression, discriminant analysis.

Pearson’s correlation coefficient, Spearman’s rho, Linearregression, Least Square method, predicting with regression equation, comparing tworegression lines, dealing with nonlinear observation, Common errors in regression,Comparing correlation and regression.

1.      Dawson, C. Practical research methods. UBS Publishers, New Delhi. 2002.

2.      Ruzin, S.E. Plant microtechnique and microscopy. Oxford University Press, New York, U.S.A., 1999.

Ethics in Science aims to provide formal training in the ethical questions and problems that arise in scientific and professional environments. The goals of this course are to contextualize standard ethics in science and to challenge and critically review current philosophies on scientific ethics. Emphasis will be placed on reasoning through conflicts and arguments through discussion, written assignments, and oral presentations.

1. Introduction to Ethics: Ethical Problem Solving, Interpersonal Relationships
2. Ethics in the Laboratory
3. Research Misconduct; professional ethics and bias in research design
4. Data acquisition, management and sharing; Sloppiness vs Fabrication
5. Publishing: Credit and responsibility in Science
6. Intellectual Property rights
7. Peer review process and Conflicts of interest
8. Funding, proposals, and manuscripts
9. Safety and the Laboratory
10. Science and Society
11. Safety and the environment
12. Hiring and the workplace: supervisors and advisors Peer review
13. the use of animals and human subjects in research
14. Bad ethics versus Bad Science

plants in medicine, its origin and development

Morphology, active principles and medicinal value of the following: i. Andrographis paniculata ii. Asparagus racemosus iii. Clitoria ternata    iv. Phyllanthus emblica   v. Gymnema sylvestre

Occurrence, distribution, Organoleptic evaluation, Microscopical evaluation, chemical constituents including tests wherever applicable and Therapeutic efficacy of following categories of drugs. a) Drugs acting on nervous system –Ashwagandha, Opium, b) Antihypertensives – Rauwolfia c) Antitussives – Vasaka, Tulsi d) Antirheumatics – Guggul, e) Antitumour – Vinca f)Antileprotics – Chaulmoogra Oil g) Antidysenterics – Holarhaena h) Antiseptics and Disinfectants -Murraya, Neem, Curcuma. i) Antimalarials – Cinchona, Andrographis j) Oxytocics – Ergot k) Vitamins –Amla l) Enzymes – Papaya

Assignment - 10 

Mini project - 20 

exam -          20

Practical course of molecular biology deals with the isolation of protein from animal and plant source using different methods and also the estimation of DNA, RNA and protein.

1.       Isolation and purification of DNA from plant, animal, Bacterial and fungal samples
2.       Isolation of plasmid DNA from the bacteria
3.       Isolation of megaplasmid from the environmental isolates
4.       Isolation of RNA from plant, animal and bacterial samples and separation on denaturing gel
5.       Primer design and PCR amplification of DNA
6.       Gel-band purification for DNA
7.       RFLP and RAPD, ISSR/SSR analysis of DNA
8.       Cloning and expression of gene in E. coli.
9.       Southern blotting and hybridization.
10.     Site directed mutagenesis
11.       Quantitative study of DNA/RNA/Proteins

Analytical tools are becoming very important tools in different fields of Biology. The paper deals with the principle, instrumentation and uses of such tools.  This course fulfils the basic knowledge in analytical techniques for those students who wish to pursue career in allied health fields and other technical programs. 

1.      Extraction of phytochemicals using Soxhlet apparatus

2.      Column Chromatography

3.      Ion exchange and affinity chromatography.

4.      HPLC- Principle and sample preparation, visit to Research Institute for analysis.

5.      Protein and DNA homology search and sequence alignment.

6.      Docking studies of ligands.

7.      Construction of dendrogram

1.      Contingency table, frequency table

2.      Simple bar chart, stem and leaf plot

3.      Histogram, Box and whisker plot

4.      Scatter plot

5.      One sample t-test, independent t-test, paired t-test

6.      Wilcoxon rank-sum test, Mann-Whitney U

7.      One way ANOVA, 2-way ANOVA, Kruskal-Wallis test

8.      Correlation, linear regression, ANACOVA.

9.      SPSS/SAS/minitab/excel

1. Visit a scientific library or documentation center and submit a report.

2. Prepare a project proposal.

3. Prepare an outline of dissertation and research paper.

4. Prepare a list of references.

2.Brown TA. Genome III. Garland Science Publ.2007

3. Azuaje F &Dopazo J. Data Analysis and Visualization in Genomics and Proteomics. John Wiley & Sons.2005

4. K. Wilson and J. Walker,Principles and Techniques of Biochemistry and Molecular Biology, 7th ed.New York: Cambridge University Press, 2010.

2. Jollès P &Jörnvall H. 2000. Proteomics in Functional Genomics: Protein

Structure Analysis

3. Campbell AM &Heyer L. 2004. Discovery Genomics, Proteomics and Bioinformatics. Pearson Education.