Practicals 1

Four Year Undergraduate Course in Biomedical Science

Four Year Undergraduate Programme Biomedical Science

Four Year Undergraduate Course in Biomedical Science

Preamble to FYUP Biomedical Science

The B.Sc.(Hons.) Biomedical Sciences started as an interdisciplinary course which is running in three colleges. The course has been very successful in terms of the career options taken up by the students after graduation over the years. The course in its annual mode prior to 2009 and in the semester mode after 2009 has been structured to reinforce the basic exposure that students get in the higher secondary school and to gradually build on this knowledge-base. The proposed syllabus has taken advantage of the four year duration to gradually make the transition from simple to complex concepts relevant to the interdisciplinary nature of undergraduate programme in Biomedical Science.

In structuring the course two points have been considered primarily: one the load on the student in each course is reduced in comparison to what was existing and other is considering the exit options provided to the students, we have aimed to offer a comprehensive skill and the knowledge base for the students keeping in mind, the employability of the students. The DC-I courses of the first two semesters are introductory courses in organic chemistry relevant to biology, biology of the cell, the basic building units of an organism, human physiology a glimpse at the orchestrated functioning of organ systems and the basic principles of genetics as seen in nature. Thus at the end of the second year, a student with an Associate Baccalaureate degree will have basic knowledge of cell biology, genetics, bioorganic chemistry, human physiology, protein chemistry, basic molecular biology and medical biochemistry. Along with this they will have hands-on training in medical lab techniques and tools used in forensic science under the AC courses. In the second year the students would build on what is introduced in the I & II semesters; for instance building on basic Bio-orgnic chemistry the students will learn more about proteins, the work-horses of the cell running the biochemical factory. This pattern is kept in focus at every exit point. The concepts in Medicinal chemistry, Pharmacology and toxicology are vital to Biomedical Sciences and these are introduced in the later semesters of the course.

In the fourth year the courses include more complex concepts of mechanisms of achieving regulated functioning of the biological systems, biophysical principles of biological systems and some of the recent excitement in biology and the application of bioinformatics in Biomedical Science, along with project work. One or two papers in the final year therefore have a longer list of learning material to be drawn from different sources; however the actual length of the material for reading/teaching is minimal. This also introduces the students to resources for self- study.

The DC-II courses are designed to give the essential exposure to the interdisciplinary nature of Biomedical Sciences to students of other disciplines within a comprehensive structure. For example, pharmocololgy and toxicology are combined into one paper, bioinformatics, pathotophysiology combining human physiology in the context of diseases are part of DC-II courses.

The syllabus before you is the joint effort of all the teachers involved in teaching Biomedical Sciences in all the colleges, in different capacities, along with all the faculty members of the Dr. B. R. Ambedkar Center for Biomedical Research of the University.

Four Year Undergraduate Course in Biomedical Science

COMPLETE COURSE STRUCTURE Semester DC-I : Theory and Practical DC-II AC Papers BMS 101: Bio-organic Chemistry I BMS 102 : Cell and Radiation Biology BMS 201: Principles of Genetics BMS 203: HIN/ENG/MIL II BMS 202: Human Physiology & Anatomy – I BMS 301: Protein Chemistry and BMS (DC-II) A : Biosafety and BMS 303: Medical Lab Function Bioethics Diagnostics (MLD) III BMS 302: Human Physiology & Anatomy - II BMS 401: Medical Biochemistry BMS (DC-II) B: Pathological BMS 403:Techniques for IV BMS 402:Genome Organization basis of diseases Forensic Sciences and Function – I OPTION OF EXIT AFTER TWO YEARS WITH DIPLOMA BMS 501: Introduction to BMS (DC-II) C: Concepts of BMS 504: Methods for Biopharmacology and in Medicinal Chemistry and epidemiological data analysis V Pharmacokinetics drug development BMS 502: Medical Microbiology BMS 503: Immunobiology BMS 601: Human Pathology BMS (DC-II) D Pharmacology BMS 604: VI BMS 602: Medicinal Chemistry & Toxicology Tools in Modern Biology BMS 603: Toxicology OPTION OF EXIT AFTER THREE YEARS WITH BACHELOR DEGREE BMS 701: Genome Organization BMS (DC-II) E Bridging and Function II Information Technology and BMS 702: Medical Biotechnology VII Biotechnology BMS 703: Research Methodology and Project Work BMS 801: Computational BMS (DC-II) F Tools and Biology and drug design model organisms in Biomedical VIII BMS 802: Biophysics Research BMS 803: Project Work EXIT AFTER FOUR YEARS WITH BACHELORS DEGREE WITH HONOURS

Foundation Course, *DC – I : Discipline Course – I, *DC – II : Discipline Course – II, *AC : Applied Course, IMBH : Integrating Mind Body & Heart, CA : Curricular Activities

Four Year Undergraduate Course in Biomedical Science

Four Year Undergraduate Course in Biomedical Science I Year Semester I and II

Four Year Undergraduate Course in Biomedical Science

Semester I

BMS 101: Bio-Organic Chemistry (DC-I)

Preamble: Bio-organic Chemistry is a discipline that integrates organic chemistry and biochemistry. It aims at understanding the relevance of biological processes using the fundamental concepts of organic chemistry. This course includes basic principles of organic chemistry like concepts of acids and bases, molecular forces responsible for the activities of biomolecules, principles of stereochemistry and their importance in understanding various biomolecular reactions and metabolic processes.

THEORY Total Lectures: 48

Unit I: Aqueous Solutions (04 Lectures) (Chapter 2: Campbell and Farrel)

Water, pH and buffers, pKa (Titration Curves of amino acids), Henderson-Hasselbach equation, buffering zone, buffer index, concept of pI and zwitter ion.

Unit II: Concept of Acids and Bases. (04 Lectures) (Chapter 8: J. D. Lee)

Arrhenius concept, Bronsted Lowry concept, Lewis concept, the levelling effect.Effect of pH onthe structure of biomolecules.

Unit III: Chemical Bonding and Molecular Forces (06 Lectures) (Chapter 2: J. D. Lee; Chapter 1: Morrison and Boyd)

Introduction to ionic interactions and covalent bond, intermolecular and intramolecular forces, types of intermolecular forces and their characteristics: ion-dipole, dipole-dipole, dipole-induced dipole and dispersion (London) forces, hydrogen bond (intramolecular and intermolecular), effect of inter/intramolecular forces on structure of different biomolecules.

Unit IV:Stereochemistry (08 Lectures) (Chapter 4 and 13: Morrison and Boyd)

Optical isomerism: Optical activity, specific rotation, enantiomerism, DandL designation, racemic modification, R and S sequence rules, diasteroisomers. Conformational isomers: conformation of ethane and butane, interconversion of projection formula, cyclohexane (mono- and di-substituted), resolution, optical purity, Walden inversion, enantiotopic and diastereotopichydrogens and prochiralcenters. Geometrical isomerism: Definition, nomenclature– E and Z.

Four Year Undergraduate Course in Biomedical Science

Unit V: Introduction to Biomolecules and their Metabolism

Analogy between organic reactions and biochemical transformations.

(i) Carbohydrates (10 Lectures) (Chapter 18: Finar, volume 1; Chapter7, 14, 16 and 19: Nelson and Cox)

Monosaccharides- cyclization of aldoses and ketoses, conformations, concept of mutarotation, anomers, epimers, derivatives-sugar phosphate, sugar alcohol, sugar acids, deoxy and amino sugars, ascorbic acid. Disaccharides- structure, reducing and non-reducing sugars. Polysaccharides- Starch, glycogen and cellulose. Carbohydrate metabolism- Glycolysis, gluconeogenesis and their regulation, tricarboxylic acid cycle, electrontransportchain, oxidative phosphorylation, hexose monophosphate shunt.

(ii) Lipids (05 Lectures) (Chapter 10, 17 and 21: Nelson and Cox; Chapter 7and 18: Campbell and Farrel)

Fatty acids, triacylglycerols, glycerophospholipids, sphingolipids, steroids (cholesterol and its derivatives). Lipid metabolism- Mobilization of triglycerides, metabolism of glycerol, β-oxidation of saturated fatty acids(palmitic acid), ketone bodies, biosynthesis of fatty acids and triglycerides.

(iii) Amino Acids (02 Lectures) (Chapter3: Nelson and Cox; Chapter 3: Campbell and Farrel)

General structure, ionization, chemistry of peptide bond, non-ribosomal peptide bond formation, essential and non-essential amino acids, amino acids as precursors of other bioactive compounds.

(iv) Nucleotides (05 Lectures) (Chapter 8 and 22: Nelson and Cox; Chapter 8 and 20: Campbell and Farrel)

Sugars and Bases, conformation of sugar phosphate backbone, hydrogen bonding by bases, Types of DNA (A, B and Z DNA), tautomers of bases, nucleotide derivatives, nucleotides as regulating molecules, concept of anti-sense molecules. Nucleotide metabolism-Outlines of purine and pyrimidine metabolism.

(v) Enzymes (04 Lectures) (Chapter6: Nelson and Cox; Chapter 5: Campbell and Farrel)

Introduction to enzyme catalysis and kinetics, mechanism of enzyme action and inhibition using specific example.

Four Year Undergraduate Course in Biomedical Science

PRACTICALS 1. Preparation of solutions based on molarity, normality, percentage, dilutions etc. 2. Preparation of buffers.

3. Estimation of Mohr’s salt/ oxalic acid by titrating with KMNO4.

4. Estimation of Cu (II) ions iodometrically using Na2S2O3. 5. Qualitative tests for carbohydrates to identify the given unknown carbohydrate solution:Mohlisch, Barfoed, Fehling/ Tollen/ Benedict, Selvinoff, Osazone, Bial’stests. 6. To determine theIodine number of the given oil/ fat. 7. To find pKa value of given acetic acid/ amino acid. 8. Absorption spectrum of DNA/ Protein

ESSENTIAL BOOKS 1. Concise Inorganic Chemistry, 5th edition (1999), J. D. Lee; Wiley-Blackwell, ISBN-13: 9780632052936. 2. Organic Chemistry, 6th edition (1996), I L Finar; ELBS, Longman Higher Education. ISBN- 13: 978-0582305601. 3. Lehninger: Principles of Biochemistry, 5th edition (2008), David L. Nelson and Michael M. Cox; Prentice Hall Publishers, ISBN-13: 978-0321707338 4. Biochemistry, 4th edition (2003), Campbell, M. K. and Farrel, S. O.;Brooks/Cole, Cengage Learning (Boston), ISBN: 0030348498

SUGGESTED READINGS 1. An Introduction to Practical Biochemistry, 3rd edition (1987), Plummer, McGraw-Hill College; ISBN-13: 978-0070841659 2. Organic Chemistry, 6th edition (1992), R. T. Morrison and R. N. Boyd; Pearson Education. ISBN-13: 9780136436690. 3. Biochemistry, J. M. Berg, J. L. Tymoczko and L. Stryer, 6th edition (2006), W. H. Freeman and Co.,ISBN-13: 978-0716787242 4. Bioorganic Chemistry, 3rd edition (1999), Hermann Dugas;Springer Verlag. ISBN-13: 978- 0387989105

Four Year Undergraduate Course in Biomedical Science

Semester I

BMS 102:Cell and Radiation Biology (DC-I)

Preamble: Biology is essentially the study of life in all of its varied forms. Because cells are the ‘basic unit of life’, the study of cells can be considered one of the most important areas of biological research. This course will provide information about cells, including their composition, their function and cell-cycle checkpoints. The module on radiation biology will help to explore and gain insight into radiation-induced biological responses at molecular, cellular and tissue levels. THEORY Total Lectures: 48

Unit I: The Cell (02 Lectures) (Chapter 1: Cooper; Chapter 1: Karp)

Historical background, significant landmarks, cell theory, structure of prokaryotic and eukaryotic cells, mycoplasma, viruses, viroids, prions.

Unit II: Cell Fractionation (02 Lectures) (Chapter 1: Cooper; Chapter 18: Karp; Chapter 11: Freifelder)

Centrifugation: types of centrifuges, principle and different types of centrifugation- differential, density gradient and equilibrium.

Unit III: Cell Membrane (04 Lectures) (Chapter 13: Cooper; Chapter 4: Karp)

Functions, different models of membrane structure, types of membrane lipids, membrane proteins: types, methods to study membrane proteins (detergents, RBC ghosts), RBC membrane as a model, membrane carbohydrates, membrane asymmetry and fluidity.

Unit IV: Membrane Transport (05 Lectures) (Chapter 13: Cooper; Chapter 4: Karp)

Transport of small molecules:Passive transport (simple diffusion and facilitated diffusion) and active transport and their types (P, V, F and ABC transporter) with example of Na+/K+ pump. Transport of macromolecules: Endocytosis (pinocytosis, phagocytosis), exocytosis.

Unit V: Cell Organelles (14 Lectures) (Chapter 9, 10, 11: Cooper)

Structure and functions of various organelles:

Four Year Undergraduate Course in Biomedical Science

A. Nucleus: Different components, nuclear envelope- its structure, pore complex, nucleo- cytoplasmic interaction (NLS and NES), nucleolous- structure and functions. Chromosome:Structure- centromere and telomere, types of chromosomes based on centromere. Diversity in structure and significance of polytene and lampbrush chromosomes. Mitosis and Meiosis:Different phases and their significance. B. Endoplasmic Reticulum: RER- biosynthesis and processing of proteins, co-translational and post-translational transport of proteins, signal hypothesis, protein sorting. SER- detoxification, biosynthesis of membrane, carbohydrate metabolism, steroid synthesis. C. Golgi Apparatus: Golgi stack (cis, trans and medial cisternae), flow of proteins through GB. Glycosylation and protein sorting. D. Lysosomes: Development of different forms of lysosomes, role in cellular digestion, lysosomal storage diseases- Hurler syndrome, Hunter syndrome, Tay-Sachs disease and Inclusion cell disease (I-cell disease). E. Peroxisomes:Assembly, functions- H2O2 metabolism, oxidation of fatty acids. Glyoxysomes. F. Mitochondria: Detailed structure, endosymbiotic theory, its genome, and functions in brief. G. Chloroplast: Detailed structure, its genome and functions in brief.

Unit VI: Cell Junctions (02 Lectures) (Chapter 14: Cooper)

Basics concepts of anchoring junctions, tight junctions, communication junctions (gap junction and plasmodesmata).

Unit VII: Cytoskeletal Elements (04 Lectures) (Chapter 12: Cooper)

Structure, assembly and functions of: A. Microtubules:Axonemal and cytoplasmic microtubules (cilia, flagella, centrioles, basal bodies). B. Microfilaments: Globular and filamentous actin. General idea about myosin. C. Intermediate Filaments: Different classes

Unit VIII: Cell Cycle (03 Lectures) (Chapter 16: Cooper)

Different phases of cell cycle and their significance.Checkpoints and regulation of cell cycle.

Unit IX: Radiation Biology (12 Lectures) (Chapters 5, 6, 13 and 20: A. H. W. Nias; Chapter 5 and 6: Freifelder)

Introduction of radiations, basic concept of radioisotopes, types of radioactive decay (gamma and beta emitter), half-life, detection and measurement of radioactivity methods based upon ionization (GM counter), methods based upon excitation (scintillation counter). Use of radioisotopes in cell biology in understanding of DNA replication (bidirectional and theta replication), transcription (labeling of RNA) and labeling of protein using labeled amino acid. Use of radioisotopes in biology: Autoradiography, radioisotopes in diagnosis (thyroid disorders, 9

Four Year Undergraduate Course in Biomedical Science

cancer) and therapy (radiotherapy). Effect of radiations (ionizing and non-ionizing) on living systems, radiation induced damage to cell (chromosome and DNA damage), precautions and safety measures in handling radioisotopes.

PRACTICALS 1. Microscopy- Theoretical knowledge of Light and Electron microscope. 2. To study the following techniques through electron/ photomicrographs: fluorescence microscopy, autoradiography, positive staining, negative staining, freeze fracture, freeze etching shadow casting, endocytosis and phagocytosis. 3. To explain mitosis and meiosis using permanent slides. 4. To cytochemically demonstrate presence of proteins in cheek cells or onion peel using mercuric bromophenol blue or fast green. 5. To cytochemically demonstrate presence of carbohydrates in cheek cells or onion peel using periodic acid Schiff’s reagent. 6. To cytochemically demonstrate presence of DNA in cheek cells or onion peel using Feulgen reagent. 7. To study the effect of isotonic, hypotonic and hypertonic solutions on cells. 8. To prepare polytene chromosomes.

ESSENTIAL BOOKS 1. The Cell: A Molecular Approach, 5th edition (2009), Cooper and Hausman. Sinauer Associates, Inc. ISBN-13: 978-0878933976. 2. Cell and Molecular Biology: Concepts and Experiments, 6th edition (2009), Gerald Karp, Wiley. ISBN-978-0470483374. 3. Physical Biochemistry: Applications to Biochemistry and Molecular Biology, David Freifelder, 2nd edition (1983), W. H. Freeman and Company. ISBN: 0716714442 / 0-7167- 1444-2. 4. An Introduction to Radiobiology, 2nd edition (1998), A. H. W. Nias, Wiley Blackwell, ISBN- 13: 978-0471975908.

SUGGESTED READINGS 1. The World of the Cell, 7th edition (2008), Becker, Kleinsmith, Hardin and Bertoni. Benjamin Cummings, ISBN-13: 978-0805393934. 2. The Cell: A Molecular Approach, 6th edition (2013), Cooper and Hausman; Sinauer Associates, Inc. ISBN-13:978-1605351551. 3. Essential Cell Biology, 7th edition (2009), Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts and Walter. Garland Science. ISBN-13:978-0815341291. 4. Molecular Cell Biology, 7th edition (2012), Lodish, Berk, Kaiser, Krieger, Bretscher, Ploegh, Amon and Scott. W. H. Freeman. ISBN-13: 978-1429234139.

Four Year Undergraduate Course in Biomedical Science

Semester II

BMS 201:Principles of Genetics (DC-I) Preamble: Genetics having its roots in mathematics thanks to Mendel, appeals to students as one of the analytical branches of biology even in senior school. Basic concepts that are essential to understand inheritance will be taught, starting from the abstract factors to physical basis of inheritance. The course aims to communicate the pivotal role of Mendelian concepts in the development of the science of genetics and also the fact that nature is full of examples that deviate from Mendelian laws starting from linkage groups. Introduction of models and the way they have contributed to our understanding of genetics will provide a perception of how forward genetics has been used to understand the basis of continuity of information transfer that is applicable to not only to the simple life forms but also to humans on one hand and to complex process of development on the other. Most of the topics will be at the introductory level, which would motivate the students to understand the molecular basis of genotype to phenotype correlation. THEORY Total Lectures: 48 Unit I: Overview of changing paradigms in genetics (02 Lectures) (Chapter 1: Snustad and Simmons)

A brief overview of how genetic principles took shape, leading to the concept of a blueprint of life within the cell to the physical entity of DNA. Also mention the surprises we have from the genomics such as genetic variation between individuals. There are popular videos/presentations that can be used. The purpose is to ignite the curiosity of the students.

Unit II:Concept of genetic inheritance (04 Lectures) (Chapter 3, 4: Snustad and Simmons)

Concept of alleles, haploid and diploid status, phenotype and genotype: Mendel’s laws of inheritance, dominant and recessive inheritance, test, back and reciprocal crosses with two examples each.

Unit III: Physical basis of inheritance (06 Lectures) (Chapter 4, 5, 7: Snustad and Simmons)

Chromosomal theory of inheritance, concept of linkage and crossing over, cytological proof of crossing over, genetic mapping: two and three point cross over. Distinguishing recombination and complementation. Allelic interactions- dominance relationships- complete, incomplete and co-dominance, gene-gene interaction.

Unit IV: Extra nuclear inheritance (03 Lectures) (Chapter 9: Klug and Cummings)

Criteria for extra nuclear inheritance, plastid inheritance in Mirabilis jalapa, kappa particles in Paramecium, maternal effect- snail shell coiling, cytoplasmic inheritance (mitochondria and chloroplast). 11

Four Year Undergraduate Course in Biomedical Science

Unit V: Mutation (04 Lectures)(Chapter 13: Snustad and Simmons;Chapter 11: Strachan and Read)

Concept of selection with examples from bacteria, prototrophy and auxotrophy, spontaneous and induced mutations, types of mutations- point, (non-sense, missense, frame shift, insertion, deletion), use of mutants to study gene functions, effects on the gene product- loss of the function and gain of function. Distinction between mutation and polymorphism.

Unit VI: Bacterial Genetics (04 Lectures) (Chapter 8: Snustad and Simmons)

Introduction togenetic exchange in bacteria: conjugation; transformation; transduction.

Unit VII: Analysis of genetic inheritance in human (05 Lectures) (Chapter 4: Strachan and Read)

Gathering family history, pedigree symbols and construction of pedigrees. Patterns of inheritance for monogenic traits and risk assessment with examples for autosomal inheritance-dominant, recessive, sex-linked inheritance, sex-limited and sex-influenced traits, mitochondrial inheritance, variation in penetrance and expressivity.

Unit VIII: Cytogenetics (05 Lectures) (Chapter 2: Strachan and Read;Chapter 6: Snustad and Simmons)

Karyotyping- banding pattern and nomenclature (G and Q banding), common syndromes due to numerical chromosome changes, common syndromes due to structural alterations (translocations, duplications, deletions)

Unit IX: Introduction to genetic basis of sex determination (04 Lectures) (Chapter 5: Snustad and Simmons;Chapter 7: Klug and Cummings)

Chromosomal theory of sex determination, mechanisms of sex determination, environmental factors and sex determination in human and Drosophila, Barr bodies, dosage compensation.

Unit X: Introduction to DNA structure and replication (04 Lectures) (Chapter 9 and 10: Snustad and Simmons)

Basicstructure of DNA, salient features of the double helix, semi-conservative replication– Messelson and Stahl experiment.

Unit XI: Introduction to developmental genetics (04 Lectures) (Chapter 18: Klug and Cummings)

Study of model systems in developmental genetics- Drosophila melanogaster and zebrafish.

Four Year Undergraduate Course in Biomedical Science

Unit XII:Basic population genetics (03 Lectures) (Chapter 23: Snustad and Simmons;Chapter 4: Strachan and Read)

Gene pool and gene frequency, Hardy Weinberg law and its application for calculating allelic and genotype frequencies.

PRACTICALS 1. Observation of wild type and mutant phenotypes in Drosophila. 2. Preparation of culture media for Drosophila and study different stages of life cycle of Drosophila. 3. Verification of Mendelian laws through Drosophila – dominant, recessive and sex-linked 4. Preparation of Barr body. 5. Karyotyping with the help of photographs (normal and abnormal karyotypes). 6. Pedigree charts of some common characters like blood group, color blindness and PTC tasting. 7. Preparation of master and replica plates with wild type and some antibiotic sensitive strain. 8. Study of polyploidy in onion root tip by colchicine treatment.

ESSENTIAL BOOKS 1. Principles of Genetics, 6th edition (2011), Snustad DP and Simmons MJ, John Wiley and Sons, Inc; ISBN-13: 978-0470903599 2. Human Molecular Genetics, 3rd edition (2003) by Tom Strachan and Andrew Read; Garland Science Publishers, ISBN -13:978-0815341826. 3. Concepts of Genetics, 10th edition, (2011). William S. Klug, Michael R. Cummings, Charlotte A. Spencer, Michael A. Palladino; Pearson Education, ISBN-13: 978-0321724120.

SUGGESTED READINGS 1. Principles of Genetics, 8th edition (2005), Gardner EJ, Simmons MJ, Snustad DP. John Wiley and Sons, Inc. ;ISBN-13: 978-9971513467. 2. An introduction to Genetic Analysis, 10th edition (2010), Griffith AJF, Miller JH, Suzuki DT, Lewontin RC, Gelbert WM.,W. H. Freeman and Co. New York. ISBN-13: 978-429229432. 3. Principles of Genetics, 6th edition (1998), Robert H. TamarinPublisher: William C Brown Pub; ISBN-13: 978-0697354624.

Four Year Undergraduate Course in Biomedical Science

Semester II

BMS 202: Human Physiology and Anatomy-I (DC-I) Preamble: The prime concern of this syllabus is to integrate the individual functions of all the cells and tissues and organs into functional whole, the human body. Since function is dependent on a structure, the curriculum lays stress on functional anatomy of the organs. It attempts to highlight the necessary bodily balances and internal bodily control so called homeostasis as well as present their abnormal function in disease. It provides a link between basic sciences and Medicine. THEORY Total Lectures: 48

Unit I: Body organization and Integumentary system (04 Lectures) (Chapter1: Fox)

General Anatomy of the body, Introduction to various kinds of body planes, Tissues level of organization (Types, origin, function and repair). Functional Anatomy and histology of human skin.Temperature regulation by skin.

Unit II: Blood (08 Lectures) (Chapter 13: Fox)

Composition and Function of blood and its components: RBC, WBC, platelets, Hematopoiesis. Hemoglobin structure and function.Hemostasisand blood coagulation mechanism, blood groups and blood banking. An overview of lymphoid tissue and lymph.Basic concepts about Anemia, Abnormal hemoglobin, polycythemia, thalassemia and leukemia

Unit III: Nerve physiology (07 Lectures) (Chapter 7: Fox;Chapter 4: Guyton)

Structure and function of neuron, Resting membrane potential, Action potential, electrophysiology of ion channels and conduction of nerve impulse, The Synapse, types of synapse, Synaptic Transmission, Neurotransmitters; types and function.

Unit IV: Nervous System I: Organization of nervous system (07 Lectures) (Chapter 8: Fox)

Structure and function of Central nervous system, Peripheral nervous(spinal and cranial nerves) system andAutonomic nervous system. An overview of concepts on Sleep, memory and Pain.Reflexes: innate and acquired with suitable examples, reflex arch. Temperature regulation of the human body by hypothalamus.

Unit V: Nervous System II: Special senses (07 Lectures) (Chapter 10: Fox)

Four Year Undergraduate Course in Biomedical Science

Concept of receptors in the body and their types, Structure, Functional anatomy, regulation and common disorders of the following sensations: Vision, Hearing, Taste, Smell and Touch.

Unit VI: Muscular system (07 Lectures) (Chapter 12: Fox;Chapter 7: Guyton)

Functional anatomy of muscular system, types of muscles, neuromuscular transmission, general and molecular mechanism of skeletal muscle excitation and contraction, Energetics of muscle contraction and characteristics of whole Muscle contraction. An overview of concepts of muscle fatigue, oxygen debt, shivering/tremor, muscle degeneration, tetany, muscular dystrophy.

Unit VII: Gastrointestinal system (08 Lectures) (Chapter 18: Fox)

Anatomy and histology of digestive tract, gastrointestinal physiology:General principles of gut motility secretion, digestion, absorption and assimilation. Gastrointestinal hormones, their formation, action and regulation.Physiological anatomy of Liver and pancreas and their functions.An overview of vomiting, gastrointestinal dysfunction: nausea, mal-absorption, Constipation, Gastritis, Ulcer, Diarrohea, jaundice and Cirrhosis.

PRACTICALS 1. Estimation of hemoglobin (Sahli’s method) and determination of blood group. 2. Determination of bleeding time and clotting time of blood. 3. Determination of total erythrocyte count. 4. Determination of total leukocyte count. 5. Preparation of blood smears and identifying various WBC 6. To perform differential leukocyte count of blood. 7. Determination of specific gravity of blood. 8. Determination of osmotic fragility of RBC. 9. Determination of reticulocyte count. 10. To study different human organs and their sections through permanent histological slides T. S. of brain, spinal cord, skeletal fibres, various parts of GIT, different tissues

ESSENTIAL BOOKS 1. Guyton and Hall Textbook of Medical Physiology, 11thedition (2006), J. E. Hall; W B Saunders and Company, ISBN-13: 978-1416045748 2. Human Physiology, 9th edition (2006), Stuart I. Fox; Tata McGraw Hill, ISBN-13: 978- 0077350062 3. Lab Mannual on Blood Analysis and Medical Diagnostics, 1stedition (2012), Dr. GayatriPrakash; S. Chand, ISBN: 81-219-3967

Four Year Undergraduate Course in Biomedical Science

4. Manual of Practical Physiology, 4th edition (2012), A. K. Jain; Arya Publication, ISBN: 8178553155.

SUGGESTED READINGS 1. Principles of Anatomy and Physiology, 13th edition (2011), Gerard J. Tortora and Bryan H. Derrickson; Wiley and Sons, ISBN-13: 978-0470565100 2. Ganong’s Review of Medical physiology, 24thedition (2012), K. E. Barett, S. M. Barman, S. Boitano and H. Brooks; Tata McGraw Hill, ISBN-13: 978-0071780032 3. Textbook of Practical Physiology, 7thedition (2007), CL Ghai; Jaypee Publication, ISBN-13: 978-8184481419

Four Year Undergraduate Course in Biomedical Science

Four Year Undergraduate Course in Biomedical Science II Year Semester III and IV

Four Year Undergraduate Course in Biomedical Science

Semester III

BMS 301: Protein Chemistry and Function (DC-I)

Preamble: Protein chemistry and function is a discipline, which aims at understanding the chemical properties of the amino acids, structural architecture of the proteins and how proteins fold to their native, functional forms. The defect in the folding of proteins and their link to various genetics/metabolic diseases is studied. This course includes various analytical techniques used in characterization of the proteins and a detailed account of how enzymes function: their kinetics, regulation and inhibition.

THEORY Total Lectures: 48

Unit I: Properties of amino acids and metabolism: (04 Lectures) (Chapter 3, 18: Nelson and Cox)

Structure and classification of amino acids, concept of pKa, zwitterion, isoelectric point, Optical properties, Lamberts-Beer Law, Molar ellipcities of chromophoric groups, overview of amino acid metabolism (phenylalanine and one branched chain amino acid).

Unit II: Peptide conformation (08 Lectures) (Chapter 4: Nelson and Cox)

Definition of peptide, peptide unit, peptide group, bond length, cis and trans conformation, Ramachandran Plot, primary, secondary (alpha helix, beta sheet, beta turn, collagen helix and other non repetitive helices), tertiary structure (with examples), Motifs, super secondary structures, Domain and Quaternary structures (with examples).

Unit III: Protein stability and folding (08 Lectures) (Chapter 4: Nelson and Cox)

Definition of native and denatured state, protein stability, forces that maintains the native state stability, Protein denaturation by chaotropic agents (urea, GdmCl), SDS and heat, Protein folding (hydrophobic collapse, Anfinsen Experiments, Levinthal Paradox), chaperone-assisted protein folding.

Unit IV: Analytical methods in protein characterization (12 Lectures) (Chapter 3: Nelson and Cox)

Paper and Thin-layer chromatography, Ion exchange chromatography, Gel filtration and Affinity chromatography, SDS-PAGE, IEF, 2D-Gel electrophoresis, Dialysis, Mass Spectrometry, N- terminal and C-terminal sequencing.

Unit V: Enzymes (12 Lectures) 18

Four Year Undergraduate Course in Biomedical Science

(Chapter 6: Nelson and Cox)

Introduction to enzyme, concept of lock and key and induced fit theory, concept of activation energy and binding energy.Enzyme kinetics, the Michaelis-Menten equation and its physiological significances, double reciprocal plots. Enzyme Inhibition, types of inhibitors of enzyme and their examples. Turnover Number.

Regulatory enzymes: General properties of allosteric enzymes, regulation by covalent modification (including co-enzymes), negative and positive cooperativity. Zymogens, Isoenzymes.

Unit VI: Protein misfolding and diseases (04 Lectures) (Chapter 4: Nelson and Cox)

How and why certain proteins misfold and how this misfolding is linked to many disease processes. Introduction to certain conformational diseases: Alzheimer’s, Parkinson, Prion Diseases, p53 disorder in cancer.

PRACTICALS 1. Verification of Beer’s Law 2. Protein estimation by any one method: Lowry’s/Bradford method. 3. Separation of amino acids by thin layer chromatography. 4. To perform salting in and salting out by ammonium sulphate, using leaf extract or any other extract and to desalt by dialysis. 5. Calculation of void volume of Sephadex G -25 column, using blue dextran 6. Assay of any one enzyme under optimal conditions. 7. To study the effect of temperature on the activity of enzyme. 8. To study the effect pH on the activity of enzyme.

ESSENTIAL BOOKS 1. Lehninger Principles of Biochemistry, 5thedition (2012), David L. Nelson and Michael M. Cox; W. H. Freeman, ISBN-13: 978-0716771081. 2. An Introduction to Practical Biochemistry, 3rd edition (1987), Plummer, McGraw-Hill College; ISBN-13: 978-0070841659.

SUGGESTED BOOKS 1. Introduction to Protein Structure, 2nd edition (1999), Carl Branden and John Tooze; Garland Science, ISBN-13: 978-0815323051. 2. Principles and Techniques of Practical Biochemistry, 5thedition (2000), Keith Wilson and John Walker; Cambridge University Press, ISBN -13: 978-0521799652. 3. Protein Folding, 1st edition (1992), Thomas E. Creighton; W. H. Freeman Company, ISBN- 13: 978-0716770275. 4. Structure and Function of Intrinsically Disordered Proteins, 1st edition (2010), Peter Tompa; CRC Press, ISBN-13: 978-1420078923.

Four Year Undergraduate Course in Biomedical Science

Semester III

BMS 302: Human Physiology and Anatomy-II (DC-I)

Unit I: Cardiovascular system (09 Lectures) (Chapter 13 and 14: Fox)

Structure and function of heart, Properties of cardiac muscle.The Cardiac Cycle, Electrocardiogram. Circulatory system: General principles of circulation and hemodynamics Cardiovascular regulatory mechanism, Lymphatic circulation and microcirculation. Basic concepts of angina, atherosclerosis and Cardiac failure

Unit II: Respiratory system (07 Lectures) (Chapter 16: Fox;Chapter 39: Guyton)

Functional Anatomy of the respiratory system.Mechanisms of pulmonary ventilation, alveolar ventilation, gaseous exchange, transport of gases, respiratory and nervous control and regulation of respiration. An overview about cough, hypoxia, asthma and bronchitis.Basic concepts of physiology of exercise.

Unit III: Renal physiology: (09 Lectures) (Chapter17: Fox;Chapter 27: Guyton)

Functional Anatomy of kidney, function and histology of nephron, Body fluid and electrolytes: their balances and imbalances. Urinary bladder: structure, Urine formation (glomerular filtration and tubular reabsorption), micturition and its regulation, renal regulation of urine volume and osmolarity, acid-base balance. Acidosis and alkalosis, basic concepts about kidney dysfunction and disorders of urination

Four Year Undergraduate Course in Biomedical Science

Unit IV: Reproductive system (09 Lectures) (Chapter 20: Fox;Chapter 81: Guyton)

Structure and function of male and female reproductive organ and tract.Function and regulation of testicular and ovarian hormones.Gametogenesis (oogenesis and spermatogenesis), fertilization, implantation, pregnancy, parturition and lactation andneonatal physiology.Basic concepts of male and female infertility, menopause and various contraceptive measures. Unit V: Endocrine system (09 Lectures) (Chapter 11: Fox;Chapter 74: Guyton)

General mechanism of hormone action, Structure, function and regulation of the following glands and their secretions: Pituitary, Hypothalamus, Pineal, Thyroid, parathyroid, adrenal, Thymus, Pancreas. Basic concepts about hypo and hyper secretion of hormones and their diseases. Unit V: Skeletal System (05 Lectures) (Chapter6: Tortora)

Cartilage: Structure, function and types. Bones: Structure, function, location and types. Joints: structure, function and types. An overview of disorders of skeletal system: arthritis, gout, fractures, osteoporosis.

PRACTICALS 1. To study the sperms and their motility (from different regions of epididymis). 2. Simple Reflex arc. 3. Physiological data acquisition based experiments. (ECG ) 4. Physiological data acquisition based experiments. (EMG ) 5. To prepare temporary slide of neuron from goat spinal cord. 6. To perform platelet count 7. To perform tests for sensations. (taste, touch and smell) 8. Blood Pressure recordings in humans. 9. Lung Function tests in humans. 10. Preparation of temporary slide of neuron from goat spinal cord. 11. To study various types of contraceptive (condoms, IUD’s, oral and injectable contraceptives) 12. To study different human organs and their sections through permanent slides. T. S. ofthyroid, liver, thymus, spleen, ovary, artery, vein, capillaries, testis, pancreas, adrenal, kidney (cortex and medulla), urinarybladder, urethra, fallopian tubes, epididymis, prostate glands, lungs, trachea, bronchioles, pititutory, heart.

Four Year Undergraduate Course in Biomedical Science

3. Principles of Anatomy and Physiology, 13th edition (2011), Gerard J. Tortora and Bryan H. Derrickson; Wiley and Sons, ISBN-13: 978-0470565100

SUGGESTED READINGS 1. Lab Mannual on Blood Analysis and Medical Diagnostics, 1st edition (2012), Dr. GayatriPrakash; S. Chand, ISBN: 81-219-3967 2. Ganong’s Review of Medical physiology, 24th Edition (2012), K. E. Barett, S. M. Barman, S. Boitano and H. Brooks; Tata McGraw Hill, ISBN-13: 978-0071780032 3. Textbook of Practical Physiology, 7th Edition (2007), CL Ghai; Jaypee Publication, ISBN-13: 978-8184481419

Four Year Undergraduate Course in Biomedical Science

Semester III DC- II Courses

Four Year Undergraduate Course in Biomedical Science

Semester III

BMS A:Biosafety and Bioethics (DC-II) Preamble: The recent advances in the field of biotechnology have brought into focus several safety and ethical issues. The inventions in the field of genetic engineering and related fields of molecular biology will affect not only us but the plants, microorganisms, animals and the entire environment and the way we practice agriculture, medicine and food processing. An increase in our ability to change life forms in recent years has given rise to the new science of bioethics. The present course focus on the biosafety and bioethical issues the modern society confronts. Topics such as biosafety levels, GM food debate, impact of biotechnology on biosafety, biotech products and ethical issues, governance of biosafety, environmentally responsible use of biotechnology, clinical ethics will be discussed in the curriculum.

THEORY Total Lectures: 48

Unit I: Introduction (03 Lectures) (Chapter 1: Sateesh)

Historical background, introduction to biological safety cabinets, primary containment for biohazards, biosafety levels of specific microorganisms, recommended biosafety levels for infectious agents and infected animals.

Unit II: Biosafety guidelines (10 Lectures) (Chapter 7, 9,20 and 21: Sateesh)

Government of India definition of genetic modified organism (GMOs) and living modified organisms (LMOs), roles of institutional biosafety committee, review committee on genetic manipulation (RCGM), genetic engineering approval committee (GEAC) for GMO applications in food and agriculture, environmental release of GMOs. The GM-food debate and biosafety assessment procedures for biotech foods and related products, including transgenic food crops, case studies of relevance. Biosafety assessment of pharmaceutical products such as drugs/vaccines etc.

Unit III: Handling and transportation of GM, infectious and radioactive materials (Chapter 7 and 10: Sateesh) (05 Lectures)

Risk analysis, risk assessment, risk management and communication, overview of national regulations and relevant international agreements including Cartagena Protocol.

Unit IV: Biosafety management (06 Lectures) (Chapter 5 and 6: Sateesh)

Key to the environmentally responsible use of biotechnology, ethical implications of biotechnological products and techniques, social and ethical implications of biological weapons.

Unit V: Concept of social science (02 Lectures) 24

Four Year Undergraduate Course in Biomedical Science

(Chapter 1 and 40: Singer and Viens)

Reason to apply its principles to study cause of health problems and suggest appropriate intervention/ solution to problem.

Unit VI: Foundation of Bioethics (02Lectures) (Chapter 1: Tristram)

Definition, historic evolution, codes and guidelines, universal principles.

Unit VII: Codes, Covenants, Declarations and Guidelines (05 Lectures) (Chapter 2 and 3: Tristram)

Define the term “Bioethics” in relation to profession, society, and biomedicine, learn about gradation of moral and ethical norms from simpler to higher levels for initiating right actions to ‘first do no harm’ and learn about prayers, oaths, covenants, declarations, guidelines and codes which have relevance to bioethics.

Unit VIII: Clinical ethics (02 Lectures) (Chapter 25, 27 and 28: Singer and Viens)

Describe the sanctity of human life and the need to preserve human life, explain about issues related to prenatal screening, clinical trials (Phase I/II/III/IV) studies.

Unit IX: Women health ethics (03Lectures) (Chapter 14 and 15: Singer and Viens)

Vulnerability of women with respect to health care, examination and screening of women for disease, social issues like domestic violence and female genital mutilation and abortion.

Unit X: Medical errors and Negligence (03 Lectures) (Chapter 34: Singer and Viens)

Medical error and medical negligence difference, remedies against medical negligence, protection and compensation related to it.

Unit XI: Critical care ethics (04 Lectures) (Chapter 58: Singer and Viens)

History and need for ICU care, functioning and ethical principles of an ICU care, triage and futility, end of life care, ethical principles related to withholding treatment and withdrawing treatment (euthanasia), legal position regarding policies in ICU and handling of conflicts in the ICU.

Unit XII. Care in HIV and AIDS (02 Lectures) (Chapter 61: Sateesh) 25

Four Year Undergraduate Course in Biomedical Science

Basics of HIV infection,identify ethical issues in clinical practice of HIV medicine and its prevention, research ethics related to HIV.

Unit XIII: Ethical use of animals in the laboratory (01 Lecture) (Chapter 23: Sateesh)

PRACTICALS 1. A case study based on genetic modified organism (Bt-Cotton). 2. A case study based on genetic modified organism (Bt-Brinjal). 3. A case study based on terminator seeds. 4. A case study based on removal of selective marker in a DNA vaccine. 5. A case study on clinical trials of drugs in India with emphasis on ethical issues. 6. A case study on women health ethics. 7. A case study on medical errors and negligence. 8. A case study on critical care ethics. 9. A case study on ethical issues in clinical practice of AIDS. 10. A case study on handling and disposal of radioactive waste.

ESSENTIAL BOOKS 1. Bioethics and Biosafety, 1st edition (2008), M. K Sateesh, I K International Pvt Ltd, ISBN- 13: 978-8190675703. 2. The Cambridge Textbook of Bioethics, 1st edition (2008), Peter A. Singer and A. M. Viens; Cambridge University Press, ISBN-13: 978-0511545566. 3. Foundation of Bioethics, 2nd edition (1996), E. H Tristram; Oxford University Press, ISBN- 13: 9780195057362.

SUGGESTED READINGS 1. Social science: An introduction to the study of society, 14th edition (2010), Hunt, E. F.,and Colander, D. C. ; Peason/Allyn and Bacon, Boston, ISBN-13: 978-020570271. 2. Principles of Biomedical Ethics, 6th edition (2011), Beauchamp Tl, Childress JF; Oxford University Press, 2001. ISBN-13: 978-0195143317. 3. A Companion to Bioethics, 2nd edition (2012), Helga Kuhse, Peter Singer; John Wiley and Sons, ISBN-13: 978-1444350845. 4. Bioethics: An Introduction to the History, Methods, and Practice, 1st edition (1997), Nancy Ann SilbergeldJecker, Albert R. Jonsen, Robert A. Pearlman; Jones and Bartlett Learning, ISBN-13: 978-0763702281. 5. Genetically Modified Organisms and biosafety, 1st edition (2004), Tomme Young. ISBN-13: 978-2831707983.

Four Year Undergraduate Course in Biomedical Science

6. Environmental Safety of Genetically Engineered Crops, 1st edition (2011), Rebecca Grumet, James F. Hancock, Karim M. Maredia, CholaniWeebadde, Michigan State University Press ISBN-13: 978-1611860085. 7. Biosafety and Bioethics, 1st edition (2006), Rajmohan Joshi; Isha Books ISBN-13: 978- 8182053779. 8. Bioethics and biosafety in biotechnology, 1st edition (2007), V. Sreekrishna; New Age International (P) Ltd.,ISBN-13: 978-8122420852.

Semester III AC Course

Four Year Undergraduate Course in Biomedical Science

Semester III

BMS 303: Medical Lab Diagnostics (MLD) (AC)

Preamble: Medical Lab Diagnostics would help students enhance their practical skills and would enable them work in a Hospital setup. The paper is divided into three modules. First of all the students would orient themselves to work in a proper diagnostic setting. Secondly students would be introduced to detection of diseases using microbiological and molecular methods. Finally they would enhance their skills by learning various cytogenetic disorders. By this time students would have been also exposed to various techniques used in Biochemistry. Therefore, after the exposure of the current paper they would find themselves equipped with a full package of skill development in order to work in a diagnostic setting.

Number of Sessions: 12 (Each session has 3 Lectures)

Unit I: Fundamentals of Clinical Diagnostics (2 sessions) (Chapter 2, 4, 9 and 11: RamnikSood)

Laboratory 1: Sterilization Techniques: Physical methods and Chemical methods. Laboratory 2: General overview of blood banking, blood typing, blood screening in transfusion medical lab.

Introduction to clinical laboratory principles and procedures.Concept of GLP and ISO labs, quality control and laboratory safety.Regulation of diagnostic labs and accreditation methods.Guidelines for collection transport, preservation processing and analysis of specimen.Overview of phlebotomy, urinalysis, basic hematology, clinical biochemistry, immune- serology and clinical microbiology.Guidelines for proper discard of biological waste and chemical wastes.

Principles and applications of important instruments used in the diagnostic laboratory: biological safety cabinets (Class I, II, III) autoclave, incubators, hot air oven, centrifuges, PCR machines, bright field microscope, fluorescence microscope, ELISA reader, Autoanalyser, Spectrophotometer Gel Electrophoresis System.

Unit II: Approaches to diagnosis of infectious diseases: (4 sessions) (Chapter 7, 8, 13, 14 and 15: Forbes, Sahm and Weissfeld)

Four Year Undergraduate Course in Biomedical Science

Classification of culture media and quality control of culture media.Innoculation, incubation and purification methods in bacteriology.Preservation of bacterial culture.Rapid identification system, Continuous monitoring culture systems: BacT/ESP/BACTEC

Use of conventional microbiological tools supplemented by most modern analytical techniques including PCR for enumeration, isolation and identification of microbes (mainly on fresh produce).

Setting up “Gold Standard” method, concepts of accuracy (efficiency), Precision, sensitivity, specificity, Prevalence positive predictive value and negative predictive value.

Unit III:Immunoserology: Principles and Application. (3 sessions) (Chapter 10: Forbes, Sahm and Weissfeld;Chapter 22 and 23: RamnikSood)

Laboratory 7, 8 and 9:Antigen-antibody interaction and its use in diagnosis:Detection and diagnosis of common diseases: Widal and typhi dot for typhoid, Acylatedhaemoglobin in Diabetes, TSH levels in Thyroid condition, Malaria antigen in Malaria, NS1 antigen in Dengue (any three immune diagnostic tests).

Concepts of Immune response to be explained.Techniques to be discussed: ELISA - direct, indirect, competitive and sandwich ELISA, Co-immunoprecipitation for protein-protein interaction studies.

Unit IV: Medical Cytogentics (3 sessions) (Chapter 4: Dracopoli and Dracopoli)

Laboratory 10, 11 and 12: Become familiar with major techniques used in clinical cytogenetics, including culture of peripheral blood and preparation of metaphase chromosomes, chromosome banding and karyotyping.

Human cytogentics and its application to medicine.cell culture and harvest, chromosome banding and staining, chromosome identification, cytogenetics nomenclature, chromosome abnormalities and aberrations, chromosomal syndromes, classification of genetic disorders, Disciplines within Clinical Genetics and integration of genetic diagnostic services with other healthcare services (Clinical Genetics, Prenatal Diagnosis, Infertility, Cancer Cytogenetics)

Students’ Presentations: Understand issues related to the interpretation of normal chromosomal variation (with the help of photographs), Examples like mosaicism, aneuploidy and other chromosomal rearrangements, ISCN nomenclature, Abnormalities of chromosome number (monosomy, trisomy, triploidy), Partial aneuploidy, microdeletion/contiguous gene syndromes, abnormal chromosomes

Skills that are developed at the end of this course:

Four Year Undergraduate Course in Biomedical Science

1. The student will demonstrate knowledge of how to obtain reliable information from a variety of sources (e. g.,web, popular media, and scientific publications). 2. Practical training to work in diagnostic setting increased. 3. The student will demonstrate knowledge of how to communicate the results of a scientific investigation.

ESSENTIAL BOOKS 1. Bailey and Scott’s Diagnostic Microbiology, 12th edition (2007), Betty A. Forbes, Daniel F. Sahm and Alice S. Weissfeld; Mosby Elsevier Publishers, ISBN-13: 978-0808923640. 2. Medical Laboratory Technology Methods and Interpretations Volume 1 and 2, 6th edition (2009), RamnikSood; Jaypee Brothers Medical Publishers, ISBN-13: 978-8184484496. 3. Current Protocols in Human Genetics, 1st edition (1994), Dracopoli and Nicolas C. Dracopoli; John Wiley and Sons, Inc.,ISBN-13: 978-0471034209.

SUGGESTIVE READINGS 1. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Michael R. Green and Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978-1936113422. 2. Microbiology: A Laboratory Manual, 10th edition (2013), James Cappuccino and Natalie Sherman, Benjamin Cummings, ISBN-13: 978-0321840226.

Four Year Undergraduate Course in Biomedical Science

Semester IV

BMS 401: Medical Biochemistry (DC-I)

Preamble: The Medical Biochemistry course has been formulated to impart medically relevant information on clinical biochemistry. Students would learn the principle and applications of the diagnostic enzymology,interplay of hormones in the metabolism and details of various biomolecules of diagnostic significance. These topics are included to educate students on the clinical significance of biochemistry. This course will also focus on the contemporary methods and practical approaches that are used in the clinical laboratories for the investigation of the diseased state.

THEORY TotalLectures = 48

Unit 1: Basic Concepts and Scope (02 Lectures) (Chapter 1: Harper)

Unit 2: Enzymes: Distribution and diagnostic significance (10 Lectures) (Chapter 1: Harper)

Properties of enzymes used in diagnosis of metabolic disorders, clinical significance of diagnostically important enzymes: creatine kinase, lactate dehydrogenase, alanine- and aspartate aminotransferases, with a detailed account of the biochemical reactions catalysed by these enzymes and of their clinical assays; kinetic assay and end point assay for the enzymes. A detailed account on: isoenzymes, their tissue distribution and clinical significance.

Unit 3: Hormones (08 Lectures) (Chapter 23: Nelson and Cox; Chapters 41 and 42: Harper)

Classification (with reference to their biochemical nature, mechanism of action (one example from each class of hormones) with special reference to epinephrine and thyroid hormones (T3 and T4); functions.

Unit 4: Structural complexities and diseases associated with carbohydrates and lipids (Chapters 7, 10 and 21: Nelson and Cox; Chapters, 15 and 26: Harper) (10 Lectures)

Carbohydrates: Sugars as information molecules; detailed account on Lectins: their role in physiological functions and their potential as drug targets in various infectious diseases. Dietary fibers. Lipids: Lipoproteins- types (chylomicron, VLDL, LDL, HDL); disorders associated with lipoprotein metabolism (hypercholesterolemia, Atherosclerosis). Metabolism of ketone bodies in diabetic patients.Prostaglandins- classification, biosynthesis, role of COX-1, COX-2, NSAIDS in synthesis; functions Steroids-Cholesterol- biosynthesis and regulation, inhibitors of cholesterol biosynthesis (Statins-structure and mechanism of action).

Four Year Undergraduate Course in Biomedical Science

Unit 5: Vitamins (06 Lectures) (Chapter 27: Tietz; Chapter 12: Chatterjea and Shinde)

Definition, classification, requirement and recommended allowances, and dietary precursors; diseases due to deficiency of water-soluble and fat-soluble vitamins: the symptoms and the clinical significance.

Unit 6: An overview of integrative metabolism (12 Lectures) (Chapter 19, 23: Nelson and Cox)

Local and global regulation in tissue specific metabolism, interplay of insulin and glucagon integration of various metabolic pathways of proteins, lipids, carbohydrates and nucleic acids, obesity and regulation of body mass, electron transport chain and inhibitors, oxidative phosphorylation: chemisosmotic theory, role of uncouplers and ionophores.

PRACTICALS 1. Preparation of serum and plasma from whole blood. 2. Quantitative determination of the following in the whole blood/plasma/serum: a). LFT: i) SGPT and SGOT ii) Creatine kinase iii) Albumin/total protein b)KFT: i) Urea ii) Uric acid c). Metabolites: i) HDL/LDL and triglycerides ii) Serum protein A: G ratio. iii) Serum glucose. 3. Five case studies based on above quantitative studies performed.

ESSENTIAL BOOKS

1. Tietz Fundamentals of Clinical Chemistry, 6th edition (2007), Carl A. Burtis, Edward R. Ashwood, and David E. Bruns;WB Saunders Co, ISBN-13: 978-0721638652 2. Harpers Illustrated Biochemistry, 29th edition (2012), Robert Murray, David Bender, Kathleen M. Botham Peter J. Kennelly, Victor Rodwell, P. Anthony Weil; McGraw-Hill Medical, ISBN-13: 978-0071765763

Four Year Undergraduate Course in Biomedical Science

3. Lehninger’s Principles of Biochemistry, David L. Nelson and Michael M. Cox, 5th edition(2008), ISBN-13: 978-0716771081 4. Textbook of Medical Biochemistry, 7thedition (2007), Chatterjea&Shinde, Jaypee Publications,.ISBN: 81-8448-134-9.

SUGGESTED BOOKS

1. Biochemistry, J. M. Berg, J. L. Tymoczko and L. Stryer, 6th edition (2006), W. H. Freeman and Co. ISBN-13: 978-0716787242 2. Fundamentals of Biochemistry: Life at the Molecular Level, 4th edition (2012), Donald Voet, Judith G. Voet, Charlotte W. Pratt; Wiley, ISBN-13: 978-0470547847

Four Year Undergraduate Course in Biomedical Science

Semester IV

BMS 402:Genome Organization and Function –I (DC-I)

Preamble: The paper Genome Organization and Function –I encompasses the basic study and understanding of the central dogma. The paper starts with the basic organization of the genome in prokaryotes and eukaryotes along with their discerning features. This is followed by chapters on prokaryotic and eukaryotic replication, transcription and translation processes.

THEORY Total Lectures = 48

Unit I: Genome structure, chromatin and nucleosome (8 Lectures) (Chapter 7: Watson;Chapter 10: Karp)

Organization of Genomes in Prokaryotes and Eukaryotes, Chromosome sequence and diversity, Chromosome duplication and segregation, Establishing the central Dogma, Nucleosomes organization and assembly, Regulation of chromatin structure, DNA topology, Denaturation and renaturation of DNA, Cot curves, Euchromatin, Heterochromatin- constitutive and facultative heterochromatin.

Unit II: The replication of DNA in Prokaryotes and Eukaryotes (12 Lectures) (Chapter 8: Watson;Chapter 13: Karp)

Chemistry of DNA synthesis, General principles -bidirectional replication, Semi-conservative, discontinuous.RNA priming, Various models of DNA replication including D-loop (mitochondrial), Theta mode of replication, rolling circle model, Replication of linear ds-DNA, Replicating the 5’ end of linear chromosome, Enzyme involved in DNA replication – DNA polymerases, DNA ligase, primase, telomerase and other accessory proteins, DNA sequencing methods– Maxam Gilbert and Sanger method.

Unit III: The mutability and Repair of DNA (6 Lectures) (Chapter 9: Watson;Chapter 13: Karp)

Replication Errors (Transitions, transversion and thymine dimer), DNA Damage (deamination, depurination and dimerization) and their repair: mismatch repair, SOS response (recombination), Excision Repair, Photoreactivation.

Unit IV: Information Transfer –I: Mechanism of Transcription (10 Lectures) (Chapter 12: Watson;Chapter 11: Karp)

Basic transcription apparatus, Initiation, elongation and termination of transcription, Eukaryotic transcription of mRNA, tRNA and rRNA, types of RNA polymerases, transcription factors, Inhibitors of transcription- rifampicin and α-amanitin.

UnitV: Information Transfer-II: Mechanism of Translation (12 Lectures)

Four Year Undergraduate Course in Biomedical Science

(Chapter 14: Watson;Chapter 11: Karp)

Features of genetic code and exceptions in some systems, Ribosome structure- rRNA and proteins, Charging of tRNA, aminoacyltRNAsynthetases, Proteins involved in initiation (both in prokaryotes and eukaryotes), elongation and termination of polypeptides, Fidelity of translation, Inhibitors of protein synthesis – tetracyclins, aminoglycosides, chloramphenicol and aminoglycosides.

PRACTICALS 1. Preparation of various stock solutions required for Molecular Biology Laboratory. 2. Preparation of culture medium (LB) for E. coli (both solid and liquid) and raise culture of E. coli. 3. Isolation of chromosomal DNA from bacterial cultures and visualization on Agarose Gel Electrophoresis. 4. Quantitative estimation of salmon sperm / calf thymus DNA using colorimeter (Diphenylamine reagent) and Spectrophotometer (A260 measurement). 5. Isolation of genomic DNA from blood / tissue. 6. Native PAGE for DNA 7. Demonstration of Polymerase Chain Reaction (PCR) technique 8. Demonstration of AMES test or reverse mutation for carcinogenicity

ESSENTIAL BOOKS 1. Molecular Biology of the Gene, 6th edition (2007), Watson, J. D.,Baker T. A.,Bell, S. P.,Gann, A.,Levine, M.,and Losick, R; Benjamin Cummings Publishers, ISBN-13: 978- 0805395921 2. Cell and Molecular Biology: Concepts and Experiments, 7th edition (2013), Gerald Karp. ; Wiley Publishers ISBN-13: 978-1118206737 3. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Michael R. Green and Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978-1936113422

Four Year Undergraduate Course in Biomedical Science

Semester IV DC-IICourses

Four Year Undergraduate Course in Biomedical Science

Semester IV

BMS B:Pathological basis of diseases (DC-II)

Preamble:Claude Bernad said “Effects vary with the conditions which bring them to pass, but laws do not vary. Physiology and pathology states are ruled by the same forces; they differ only because of the special conditions under which the vital laws manifest themselves” Thus the syllabi of Pathology compliments and supplements the necessary knowledge students have gained in Physiology. Consequently it incorporates topics like cellular adaptations, inflammation, neoplasia, cellular ageing and other infectious diseases. Pathology also provides the necessary inputs for the other disciplines like Pharmacology, social and preventive medicine, medicinal biochemistry etc. All the topics and experiments are introductory in nature and lay stress on introducing Students with basic concepts of pathology

THEORY Total Lectures = 48

Unit I: Introduction (2 Lectures) (Chapter 1: Underwood and Underwood)

History of pathology, Basic definitions and common terms used in pathology, Survival mechanism and disease, microscopic and cellular pathology, scope and techniques used.

Unit II: Cell Injury and responses of cells: Cellular Adaptations, and Cell Death (Chapter 1: Robbins, Kumar and Cotran) (4 Lectures)

An overview of cellular adaptation: Hyperplasia, Hypertrophy, Atrophy, Metaplasia; Causes and mechanisms of cell injury, reversible and irreversible injury, Necrosis, Apoptosis, Types of apoptosis, Intracellular accumulations, Cellular ageing

Unit III: Role of Inflammation in disease (with suitable examples) (7 Lectures) (Chapter 2: Robbins, Kumar and Cotran)

Basic concepts with suitable examples of general features of acute and chronic inflammation: Vascular Changes, cellular events, important chemical mediators of inflammation, Morphological effects inflammation response, Granulomatus Inflammation.

Unit IV: Role of Tissue repair Healing and Fibrosis (with suitable examples) (5 Lectures) (Chapter 3: Robbins, Kumar and Cotran)

Basic mechanism of tissue regeneration, and repair by healing, scar formation and fibrosis

Unit V: CommonHemodynamic Disorders in diseases (with suitable examples) (6Lectures) (Chapter 4: Robbins, Kumar and Cotran)

An overview of Edema, hyperemia, congestion, hemorrhage, hemostasis and thrombosis, Embolism, Infarction and shock with suitable examples

Four Year Undergraduate Course in Biomedical Science

Unit VI: Nutritional diseases (5 Lectures) (Chapter 9:Robbins, Kumar and Cotran)

Protein energy malnutrition, deficiency diseases of vitamins, minerals, nutritional excess and imbalances.Role and effect of metals .

Unit VII: Cancer (7 Lectures) (Chapter 7:Robbins, Kumar and Cotran)

Definitions, Nomenclature, charactersitics of benign and malignant neoplasms, grading and staging of cancer, biology of tumor growth, invasion and metastasis, carcinogens and cancer, concept of oncogenes, tumor suppressor genes, DNA repair genes and cancer stem cells.

Unit VIII: Infectious diseases epidemiology (12 Lectures) (Chapter 8: Robbins, Kumar and Cotran,.Chapter 5 and 16:Park)

Modes of infections with suitable examples.Overview of cause, extent, prevention, treatment and control of the diseases: Respiratory infections, Intestinal infections, Arthropod-borne infections, Zoonosis and Surface infections

PRACTICALS 1. Urine analysis for abnormal constituents: protein, fats and glucose 2. Measuring Erythrocyte sedimentation rate. 3. Tissue Processing, embedding and sectioning. 4. Staining and preparation of permanent histological slide. 5. Diagnostic tests for detection of various Diseases – CRP, VDRL, RA, Pregnancy, Dengue and HIV (any four) 6. PCR based diagnostics (for any one disease)

ESSENTIAL BOOKS 1. Robbins and Cotran Pathologic Basis of Disease, 8th edition (2009), Vinay Kumar, Abul. K. Abbas, Jon C. Aster, Nelson Fausto; Saunders Publishers, ISBN-13: 978-1416031215 2. Robbins Basic Pathology, 9th edition (2012), Kumar, Abbas, Fausto and Mitchell; Saunders Publication, ISBN-13: 978-1437717815 3. General And Systematic Pathology, 2nd edition (1996) J.,Ed. Underwood and J. C. E. Underwood; Churchill Livingstone, ISBN-13: 978-0443052828 4. Textbook of preventive and social medicine, 20th edition, J. E Park; Banarsi Das Bhanot. Publishers. ASIN B0007CBHKI.

SUGGESTED READING

Four Year Undergraduate Course in Biomedical Science

1. Medical Laboratory Technology Methods and Interpretations, 6th edition (2009), Ramnik. Sood;.Jaypee Brothers Medical Publishers, ISBN-13: 978-8184484496. 2. Pathophysiology, 3rd edition (2012), Lee-Ellen C. Copstead-Kirkhorn and Publisher. Saunders. ISBN-13: 978-1455726509.

Semester IV ACCourse

Four Year Undergraduate Course in Biomedical Science

Semester IV

BMS 403: Techniques for Forensic Science (AC)

Preamble: Forensic science is the application of scientific knowledge to questions of civil and criminal law. Interest in forensic science has grown considerably in recent years. Keeping this in view, the present forensic science course is designed for students to explore how forensic scientist’s work, the tools and techniques they use and how they reach the conclusions they present in court. This engage students in using a creative, problem solving and inquiry based approach to investigate the crime scene. It also explains the characteristics of a fingerprint collect, process, and analyze fingerprint evidence and explain DNA analysis.

Number of Sessions: 12 (Each session has 3 Lectures)

Unit I: Crime Scene Investigation (2 Sessions) (Chapter 10 and 18 Nordby)

Laboratory 1:Documentation of crime scene by photography, sketching and field notes. Laboratory 2a: Simulation of a crime scene for training. Laboratory 2b: To lift footprints from crime scene.

Introduction and principles of forensic science, Forensic science laboratory and its organization and service, tools and techniques in forensic science, branches of forensic science, causes of crime, role of modus operandi in criminal investigation

Unit 2: Types of injuries and death (1 session) (Chapter 4: Nordby)

Laboratory 3: Case studies to depict different types of injuries and death.

Classification of injuries and their medico-legal aspects, method of assessing various types of deaths.

Unit 3: Forensic chemistry and Ballistics (2 sessions) (Chapter 4 and 5: Heard)

Laboratory 4a: Comparison of bullets and cartridges in museum Laboratory 4b: Separation of nitro compounds (explosives) by thin layer chromatography. Laboratory 5: To perform the preliminary examination of blood in a given sample.

Classification of fire arms and explosives, introduction to internal, external and terminal ballistics. Chemical evidence for explosives.

Unit 4: Forensic Graphology (2 sessions) (Chapter 2, 3, 4 and 15: Morris)

Four Year Undergraduate Course in Biomedical Science

Laboratory 6: Identification and comparison of handwriting characters Laboratory 7: To perform thin layer chromatography of ink samples.

General and individual characteristics of handwriting, examination and comparison of handwritings and analysis of ink various samples.

Unit 5:Forensic Toxicology (1 session) (Chapter 5: Nordby)

Laboratory 8: Identification techniques of common toxins, drugs, pesticides, Volatile poisons, vegetable poisons etc. in given biological samples and crime scene.

Role of the toxicologist, significance of toxicological findings

Unit 6:Fingerprint analysis (1 session) (Chapter 8: Wheeler)

Laboratory 9a: Investigate method for developing fingerprints by Iodine crystals. Laboratory 9b: To observe the effects of surface temperature on fingerprints.

Fundamental principles of fingerprinting, classification of fingerprints, development of finger print as science for personal identification.

Unit 7: DNA Fingerprinting (2 sessions) (Chapter 15: Nordby)

Laboratory 10: DNA isolation in minimal available biological samples Laboratory 11: PCR amplification on target DNA and DNA profiling

Principle of DNA fingerprinting, application of DNA profiling in forensic medicine.

Unit 8:Cyber Forensic Investigation (1 session) (Chapter 27: Nordby)

Laboratory 12a: Digital Evidence Collection Laboratory 12b:E-Mail Investigation, E-Mail Tracking, IP Tracking, E-Mail Recovery,Recovering deleted evidences, Password Cracking

Investigation Tools, eDiscovery,, Evidence Preservation, Search and Seizure of Computers,Introduction to Cyber Security

ESSENTIAL BOOKS 1. Forensic Science – An introduction to Scientific and Investigative Techniques, 3rd edition (2009), James SH, Nordby JJ and Bell S; CRC Press, ISBN-13: 978-1420064933.

Four Year Undergraduate Course in Biomedical Science

2. Practical Forensic Microscopy: A laboratory manual, 1st edition (2008), Barbara Wheeler and Lori J Wilson; Bios Scientific Publisher, ISBN-13: 978-0470031766. 3. Forensic Handwriting Identification: Fundamentals, Concepts and Principals 1st edition (2000)Ronald N. Morris, Academic press ISBN-13: 978-0125076401 4. Handbook of Firearms and Ballistics: Examining Interpreting Forensic Science by Brian J Heard 2nd edition (2008), John Wiley and Sons ISBN-13: 978-0470694602.

SUGGESTEDREADINGS 1. Principles of Forensic Medicine and Toxicology, 1st edition (2011) Rajesh Bardale; Jaypee Brothers Medical Pub, ISBN-13: 978-9350254936. 2. Practical Crime Scene Processing and Investigation, 2nd edition (2011), Ross M Gardner, CRC press ISBN-13: 978-1439853023. 3. Forensic Medicine and Toxicology: Oral, Practical And Mcq, 3rd edition (2006), Karmakar,Jaypee Brothers, ISBN-13:978-8171797350. 4. Fundamentals of Forensic Science, 2nd edition (2010), Houck, M.M. and Siegel, JA; Academic Press, ISBN-13: 978-0123749895. 5. Criminalistics- An Introduction of Forensic Science, 10th edition (2010), Prentice Hall Inc; ISBN-13: 978-0135045206.

Four Year Undergraduate Course in Biomedical Science

Four Year Undergraduate Course in Biomedical Science III Year Semester V and VI

Four Year Undergraduate Course in Biomedical Science

Semester V

BMS 501: Introduction to Biopharmacology and Pharmacokinetics (DC-I) Preamble: Pharmacology is the science concerned with the study of drugs and how they can best be used in the treatment of disease in both humans and animals. The course starts with the general considerations and lead to understanding of various drugs acting on different body systems. It is a very important biomedical discipline, with roots both in basic biology and chemistry, and plays a vital role in helping to safeguard our health and welfare.

THEORY Total Lectures: 48 Unit I: General Pharmacology (08 Lectures) (Chapter 1: Tripathi; Chapter 1, 2 and 3: Rang and Dale)

Nature and Source of drugs, Routes of drug administration and their advantages, receptor and receptor subtypes.

Unit II: Pharmacokinetics (08 Lectures) (Chapter 2 and 3: Tripathi)

Drug absorption, distribution, metabolism, and excretion, bioavailability, First Pass metabolism, excretion and kinetics of elimination, Bioavailability, Biological half life of drug and its significance, Drug-drug interactions.

Unit III: Pharmacodynamics (06 Lectures) (Chapter 4: Tripathi)

Principles and mechanism of drug action,Factors affecting drug action. General considerations, pharmacological classification, mechanism of action and uses of following classes of drugs acting on various systems.

Unit IV: Drugs acting on CNS (10 Lectures) (Chapter 27, 29, 34 and 35: Tripathi) (a) Mechanism of General anaesthesia, Stages of anaesthesia, General anaesthetics (Nitric oxide, halothane), (b) Principles of hypnosis and sedatives: sedative and hypnotics drugs (Phenobarbitone, diazepam), (c) Opioid analgesics (Morphine) (d) CNS stimulants (strychnine, amphetamine).

Unit V: Brief introduction to autocoids (04 Lectures) (Chapter 13 and 14: Tripathi)

Drug therapy of inflammation, NSAID and other drugs (aspirin, celecoxib).

Unit VI: Chemotherapy of microbial diseases (06 Lectures) 44

Four Year Undergraduate Course in Biomedical Science

(Chapter 49, 50 and 57: Tripathi)

Antibacterial (sulfonamides), antifungal (amphotericin B).

Unit VII: Horomones and hormone antagonists (08 Lectures) (Chapter 18, 19 and 20: Tripathi)

Insulin and oral hypoglycaemic agent (tolbutamide, rosiglitazone), thyroid and anti-thyroid drugs (eltroxin, carbimazole), estrogen and progestins (progesterone, hydroxyprogesteronecaproate).

*PRACTICALS 1. Handling of laboratory animals. 2. Routes of drug administration (Oral, I.M.) 3. To study the presence of acetaminophen in given sample. 4. To study the stages of general anesthesia. 5. To determine partition coefficient of general anesthetics. 6. Effect of analgesic (Tail-flick test). 7. Anti-anxiety effect of valium (Plus maze test). 8. Fixing of organ bath and kymograph. 9. To record CRC of acetylcholine using guinea pig ileum / rat intestine. 10. Determination of dose ratio. 11. Study of competitive antagonism using acetylcholine and atropine. *Experiments to be conducted in Virtual mode and through providing data.

ESSENTIAL BOOKS 1. Essentials of Medical Pharmacology, 7th edition (2010), K.D. Tripathi, Jaypee Brothers, ISBN: 9788184480856. 2. Pharmacology, 7th edition (2011), H.P. Rang, M.M. Dale, J.M. Ritter and P.K. Moore, Churchill Livingstone. ISBN: 9780702045042. 3. Hand book of Experimental Pharmacology, 4th edition (2012), S.K. Kulkarni, VallabhPrakashan, 2012. ISBN 13: 9788185731124.

Four Year Undergraduate Course in Biomedical Science

Semester V

BMS 502: Medical Microbiology (DC – I)

Preamble: The Medical Microbiology course has been formulated to impart basic and medically relevant information on the microbes. The microbial structure, growth and development, methods and role of sterilization in the context of study of microbes are included. The pathogenic microbes and the diseases caused by them are included to broaden the perspective of the subject. This course will also focus on mechanisms of microbial pathogenesis and the host response, and the scientific approaches that are used to investigate these processes. Lastly the course deals with the problem of emerging antimicrobial resistance with reference to known pathogens.

THEORY Total Lectures = 48

Unit I: Fundamental Concepts (8 Lectures) (Chapter 1, 6, 7, 8 and 17: Willey) a) History of microbiology, Discovery of microorganisms, Contributions of Louis Pasteur and Robert Koch in Medical Microbiology. b) Molecular methods of assessing microbial phylogeny- molecular chronometer, phylogenetic trees, rRNA, DNA and proteins as indicator of phylogeny. Major Divisions of life- Domains, Kingdoms. c) Requirements for microbial growth, growth factors, culture media- synthetic and complex, types of media. Obtaining Pure Cultures, Preserving Bacterial Cultures, Growth Curves and generation time, Control of microbial growth, general concept of effect of environmental factors on growth of microbes.

Unit II: Bacterial Cells - fine structure and function. (5 Lectures) (Chapter 3: Willey)

Size, shape and arrangement of bacterial cells. Cell membrane, cytoplasmic matrix, inclusion bodies (egmagnetosomes), nucleoid, Ultrastructure of Gram +ve and Gram –ve bacterial cell wall, Pili, Capsule, Flagella and motility

UnitIII: Microbial Genetics (5 Lectures) (Chapter 14: Willey)

Mutations, Bacterial recombination: general and site specific and replicative, bacterial plasmids fertility factor, col plasmid, bacterial conjugation (Hfr, F′, F+, F-), transformation, transduction- generalized and specialized.

UnitIV: Principles of Diseases and Epidemiology (3 Lectures) (Chapter 14: Tortora)

Four Year Undergraduate Course in Biomedical Science

Relationship between Normal microbiota and host, Opportunistic microorganisms, nosocomial infections, Development and spread of infectious disease: invasion, pathogen, parasite, pathogenicity, virulence, carriers and their types

Unit V: Bacterial Diseases (with reference to etiology, clinical symptoms, virulence factors involved, detection and prevention) (7 Lectures) (Chapter 38: Willey)

Respiratory tract infections: Diphtheria and Tuberculosis, Gastrointestinal tract infections, staphylococcal food poisoning and E. coli gastroenteritis, Urinary tract infections: gonorrhea and syphilis

Unit VI: Viruses, viroids, prions (5 Lectures) (Chapter 25 and 37: Willey)

General characteristics of viruses, structure, isolation, cultivation and identification of viruses, viral multiplication, one step multiplication curve, lytic and lysogenic phages (lambda phage), concept of early and late proteins, clinical virology with reference to HIV virus and hepatitis virus (Life cycle and clinical symptoms), viroids and prions

Unit VII: Medical Mycology (with reference to Life Cycle and clinical symptoms) (Chapter 50: Forbes, Sahm and Weissfeld) (5 Lectures)

General and detailed life cycle of Aspergillusand Candida albicans in relation to human diseases caused by them.

Unit VIII: Parasitology (with reference to Life Cycle and clinical symptoms) (3 Lectures) (Chapter 49: Forbes, Sahm and Weissfeld)

Classification of medically important parasites. Common protozoan disease: Malaria, Infections caused by Taeniasolium / Taeniasaginata, Fasciola hepatica and Ascarislumbricoides.

Unit IX: Antimicrobial chemotherapy and emerging antimicrobial resistance (7 Lectures) (Chapter 34: Willey)

Spectrum of antimicrobial activity, action of antimicrobial drugs, inhibitors of cell wall synthesis, anti-mycobacterial antibiotics, inhibitors of protein synthesis and nucleic acid synthesis, competitive inhibitors of essential metabolites, antifungal, antiviral, anti-protozoan drugs; effectiveness of chemotherapeutic agents, concepts of antimicrobial resistance, novel methods to combat increasing antimicrobial resistance.

PRACTICALS 1. Preparation of different media: synthetic media, Complex media-nutrient agar, Luria Agar.

Four Year Undergraduate Course in Biomedical Science

2. Staining methods: Gram’s staining, Acid fast staining (permanent slide only), Capsule staining and spore staining. 3. Study and plot the growth curve of E coli using turbidometric method and to calculate specific growth rate and generation time. 4. To perform antibacterial testing by Kirby-Bauer method. 5. Staining and morphological characterization of Aspergillus sp., Pencillium sp. and Saccharomyces sp. 6. Demonstration of PCR based method of detection. 7. Isolation of bacteriophages (any with a non-pathogenic host) and calculation of the plaque forming units (pfu).

ESSENTIAL BOOKS 1. Microbiology: An Introduction, 9th edition (2008), Gerard J. Tortora, Berdell R. Funke, Christine L. Case; Benjamin Cummings. ISBN-13: 978-0321733603. 2. Prescott, Harley, and Klein's Microbiology, 8th edition, (2011), Joanne M. Willey, Linda M. Sherwood, Christopher J. Woolverton, McGraw Hill International. ISBN-13:978- 0071313674. 3. Bailey and Scott’s Diagnostic Microbiology, 12th edition (2007), Betty A. Forbes, Daniel F. Sahm and Alice S. Weissfeld; Mosby Elsevier Publishers, ISBN-13: 978-0808923640.

SUGGESTED READINGS 1. Microbiology, 6th edition (1993), Pelczar, Chan and Krieg; McGraw Hill International, ISBN-13: 978-0070492585. 2. Brock Biology of Microorganisms, 13th edition (2010), Michael T. Madigan, John M. Martinko, David Stahl and David P. Clark, Pearsons, Benjamin Cummings, ISBN-13: 978- 0321649638. 3. Microbiology: A Laboratory Manual, 10th edition, (2013), James Cappuccino and Natalie Sherman, Benjamin Cummings. ISBN-13: 978-0321840226.

Four Year Undergraduate Course in Biomedical Science

Semester V

BMS 503: Immunobiology (DC-I) Preamble: The immune system distinguishes between self and foreign molecules and thus alerts and mediates protection against attack by potentially infectious organisms. Malfunctioning of the immune system leads to a number of disorders and diseases. Immunobiology is a comprehensive study of the organization and functioning of the immune system with its network of cells and molecules. Understanding the biology of the immune system is, therefore, key to developing strategies towards prevention and cure to a number of disorders and diseases that result due to interference in the functioning and regulation of the immune system. This paper covers the structure, organization, function and regulation of and by the immune system keeping the above aspects in mind.

THEORY Total Lectures: 48

Unit I: Introduction (2 Lectures) (Chapter 1 and 3: Kuby)

Historical background, general concepts of the immune system, innate and adaptive immunity; active and passive immunity; primary and secondary immune response.

Unit II: Structure, properties and functions of the immune system (10 Lectures) (Chapter 2 and 7: Kuby)

(a) Hematopoeisis, T and B lymphocyte, NK cells, monocytes and macrophages; neutrophils, eosinophils, basophils, mast cells and dendritic cells; thymus and bone marrow; lymph nodes, spleen, MALT, GALT and SALT; pattern recognition receptors. (b) Mechanisms of pathogen killing by macrophages and neutrophils. (c) Complement system: Components of the complement activation classical, alternative and lectin pathways; biological consequence of complement activation, methods to study complement fixation. (d) Inflammation

Unit III: Adaptive immune response (20 Lectures) (Chapter 4, 8, 10, 11, and 12: Kuby)

(a) Antigens and haptens: Properties (foreignness, molecular size, heterogeneity); B and T cell epitopes; T dependent and T independent antigens. (b) Major Histocompatibility Complex: Organization of MHC and inheritance in humans; concepts of polygeny and polymorphism with respect to MHC. (c) Antigen presenting cells, antigen processing and presentation pathway (cytosolic and endocytic), MLRs. (d) Humoral immune response: Concepts of B cell development in bone marrow, generation of plasma cells and memory B cells in lymphoid organs. Antibodies: Historical perspective of antibody structure; structure, function and properties of the antibodies; different classes and subclasses and biological activities of antibodies; concepts of antibody diversity and class 49

Four Year Undergraduate Course in Biomedical Science

switching. (isotype, allotype and idiotype); transport of IgA, Hybridoma technology, monoclonal antibodies; basic concepts of abzymes, immunotoxin, chimera, hybrid antibodies, antigen- antibody interactions. (e) Cell mediated immune response:T cell maturation in thymus, thymic selection, self MHC restriction of T cells, T cell receptor complex.T cell sub-types and their effector function. Trimolecular complex formation between APC and Naïve T cells, clonal expansion. Cytokines properties and functions of Interferon and Interleukins (IL1, IL2, IL4).

Unit IV: Immunological principles of various reactions and techniques (8 Lectures) (Chapter 6: Kuby)

Affinity and avidity, cross reactivity, precipitation, agglutination, immunodiffusion, immunoelectrophoresis, ELISA (indirect, sandwich, competitive, chemiluminescence, and ELISPOT assay), western blotting, immunofluorescence, flow cytometry and fluorescence, and immunoelectron microscopy.

Unit V: Vaccines and Immunotherapeutics (4 Lectures) (Chapter 19: Kuby)

Types and their characteristics, adjuvants, overview of National Immunization Course.

Unit VI: Dysfunctions of immune system (4 Lectures) (Chapter 15 and 16: Kuby)

Types of hypersensitivity, overview of autoimmunity. Immunodeficiency disorders: Animal models of primary immunodeficiency (nude mouse and SCID mouse); specific impaired functions in lymphoid and myeloid lineage.

PRACTICALS 1. To perform immunodiffusion by Ouchterlony method. 2. Immunodiffusion by Mancini method 3. Analysis of the ouchterlony and Mancini method 4. To perform ELISA checkerboard experiment. 5. To perform Complement fixation assay 6. To perform Agglutination inhibition Assay 7. To perform sandwich ELISA. 8. To perform Widal test.

ESSENTIAL BOOKS

Four Year Undergraduate Course in Biomedical Science

1. Immunology, 6th edition, (2006), J. Kuby et al, W.H. Freeman and Company, New York. ISBN-13: 978-1429202114.

SUGGESTED READINGS 1. Microbiology, 7th edition, (2008), Prescott, L., John Ii Harley, Donald A. Klein, McGraw Hill. ISBN-13: 978-0071102315. 2. Roitt’s Essential Immunology, 12th edition, (2011), Wiley-Blackwell Science. ISBN-13: 978-1405196833. 3. Immunology, 8th edition, (2012), Male, D., Brostoff, J., Roth, D.B. and Roitt, I., Elseivier- Sauders. ISBN-13: 978-0323080583. 4. An Introduction to Immunology, Immunochemistry and Immunobiology, 5th edition, (1988), Barrett, James T., Mosby Company, St. Louis. ISBN-13: 978-0801605307. 5. Immunology: An Introduction,4th edition, (1994), Tizard, I.R., Saunders College Publishing, Philadelphia. ISBN-13: 978-0030041983.

Four Year Undergraduate Course in Biomedical Science

Semester V DC-II Course

Four Year Undergraduate Course in Biomedical Science

Semester V

BMS C: Concepts in Medicinal Chemistry and Drug Development (DC-II) Preamble: The course emphasizes on various drug targets in the body and highlights the importance of drug-receptor interactions, lead discovery, drug design and drug development strategies.

THEORY Total Lectures: 48

Unit I: General Introduction (2Lectures) (Chapter 1: Silverman)

Definition and scope of drug design.

Unit II: Drug target classification (8Lectures) (Chapter 7-9: Patrick; Chapter 3, 4, and 6: Silverman)

Proteins as drug targets: Receptors - receptor role, ion channels, membrane bound enzyme activation, agonist and antagonists, concept of inverse agonist, desensitization and sensitization of receptors, affinity, efficacy and potency. Enzymes - Enzyme inhibitors (competitive, non- competitive, suicide inhibitors), medicinal use of enzyme inhibitors.Nucleic acids as drug targets:Classes of drugs that interact with DNA: DNA intercalators and DNA alkylators.

Unit III:Physicochemical principles of drug action (8 Lectures) (Chapter 2: Silverman)

Partitioncoefficient,drugdissolution,acidbaseproperties,surfaceactivity,bioavailablity,stereochemi calaspectsofdrugaction.

Unit IV: Drug receptor interactions (8Lectures) (Chapter 2 and 3: Nogrady)

Kinetic analysis of ligand receptor interactions using scatchard plot, double reciprocal plot, Hill plot, forces involved, relationship between dose and effect (graded and quantal response).

Unit V: Principles of drug design (8Lectures) (Chapter 13, 14 and 15: Patrick)

Introduction to SAR, strategies in the search for new lead compounds, analogue synthesis versus rational drug design, concept of prodrugs.

Unit VI: Drug discovery and pharmainformatics (14Lectures) (Chapter 2: Silverman; Chapter 15, 17 and 18: Patrick)

Drug discovery pipeline, drug target identification and validation for microbial pathogen, selection of gene unique to the pathogen, screening for its presence in other microbes and human 53

Four Year Undergraduate Course in Biomedical Science

host, Drug Databases, PubChem, Calculating drug-like properties, introduction to rational drug design methods, optimization of lead compounds, protein 3D structure and binding site analysis, similarity based virtual screening using online tools.

PRACTICALS 1. Preparation of Benzocaine. 2. Preparation of Aspirin and determination of partition coefficient in octanol-water system. 3. Preparation of Paracetamol. 4. Preparation of Phenacetin. 5. Visualization and analysis of 3D structures of proteins. 6. Finding the active sites in a receptor. 7. Molecular docking using AutoDock or HEX. 8. Searching databases for drug like compounds and computing drug like properties of small molecules.

ESSENTIAL BOOKS 1. Introduction to Medicinal Chemistry, 4th edition (2009), Graham l. Patrick, Oxford University Press. ISBN-13: 978-0199234479. 2. The Organic Chemistry of Drug Design and Drug Action,2nd edition (2004), Richard B. Silvermann, Elsevier, Academic Press. ISBN-13: 978-0126437324. 3. Medicinal Chemistry: A Molecular and Biochemical Approach, 3rd edition (2005), Thomas Nogrady and Donal F. Weaver, Oxford University Press. ISBN-13: 978-0195104561.

Four Year Undergraduate Course in Biomedical Science

Semester V AC Course

Four Year Undergraduate Course in Biomedical Science

Semester V

BMS 504: Methods for Epidemiological Data Analysis (AC) Preamble: In public health work, one may be concerned with planning of experiments and the analysis of their results. Therefore, one has to deal with statistical data analyses that come from no deliberate experiment but that arise because of the data collected from the population in the course of public health study and survey. This course therefore provides training to the students on how to conduct epidemiological surveys, design questionnaire and analyze the data. The students will get hands-on-training on ‘R’, a free software environment for statistical computing and graphics. Total sessions: 12 (Each session of 3 Lectures) Unit I: Understanding Epidemiological Data (1 session) (Chapter 2, 3, 9: Park;Chapter 7: Glantz; Website for NCRP: http://www.ncrpindia.org/) 1. Analysis of data from National Cancer Registry Program (NCRP) 2. Understanding incidence, mortality (rates, ratios and proportions) Components of epidemiology: disease frequency, distribution of disease and determinants of disease. Epidemiological approach and measurements- vital statistics (rates, ratios and proportions), measurements of health indicators (morbidity, mortality and fertility rates). Unit II: Epidemiologic Methods and Survey (4 sessions) (Chapter 3, 5, 6: Park) 1. Designing a questionnaire for survey of prevalence diabetes/ hypertension/ allergy/ respiratory disorders/etc. 2. Defining the parameters for ethical issues in a study 3. Determining the target and control populations 4. Surveying the population for the diseases mentioned above Data collection: observational (descriptive and analytical) and experimental studies. Epidemiology study designs- case control and cohort studies (prospective and retrospective), techniques of sampling and matching, sources of bias. Unit III: Data Organization and Presentation (2 sessions) (Chapter 19: Park; Chapter 2: Glantz; Website for ‘R’: www.r-project.org) 1. Introduction to ‘R’ software 2. Analysis of data from NCRP data and survey conducted by the students Basic principles of ‘R’ software for tabulation and graphical representations (bar diagrams, histograms, pie charts, box plot, etc.), measures of central tendency (mean, mode, median and partition values), dispersion (range, standard deviation, coefficient of variance and covariance) and skewness. Unit IV: Statistical Modeling and Analysis using ‘R’ on NCRP data and survey conducted by the students (5 sessions) (Chapter 19: Park; Chapter 3-10: Glantz; Website for ‘R’: www.r-project.org)

Four Year Undergraduate Course in Biomedical Science

1. Correlation studies 2. Regression studies 3. Probabilistic distribution studies 4. Comparison of groups and ascertaining statistical significance of differences Correlation analysis (scatter diagrams and Karl Pearsons coefficient of determination, standard and probable errors) and regression analysis. Inferential statistics: sampling distributions and standard error, null and alternate hypothesis, basic concept and illustrations of type I and type II errors, concept of confidence interval estimation, large sample tests for single mean and difference of means, single proportion and difference of proportions, students t-distribution (test for single mean, difference of means and paired t-test), chi-square distribution, F-distribution, one-way and two-way ANOVA, non parametric analysis (sign and rank tests), p-value.

ESSENTIAL BOOKS 1. Park’s Textbook of Preventive and Social Medicine, 21st edition (2011), K. Park, M/s Banarsi Das Bhanot Publishers. 2. Primer of Biostatistics, 7th edition (2011), Stanton Glantz, McGraw-Hill Medical. ISBN-13: 978-0071781503.

SUGGESTED READINGS 1. Basic epidemiology,2nd edition (2006), R. Bonita, R. Beaglehole, TordKjellstrèom, Contributor; World Health Organization, illustrated, Publisher: World Health Organization, ISBN-13: 978-9241547079. 2. Biostatistics: A Foundation for Analysis in the Health Sciences,10th edition (2013), Wayne W Daniel and Chad L. Cross, Wiley. ISBN-13: 978-1118302798. 3. Principles of Biostatistics,2nd edition (2000), Marcello Pagano and KimberleeGauvrean, Thompson learning. ISBN-13: 978-0534229023. 4. Biostatistical Analysis, 5th edition (2009), Jerrold H. Zar, Pearson. ISBN-13: 978- 0131008465. Website for ‘R’: www.r-project.org Website for NCRP: http://www.ncrpindia.org/

Four Year Undergraduate Course in Biomedical Science

Semester VI

BMS 601: Human Pathology (DC-I)

Preamble: The curriculum of pathology aims at preparing the students in basic understanding of diseases and their pathogenesis. The topics are of introductory nature and build the concepts of how human system work in altered and diseased stage under the influence of various internal and external stimuli Thus the syllabi of pathology compliments and supplements the necessary knowledge students have gained in Physiology. Consequently it incorporates topics like cellular adaptations, inflammation, neoplasia, cellular ageing and other infectious diseases. Laboratory exercises have been designed to substantiate and clarify the theoretical concepts.

THEORY Total Lectures: 48

Unit I: Introduction (2 Lectures) (Chapter 1: Underwood and Underwood)

History of pathology, basic definitions and familiarization with the common terms used in pathology, techniques used in pathology.

Unit II: Cellular Adaptations, Cell Injury and Cell Death (6 Lectures) (Chapter 1: Robbins, Kumar and Cotran)

Causes and mechanisms of cell injury: reversible and irreversible injury, Cellular responses: Hyperplasia, Hypertrophy, Atrophy, Metaplasia, Necrosis, Apoptosis, subcellular and intracellular response, (with suitable examples of diseases), Cellular ageing.

Unit III: Role of Inflammation in diseases (with suitable examples) (8 Lectures) (Chapter2: Robbins, Kumar and Cotran)

General features of acute and chronic inflammation: Vascular changes, cellular events, termination of acute inflammatory response. Cells and molecular mediators of inflammation, morphological effects and outcome of acute inflammation., systemic effects of chronic inflammation, granulomatous inflammation.

Unit IV: Tissue Renewal And Repair, Healing And Fibrosis (6 Lectures) (Chapter 3: Robbins, Kumar and Cotran)

Mechanism of tissue regeneration, role of ECM, repair by healing, scar formation and fibrosis, cutaneous wound healing, tissue remodeling in liver (mechanism of fibrosis and cirrhosis).

Unit V: Hemodynamic Pathology (5 Lectures) (Chapter 4: Robbins, Kumar and Cotran)

Four Year Undergraduate Course in Biomedical Science

Edema, hyperemia, congestion, hemorrhage, hemostasis and thrombosis, Embolism, Infarction and shock and hypertension.

Unit VI: Nutritional diseases (5 Lectures) (Chapter 9: Robbins, Kumar and Cotran)

Protein energy malnutrition, deficiency diseases of vitamins and minerals, nutritional excess and imbalances. Role and effect of metals (Zinc Iron and Calcium) in pathogenesis of cardiovascular and neurodegenerative diseases.

Unit VII: Cell proliferation: Cancer (6 Lectures) (Chapter 7: Robbins, Kumar and Cotran)

Definitions, nomenclature, characteristics of benign and malignant neoplasms, grading and staging of cancer, biology of tumor growth, mechanism of tumor invasion and metastasis, carcinogens and cancer, concept of oncogenes, tumor suppressor genes, DNA repair genes and cancer stem cells.

Unit VIII: Pathophysiology diseases (10 Lectures) (Chapters 17, 11 and 15: Robbins, Kumar and Cotran)

Diaorrhea, typhoid, arteriosclerosis, restrictive and obstructive respiratory diseases (COPD), silicosis.

PRACTICAL S 1. Urine Analysis: Gross examination of urine for colour, odour etc. Abnormal constituents like protein,ketone bodies, glucose, blood, urea (any three) 2. Tissue Processing, embedding, sectioning. Staining and preparation of permanent histological slide. 3. Study of histological slides showing hypertrophy, hyperplasia, dysplasia, leukemia, cirrhosis and any common cancer. 4. Diagnostic tests for detection of various Diseases – CRP, VDRL, RA, Pregnancy, Dengue and HIV (any four) 5. Physiological data acquisition like EMG, PFT, Temperature EEG (any two) 6. PCR based diagnostics (for any one disease) 7. Measurement of Erythrocyte Sedimentation Rate.

ESSENTIAL BOOKS 1. Robbins and Cotran Pathologic Basis of Disease, 8th edition (2009), Vinay Kumar, Abul K. Abbas, Jon C. Aster, Nelson Fausto; Saunders Publishers, ISBN-13: 978-1416031215 2. General And Systematic Pathology, 2nd edition (1996), J., Ed. Underwood and J. C. E. Underwood; Churchill Livingstone, ISBN-13: 978-0443052828. 59

Four Year Undergraduate Course in Biomedical Science

3. Robbins Basic Pathology, 9th edition (2012), Kumar, Abbas, Fausto and Mitchell; Saunders Publication, ISBN-13: 978-1437717815.

SUGGESTED READINGS 1. Medical Laboratory Technology Methods and Interpretations Volume 1 and 2, 6th edition (2009), RamnikSood; Jaypee Brothers Medical Publishers, ISBN-13: 978-8184484496. 2. Pathophysiology, 3rd edition (2012), Lee-Ellen C. Copstead-Kirkhorn and Publisher Saunders, ISBN-13: 978-1455726509.

Four Year Undergraduate Course in Biomedical Science

Semester VI

BMS 602: Medicinal Chemistry (DC-I) Preamble: The course highlights the importance of Medicinal Chemistry in all our lives and the fascination of working in a field that overlaps the disciples of chemistry, biology, biochemistry, pharmacology etc. It gives brief understanding about drug-receptor interactions, lead discovery, drug design and molecular mechanism by which drug act in the body. The course emphasizes on various drug targets in the body and drug development strategies with mechanism of action of antibacterial agents and concept of drug resistance.

THEORY Total Lectures: 48 Unit I:General Introduction (2 Lectures) Chapter 1: Silverman)

Definition and scope of medicinal chemistry

Unit II: Drug target classification (12 Lectures) (Chapter 7-9: Patrick; Chapter 3-6: Silverman)

Proteins as drug targets Receptors: The receptor role, ion channels, membrane bound enzyme activation, agonist and antagonists, concept of inverse agonist, desensitization and sensitization of receptors,affinity, efficacy and potency. Enzymes: Enzyme inhibitors(competitive, non-competitive, suicide inhibitors),medicinal use of enzyme inhibitors. Nucleic acids as drug targets Classes of drugs that interact with DNA: DNA intercalators (amsacrine), Groove binders(netropsin),DNAalkylators(amines:mechlorethamine; nitrosoureas:carmustine), concept of antisense therapy.

Unit III:How drug acts: Molecular aspects (6 Lectures) (Chapter 5: Patrick; Chapter 3: Silverman)

Structure and functions of cell surface receptors, signal transduction mechanism (GPCRs, Tyrosine kinase, guanylate-cyclase linked receptors and intracellular receptors that regulate DNA transcription).

Unit IV: Physicochemical principles of drug action (8 Lectures) (Chapter 2: Silverman)

Partitioncoefficient,drugdissolution,acidbaseproperties,surfaceactivity,bioavailability,stereochemicalaspectsofdrugaction,electronicstruct ure(Hammetcorrelations),determiningrelationshipbetweenchemicalandbiologicaldata(Hanschapp roach)

Four Year Undergraduate Course in Biomedical Science

Unit V:Measurement of drug effects (8 Lectures) (Chapter 2 and 3: Nogrady)

Kinetic analysis of ligand receptor interactions using scatchard plot, double reciprocal plot,Hillplot,forcesinvolved,relationshipbetweendoseandeffect(gradedandquantalresponse)

Unit VI:Principles of drug design (8 Lectures) (Chapter 12-14: Patrick)

Introduction to SAR, strategies in the search for new lead compounds, analogue synthesis versus rational drug design, concept of prodrugs.

Unit VII:Antibacterial agents (4 Lectures) (Chapter 19: Patrick)

Mechanism of action, antimetabolites (sulphonamides), cell wall synthesis inhibitors (penicillins), agents that act on plasma membrane (valinomycin), protein synthesis inhibitors (streptomycin and chloramphenicol), nucleic acids transcription and replication inhibitors (quinolones and fluoroquinolones), drug resistance.

PRACTICALS 1. Preparation of Benzocaine. 2. Preparation of Benzoquinone. 3. Preparation of Aspirin and determination of partition coefficient in octanol-water system. 4. Preparation of Paracetamol. 5. Preparation of Phenacetin. 6. Preparation of Hippuric acid. 7. Preparation of s-benzyl thiouronium salt. 8. Extraction of caffeine from tea leaves and study its absorption properties. 9. Phytochemical screening and qualitative chemical examination of various plant constituents by Solvent extraction. (Detection of alkaloids, carbohydrates, glycosides, phytosterols, oils and fats, tannins, proteins, gums and mucilages).

Four Year Undergraduate Course in Biomedical Science

3. Medicinal Chemistry: A Molecular and Biochemical Approach,3rd edition (2005), Thomas Nogrady and Donal F. Weaver, Oxford University Press. ISBN-13: 978-0195104561.

SUGGESTED READINGS 1. Wilson Gisvold textbook of Organic Medicinal and Pharmaceutical Chemistry, 11th edition (2003), edited by Block and Beale, Baltimore, Lippincot. ISBN-13: 978-0781734813. 2. The Practice of Medicinal Chemistry,2nd edition (2003), Camille G. Wermuth, Academic Press. ISBN-13: 978-0127444819. 3. Principles and Practice of Medicinal Chemistry,2nd edition (2003), Frank. D. King. The Royal Society of Chemistry.ISBN-13: 978-0854046317. 4. Introduction to Medicinal Chemistry: How Drugs Act and Why, 1st edition (1996), Alex Gringauz, Wiley VCH. ISBN-13: 978-0471185451.

Four Year Undergraduate Course in Biomedical Science

Semester VI

BMS 603: Toxicology (DC – I) Preamble: Different types of poisons have been known to humans since ages. Even in early times when science was in its infancy, curious people such as “Paracelsus” could predict “Every substance is a poison and, it is the right dose of the substance which differentiates remedy from poisons”. This thought is fundamental even to modern toxicology and pharmacology. There is an increasing use of chemicals in the modern society and hence, toxicology is becoming a more important subject to study with the passage of time. Modern toxicology is a vast, multidisciplinary subject encompassing various other basic fields of science. The present course content is designed to provide the basics of toxicology. Relevant importance has been given to those topics which can build a strong foundation in the subject, based on which, facts can be assimilated during subsequent higher studies. THEORY Total Lectures 48 Unit I: Introduction (2 Lectures) (Chapter 2: Cassarett)

Brief history, Different areas of modern toxicology, classification of toxic substances, various definitions of toxicological significance.

Unit II: Toxic exposure and response (5 Lectures) (Chapter 2: Cassarett)

Effect of duration, frequency, route and site of exposure of xenobiotics on its toxicity.Characteristic and types of toxic response.Types of interactions between two and more xenobiotics exposure in humans.Tolerance and addiction.

Unit III: Evaluation of toxicity (2 Lectures) (Chapter 3: Cassarett; Chapter 1: Timbrell)

Various types of dose response relationships, assumptions in deriving dose response, LD50, LC50, TD50 and therapeutic index.

Unit IV: Mechanism of toxicity (10 Lectures) (Chapter 3: Cassarett)

Delivery of the toxicant, mechanisms involved in formation of ultimate toxicant, detoxification of ultimate toxicant.

Unit V: Fate of xenobiotics in human body (10 Lectures) (Chapter 5 and 6: Cassarett; Chapter 2: Timbrell)

Four Year Undergraduate Course in Biomedical Science

Absorption, Distribution, Excretion and Metabolism of xenobiotics (biotransformation, Phase- I reactions including oxidations, hydrolysis, reductions and phase II conjugation reactions).Toxic insult to liver, its susceptibility to toxicants with reference to any two hepatotoxicants.

Unit VI: Toxic agents (8 Lectures) (Chapter 22 and 23: Cassarett; Chapter 8: Timbrell) Human exposure, mechanism of action and resultant toxicities of the following xenobiotics: Metals: lead, arsenic, Pesticides:organophosphtes, carbamates, organochlorine, bipyridyl compounds and anticoagulant pesticides.

Unit VII: Eco-toxicology (7 Lectures) (Chapter 29: Cassarett; Chapter 8 and 9: Timbrell)

Brief introduction to avian and aquatic toxicology, movement and effect of toxic compounds in food chain (DDT, mercury), bioaccumulation, biomagnification, acid rain and its effect on ecosystems, concept of BOD and COD.

Unit VIII: Clinical toxicology (4 Lectures) (Chapter 22: Cassarett)

Management of poisoned patients, clinical methods to decrease absorption and enhance excretion of toxicants from the body use of antidotes.

PRACTICALS 1. Separation of a mixture of benzoic acid, beta- napthol and napthelene by solvent extraction and identification of their functional Groups. 2. Determination of Dissolved oxygen (DO) using Winkler’s method. 3. Determination of Biological oxygen demand (BOD) of water. 4. To perform quantitative estimation of residual chlorine in water samples. 5. To determine the total hardness of water by complexo-metric method using EDTA. 6. To determine acid value of the given oil sample. 7. To estimate formaldehyde content of given sample. 8. Calculation of LD50 value of an insecticide from the data provided. 9. Determination of COD (chemical oxygen demand) of the given water sample.

ESSENTIAL BOOKS 1. Cassarett and Doull’s Toxicology “The Basic Science of The Poisons” 7th edition (2008), Curtis D. Klaassen Editor, McGrawHill Medical. ISBN: 9780071470513. 2. Cassarett and Doull’s “Essentials of Toxicology” 2nd edition (2010), Klaassen and Whatkins, McGraw Hill Publisher. ISBN-13: 978-0071622400. 65

Four Year Undergraduate Course in Biomedical Science

3. Introduction to Toxicology,3rd edition (2001), John Timbrell, Taylor and Francis Publishers. ISBN 13: 9780415247627.

SUGGESTED READINGS 1. Principles of Toxicology, 2nd edition (2006), Stine Karen and Thomas M Brown, CRC press. ISBN-13: 978-0849328565. 2. Lu’s basic toxicology: Fundamentals target organ and risk assessment, 5th edition (2009), Frank C Lu and Sam Kacow, Informa Health care. ISBN: 9781420093117.

Four Year Undergraduate Course in Biomedical Science

Semester VI DC-II Courses

Four Year Undergraduate Course in Biomedical Science

Semester VI

BMS D: Pharmacology and Toxicology (DC-II) Preamble: The course provides basic insight into principles of pharmacology and toxicology. It also highlights the pharmacodynamics and pharmacokinetics aspect of drugs in general. The emphasis will be on evaluation of toxicity and mechanism of toxicity of xenobiotics.

THEORY Total Lectures: 48 Unit I: General pharmacology and toxicology (6 Lectures) (Chapter 1: Tripathi; Chapter 1-3: Rang and Dale; Chapter 2, 29: Casarett) Nature and source of drugs, routes of drug administration and their advantages, definitions and scope of toxicology.Introduction to ecotoxicology.

Unit II: Mechanism of toxicity (6 Lectures) (Chapter 3: Casarett) Formation of ultimate toxicant of xenobiotics and its interaction with target molecules.

Unit III: Pharmacokinetics (6 Lectures) (Chapter 5 and 6: Casarett; Chapter 2: Timbrell)) Membrane transport, absorption, distribution of xenobiotics. Brief introduction to biotransformation, Phase- I reactions including oxidations, hydrolysis, reductions and phase II conjugation reactions and excretion of drugs.

Unit IV: Pharmacodynamics (6 Lectures) (Chapter 2: Rang and Dale; Chapter 2: Casarett) Mechanism of drug action, receptors and receptors subtypes, Dose response relationship and combined effect of drugs. Concept of LD50, LC50, TD50 and therapeutic index.

Unit V: Introduction and classification of the drugs acting on: a. Central and autonomic nervous system, neurotoxic agents. (6 Lectures) (Chapter 29, 32 and 33: Tripathi; Chapter 16: Casarett) b. Cardiovascular system and cardiotoxic agents. (6 Lectures) (Chapter 37-40: Tripathi; Chapter 18: Casarett) c. Kidney and nephrotoxic agents. (4 Lectures) (Chapter 41 and 42: Tripathi; Chapter 14: Casarett)

Four Year Undergraduate Course in Biomedical Science

Unit VI: Introduction and classification a. Anti-inflammatory and analgesic drugs and their related toxicity. (4 Lectures) (Chapter 14 and 15: Tripathi; Chapter 13 and 14: Casarett) b. Endocrine drugs (Tripathi, Chapter 18, 19, 20) (2 Lectures) (Chapter 18-20: Tripathi) c. Antimicrobial chemotherapeutic drugs (Tripathi, Chapter 49) (2 Lectures) (Chapter 49: Tripathi)

PRACTICALS 1. Handling of laboratory animals and various routes of drug administration. 2. To study presence of paracetamol/aspirin in the given sample. 3. Separation of a mixture of benzoic acid, beta- napthol and napthelene by solvent extraction and identification of their functional groups. 4. Determination of Dissolved water (DO) using Winkler’s method. 5. To determine the total hardness of water by complexometric method Using EDTA. 6. To determine Acid value of the given oil sample. 7. Calculation of LD50 value of an insecticide from the data provided.

ESSENTIAL BOOKS 1. Essentials of Medical Pharmacology, 7th edition (2010), K.D. Tripathi, Jaypee Brothers, ISBN-13: 978-8184480856. 2. Pharmacology, 7th edition (2011), H.P. Rang, M.M. Dale, J.M. Ritter and P.K. Moore, Churchill Livingstone, ISBN-13: 978-0702045042 3. Cassarett and Doull’s Toxicology “The Basic Science of The Poisons” 7th edition (2008), Curtis D. Klaassen Editor, McGrawHill Medical. ISBN-13: 978-0071470513. 4. Introduction to Toxicology, 3rd edition (2001), John Timbrell, Taylor and Francis Publishers. ISBN-13: 978-0415247627. SUGGESTED READINGS 1. Cassarett and Doull’s “Essentials of Toxicology”,2nd edition (2010), Klaassen and Whatkins, McGraw Hill Publisher. ISBN-13: 978-0071622400. 2. Principles of Toxicology, 2nd edition (2006), Stine Karen and Thomas M Brown, CRC press. ISBN-13: 978-0849328565.

Four Year Undergraduate Course in Biomedical Science

3. Lu’s basic toxicology: Fundamentals target organ and risk assessment,5th edition (2009), Frank C Lu and Sam kacow, Informa Health care. ISBN: 9781420093117.

Semester VI AC Course

Four Year Undergraduate Course in Biomedical Science

Semester VI

BMS 604: Tools in Modern Biology (AC)

Preamble: This course has been designed to introduce the various tools and techniques in modern era of biology and biotechnology. The philosophy behind this course is to make the students appreciate various processes and techniques they learn in other courses with hands-on training and experience. The emphasis is laid on techniques and tools in understanding DNA and proteins- the building blocks of life. It focuses on the principles of amplification, purification and analysis of DNA sequences by the means of plasmids, PCR and mapping. It also accounts for purification and study of protein-protein interactions besides giving an overview of cell culture. Total sessions: 12 (Each session of 3 Lectures)

Unit I: Plasmids and Biotechnology (3 sessions) (Chapter 2, 3 and 4: T. A. Brown; Chapter 5: Strachan and Read) 1. Isolation of Plasmid (mini-prep) from E. coli culture 2. Restriction digestion of plasmid and its analysis 3. Extraction of DNA from agarose gel 4. Construction of restriction maps from the data provided

Significance of plasmids in biotechnology; different methods of plasmid isolation; types and relevance of restriction sites and their potential in mapping.

Unit II: Amplification and Analysis of DNA sequences (3 sessions) (Chapter 9 and 10: T. A. Brown; Chapter 5: Strachan and Read) 1. Primer designing 2. Optimization of PCR conditions for temperature (gradient PCR) and Mg2+ concentration 3. Detection of bacteria specific genes using colony PCR 4. Analysis of DNA sequences with electropherograms

Principle, applications and modifications of PCR; essentials for a primer; concept of DNA sequencing and analysis of electropherograms.

Unit III: Purification and Analysis of Proteins (4 sessions) (Chapter8 and 9: Freifelder) 1. Comparative analysis of protein on native and denaturing gels 2. Protein purification by affinity chromatography 3. Separation of proteins by ion exchange chromatography

Concept of protein structure and denaturation with relevance to its resolution on gel; principle of chromatography and its application in purification and studying interactions

Four Year Undergraduate Course in Biomedical Science

Unit IV: Cell culture and Imaging (2 sessions) (Chapter 2: Wilson and Walker) 1. Preparation of media and culturing of cells 2. Fluorescence imaging demonstration in E coli with GFP and mammalian cells with PI/DAPI.

Essentials of cell culture, composition of media and the variations therein, analysis of the status within using fluorescence microscopy.

ESSENTIAL BOOKS 1. Gene cloning and DNA analysis, 6th edition (2010), T.A. Brown. Wiley-Blackwell ISBN-13: 978-1405181730. 2. Human Molecular Genetics, 3rd edition (2003), Tom Strachan and Andrew Read; Garland Science Publishers, ISBN -13:978-0815341826. 3. Physical Biochemistry: Applications to Biochemistry and Molecular Biology, 2nd edition (1982), David Freifelder, W.H. Freeman and Company. ISBN-13: 978-0716714446. 4. Principles and Techniques of Biochemistry and Molecular Biology 7th edition (2010), Wilson K and Walker J. Cambridge University Press, 2010. ISBN-13: 9780521516358. SUGGESTED READINGS 1. Principles of Gene Manipulation and Genomics, 7th edition (2006), S.B. Primrose and R.M. Twyman. Blackwell Scientific ISBN-13: 978-1405135443. 2. Molecular Biotechnology: Principles and Applications of Recombinant DNA, 4th edition (2009), Bernard R. Glick, Jack J. Paternack, Cheryl I. Patten. ASM press, ISBN- 13:9781555814984. 3. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Three-volume set by Michael R. Green, Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978- 1936113422. 4. Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications, 6th edition (2010), ISBN-13: 978-0470528129.

Four Year Undergraduate Course in Biomedical Science

Four Year Undergraduate Course in Biomedical Science IV Year Semester VII and VIII

Four Year Undergraduate Course in Biomedical Science

VII Semester

BMS 701: Genome Organization and Function –II (DC-I)

Preamble: The paper Genome Organization and Function –II deals with the more intriguing concepts of gene regulation (transcriptional, translation and genomic), gene silencing, RNAi and forms and mechanisms of regulatory RNAs. The organization of the genome from overlapping gens in bacteria and DNA of cell organelles to the abundance of repetitive DNA in higher organisms will be discussed. Jumping Genes will also be introduced to students here. The paper concludes with view to various genomes and their sequencing, special emphasis on the Human genome project, its goals and features.

THEORY Total Lectures = 48

Unit I: Gene Architecture (5 Lectures) (Chapter 13: Watson)

Split Genes, Concept of introns and exons, RNA splicing, Spliceosomes and Self splicing introns, alternative splicing and exon shuffling, RNA editing, mRNA transport and metabolism.

Unit II: Gene Regulation in Prokaryotes and Eukaryotes (15 Lectures) (Chapter 16 and 17: Watson; Chapter 23: Becker) a) Transcriptional regulation in prokaryotes: Principles of Transcriptional regulation, Bacterial gene regulation with reference to lactose, tryptophan and arabinose operon. Role of sigma factors in gene expression. b) Eukaryotic gene regulation: Transcriptional control - Conserved mechanism of regulation, activators, signal integration, combinatorial control, transcriptional repressors, signal transduction and control of transcriptional regulators, examples of steroid receptors, MAP kinase and STATs pathways, c) Eukaryotic gene regulation: Post-transcriptional control - Regulation of translation, translation-dependent regulation of mRNA and protein stability, post translational control and role of ubiquitin. d) Eukaryotic gene regulation: Genomic control – gene amplification and deletions, DNA rearrangements, chromosome puffs, DNA methylation, changes in histone and chromosome remodeling proteins.

Unit III: Regulatory RNAs (4 Lectures) (Chapter 18: Watson)

Riboswitches, RNA interference, miRNA, siRNA, Regulatory RNA and X-inactivation (reference of calico cats)

Four Year Undergraduate Course in Biomedical Science

Unit IV: Transposable genetic elements (4 Lectures) (Chapter 18: Snustad and Simmons)

Prokaryotic transposable elements- IS elements, Composite transposons, Tn-3 elements; Eukaryotic transposable elements- Ac-Ds system in maize and P elements in Drosophila; Uses of transposons; Eukaryotic Viruses.

Unit V: Human Genome Project (8 Lectures) (Chapter 5, 8 and 18: Strachan and Read)

Introduction to Genome Projects, organization and goals of human genome project, Tools (Vectors- BAC, PAC, YAC and sequencing techniques) and approaches (Hierarchical and shotgun sequencing), Outcomes and ethical issues, Applications in human diseases with an example of CFTR

Unit VI: Organization of the Human Genome (12 Lectures) (Chapter 9 and 13: Strachan and Read)

General features: Gene density, CpG islands, RNA-encoding genes, Gene clusters, Diversity in size and organization of genes, Types of repetitive DNA, Pseudogenes, gene families, Genetic markers and their applications

PRACTICALS 1. Preparation of various stock solutions for mentioned experiments. 2. Comparative analysis of genomic DNA and plasmid DNA by restriction enzyme digestion and estimation of size of a DNA fragment after electrophoresis using DNA markers 3. Preparation of human metaphase chromosome and Giemsa Staining 4. Perform Southern Hybridization. 5. Isolation of RNA from E. coli or mammalian cells and cDNA preparation 6. Perform RT-PCR of the cDNA prepared 7. Demonstration of Northern Blotting 8. Demonstration of Western Blotting

ESSENTIAL BOOKS 1. Molecular Biology of the Gene, 6th edition (2007), Watson, J. D., Baker T.A., Bell, S. P., Gann, A., Levine, M., and Losick, R; Benjamin Cummings Publishers, ISBN-13: 978- 0805395921. 2. Principles of Genetics, 6th edition (2011), D. Peter Snustad, Michael J. Simmons; John Wiley and Sons, ISBN-13: 978-0470903599.

Four Year Undergraduate Course in Biomedical Science

3. The World of the Cell, 7th edition (2008), Becker, Kleinsmith, Hardin and Bertoni. Benjamin Cummings, ISBN-13: 978-0805393934. 4. Human Molecular Genetics, 3rd edition (2003), Tom Strachan and Andrew Read; Garland Science Publishers, ISBN -13:978-0815341826.

SUGGESTED READINGS 1. The Cell: A Molecular Approach, 6th edition (2013), Cooper and Hausman; Sinauer Associates, Inc. ISBN-13: 978-1605351551. 2. DNA Replication, 2nd edition (2005), Arthur Kornberg; University Science Books ISBN-13: 978-1891389443 3. Cell and Molecular Biology: Concepts and Experiments, 7th edition (2013), Gerald Karp; Wiley Publishers, ISBN-13: 978-1118206737. 4. Gene cloning and DNA Analysis: An Introduction, 6th edition (2010) T.A. Brown; Wiley - Blackwell Publishing, ISBN-13: 978-1405181730. 5. Genomics: The Science and Technology behind the Human Genome Project, 1st edition (1999), Cantor and Smith; John Wiley and Sons, ISBN-13:978-0471599081. 6. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Michael R. Green and Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978-1936113422. 7. Concepts of Genetics, 10th edition, (2012). William S. Klug, Michael R. Cummings, Charlotte A. Spencer, Michael A. Palladino. ISBN-13: 978-0321724120.

Four Year Undergraduate Course in Biomedical Science

VII Semester

BMS 702: Medical Biotechnology(DC-I)

Preamble: The unique preposition of this paper is that the students learn the basic techniques and methods used in the diagnosis and therapy of various human diseases and in the production of biopharmaceuticals. The concepts of cloning and expression of the desired gene is explored. This paper aims to train students to understand how biological systems are applied in the advancement of medical biotechnology.

THEORY Total No of Lectures = 48

Unit I: Introduction to Biotechnology (1 Lecture) (Chapter 1: T.A. Brown; Chapter 1: Primrose)

Brief history and Importance

Unit II: Basic techniques (4 Lectures) (Chapter 2: Primrose)

Agarose gel electrophoresis, Southern, Northern and Western blotting and hybridization, use of enzymatic and chemiluminiscent methods for detection of proteins, detection of nuclei acids by radioactive and fluorescent probes.

Unit III: Manipulation of DNA (5 Lectures) (Chapter 3, 4 and 5: T. A. Brown; Chapter 3 and 4: Primrose)

Isolation and purification of genomic and plasmid DNA, Restriction and modification systems, type I-IV restriction endonucleases, nomenclature and sequence recognition, restriction mapping. Joining of DNA molecules: role of DNA ligase, adaptors, linkers, homopolymer tailing

Unit IV: Cloning Vectors (8 Lectures) (Chapter2, 6 and 7: T.A.Brown; Chapter 5: Primrose)

Basic biology of plasmids, brief life cycle of phages (lambda and M13), Plasmid vectors (pBR322 and pUC vectors, T-vectors) and phage vectors (Bacteriophage vectors- replacement and insertion vectors), cosmids, phasmids, in vitro packaging, expression vectors, example of prokaryotic and eukaryotic expression vectors, inducible and constitutive expression vectors with one example each.

Unit V: Cloning and expression of cloned genes in prokaryotic and eukaryotic Cells(Chapter 6, 7 and 11: T.A.Brown) (6 Lectures)

Challenges in expression of foreign proteins in heterologous host, factors affecting the expression host cell physiology, promoters, codon choice, plasmid copy no. etc., expression in eukaryotic cells (yeast and mammalian expression system, Baculovirus system), Shuttle vectors, 77

Four Year Undergraduate Course in Biomedical Science

Bacterial transformation and selection and screening of transformants (blue/white and antibiotic selection methods).

Unit VI: Polymerase chain reaction (PCR) (4 Lectures) (Chapter 9: T.A. Brown)

Principle and applications, primer-design, detailed understanding of PCR and RT- (Reverse transcription) PCR.

Unit VII. Construction of genomic and cDNA libraries, screening and selection of recombinants (6 Lectures) (Chapter 5 and 6: Primrose; Chapter 8: T.A.Brown)

Immunochemical methods of screening, nuclei acid hybridization (Colony and Plaque hybridization), different methods of preparation of gene probe. Hybrid Release Translation and Hybrid Arrest Translation.

Unit VIII. Random and site-directed mutagenesis (Chapter 8: Primrose) (4 Lectures)

Methods in Random mutagenesis: any two, methods in Site-directed mutagenesis: oilgonucleotide-directed mutagenesis, PCR-based method, screening and identification of mutants. Protein engineering concept and examples of Subtilisin, and alpha-Antitrypsin (AAT)

Unit IX:Application of Medical Biotechnology (8 Lectures) (Chapter 26: T.A.Brown)

(a) Production of recombinant biomolecules: Insulin, somatostatin, Factor VIII and interferons. (b) DNA Profiling: Introduction, DNA profiling based on STRs, minisatellites, RFLP, AFLP, VNTRs, SNPs and their applications. (c) Gene Therapy: Strategies and limitations, somatic and germline gene therapy, different vectors (viral and non viral) and their comparison, treatment for genetic and infectious diseases.

Unit X: Biosafety and ethical issues in biotechnology (2 Lectures) (Chapter 13 and 14:T. A. Brown)

PRACTICALS 1. To understand the method of digesting DNA with different restriction enzymes. 2. To maintain and store the E.coli DH5 alpha cells. 3. Preparation of Competent Cell (Calcium Chloride Treatment). 4. To prepare insert and vector for ligation. 5. To perform ligation reaction using T4 DNA ligase. 6. Transform competent bacterial cells with foreign DNA.

Four Year Undergraduate Course in Biomedical Science

7. To identify recombinants by blue-white screening and PCR.

ESSENTIAL BOOKS 1. Gene cloning and DNA analysis, 6th edition (2010), T.A. Brown. Wiley-Blackwell ISBN-13: 978-1405181730. 2. Principles of Gene Manipulation and Genomics, 7th edition (2006), S.B. Primrose and R.M. Twyman. Blackwell Scientific ISBN: 978-1405135443.

SUGGESTED READINGS 1. Molecular Biotechnology: Principles and Applications of Recombinant DNA, 4th edition (2009),Bernard R. Glick, Jack J. Paternack, Cheryl I. Patten. ASM press, ISBN- 13:9781555814984. 2. DNA Replication, 2nd edition (1992), Arthur Kornberg; University Science Books, ISBN - 13:978- 0716720034. 3. Genomics: The Science and Technology behind the Human Genome Project, 1st edition (1999), Cantor and Smith; John Wiley and Sons, ISBN-13:978-0471599081. 4. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Three-volume set by Michael R. Green, Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978- 1936113422.

Four Year Undergraduate Course in Biomedical Science

Semester VII DC-II Course

Four Year Undergraduate Course in Biomedical Science

VII Semester

BMS E: Bridging Information Technology and Biotechnology (DC-II)

Preamble: This course has been designed to reflect how information technology synergizes biotechnology. The course will focus on information retrieval from various databases, the basis of sequence data analysis, use of Hidden Markov Model to solve various sequence analysis problems, such as pairwise and multiple sequence alignments, gene annotation etc. Total Lectures: 48 Unit I: Convergence of biotechnology and information technology (2 Lectures) (Chapter 1: Mount) Introduction to bioinformatics and its applications, Internet and bioinformatics.

Unit II: Databases and genome browsers (8 Lectures) (Chapters 2 and 6: Mount) Introduction to various databases and their classification (primary and secondary databases) e.g. NCBI, DDBJ, EMBL, ENSEMBL, UCSC and their use in laboratories: literature, sequence, structure, medical, enzymes and metabolic pathways databases.

Unit III: Sequence alignment and visualization (8 Lectures) (Chapters 3 and 4: Mount) Local and global sequence alignments (Needleman-Wunsch and Smith-Waterman algorithms), pair-wise (BLAST and FASTA algorithms) and multiple sequence alignment (Clustal W) and its importance.

Unit IV: Theory behind BLAST (4 Lectures) (Chapter 4: Mount) How Hidden Markov Model (HMM) can be used to model a family of unaligned sequences or a common motif within a set of unaligned sequences and further be used for discrimination and multiple alignment.

Unit V: Phylogenetic analysis (5 Lectures) (Chapter 14: Baxevanis and Ouellette) Basics and tools for phylogenetic analysis, cladistics and its assumptions, tree-building methods (Character and distance based methods), construction of phylogenetic trees (PHYLIP).

Unit VI: Gene ontology (3 Lectures) (Chapter 9: Baxevanis and Ouellette) The Ontologies: cellular component, biological process and molecular function.

Unit VII: Genome analysis (5 Lectures) (Chapter 11: Mount) Features of DNA sequence analysis, gene prediction methods, SNP analysis (dbSNP), sequence assembly and genome annotation.

Unit VIII: Restriction site mapping and primer design (6 Lectures) 81

Four Year Undergraduate Course in Biomedical Science

(Chapter 13: Baxevanis and Ouellette) In silicorestriction mapping, cloning and expression, identification of cDNA from databases, design of primers for standard and real time PCR, e-PCR.

Unit IX: Introduction to machine learning (4 Lectures) (Chapter 12: Mount) Learning from data, how can we extract knowledge from data to take decisions, and program the computer to be able to learn from examples and adapt systems dynamically to enable better user experiences.

Unit X: Application of bioinformatics in biotechnology (3 Lectures) PCR diagnostic design, design strategy for over-expression of a therapeutic protein using specific examples to illustrate the strategy.

PRACTICALS 1. Retrieval of information from nucleotide databases. 2. Sequence alignment using BLAST. 3. Multiple sequence alignment using Clustal W. 4. Phylogenetic analysis using PHYLIP 5. Gene Ontology 6. Gene prediction and ORF finding. 7. In silicoprimer designing for standard and real time PCR and performing e-PCR.

ESSENTIAL BOOKS 1. Bioinformatics: Sequence and Genome analysis, 2nd edition (2004), David W. Mount, Cold Spring Harbour Laboratory Press. ISBN-13: 978-0879697129. 2. Bioinformatics: A practical guide to the analysis of genes and proteins, 3rd edition (2004), Andreas D. Baxevanis and B.F. Francis Ouellette, John Wiley and Sons. ISBN: 978- 0471478782.

Four Year Undergraduate Course in Biomedical Science

VIII Semester

BMS-801: Computational Biology and Drug Design (DC-I) Preamble: This course will introduce the discipline of computational biology and drug design. It has been designed to explain the different aspects of nucleotide and protein sequence analyses, sequence alignments and their applications in understanding biology. The course will also emphasize on the strategic issues in drug discovery and development, principles of computational methods involved in lead generation virtual screening, quantitative structure- activity relationship and molecular docking.

THEORY Total Lectures: 48 Unit I: Introduction to computational biology (2 Lectures) (Chapter 1: Mount) What is computational biology and bioinformatics, internet and bioinformatics, chemoinformatics. Introduction to linux and common terminal commands.

Unit II: Biological databases and genome browsers (10 Lectures) (Chapter 2 and 6: Mount) Introduction to various databases and their classification (primary and secondary databases) e.g. NCBI, DDBJ, EMBL, ENSEMBL, UCSC and their use in laboratories: literature, sequence, structure, medical, enzymes and metabolic pathways databases.

Unit III: Sequence alignment and visualization (8 Lectures) (Chapters 3, 4 and 5: Mount) Local and global sequence alignments (Needleman-Wunsch and Smith-Waterman algorithms), pair-wise (BLAST and FASTA algorithms) and multiple sequence alignment (Clustal W) and its importance.Theory behind BLAST- how Hidden Markov Model (HMM) can be used to model a family of unaligned sequences or a common motif within a set of unaligned sequences and further be used for discrimination and multiple alignment, BLAST score, aminoacid substitution matrices, s-value and e-value, calculating the alignment score and significance of e and p value.

Unit IV:Phylogenetic analysis (4 Lectures) (Chapter 14: Baxevanis and Ouellette) Basics and tools for phylogenetic analysis, cladistics, tree-building methods (character and distance based methods), construction of phylogenetic trees (PHYLIP) and identifying homologs.

Unit V:Microarray analysis (3 Lectures) (Chapter 13: Mount; Chapter 9 and 16: Baxevanis and Ouellette) Introduction and use of DNA microarray to assay gene expression, designing of the experiment, analysis and biological interpretation, principle and applications of protein microarray.

Four Year Undergraduate Course in Biomedical Science

Unit VI:Drug discovery pipeline (3 Lectures) (Chapter 1, 2: Smith and O’Donnell) Drug life cycle, stages of drug discovery and strategic issues in drug discovery.

Unit VII:Lead generation (6 Lectures) (Chapter 12, 18: Patrick) 2D and 3D molecular structures, molecular descriptors and fingerprints, molecular similarity and diversity, topological descriptors, quantitative structure-property relationships.

Unit VIII:Overview of drug development (12 Lectures) (Chapter 15, 17, 18: Patrick) HTS, clinical trials, applications of chemoinformatics in drug research (chemical libraries, protein 3D modeling, characterization of binding site, virtual screening, protein-ligand interactions, prediction of pharmacological properties, Introduction to drug databases, PubChem and their use in drug development, Lipinski’s rule of five, concept of energy minimization and forcefields, introduction to rational drug design using example.

PRACTICALS 1. Retrieval of information from databases. 2. Sequence alignment using BLAST and Clustal W. 3. Phylogenetic analysis using PHYLIP. 4. Microarray analysis using Bioconductor. 5. Molecular format conversion and hands-on molecular visualization program for displaying, animating and analyzing large bio-molecular systems using 3-D graphics. 6. Homology Modeling using SPDBV, model structure refinement using SPDBV and model validation using What Check and Pro Check. 7. Comparing structures, mutations, studying interactions creating electrostatic potential diagrams. 8. Virtual screening and molecular docking using AUTODOCK.

Four Year Undergraduate Course in Biomedical Science

4. The Process of New Drug Discovery and Development, 2nd edition (2006), C.G. Smith and J.T. O’Donnell, Informa Healthcare, ISBN-13: 978-0849327797.

SUGGESTED READINGS 1. Cheminformatics (2003), J. Gasteiger, Thomas Engel; Wiley-VCH . ISBN: 9783527618279. 2. Molecular modeling - Principles and Applications, 2nd edition (2003), A. R. Leach, Pearson Education Limited, UK. ISBN 13: 9780582382107. 3. Cheminformatics in Drug Discovery(2006), edited by. T.I. Opera; Wiley Publishers,ISBN: 9783527604203. 4. Molecular dynamics simulation: elementary methods(1992), J. M. Haile, Wiley- Interscience, New York. ISBN-13: 978-0471184393.

Four Year Undergraduate Course in Biomedical Science

VIII Semester

BMS-802: Biophysics (DC-I) Preamble: Biological phenomena cannot be understood fully without physical insight. Biophysics is an interdisciplinary frontier of science in which the principles and techniques of physics are applied to understand biological problems at every level, from atoms and molecules to cells, organisms and environment. The work always aims to find out how biological systems work. This paper covers various spectroscopic techniques, hydrodynamic methods, molecular biophysics and introduction to various physical principles responsible for maintaining the basic cellular function and integrity of biological membranes including transport across them.

THEORY Total Lectures: 48 Unit I: Biophysical techniques (20 Lectures) (Chapter 3, 4 and 6: Sheehan; Chapter14-17: Freifelder)

Basic principles of electromagnetic radiation: Energy, wavelength, wave numbers and frequency, review of electronic structure of molecules. UV-visible spectrophotometry: Beer Lambert law, light absorption and its transmittance, factors affecting absorption properties of a chromophore, structural analyses of DNA/ protein using absorption of UV light. Fluorescence spectroscopy: Theory of fluorescence, static and dynamic quenching, resonance energy transfer, fluorescent probes in the study of protein and nucleic acids. Optical rotatory dispersion and Circular dichroism: Principle of ORD and CD, analysis of secondary structure of proteins (denatured and native form) and nucleic acids using CD. Infra red spectroscopy: Theory of IR, identification of exchangeable hydrogen, number of hydrogen bonds, tautomeric forms. Magnetic resonance spectroscopy: Basic theory of NMR, chemical shift, medical applications of NMR. Mass spectrometry (MALDI-TOF): Physical basis and uses of MS in the analysis of proteins/ nucleic acids. X-ray crystallography: Diffraction, Bragg’s law and electron density maps (concept of R-factor and B-factor), growing of crystals (Hanging drop method).

Unit II: Hydrodynamic methods (10 Lectures) (Chapter 7: Sheehan; Chapter11, 13: Freifelder)

Viscosity: Methods of measurement of viscosity, specific and intrinsic viscosity, relationship between viscosity and molecular weight, measurement of viscoelasticity of DNA. Sedimentation: Physical basis of centrifugation, Svedberg equation, differential and density gradient centrifugation, preparative and analytical ultracentrifugation techniques, fractionation of cellular components using centrifugation with examples. Flow Cytometry: Basic principle of flow cytometry and cell sorting, detection strategies in flow cytometry.

Four Year Undergraduate Course in Biomedical Science

Unit III: Molecular biophysics (10 Lectures)

(Chapter 6: Sheehan; Chapter1: Freifelder; Chapter 2 and 3:Tinoco; Chapter 6: Watson)

Basic thermodynamics: Concept of entropy, enthalpy, free energy change, heat capacity. Forces involved in biomolecular interactions with examples: Configuration versus conformation, Van der Waals interactions, electrostatic interactions, stacking interactions, hydrogen bond and hydrophobic effect. Supercoiling of DNA: Linking number, twist and writhe. Protein folding: Marginal stability of proteins, thermodynamic and kinetic basis of protein folding, protein folding problem (Levinthal’s paradox), role of molecular chaperones in cellular protein folding, basics of molecular and chemical chaperones, protein misfolding and aggregation, diseases associated with protein misfolding.

Unit IV: Biological membranes (08 Lectures) (Chapter 12: Hoppe)

Colloidal solution, Micelles, reverse micelles, bilayers, liposomes, phase transitions of lipids, transport of solutes and ions, Fick’s laws of diffusion, ionophores, transport equation, membrane potential.

PRACTICALS 1. Effect of different solvents on UV absorption spectra of proteins. 2. Study of structural changes of proteins at different pH using UV spectrophotometry. 3. Study of structural changes of proteins at different temperature using UV spectrophotometry. 4. Determination of melting temperature of DNA. 5. Study the effect of temperature on the viscosity of a macromolecule (Protein/DNA). 6. Use of viscometry in the study of ligand binding to DNA/protein. 7. Crystallization of enzyme lysozyme using hanging drop method. 8. Analysis, identification and comparison of various spectra (UV, NMR, MS, IR) of simple organic compounds.

ESSENTIAL BOOKS 1. Physical Biochemistry: Principles and Applications, 2nd edition (2009), David Sheehan, JohnWiley. ISBN-13: 978-0470856031. 2. Physical Biochemistry: Applications to Biochemistry and Molecular Biology, 2nd edition (1982), David Freifelder, W.H. Freeman and Company. ISBN-13: 978-0716714446. 3. Physical Chemistry: Principles and Applications in Biological Sciences, 4th edition (2001), I. Tinoco, K. Sauer, J.C. Wang and J.D. Puglisi, Prentice Hall, ISBN-13: 978-0130959430.

Four Year Undergraduate Course in Biomedical Science

4. Molecular Biology of the Gene, 7th edition (2007), Watson, J. D., Baker T.A., Bell, S. P., Gann, A., Levine, M., and Losick, R, Benjamin Cummings Publishers, ISBN-13: 978- 0805395921. 5. Biophysics, 1st edition (1983), W. Hoppe, W. Lohmann, H. Markl and H. Ziegler, Springer- Verlag, ISBN-13: 978-3540120834. SUGGESTED READINGS 1. The Physics of Proteins: An introduction to Biological Physics and Molecular Biophysics, 1st edition (2010), H. Frauenfelder, S.S. Chan and W.S. Chan, Springer, ISBN-13: 978- 1441910431. 2. Principles of Instrumental Analysis, 6th edition (2006), D.A. Skooget. al., Saunders College Publishing. ISBN-13: 978-0495012016. 3. Principles of Physical Biochemistry, 2nd edition (2005), K.E. Van Holde, W.C. Jhonson and P. Shing Ho, Prentice Hall Inc. ISBN-13: 978-0130464279. 4. Biophysical Chemistry, 1st edition (1980), C.R. Cantor, P.R. Schimmel, W.H. Freeman andCompany. ISBN-13: 9780716711889. 5. Crystallography Made Crystal Clear: Guide for Users of Macromolecular Models, 3rd edition (2010), Gale Rhodes, Academic Press. ISBN: 9780080455549. 6. Introduction to Protein Structure, 2nd edition (1999), C. Branden and J. Tooze, Garland Publishing, ISBN-13: 978-0815323051.

Four Year Undergraduate Course in Biomedical Science

Semester VIII DC-II Course

Four Year Undergraduate Course in Biomedical Science

VIII Semester

BMS F:Tools and Model Organisms in Biomedical Research (DC-II)

Preamble: This course has been designed to introduce the various tools and techniques in modern era of biology. It focuses on the principles of microscopy, spectroscopy, chromatography, various molecular biology and immunological techniques. This course also aims to give the students an introduction to different model organisms, what they areused for, which techniques that can be applied to modify their genome, and how the students may use these organisms employing modern technological approaches for research and understanding of biology. It’s a motley collection of creatures: They fly, swim, wiggle, scurry, or just blow in the wind.But to the scientific community, this compilation has been elevated above all other species.They are the model organisms.-The Scientist, June 2, 2003 THEORY Total Lectures: 48

Unit I:Spectroscopy (5Lectures) (Chapter 3, 4 and 6: Sheehan) Principles and biological applications of UV, visible spectroscopy, Fluorescence spectroscopy, Infrared spectroscopy, NMR and Mass spectroscopy Unit II: Microscopy (3Lectures) (Chapter 18: Karp) Principles of Light microscopy, Phase contrast microscopy, Electron microscopy (EM)- scanning EM,transmission EM and scanning transmission EM (STEM); Fluorescence microscopy. Unit III: Analytical methods (5Lectures) (Chapter 18: Karp) Chromatography: Principle and applications of affinity, gel filtration and ion exchangechromatography, HPLC Centrifugation: Principle and different types of centrifugation- differential, density gradient and equilibrium. Flow cytometry:Flurochromes, fluorescent probe and principle, application in biomedical science. Unit IV: Molecular Biology Methods (8Lectures) (Chapter 2, 3, 4, 9 and 10: T. A. Brown; Chapter 2: Primrose; Chapter 5: Strachan and Read) Isolation, purification and quantification of nucleic acids; Agarose and PAGE; Hybridization techniques- Southern, Northernand Western; Restriction enzymes, Gene cloning and RFLP; Principles of PCR, RT PCR, Real time PCR;DNA sequencing- Maxam Gilbert and Sanger methods Unit V:Immunological methods (3Lectures) (Chapter6: Kuby)

Four Year Undergraduate Course in Biomedical Science

Monoclonal antibody generation, isolation of various immune cells and their functional assays, generation and applications of nude mice.ELISA - direct, indirect, competitive and sandwich ELISA,Co-immunoprecipitation for protein-protein interaction studies. Unit VI: Introduction to model organisms (2 Lectures) (Chapter 1: Pierce; Chapter 8: Strachan and Read) What are model organisms? Why there is a need to study model organisms?How to choose a model organism? Unit VII:Different model organisms (Chapter 1: Pierce; Chapter 8: Strachan and Read) The following aspects will be discussed under each model organism listed below. Brief history of model organisms, life cycle,culture conditions/maintenance, advantages and disadvantages of the organism as a model, fundamental discoveries made so far using these organisms, discussion onsuitability of each for genetic, developmental biology and as disease models: Escherichia coli (2 Lectures) Utilization in discovery of fundamental metabolic pathways. Saccharomyces cerevisiae(Baker’s yeast) (6Lectures) Mating types and their inheritance. Discovery of cell division cycle genes-cdc mutants,Yeast two hybrid system for protein-protein interactions. Overview of saccharomyces genome database (SGD), commonly used yeast assays, the 'Yeast Genome Deletion Collection'. Caenorhabditiselegans(Nematode worm) (2 Lectures) Insights into the role of proteases (ced genes) in Coursed cell death, cell-fate mapping and lineage studies.Discovery of RNAi in C.elegans, Overview of Wormbase database Drosophila melanogaster (Fruit fly) (4Lectures) Insights into forms of cancer and neurodegenerative diseases.Flybase, the Gene disruption project, transgenic flies. Musmusculus(Mouse) (4 Lectures) “Premier” model organism for studying complex physiological processes. Generation and application of knock outand transgenic mice as disease models. Knockout database. Introduction to other model organisms (4 Lectures) Dictyosteliumdiscoideum (Social amoeba) as amodel for induced multicellularityand differentiation. Daniorerio (Zebra fish)as a model for humandisease (any 2).Introduction to tools for Standard mutagenesis andGenetic screening. Daphnia (Water flea)as a model for ecotoxicological studies.

PRACTICALS

Four Year Undergraduate Course in Biomedical Science

1. Isolation and spectroscopic quantification of genomic DNA from blood/tissue/E.coli,determination of melting temperature of DNA. 2. Optimization of PCR conditions for temperature (gradient PCR) and Mg2+ concentration. 3. Restriction digestion of DNA for RFLP and DNA fingerprinting. 4. To perform Southern hybridisation. 5. Protein purification by affinity/ion exchange/gel filtration chromatography. 6. To perform sandwich ELISA. 7. Preparation of culture media for Drosophila and study different stages of life cycle of Drosophila. 8. Study of life cycle of Dictyosteliumdiscoideum.

ESSENTIAL BOOKS 1. Physical Biochemistry: Principles and Applications, 2nd edition (2009), David Sheehan, JohnWiley. ISBN-13: 978-0470856031. 2. Cell and Molecular Biology: Concepts and Experiments, 6th edition (2009), Gerald Karp, Wiley. ISBN-978-0470483374. 3. Gene cloning and DNA analysis, 6th edition (2010), T.A. Brown. Wiley-Blackwell ISBN-13: 978-1405181730. 4. Principles of Gene Manipulation and Genomics, 7th edition (2006), S.B. Primrose and R.M. Twyman. Blackwell Scientific ISBN: 978-1405135443. 5. Human Molecular Genetics, 3rd edition (2003), Tom Strachan and Andrew Read; Garland Science Publishers, ISBN -13:978-0815341826. 6. Immunology, 6th edition, (2006), J. Kuby, W.H. Freeman and Company, New York. ISBN- 13: 978-1429202114. 7. Genetics: A Conceptual Approach, 4th edition (2010), Benjamin A. Pierce, W. H. Freeman,ISBN-13: 978-1429232524. SUGGESTEDREADINGS 1. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Three-volume set by Michael R. Green, Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978- 1936113422. 2. Concepts of Genetics, 10th edition, (2012). William S. Klug, Michael R. Cummings, Charlotte A. Spencer, Michael A. Palladino. ISBN-13: 978-0321724120. 3. Physical Biochemistry: Applications to Biochemistry and Molecular Biology, 2nd edition (1982), David Freifelder, W.H. Freeman and Company. ISBN-13: 978-0716714446. 4. Principles and Techniques of Biochemistry and Molecular Biology, 7th edition (2010), Wilson K and Walker J., Cambridge University Press, 2010. ISBN-13: 978-0521516358. 5. Emerging Model Organisms: A Laboratory Manual, Volume 2, Lab manual edition (2010),Cold Spring Harbor Laboratory Press, ISBN-13: 978-0879698652.

Syllabus (Revised on 29-6-2009)

M.Sc. in Biomedical Sciences (Four Semester Course)

Dr. B.R. Ambedkar Center for Biomedical Research University of Delhi, Delhi-110 007

Master of Science Biomedical Science

TWO YEAR FULL TIME PROGRAMME

Rules, Regulations and Course Contents

Dr. B.R. Ambedkar Center for Biomedical Research (Faculty of Science) University of Delhi Delhi-110 007

University of Delhi Examination Branch

Date: 30th June, 2009 Course: M.Sc. in Biomedical Science

Check List of New Course Evaluation for AC Consideration

S.No. Parameters Status

1 Affiliation 2 Programme Structure 3 Codification of Papers 4 Scheme of Examinations 5 Pass Percentage 6 Promotion Criteria 7 Division Criteria 8 Span Period 9 Attendance Requirements 10 Course content for each paper along with reading list

2 MASTER OF SCIENCE (Biomedical Science)

TWO YEAR FULL TIME PROGRAMME

AFFILIATION

The proposed programme shall be governed by the Dr. B.R. Ambedkar Center for Biomedical Research, Faculty of Science, University of Delhi, Delhi-110 007.

PROGRAMME STRUCTURE

The M.Sc. Programme is divided into two parts as under, each part will consist of two Semester as given below.

Semester Odd Semester-Even Part I First Year Semester I Semester II Part II Second Year Semester III Semester IV

Each semester would consist of five papers and one practical through Semester I and II (Part I) and semester III. Semester IV (Part II) would comprise of Optional Papers from which each student has to select two papers and undertake Dissertation work. Selection of papers in Semester IV would be based on merit (performance in the Part I Examinations), choice and other specific guidelines as outlined below. It is mandatory for each student to complete a Dissertation, assigned at the end of 2nd Semester and complete at the end of 4th Semester. It would comprise of bench work.

The schedule of papers prescribed for various semesters shall be as follows:

CLASSIFICATION OF PAPERS

Part I: Semester I

S.No. Code Subject Maximum Marks Credits 1 MBS 101 Organic Chemistry-I 100 4 2 MBS 102 Biochemistry 100 4 3 MBS 103 Cell Biology 100 4 4 MBS 104 Medical Microbiology 100 4 5 MBS 105 Genetics 100 4 6 MBS 106 Practicals 100 4 Total 600 24

Part I: Semester II

S.No. Code Subject Maximum Marks Credits 1 MBS 201 Organic Chemistry-II 100 4 2 MBS 202 Molecular Biology and Biotechnology 100 4 3 MBS 203 Application of Statistics & Mathematics for 100 4 Biology 4 MBS 204 Immunology 100 4 5 MBS 205 Human Physiology-I 100 4 6 MBS 206 Practicals 100 4 Total 600 24

Part II: Semester III

S.No. Code Subject Maximum Marks Credits 1 MBS 301 Human Physiology-II 100 4 2 MBS 302 Principles of Medicinal Chemistry 100 4 3 MBS 303 Analytical and Biomedical Techniques & 100 4 Instrumentation 4 MBS 304 Molecular Oncology 100 4 5 MBS 305 Toxicology & Pharmacology 100 4 6 MBS 306 Practicals 100 4 Total 600 24

Part II: Semester IV

1 MBS 401 Dissertation 400 16 2 MBS 402 Genome Biology (Compulsory) 100 4 3 MBS Special Paper I (Optional) 100 4 Total 600 24

Special Papers* being offered (based on choice cum merit basis)

1 MBS 403 Concepts in drug discovery and mechanism Interdisciplinary Chemistry 2 MBS 404 Advanced Medicinal Chemistry Interdisciplinary Chemistry 3 MBS 405 Radiation Biology Interdisciplinary Zoology 4 MBS 406 Topics in Clinical Research 5 MBS 407 Advanced Toxicology & Pharmacology 6 MBS 408 Advanced Immunology Interdisciplinary Zoology

SCHEME OF EXAMINATION

1. English shall be the medium of instruction and examination. 2. Examinations shall be conducted at the end of each semester as per the Academic Calendar notified by the University of Delhi. 3. Each course will carry 100 marks and will have two components: Internal assessment (25 marks) and end of semester examination (75 marks)

Theory

i. Internal Assessment 30 marks

a. Attendance 05 marks b. Test / Assignments 25 marks

ii. End of semester examination 70 marks

End Semester Examination (Practicals) 100 marks

4 4. The system of evaluation shall be as follows:

4.1 Internal assessment will be broadly based on attendance in theory (5 marks), assignments and tests in the theory component (20 marks). These criteria are tentative and could be modified by the faculty members associated with teaching of a paper based on guidelines approved by the academic council.

4.2 The scheme of evaluation for dissertation shall be as follows:

4.2.1 Dissertation will formally begin from end of Semester II and will consist of bench work.

4.2.2 Dissertation work will consist of internal evaluation by the concerned supervisor based on general performance, written assignments, student seminar, in-class examination during the duration of the dissertation (100 marks), Project work (200 marks) and viva-voce (100 marks) the last two being evaluated by a board comprising of all teachers in the Department and /or external experts.

5. Examinations for courses shall be conducted only in the respective odd and even Semester as per the Scheme of Examinations. Regular as well as Ex-students shall be permitted to appear / re-appear / improve in courses of Odd Semesters only at the end of Odd Semesters and courses of Even-Semesters only at the end of Even Semesters.

PASS PERCENTAGE

Minimum marks for passing the examination in each semester shall be 40% in each paper and 45% in aggregate of a semester.

However, a candidate who has secured the minimum marks to pass in each paper but has not secured the minimum marks to pass in aggregate may reappear in any of the paper/s of his choice in the concerned semester in order to be able to secure the minimum marks prescribed to pass the semester in aggregate.

No student would be allowed to avail of more than two chances to pass a paper inclusive of the first attempt.

PROMOTION CRITERIA

Semester to Semester: Students shall be required to fulfill the Part to part Promotion Criteria. Within the same part, students shall be promoted from a semester to the next semester, provided she/he has passed at least three out of the five theory examinations of the current semester. However passing in practical is mandatory for promotion from one semester to next. There shall not be any repeat/improvement allowed for practical examination.

Part I to Part II: Admission to Part II of the programme shall be open to only those students who have successfully passed at least 6 theory papers out of papers offered for the Part I courses comprising of Semester-I and Semester-II taken together and two practical papers. However, she/he will have to clear the remaining papers while studying in Part-II of the programme.

5 DIVISION CRITERIA

Successful candidates will be classified on the basis of combined results of Part-I and Part-II examinations as follows:

Candidates securing 60% and above : I Division Candidates securing between 50% and 59.99% : II Division All others between 40-49.99% : Pass

QUALIFYING PAPERS

None

SPAN PERIOD

No students shall be admitted as a candidate for the examination for any of the Parts/Semesters after the lapse of four years from the date of admission to the Part-I/Semester-I of the M.Sc. in Biomedical Programme.

ATTENDANCE REQUIREMENT

No student shall be considered to have pursued a regular course of study unless he/she is certified by the Head /Director of the Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, to have attended 75% of the total number of lectures and seminars conducted in each semester, during his/her course of study. Provided that he/she fulfils other conditions, the Head/Director, Dr. B.R. Ambedkar Center for Biomedical Research may permit a student to the next Semester who falls short of the required percentage of attendance by not more than 10% of the lectures and seminars conducted during the Semester.

COURSE CONTENT FOR EACH COURSE

Is Enclosed.

LIST OF READINGS

The latest editions of each book will be referred to the class. List is enclosed at the end of each paper.

6 MBS 101: Organic Chemistry I

Reactive Intermediates in Organic Reactions Carbocations, carbanions, Free Radicals their stability and applications to biological systems, benzynes, carbenes, radical cations and radical anions; their generations and reactions exemplified with suitable case study leading to C-C bond formation.

Stereochemistry of Organic Compounds The definition of the following terms with suitable examples; Elementary treatment of symmetric elements, Chirality, prochirality; (enantiomer, epimer,diastereomer). Absolute and relative configuration; r and s notation; enantiotopic and diastereotopic faces, endo and exo faces, Regioselective, enantioselective, stereoselective and stereospecific reactions, Confirmation of 2,3 dibromomutane, E & z notations, Cyclohexane diols.

Mechanism and stereochemistry of following reactions Substitution, elimination and addition reactions; oxidation and reduction, Ester formation and ester hydrolysis, Aromaticity, aromatic and Nucleophilic substitution (with appropriate examples; Woodward Hoffman rules and photocyclization,

Asymmetric synthesis Cram and Prelog rule, Chiral synthesis (with suitable examples) asymmetric epoxidation.

Heterocyclic Chemistry Structure, synthesis and reactivity of the following heterocycles and their significance in biology and drugs and materials: furan, pyrrole, thiophene, imidazole, oxazole, thiazole, azepine, thiazine, carbazole, indole pyridine, quinoline and isoquinoline, acridine, phenothiazine, pteridine, purines and pyrimidines

Reading List

7 MBS 102: BIOCHEMISTRY

Structure Of Protein Secondary and tertiary structure of protein: a helix, ß sheets, examples of proteins, Ramachandran plot, factors effecting secondary and tertiary structure (disulphide bonds, heat, organic solvents, detergents). Examples of some common structural motifs in proteins.

Separation techniques for proteins: Ion exchange chromatography, dialysis, molecular sieving, polyacrylamide gel electrophoresis (determination of subunits and molecular weight), electrofocussing affinity chromatography.

Structure and function of hemoglobin: Conformational studies, binding of oxygen and its release, oxygen saturation curves. Methods of protein sequencing. Disorder of Amino Acid and protein metabolism

Enzymology Introduction: General characteristics of enzymes, definition of coenzyme, holoenzyme, prosthetic groups, classification. Enzyme Kinetics: Substrate, active site, transition state, activation energy, equilibrium constant Km, Vmax, specificity, Michaelis-Menten equation. Reaction Mechanism: Acid-base catalysis and colvalent catalysis (giving examples). Regulation of enzyme activity: Reversible and irreversible inhibition (non-competitive, uncompetitive) and their effects on Km and Vmax, effect of pH, heat, PMSF and other inhibitors. Allosteric enzymes: Models to explain their kinetic behaviour. Problems on enzyme kinetics: Determination of active sites and turnover number.

DNA replication and its regulation Concept of origin of replication, semiconservative hypothesis.

Mechanism of DNA Replication: Structure and function of DNA polymerases. Role of helicase, primase, gyrase, topoisomerase and other proteins in DNA replication in E.coli. replication of viruses and eukaryotes, initiation of replication, elongation and termination of DNA synthesis. DNA Repair

RNA Synthesis Transcription in prokaryotes using E-coli as an example, Structure & function of RNA polymerases. Transcription initiation, elongation and termination.

Transcription in eukaryotesStructure of TFIID, and other transcription factors, enhancers, silencers, insulators, general concept of regulation of transcription (in brief). Post-transcritional modifications, RibozymesStructure and mechanism of action.

Translation Translation in Prokaryotes-initiation: activation of amino acid, role of 30s and 50s ribosomal subunits, initiation factors) shine-dalgarno sequences. Elongation factors, peptidyl transferase termination signal, release factors. Inhibition of protein sunthesis - by antibiotics.

Translation in eukaryotes recent concept in initiation and termination, regulation of protein synthesis, comparison with prokaryotic system. Post translation modification Methylation, glycosylation, phosphorylation, acetylation, proteolytic processing, addition of prosthatic groups, disulphide bond etc. protein degradation.

Reading List

1 Harpers biochemistry by Robert K. Murray and Daryl K. Granner and Peter A. Mayes and Victor W. Rodwell; Ed. 25th; McGraw-Hill; 2000.

8 2 Biochemistry by Donald Voet and Judith G. Voet; Ed. 3rd; Wiley; 2008. 3 Lehninger principles of biochemistry by David L. Nelson and Michael M. Cox; Ed. 5th; W.H. Freeman, 2004. 4 Biochemistry by Christopher K. Mathews and Kensal E. van Holde and Kevin G. Ahern; Ed. 3rd; Prentice Hall, 1999. 5 Textbook of biochemistry with clinical correlations by Thomas M. Devlin; Ed.6th; Wiley-Liss; 2005. 6 Biochemistry by Jeremy M. Berg and John L. Tymoczko and Lubert-Stryer; Ed. 6th; W.H. Freeman, 2008.

9 MBS 103: CELL BIOLOGY

Biomembranes: Basic structure, lipid and protein composition and their basic functions Transport of molecules across membranes. Passive and active transport across membranes. Factors regulating them, ion chanells, ABC pumps of bacteria.

Organelles of eukaryotic cells Introduction basic structure and function of various organelles, ER, golgi bodies, chloroplasts, mitochondria endosomes, lysosomes etc. separation and visualization methods of various cell organelles.Muscle & Nerve Cells.

Nucleus and Chromosome Structure Introduction: Prokaryotic and Eukaryotic genome and its organization, eukaryotic chromosome. Basic structure of DNA; hairpins and cruciform, Z-DNA, triple helix.

DNA Supercoiling: Histones, nonhistone proteins, topoisomerases and telomerase and their functions in chromatin structure. Yeast artificial chromosome.

The Cytoskeleton Cytoskeleton proteins, Cell motility and shape, protein sorting, Transport of proteins. Microfilaments and actin filaments

ECM Proteins and Cell Adhesion Cell-cell interaction, Cell junctions, Adhesion proteins, Cell matrix interaction, Integrins, Functional role of adhesion proteins.

Eukaryotic Cell Cycle Cell cycle and its control: Loss of cell regulation by viral infection, checkpoints in cell cycle regulation.

Cell to Cell Signaling Cell surface receptors, G-protein mediated signaling, camp, receptors tyrosine kinases, second messengers.

Cell death Apoptosis, Necrosis, Proapoptotic and Antiapoptotic proteins and mechanism of action Autophagy, Senescence, Cell death mechanisms in health and diseases.

Cell Differentiation

Cellular Stress Response Stress response proteins and pathways, Post translational modifications in stress response, General responses to hyperthermia nutritional deprivation and other stressors.

Reading List

1. Molecular biology of the cell by Bruce, Alberts and Alexander Johnson and Julian Lewis, and Martin Raff; Ed. 5th; Garland Science; 2008. 2. Molecular biology of the cell: the problem book by John Wilson and Tim Hunt; Ed. 5th; Garland Science; 2008. 3. Molecular cell biology by Harvey Lodish and Arnold Berk, Chris A. Kaiser, and Monty Krieger; Ed. 6th; W H Freeman and Company; New York; 2008. 4. Cell: molecular approach by Geoffrey M. Cooper and Robert E. Hausman; Ed. 4th; ASM Press; 2007. 5. Cell biology by Thomas D. Pollard and William C. Earnshaw; Ed. 2nd; Saunders; 2008.

10 MBS 104 : MEDICAL MICROBIOLOGY

Bacteriology Introduction, Taxonomy, nomenclature and identification of bacteria, Reproduction and growth, Organization and ultrastructure of micro-organisms and various antibiotics, Antimicrobial used in clinical practical, Normal human flora, Pathogenesis and virulence factors of bacteria, Human diseases caused by bacteria in the following: Respiratory tract infections, Urinary tract infections, Genital tract infections, Gastrointestinal tract infections, Blood stream and CNS infections. Epidemiology of bacterial diseases.

Parasitology Classification of parasitic protozoa. Cellular organization of parasitic protozoa. Epidemiology of parasitic infections. Immunology and immunopathology of parasitic infections, Control of parasites and parasitic infections. Common parasitic disease: Trypanosomiasis, Leishmaniasis, Malaria, Opportunistic parasitic infections, Helminths.

Medical Mycology Classification, Cryptococcosis, Candidiasis, Blastomycosis, Histoplasmosis, Coccidiomycosis, Phycomycosis.

Clinical Virology The structure, components and classification of viruses. Viral multiplication cycle, effect of virus infection on the host cell, cytopathic effects, inhibition of host cell cytopathic effects, inhibition of host macromolecular biosynthesis, changes in regulation of gene expression. Genetics of animal viruses. History, epidemiology, diagnosis, clinical features, treatment and prevention of small pox, herpes, adenoviruses, arboviruses, picornaviruses, myxoviruses.

Reading List

1 Microbiology by Lansing M. Prescott and John P. Harley and Donald Klein; Ed. 6th; McGraw-Hill Science, 2004. 2 Color ATLAS and textbook of diagnostic microbiology by Elmer W Koneman and Stephen D Allen and William M Janda and Paul C Schreckenberger and Washington C Winn; Ed. 6th; Lippincott Williams & Wilkins, 2005. 3 Medical microbiology: a guide to microbial infections: pathogenesis, immunity, laboratory diagnosis and control by David Greenwood and Richard C. B. Slack and John F. Peuthere, ed. 17th Ed. Churchill Livingstone; 2007. 4 Essentials of diagnostic microbiology by Lisa Anne Shimeld and Anne T. Rodgers; Delmar Publishers, 1999. 5 Medical Microbiology by Geo. Brooks and Karen C. Carroll and Janet Butel and Stephen Morse; Ed. 24th; McGraw-Hill Medical, 2007. 6 Topley and Wilson's Microbiology and Microbial Infections by Leslie Collier and Albert Balows and Max Sussman; Ed. 9th; 6-Volume Set; A Hodder Arnold Publication, 2000.

11 MBS 105: GENETICS

SECTION A

Introduction to the Science of Genetics Genetic terminology Impact of Genetics on other disciplines.

Mendelian Genetics Mendelian Laws of inheritance, its application in animal Genetics, analysis of results of Genetic crosses by various methods.

Chromosomal basis of inheritance and data analysis Sex chromosomes in grasshopper, maize and co-linearity of genes on chromosomes, Non-disjunction in Drosophila and its role in deciphering chromosomal basis of inheritance. Analysis of patterns of inheritance, Punnett square, statistical methods.

Deviations from Mendelian Genetics I Codominance, incomplete dominance, RFLP markers, gene interactions, multiple alleles.

Mutation and mutational analysis Spontaneous occurrence of mutations in bacteria Lederberg and Lederberg experiment, Types of mutations i.e. point mutations, deletions, rearrangements, insertions, dynamic mutations (repeat expansions) with appropriate examples, Chromosomal anomalies. Mutation mapping suing balancers, Clb technique in Drosophila.

Linkage as a deviation from Mendelian Genetics Recombination, Gene mapping using Drosophila as an example, experiments demonstrating physical basis of recombination, crossing over. Gene mapping using special systems, yeast and Neurospora.

Bacterial genetics Transformation, Conjugation, genetic map construction in E.coli. Phage genetics, fine structure of rII region, work of Seymour Benzer.

Genetic Variation Transposition and its application in genetic studies. Extra chromosomal inheritance, chloroplast and mitochondrial inheritance, mitochondrial mutations in yeast, human genetic disorders related to mitochondrial inheritance.

Deviations from Mendelian Genetics II Genomic imprinting in mice, understanding molecular basis of epigenetic inheritance, human disorders related to imprinting, Prader Willi and Angelmen syndrome, Molecular basis of Epigenetic regulation in H19 and Igf2 region, histone modification marks, Position effect variegation.

Genetic control mechanisms and generation of cellular asymmetry The lambda phage control of lytic and lysogenic phase, molecular basis of regulatory mechanisms in phage lambda. Mating type switching in Saccharomyces cerevisiae.

Sex determination in Drosophila and humans Chromosomal basis to genetic basis, genetics of dosage compensation in Drosophila. X inactivation and its molecular basis in humans.

Introduction to developmental genetics Early embryonic development in Drosophila. Maternal inheritance, genetic basis of axis determination, regulatory cascade in development in Drosophila, Homeotic genes.

12 Introduction to human Genetics Pedigree analysis and basic inheritance patterns in humans.

SECTION B

POPULATION GENETICS

Definition, aim and scope of population genetics, population structure, factors maintaining population boundaries, effective breeding size, gene pool. The Hardy-Weinberg Law and its application, factors affecting the Hardy-Weinberg equilibrium. Human polymorphism (transient and balanced), relationship between sickle cell polymorphism and malaria, other ploymorphisms that may be an adaptation to malaria eg. G6PD deficiency. Duffy blood groups, thalassemia and haptoglobins. X linked polymorphism (G6PD and colour blindness). Incompatibility Selection. Non-random mating, inbreeding and its consequences. Migration and Genetics, types of migration, models to study genetic effects of migration, gene flow, effects of gene flow, admixture and natural selection, calculation of admixture.

Reading List

1. Principles of genetics by D. Peter Snustad and Michael J. Simmons; Ed.5th; John Wiley & Sons Ltd; 2008. 2. Principles of genetics by Eldon John Gardner and Michael J. Simmons and D. Peter Snustad Ed.8th; John Wiley; 2005. 3. Introduction to genetic analysis by Anthony J.F. Griffiths and Susan R. Wessler and Richard C. Lewontin and Sean B. Carroll; Ed.9th; W. H. Freeman,2008. 4. An Introduction to Genetic Analysis by Anthony J.F. Griffiths; Susan R. Wessler; Richard C. Lewontin; William M. Gelbart; David T. Suzuki and Jeffrey H. Miller; W. H. Freeman, 2004. 5. Developmental biology by Scott F. Gillbert; Ed.8th; Sinauer Associates; 2006. 6. Genes by Benjamin Lewin; Ed.9th; Jones and Bartlett Publishers; 2006.

13 MBS-201: ORGANIC CHEMISTRY-II

Bio-organic Chemistry Aminoacids, peptides and Proteins structure and Functions. Formation of Peptide Bonds. Activation and Protecting groups and peptide bond formation, protein degradation and sequencing of amino acids,DNA and RNA bases, nucleosides and nucleotides, formation of N- and C- glycosides, phosphodiesters, conformation and configuration of 5-carbon and 6-carbon sugars, maltose, sucrose and lactose, glucosylamine, neuraminic and muramic acids.

Synthetic macromolecules and Polymers in Biology Building of macromolecules and molecular frameworks and their biomedical applications. Synthetic strategies for artificial systems that mimic biological entities, applications of supramolecular principles to molecular diagnosis, therapeutic applications of supramolecular chemistry. Nanotechnology and its applications in drug delivery and the potential for synthetic peptides to form antibiotic tubes

Mechanisms in Biological Chemistry Active methylene groups, aldol and retroaldol reactions, schiff bases and enamine reactions, nitrogen, phosphorous and sulfur ylides, Umpolung reaction, Michael addition, Polymer supported organic reactions, phase transfer catalysis, Equivalence of these reactions in biological systems

Enzyme systems Enzyme classifications, EC number, Inhibitors, Mechanism of Enzymes. Mechanism of coenzyme catalysis: Coenzyme A, NAD+ and NADPH, FMN and FAD, biotin, pyridoxal, TPP, lipoic acid, tetrahydrofolate, ascorbic acid, cyanocobalamine and cytochrome P-450.

Hammett and Taft Equation Steric and Solvent effects Role of pH, reaction media on certain reactions.

Reading List

1 Marchs advanced organic chemistry: reactions, mechanisms and structure by Jerry March and Michael B. Smith; Ed.6th; Wiley-Interscience; 2007. 2 Advanced organic chemistry: Part A: structure and mechanisms by Francis A. Carey and Richard J. Sundberg; Ed. 5th; Springer; 2008. 3 Organic chemistry by Thomas N. Sorrell; Ed.2nd; University Sceince Books, 2005 4 Organic chemistry by Robert Thorton Morrison and Robert Neilson Boyd; Ed. 6th; Prentice Hall of India; New Delhi; 2002. 5 Organic chemistry by T. W. Graham Solomons and Craig B. Fryhle; Ed. 9th; Wiley, 2007 6 Modern methods of organic synthesis by W. Carruthers and Iain Coldham; Ed. 4th; Cambridge University Press; London; 2005. 7 Introduction to General, Organic and Biochemistry by Frederick A. Bettelheim, William H. Brown, Mary K. Campbell, Shawn O. Farrell; Ed.9th; Brooks Cole, 2009. 8 Biological and Pharmaceutical Nanomaterials: Nanotechnologies for the Life Sciences by Challa S. S. R. Kumar; Ed.1st; Wiley-VCH, 2006.

14 MBS 202: MOLECULAR BIOLOGY AND BIOTECHNOLOGY

Regulation of gene expression in Prokaryotes Coordinated control of clustered genes-operon model, with example of inducible systems like Lac Operon. Arabinose operon and repressible systems like Trp operon. Role of cyclic AMP.

Role of repressors and activators of transcription in regulation of phage-lytic and lysogeic pathways, lambda repressor.

Regulation of Gene expression in Eukaryotes Introduction-Organization of genes in eukaryotic DNA; Repetitive DNA sequences, Activators, enhancers. Modular structure of transactivators, repressor complexes, mechanism of their function in gene regulation.

Post transcriptional regulation of transcription regulators by methylation, acetylation, hormones and protein-protein interactions.

Methods used to study protein-protein interactions (yeast two hybrid and co-Immunoprecipitation) and protein-DNA interactions (EMSA and DNA footprinting)

Diseases linked with gene expression.

Chromatin remodeling Role of various remodeling proteins such as NURF, ACF, CHRAC, SWI-SNF and locus control regions in gene regulation.

Oncogenes Retroviral and cellular oncogenes, their function and mechanism of action in regulating cell growth and development (using P53 and Ras protein as example).

Recombinant DNA technology and Biotechnology Types of Restriction endonucleases and how to make restriction maps. Other enzymes used in genetic engineering such as S1 nuclease, polynuceotide kinase, mung bean nuclease etc. Vectors - cloning and expression vectors, prokaryotic and eukaryotic cloning vectors, yeast vectors, shuttle vectors, YAC & BAC. Principles of selection of specific cloned DNA - blue white selection, insertional inactivation, antibiotic markers used in prokaryotic and eukaryotic cloning. Detection and identification of cloned DNA sequences, methods of sequencing of DNA. Application and principles of Polymerase Chain Reaction, RT-PCR, RFLP analysis, real time PCR. Mutagenesis different methods used to generate mutants (deletion and point mutations). Application of recombinant DNA technology: DNA fingerprinting, gene therapy, diagnostics. Bio-safety and ethics for recombinant DNA technology.

Reading List

1 Gene VIII by Benjamin Lewin Ed.7th; Oxford; 2008. 2 Molecular cell biology by Harvey Lodish and Arnold Berk, Chris A. Kaiser, and Monty Krieger; Ed.6th; W H Freeman and Company; New York; 2008 3 Cell: a molecular approach by Geoffrey M. Cooper; Ed.3rd; ASM Press; 2004

15 MBS 203: APPLICATION OF STATISTICS AND MATHEMATICS FOR BIOLOGY

Bio-Statistics Introduction to Mean, mode, median, mean deviation, Standard deviation, coefficient of variation.

Correlation (Karl Passions, Co-efficient of correlation, Rank correlation) and Regression analysis, Regression equations, taking suitable examples from biological data.

Probability: Theorems on probability, Binomial and normal distribution .

Methods of Sampling of biological data and analysis using t and Z and F tests of significance for small and large samples.

Bio-Mathematics Functions, Limits and continuity, differentiation and integration, Maxima & Minima and their use in biological problems.

Differential Equations, separable variables, homogeneous, exact and linear equations of second order, application of differential equations of Biochemistry.

Matrices and determinants, characteristic roots and characteristic equations, Caley Hamilton theorem.

Reading List

1 Basic statistics by A. L. Nagar and R. K. Das; 2nd Ed.; Oxford; 2002. 2 Biostatistics: a manual of statistical methods for use in health, nutrition and anthropology by K. Visweswara Rao; Jaypee Borthers, 1996. 3 Introductory statistics by Prem S. Mann; 5th Ed.; John Wiley; 2003. 4 Biostatistics: a foundation for analysis in the health sciences by Wayne W. Daniel; 8th Ed.; John Wiley; 2005. 5 John E. Freunds mathematical statistics with application by Irwin Miller and Marylees Miller; Ed.7th; Pearson; 2006. 6 Essential Mathematical Biology by Nicholas F. Britton; Ed.1st; Springer; 2004.

7 Differential Calculus by Shanti Narayan ; Ed. 30th; S. Chand & Co Ltd; 2005.

16 MBS 204 : IMMUNOLOGY

Introduction to Immune System Innate and acquired Immunity, Active and passive Immunity

Lymphoid System Lymphoid Tissue: Primary or Secondary, Primary Lymphoid Organs, Secondary Lymphoid organs, Lymphocyte Traffic

Cells involved in the Immune Response Lymphocytes, Mononuclear Phagocyte, Antigen- presenting cells, Polymorphs and mast cells, Cluster designation Ag specific receptors (comparison of Human and Mouse Lineages)

Antibody Generation, structure and Function Humoral immunity, Clonal Selection Theory, Immnoglobulins, Antibody Structure and Function, Antibody Effector Mechanism, Antibody Receptors, Antibody Diversity, Immunogolubin Gene Recombination, Effect of Somatic Mutations or the Antibody Diversity, Ab Class switching, Antibody Responses in vivo, Enhanced Secondary Responses Isotype switching, Affinity Maturation Development of Memory

Major Histocompatibility Complex Structure of MHC Class I Molecules, Structure of MHC Class II Molecules, Genomic Organisation of the MHC locus in Mice and Humans, Ontogeny and T-cell Receptors, Genomic Organization of TCR Locus

Antigen Recognition and Presentation Structure and assembly of MHC molecules/Peptide Complexes. Antigen Processing and Presentation of T-lymphocytes (CD4+ and CD8+)

Complement System Nomenclature of classical Complement, Alternative Activation of pathway, Biological Effects of Complement

Cytokines Network Molecular basis of t- cell activation, Cytokine production from TH1 and TH2 CD4+ T-cells, Structure and function of various cytokines, cytokine receptors

Cell Mediated Immune Response T -Cell independent Defence Mechanisms, T- Cell dependent Defence Mechanisms, Cell Mediated Cytotoxicity, Role of Macrophages in Immune Response

Regulation of Immune Response Role of Antigen, Antigen Presenting Cell, Antibody, Lymphocytes, Idiotypic Modulation of Response, Neuroendocrine Modulation of Responses, Genetic control of Immune Response.

Cell Migration and Adhesion Patterns of Cell Migration, Structure and function of various adhesion Molecules, Mechanism of Cell Migration and their involvement in disease

Immunopathology Rh- blood groupings, Autoimmune Diseases, Immuno deficiencies, Genetic disorders congenital and acquired, Hypersensitivity Reactions (type I and type IV), Role of 1gE, Mast cells, Genetic Allergic Response, Tumors

Immune Tolerance Self Tolerance, Transplantation and Rejection.

17 Antigen Antibody Interaction

Immunological Techniques Haemagglutination, Direct/Indirect Immunoflorescence, Isolation of pure antibodies, Hybridoma Technology for Mab Production, Assays for Complement

Gene Targeting: Knock out and Transgenic Animals.

Tumor Immunology

FACS

Vaccines

Reading List

1 Kuby Immunology by Thomas Kindt and Richard A. Goldsby and Barbara A. Osborne; Ed. 6th; W.H. Freeman and Company, New York; 2007. 2 Cellular and molecular immunology by Abul K. Abbas and Andrew H. Lichtman and Shiv Pillai; Ed. 6th; Saunders, 2007. 3 Immunology; Ed.7th by David Male and Jonathan Brastoff and David B. Both and Ivan Roitt; Mosby Elsevier; 2006. 4 Immuno biology: the immune system in health and disease by Charles A. Janeway and Paul Travers and Mark Walport and Mark J. Shlomchik; 7th Ed; Garland Science; 2008. 5 Immunology of infection diseases by Stefan H. E. Kaufmann and Alan Sher and Rafi Ahmed; ASM Press, Washington; 2002. 6 Essentials of immunology & serology by Jacqueline H. Stanley; DELMAR; Australia; 2002.

18 MBS 205: HUMAN PHYSIOLOGY

Membrane physiology, nerve and muscle Organization and functional systems of the cell with refers to nerve and muscle cells. Transport of ions and molecules through cell membrane: diffusion and active transport. Membrane potentials and action potentials: Resting membrane potential of nerves. Nerve action potential. Excitation and Contraction of skeletal muscle: Physiologic anatomy of skeletal muscle. Molecular mechanisms of muscle contraction. Energetics of muscle contraction. Excitation of skeletal muscle. Neuromuscular transmission and excitation-contraction coupling.

Blood physiology Blood cells, and blood clotting, red blood cells. Blood groups, transfusion, tissue and organ transplantation. Resistance of body to infection. Leukocytes, granulocytes, monocyte-macrophage system and inflammation. Hemostasis and blood coagulation.

Heart and circulation Physiology of cardiac muscle. Cardiac cycle, Regulation of heart pumping, Rhythmical excitation of heart, Control of excitation and conduction in heart, Characteristics of normal electrocardiogram, Cardiac arrhythmias, Physical characteristics and basic theory of circulation, Vascular distensibility and functions of arterial and venous systems, Microcirculation and lymphatic system, Capillary fluid exchange, interstitial fluid and lymph flow, Local control of blood flow by tissues and humoral regulation, Nervous regulation of circulation, Cardiac output, venous return and their regulation, Heart sounds, dynamics of valvular and congenital heart defects, Cardiac failure and circulatory shock.

Respiration Pulmonary ventilation: mechanisms of pulmonary ventilation, pulmonary volumes and capacities, alveolar ventilation. Functions of respiratory passageways. Pulmonary circulation, pulmonary edema and pleural fluid. Physical principles of gas exchange, Diffusion of gases through respiratory membrane, Transport of oxygen and carbon dioxide in blood and body fluids. Regulation of respiration: respiratory center, peripheral chemoreceptor system, central chemoreceptor system and their regulatory function.

Gastrointestinal physiology General principles of gastrointestinal function - motility, nervous control, and blood circulation, Transport and mixing of food in the alimentary tract, Ingestion of food. Motor functions of stomach. Movements of small intestine. Movements of colon. Secretary functions of alimentary tract: Secretion of saliva, Gastric secretion, Pancreatic secretion, Secretion of bile by liver, Secretions of small and large intestine. Digestion and absorption in gastrointestinal tract: Digestion of various foods, Absorption in small intestine.

Kidneys and body fluids Body fluid compartments: Basic principles of osmosis and osmotic pressure: Extracellular and intracellular fluids. Interstitial fluid and edema. Urine formation by kidneys: Glomerular filtration, renal blood flow and their control, Functions of kidneys in homeostasis, Determinants of glomerular filtration rate, Renal blood flow, Tubular processing of glomerular filtrate, Reabsorption and secretion by renal tubules. Reabsorption and secretion along different parts of nephron, Regulation of tubular reabsorption.

Regulation of extracellular fluid osmolarity and sodium concentration. Role of thirst in controlling extracellular fluid osmolarity and sodium concentration. Integration of renal mechanisms for control of blood volume and extracellular fluid volume. Renal regulation of potassium, calcium, phosphate and magnesium. Regulation of acid-base balance.

19 Reading List 1 Textbook of medical physiology by Arthur C. Guyton and John E. Hall; Ed.11th; Saunders; 2005. 2 Review of medical physiology by William F. Ganong; Ed. 22nd; McGraw Hill; 2005. 3 Essential medical physiology by Leonard R. Johnson and Ed. 3rd; ELSEVIER; 2003. 4 Principles of anatomy and physiology by Gerard J. Tortora and Bryan Derrickson; Ed.1th; John Wiley; 2006. With (Brief atlas of the skeleton surface anatomy, and selected medical images) 5 Best and Taylors physiological basis of medical practice by John B. West; 12th; B I Waverly Pvt Ltd.; New Delhi; 1990. 6 Medical Physiology: A cellular and molecular approach by Walter F. Boron and Emile L. Boulpaep; Saunders; 2003. 7 Physiology by Robert M. Berne and Matthew N. Levy; Mosby; 1998.

20 MBS 301: ADVANCE HUMAN PHYSIOLOGY

Sensory Physiology Central nervous system synapses. Some special characteristics of synaptic transmission, Sensory receptors. Neuronal circuits for processing information. Somatic sensations: Tactile and position senses. Sensory pathways for transmission of somatic signals into the central nervous system. Transmission in dorsal column medial lemniscal system. Pain, headache, and thermal sensations: Pain receptors and their stimulation, Dual transmission of pain signals into the central nervous system. Referred and visceral pain. Eye: Optics of vision, Receptor and neural function of retina, Photochemistry of vision, Color vision, Neural function of retina. Central neurophysiology of vision, Organization and function of visual cortex. Hearing: Tympanic membrane and ossicular system, Cochlea, Central auditory mechanisms, Vestibular sensations and maintenance of equilibrium. The chemical senses - taste and smell.

Nervous system: motor and integrative neurophysiology Motor functions of spinal cord. Spinal cord reflexes. Muscle sensory receptors - muscle spindles and Golgi tendon organs and their roles in muscle control, Flexor reflexes and withdrawal reflexes, Reflexes of posture and locomotion. Cortical and brain stem control of motor function: Motor cortex and corticospinal tract, Role of brain stem in controlling motor function. Cerebellum, basal ganglia and motor control. Integration of all parts of total motor control system. Cerebral Cortex: intellectual functions of brain, learning and memory. Physiologic anatomy of cerebral cortex. Functions of specific cortical areas, Association areas. Function of brain in communication - language input and output. Function of corpus callosum and anterior commissure. Thoughts, consciousness and memory. Behavioral and motivational mechanisms of brain. Limbic system and hypothalamus. Activating-driving systems of brain. Functional anatomy and functions of limbic system and hypothalamus. States of brain activity. Sleep. Slow-wave sleep. REM sleep. Basic theories of sleep. Brain waves. Origin in brain of brain waves (EEG). Epilepsy, Psychotic behavior and dementia - roles of specific neurotransmitter systems.

Metabolism and Temperature Regulation Metabolism of carbohydrates and formation of adenosine triphosphate. Lipid metabolism. Dietary balances, regulation of feeding, obesity and starvation. Vitamins and minerals. Energetics and metabolic rate. Body temperature, temperature regulation and fever.

Endocrine glands & Hormones Endocrine glands & Hormones, Pituitary: Structure and function, Hypothalamic control of pituitary glands. Thyroid structure, function of parathyroid hormones. Adernal Cortex, Structure and function of its hormones; Adrenal Medullar; function of its hormones. Pancreas: Function of its hormones.

Environmental Physiology High altitude, space and Deep Sea Diving Physiology: Effect of low oxygen pressure on the body, Effects of Acceleratory forces on the body in aviation and space physiology, Effect of High partial pressure of gases on the body.

Reading List

1 Textbook of medical physiology by Arthur C. Guyton and John E. Hall; Ed.11th; Saunders; 2005. 2 Review of medical physiology by William F. Ganong; Ed. 22nd; McGraw Hill; 2005. 3 Essential medical physiology by Leonard R. Johnson and Ed. 3rd; ELSEVIER; 2003. 4 Principles of anatomy and physiology by Gerard J. Tortora and Bryan Derrickson; Ed.1th; John Wiley; 2006. With (Brief atlas of the skeleton surface anatomy, and selected medical images) and 5 Best and Taylors physiological basis of medical practice by John B. West; 12th; B I Waverly Pvt. Ltd.; New Delhi; 1990. 6 Medical physiology: a cellular and molecular approach by Walter F. Boron and Emile L. Boulpaep; Saunders; 2003. 7 Physiology by Robert M. Berne and Matthew N. Levy; Mosby; 1998.

21 MBS 302: PRINCIPLES OF MEDICINAL CHEMISTRY

Role of Medicinal Chemistry in discovery of drugs

Drug Design Discovery of lead compound, lead modification, conventional drug screening, structural modification, bioisosteres, structure activity relationship, Quantitative structure activity relationships, introduction to molecular modeling and molecular graphics, pharmacophore descriptors

Receptors Chemical nature of receptors, Neurotransmitters and their receptors, Receptor modulation and mimics, Receptor sites, Drug receptor interactions, active transport, affinity and efficacy, antagonism, partial antagonism, inverse agonism, allosteric binding sites Chirality and receptor binding, Signal transduction and second messenger systems, classification of receptors and receptor subtypes.

Introduction of various classes of drugs based on their interaction with target site. Drugs interacting with receptors, enzymes, DNA, carbohydrates etc with suitable examples.

Structure activity relationship illustrated with examples from Sulphonamides, E-lactams, Quinolones, Nucleosides and Alkaloids.

Drug Metabolism Biotransformations and their mechanisms, Phase I and Phase II metabolism, Oxidation, Reduction, Hydrolysis, Deamination and Conjugation (GSH, Sulfate, Glucuronide and Amino acids), Role of non- specific enzymes: Oxidases, Mono-oxygenases, Di-oxygenases and Peroxidases: Biotransformations illustrated by suitable examples of commonly used drugs, Chirality and drug metabolism.

Enzyme Inhibition Reversible and irreversible, Adverse drug reactions, Drugs acting on cell wall, Fungal membrane and Nuclear membrane, Drugs inhibiting protein synthesis.

Reading List

1 Organic chemistry of drug design and drug action by Richard B. Silverman; Ed. 2nd; ELSEVIER; 2004. 2 Foye's Principles of Medicinal Chemistry by Thomas L Lemke and David A Williams; Ed. 6th; Lippincott Williams & Wilkins; 2007. 3 Medicinal chemistry: principles and practice by Frank D. King; Ed. 2nd; The Royal Society of Chemistry; 2002. 4 Introduction to medicinal chemistry by Graham L. Patrick; Ed. 3rd; Oxford; 2006. 5 Chemical aspects of drug delivery systems by D. R. Karsa and R. A. Stephenson; The Royal Society of Chemistry; 1996.

22 MBS 303: ANALYTICAL & BIOMEDICAL TECHNIQUES AND INSTRUMENTATION

Introduction Principles of Instrumental Analysis, Types of Instrumental Methods to be covered in the course. Selecting an analytical method and developing a new Analytical Technique.

Separation Methods An introduction to chromatographic separation, Gas Chromatography, High Pressure Liquid Chromatography and FPLC, Supercritical fluid chromatography

Mass Spectrometry Explanation of mass Spectrometry. Forming charged particles: Electron impact (EI) and Chemical Ionization(CI), Fast Atom Bombardment (FAB), Field Desorption (FD), Electrospray Ionization, Matrix Assisted Laser Desorption Ionization (MALDI). Mass Analyzers: Magnetic sector mass spectrometers, Double focusing mass spectrometers, Quadrupole pole mass spectrometers, ion cyclotron resonance, Time of Flight mass analyzers. Combine the mass spectrometer with Gas Chromatography (GC/MS) and with liquid chromatography (LC/MS). Applications of mass spectrometry in Biomedical field.

Nuclear Magnetic Resonance Spectroscopy Theory of NMR: Quantum description, Classical description Processional motion, Larmour frequency, Relaxation processes, T1 and T2 and their measurement. Fourier Transform NMR: Pulsed excitation, FID, Types of NMR Spectra Wild line and high resolution spectra. NMR Spectrometers: Instrumentation. Environmental Effects: Types, Chemical shift theory, Magnetic anisotropy, Spinspin splitting, first order and second order spectra, Double Resonance Techniques, Proton on heteroatom. Application of proton NMR: Identification of compounds. 13C NMR: Proton decoupling: Broad band, off-resonance, Pulsed decoupling, NOE, application to structure determination. Magnetic Resonance Imaging: The concept of MRI, Application in Muscle Physiology, functional mapping of brain. Other nuclei : 31P, 19F, 23Na, 15N

Optical Methods and their applications in Biomedical Sciences Ultraviolet / Visible molecular absorption spectroscopy, Fluorescence and Phosphorescence, Infrared, CD and ORD

Miscellaneous Confocal Microscopy: Applications in Cell Biology, Electron Microscopy, Tracer Techniques in Biology: tumor diagnosis and imaging, infectious diseases such as tuberculosis, Flow Cytometry, Mangetic Assisted Cell Sorting

Reading List

1 Spectrometric identification of organic compounds by Robert M. Silverstein and Francis X. Webster; Ed. 6th; John Wiley; 1997. 2 Principles of instrumental analysis by Douglas Skoog and F. James Holler and Timothy A. Nieman; Ed. 5th; Saunders; 1998. 3 Contemporary instrumental analysis by Kenneth A. Rubinson and Judith F. Rubinson; Prentice Hall 2000. 4 Organic spectroscopy by William Kemp; Ed. 3rd; Palgrave; 1991. 5 Basic one and two dimensional NMR spectroscopy by Horst Friebolin; Ed.3rd; Wiley-VCH; 1998. 6 NMR and its applications to living systems by David G. Gadian; Ed. 2nd; Oxford; 1995. 7 Structure determination of organic compounds: tables of spectral data by E. Pretsch and P. Buhlmann and C. Affolter; Springer; 2005. 8 MRI principles by Donald G. Mitchell; W S Saunders; 1999. 9 HPLC: a practical users guide; Ed.2nd by Marvin C. McMaster; Wiley-Interscience; 2007.

23 MBS 304: MOLECULAR ONCOLOGY (Interdisciplinary)

The Cancer Problem Epidemiology, Environmental carcinogens and risk factors, life style, changing patterns, the Indian scenario.

Mechanisms of Carcinogenesis Various theories, multi-step and multistage processes, Initiation, Promotion and Progression. Role of DNA damage, repair and mutations by physicochemical agents and viruses, interaction of various agents. Differentiation: hyperplasia and precancerous lesions. Strategies of chemoprevention.

Tumor types and leukemia Benign and malignant tumors, localized and metastatic disease, Schemes of classification, WHO classification, staging and grading, degree of malignancy. Classification of leukemia, types of chromosomal translocations.

Tumor Immunology Immune suppression and role of immune survelliance in growth of tumors. Tumor specific antigens and immune response. Modulation of immune response and immunotherapy, cancer vaccines.

Modulation of the Eukaryotic Cell Cycle and cell death in cancer Cell cycle and its control: Mechanism of deregulation of cell cycle during cancer. Apoptosis, Necrosis, Proapoptotic and Antiapoptotic proteins and mechanism of action.

Cell Interactions in Development of cancer Cell-cell interaction, integrins, invasions, invasions by cancerous cells. Angiogenesis, Neoarrgiogenesis, Stem Cell Differentiation, Morphogens

Experimental Model Systems in Cancer Research Microbial Models, Primary Cell Cultures, Established Cell Lines, Organ Cell Cultures, Spheroids.

Tumor suppressor genes and Viral oncogenes Mechanisms of P53, Rb, Ras action in normal and transformed cells and viral oncogenes, Role of oncogenes in gene regulation using examples erb, rel, jun-fos, large Tantigen etc.

Growth factor-signalling pathways in cancer Relationship between oncogene products and growth factors, using example of Src, Wnt, Abl, GAP and growth factors. Effect of viral infection on signal transduction.

Cancer genetics, familial cancers.

Emerging Cancer Therapy Cellular, tissue and molecular markers, potential targets for Cancer Therapy, Drug Discovery Strategy.

Reading List

1 Genes by Benjamin Lewin Ed. 7th; Oxford; 2000. 2 Principles of Genetics by Eldon J. Gardner and Michael J. Simmons and D. Peter Snustad; Ed. 8th; John Wiley, 2005. 3 Molecular cell biology by Harvey Lodish and Arnold Berk, Chris A. Kaiser, and Monty Krieger; Ed. 6th; W H Freeman and Company; New York; 2008. 4 Principles of molecular oncology by Miguel H. Bronchud and Others; Humana Press; 2000.

24 MBS 305: TOXICOLOGY & PHARMACOLOGY

Introduction to pharmacology, scope of pharmacology. Routes of administration of drugs, their advantages and disadvantages. Various processes of absorption of drugs and the factors affecting them; Adsoption, metabolism, distribution and excretion of drugs. Pharmacodynamics: General mechanism of drug action and the factors, which modify drug action.

Pharmacological classification of drugs; the discussion of drugs should emphasize the following aspects:

Drugs acting on the central nervous system: Anesthetics, pshychopharmacological agents

Drugs acting on the autonomic nervous system: Cholinergic drugs, anticholinergic drugs, anticholinesterase drugs, Adrenergic drugs and adrenergic receptor blockers, Neuron blockers and ganglion blockers, Neuromuscular blockers, drugs used in myasthenia gravis.

Hormones and hormone antagonists, Drugs acting on the respiratory system- bronchodilators, expectorants and antitussive agents, Drugs acting on the digestive system, Cardiovascular drugs, cardiotonics, antianginal agents, antihypertensive agents, peripheral vasodilators and drugs used in atherosclerosis, coaogulants and anticoaogulants.

Principles of Toxicology

Definition, scope and different branches of toxicology.

A brief review of toxic substances: Synthetic organic compounds: Chemical additives in food, Chemicals in the work place, Solvents, Pesticides, Cosmetics, Drugs of abuse. Inorganic chemicals: Industrial and chemical environmental inorganic toxicants polluting air/ water/ food. Naturally occurring poisons: Mycotoxins, Bacterial toxins, Plant toxins and Animal toxins.

Types of toxicity and its measurement: Acute, Sub-acute or Chronic and its manifestations. Acute toxicity: Mode of application/ administration/ exposure, in-vitro tests, Dose response relationship, Measurement of TD 50/ TC 50 and LD 50/ LC 50. Subacute and chronic toxicity. Risk and safety analysis: Margin of safety, Therapeutic index, Ideal therapeutic index. Inter-species extrapolation of dose-response data, NOEL, ADI, TLV, WHO standards. Special toxicity studies: Carcinogenecity, teratogenicity, in-vitro mutagenicity tests.

Epidemiology of toxicity: Cohort study, Retrospect study, Case-control study, Cross-sectional study, Confounding.

Pharmacokinetic aspects of toxicants: Absorption, Distribution, Metabolism and Excretion (ADME) of drugs and chemicals. A general study only. Site of metabolism, Metabolizing enzymes of liver, kidney, lung, GI tract, skin and their role in activation and detoxification of drugs and chemicals. Physiological (route of exposure, species, sex and age), Nutritional and environmental (temperature, altitude and circadian rhythms related) factors affecting metabolism, detoxification and toxic responses of drugs and chemicals.

Organ toxicities Hepatotoxicity: A brief description of morphological and functional aspects of liver with special reference to hepatotoxicity, various hepatotoxic agents, types of liver injuries- Fatty liver formation, Necrosis, Cholastosis, Hepatitis, Fibrosis, Cirrhosis, Carcinogenesis. Nephrotoxicity: A brief description of morphological and functional aspects of kidney in relation of nephrotoxicity, nephrotoxic agents, Detailed mechanisms of chemical induced nephrotoxicity. Cardiovascular toxicity: A brief description of mechanisms of cardiovascular toxicity and cardiotioxic agents- subcellular and biochemical mechanisms.

25 Neurotoxicity: A brief description neurotoxic agents and types of neurotoxic effects- Axanopathy, Neropathy, Neuronopathy, Mylenopathy. Broncho-pulmonary (inhalation) toxicity. Gastro-intestinal toxicity. Skin toxicity/ photosensitivity. Tests for evaluation of toxicities in different organs. Therapeutic aspects: General measures and treatment of poisoning cases, Specific antidotes, Agents of first choice, Contraindications.

Reading List

1 Essential of medical pharmacology; 6th Ed. By K.D. Tripathi; Jaypee Brothers; New Delhi; 2008. 2 Goodman & Gilmans the pharmacological basis of therapeutics by Laurence Brunton and John Lazo and Keith Parker; Ed. 11th; McGraw-Hill Professional; 2005. 3 Pharmacology H. P. Rang and M.M. Dale and J.M. Ritter and P.K. Moore; Ed. 5th; Churchill Livingstone, 2003. 4 Integrated Pharmacology: With Student Consult Access by Clive P. Page and M.J. Curtis and M.C. Sutter and M.J. Walker and B.B. Hoffman; Ed. 3rd; Mosby; 2006. 5 Principles of toxicology by Karen E. Stine and Thomas M. Brown; Ed. 2nd; CRC Press; 2006. 6 Lus basic toxicology: fundamentals, target organs and risk assessment by Frank C. Lu and Sam Kacew; Ed. 5th; Informa Healthcare; 2009. 7 Casarett and Dulls toxicology: the basic science of poisons by Curties D. Klaassen; Ed. 7th; McGraw Hill; New York; 2007. 8 Toxicology by Hans Marquradt and S.G. Schafer and R.D. McClellah and Academic Press; 1999. 9 Principles and practice of toxicology in public health by Ira R. Richards; Jones and Bartlett Publishers; 2007. 10 Handbook of human toxicology by E.J. Massaro; CRC Press; 1997.

26 MBS 401: DISSERTATION

27 MBS 402: GENOME BIOLOGY (Interdisciplinary)

Introduction Overview of Genomics. To highlight how biology is a network of interactions direct and indirect. What is the difference between genetics and genome biology? The transition from reductionist to comprehensive approach in understanding biological systems.

Role of model organisms in genetic studies in the pre-genomic era E.coli: Mutation analysis through mutant selection and deciphering metabolic pathways. Saccharomyces cerevisea: Tetrad analysis, isolation of mutants (e.g. cell cycle mutants) and their characterization. Caenorhabditis elegans: Discovery of RNAi/miRNA in developmental context. Drosophila melanogaster: from chromosomal basis of inheritance to sharing themes in developmental biology. (Note: students have studied this under Concepts in genetics (II semester), during these lectures the teacher is expected to reflect the integration of regulatory loops shared between Drosophila and humans, to show how this Cinderella of genetics remains relevant in the genomics era). Mus musculus: Generation of knockouts and transgenic for tissue expression analysis: Conventions of nomenclature of genes and gene products in different model systems (www.ncbi.nlm.nih.gov).

Pedigree Analysis Basic concept, Gathering family history, Pedigree symbols and construction of pedigrees, Interpretation of pedigree data.

Patterns of inheritance for monogenic traits Deviations from the basic pedigree patterns-Variable penetrance and expressivity, pleiotropy, late onset, dominance problems, anticipation, genetic heterogeneity, genomic imprinting and uniparental disomy, spontaneous mutations and X-inactivation (Website: OMIM)

Human Genome and beyond History, organization and goals of human genome sequence. Tools (Vectors- BAC, PAC, YAC and sequencing techniques) and approaches (Hierarchial and shotgun sequencing used). Outcomes and ethical issues. (For topics 1 and 3 refer to Human Genome Project site also.)

Organization of the Human Genome General features: Gene density, CpG islands, RNA-encoding genes. Gene clusters, Pseudogenes. Diversity in size and organization of genes. Types of repetitive DNA: LINES, SINES. Genetic markers and their applications

Techniques for Genomics Cytogenetic techniques (Karyotyping and FISH). Polymorphism screening (Genotyping of SNPs and Microsatellite markers). Expression analysis and proteome analysis

Mapping strategies Physical Maps (Cytogenetic maps, Radiation hybrids). Genetic Maps (Marshfield and DeCode maps)

Identification of Genetic Basis of Disease Forward and Reverse Genetics; Top-down and Bottom- up approaches. Parametric and non-parametric approach, TDT, Polymorphism based analysis. Positional and Candidate Gene approaches, Positional- cloning approach [Examples like Huntington disease, Cystic fibrosis, but not restricted to these]. Genotypic and Allelic frequencies. Haplotype construction (using SNPs and/or microsatellites polymorphism data). Introduction to Copy number variation (to be covered through paper presentations)

Genome of model organisms & pathogens & Comparative Genomics Overview of prokaryotic and eukaryotic genome organization and complexity: E. coli, Yeast, Drosophila, Mouse, M. tuberculosis and Plasmodium. Conservation and diversity of genomes

Implications of Genome Research: Diagnosis and screening of Genetic Disorders. Prenatal genotyping for mutations in ȕ- globin gene and sickle cell aneamia. Applications in pharmacogenetics (Genetic polymorphism in drug metabolism genes and their effect on drug metabolism and drug response, toxicity)

Website based analysis and seminars: www.ncbi.nlm.nih.gov, www.ensembl.org, HAPLORE for haplotype construction. Epigenome analysis [Concepts are taught in II semester]

Reading List

1 Human molecular genetics by Tom Strachan and Andrew P. Read; Ed. 3rd; Garland Science; 2004. 2 Vogel and Motulsky's Human Genetics: Problems and Approaches by Michael Speicher and Stylianos E. Antonarakis and Arno G. Motulsky; Ed. 4th; Springer; 2009. 3 Genomics: the science and technology behind the human genome project by Charles R. Cantor and Cassandra L. Smith; Ed. 2nd; John Wiley; 2002. 4 Genetics: From Genes to Genomes by Leland Hartwell, Leroy Hood, Michael L. Goldberg, and Ann E. Reynolds; Ed. 3rd; McGraw Hill Higher Education; 2006. 5 Basic human genetic by Elaine Johnsoen, Mange and Arthur P. Mange; Rastogi Publications; 2005. 6 Molecular and Genetic Analysis of Human Traits by Gustavo Maroni; Ed.1st; Wiley-Blackwell; 2001. 7 Human Genetics: The Molecular Revolution by McConkey; Jones and Bartlett; 1993. 8 Thompson & Thompson Genetics in Medicine by Robert L. Nussbaum and Roderick R. McInnes and Huntington F. Willard; Ed. 6th; Saunders; 2004.

29 MBS 403: CONCEPTS IN DRUG DISCOVERY AND MECHANISM (Interdisciplinary)

Existing drugs as lead compounds for new discovery: Case histories to be illustrated with examples from sulfonamides, E-lactams, Quinolones, Nucleosides, Alkaloids etc.

Combinatorial Chemistry: Methodology of combinatorial Synthesis, Parallel synthesis and Combinatorial Library.

Concepts in drug delivery systems., drug delivery devices: implants, minipumps, mechanism of controlled drug release, soluble delivery systems: micro and nano systems, routes of drug delivery systems .

Pharmacogenetics: Population variation in drug metabolism; genetic variability; polymorphism relating to receptors and genes in drug metabolism; molecular markers and Single nucleotide polymorphism as markers for emerging concepts in pharmacogenetics.

Receptor Chemistry and Biology: Chemistry of membrane and intracellular receptors; Isolation and characterization of receptors; Regulation of receptor number and affinity; Receptor cross-talk; Organ Receptors; Non-liganded and constitutive receptor activation; r-DNA receptor bioassays; Desensitization of receptors; Receptors as targets for vaccines and newer drug development.

Student seminar

Reading List

1 Organic chemistry of drug design and drug action by Richard B. Silverman; Ed. 2nd; ELSEVIER; 2004. 2 Combinatorial chemistry and molecular diversity in drug discovery by Eric M. Gorden and James F. Kerwin; Wiley-Liss; 1998. 3 Molecular diversity and combinatorial chemistry: principles and applications by Michael C. Pirrung; ELSEVIER; 2004. 4 Textbook of drug design and discovery by Povl Krogsgaard-Larsen and Kristian Stromgaard and Ulf Madsen; Ed. 4th; CRC; 2009. 5 Nanobiotechnology in molecular diagnostics: current techniques and applications by K.K. Jain, Horizon Bioscience; 2006. 6 Burgers medicinal chemistry and drug discovery by Donald J. Abraham; Ed. 6th; John Wiley; 2003. 7 Polymeric drugs & drug delivery systems by Raphael M. Ottenbrite and Sung Wan Kim; Technomic, 2001.

30 MBS 404: ADVANCED MEDICINAL CHEMISTRY (Interdisciplinary)

Metal Complexes in Medicine Chemistry of Metal Species, Biochemistry, SAR. Complexes in Clinical Trial. Metal containing imaging agents

Drugs acting on Novel Targets (examples from past one decade or so) E-tubulin inhibitors and their mechanism. Kinase inhibitors e.g. AKt inhibitors, discovery of gleevac etc. HIV inhibitors: integrase inhibitors, CCR5 inhibitors etc. New drugs developed for tuberculosis and other infectious diseases. New drugs developed for cardiovascular disease Cholesterol, absorption inhibitors e. g. ezetimibe, glycoprotein inhibitor e.g. abciximab, Renin inhibitors e.g. aliskerin

Drug Discrimination Subjects, Dose and the parameters, Nature of the stimulus, Stereoselectivity, Specificity, Locus and mechanism of action, Structure activity studies

Role of Biotechnology in Drug Discovery The impact of biotechnology on small-molecular drug discovery and development. Examples of approved biotechnology based drugs: Monoclonal antibodies, Interferon alpha, Interferon beta, Interferon gamma, Inter leukins, Growth hormones, Antisense nucleotides, Use of Transgenic animal models for drug evaluation

Molecular Modelling and Computer Aided Design of Macro-moleculas for Medical Application. Basic elements contributing to 3D-structure, Macromolecular structure database: Its constitution and attributes, Sequence Homology and Homology based modeling, Modeling Ligand Protein association: Docking methods, Molecular Mechanics, Molecular Dynamics.

Students Seminar

Reading List

1 Introduction to Medicinal Chemistry: How drugs act and why by Alex Gningauz and Bruce S. Burnham and Iris H. Hall; Ed. 2nd; Wiley-Interscience; 2007. 2 Chemoinformatics: a textbook by Johann Gasteiger and Thomas Engel; Wiley-VCH; 2003. 3 Molecular modeling: basic principles and applications by Hans-Dieter Holtje and Wolfgang Sippl and Didier Rogan and Gerd Folkers; Ed. 3rd; Wiley-VCH; 2008. 4 Biopharmaceuticals: Biochemistry and Biotechnology by Gary Walsh; Ed. 2nd;Wiley; 2003. 5 Targeted & Controlled Drug Delivery: Novel Carrier Systems by S. P. Vyas, and R.K. Khar; CBS; 2006.

31 MBS 405: RADIATION BIOLOGY

PART I

Fundamentals of Radiation Physics Electromagnetic radiation and radioactivity. Radiation sources and radionuclides. Measurement units of exposed and absorbed radiation.

Radiation and Photochemistry Interaction of radiation with matter, excitation and ionization. Radiochemical events relevant to radiation biology. Dosimetry

Interaction of radiation with Biomolecules Nucleic acids, proteins, lipids and carbohydrates

Cellular effects of radiation Effects of Ionizing and non-ionizing radiation on cells, DNA, chromosomes and membrane, cell survival (including biophysical models). Division delay and cell cycle check points. Mutation

DNA repair processes Various repair pathways and their regulation. Mechanistic and regulatory aspects of DNA repair. Role of DNA repair in aging and genetic diseases

Biology Dosimetry Micronuclei formation, Chromosome aberration and mutation assays.

Systemic effects of radiation Acute, delayed and late radiation effects (with particular reference to nervous system, gastrointestinal and hematopoitic syndrome). Carcinogenesis and teratogenesis.

Modification of cellular and systemic response to radiation Radiosensitization and Radioprotection.

Behavioral Radiation Biology Effects of radiation on nervous systems (in vitro studies). Effects of low and high doses of radiation on nervous system and behaviour.

Radiation Safety Biological basis of ICRP recommendations

Radio-ecology and environmental radiation biology Low dose effects of natural and man made radiation, Ultraviolet radiation and environment.

PART II

Application in Biomedicine

Radiation Medicine Radiation Therapy, Therapeutic nuclear medicine, Management of radiation injuries

Current Area of Research Tumor Physiology and Radiation Response, Predictive Assays, Adaptive response, Improvement in Tumor Radiotherapy, Emerging new applications

32 Others Low-dose hypersensitivity, Bystander effects, Radiation induced alterations in signal transduction

Reading List

1 Radiobiology for the Radiobiologist by Eric J. Hall and Amato J. Giaccia;Ed. 6th; Lippincott; 2005. 2 Basic Clinical Radiobiology by G. Gorden Steele; Hodder Arnold Publication; 2002. 3 Introduction to Radiobiology by A. Wambersie; Ed. 1st; Taylor & Francis; 2007. 4 Introduction to Radiobiology by A.H.W. Nias; Ed. 2nd; Wiley; 1998.

33 MBS 406: TOPICS IN CLINICAL RESEARCH

Introduction to Clinical Research Definition, Scope and Types of Clinical Research, Understanding Epidemiology, (infectious disease, cancer and genetics) Pharmacology and Pharmaceuticals, Good Clinical Practices (GCP), Process of Drug Development and Drug Safety. Introduction to Bioavailability and Bioequivalence.

Methods in Clinical Research and Clinical Trial: Design Designing of protocol, Pharmaco-epidemiology, Introduction to Quality Assurance and quality control, Good Laboratory Practice (GLP) and Accreditation, Study population and sample size, Medical report writing and publication of results.

Ethics in Clinical Research Definition and theories of Ethics and Foundation, Independent Ethics Committee, Informed Consent, Integrity in Clinical Research, Conflicts of Interest.

Regulatory Process in Clinical Research History and Role of Regulations in Clinical Research, US and Indian Regulatory system, EU Regulatory Affairs, Non-Disclosure Agreement, GMP regulations, Patent and Patent laws

Clinical Research and Management Clinical Study Preparation, Pre-clinical Trials, Clinical trial phase I/II/III/IV, Documentation, Monitoring, Audit and Inspection of trial study, Pharmaco-vigilance, Drug Safety.

Biostatistics and Data Management Role of Statistics in clinical research, Trial design and analysis, Data management and validation, Consideration of SAE (serious adverse effects), Bioinformatics, software and IT in Clinical Research.

Reading List

1 Ethical and Regulatory Aspects of Clinical Research: Readings and Commentary, Ezekiel J. Emanuel, 1st Ed., The Johns Hopkins University Press; 1 Edition, 2003. 2 The Pharmaceutical Regulatory Process (Drugs and the Pharmaceutical Sciences), Ira R. Berry, 1st Ed., Informa HealthCare, 2004. 3 Fundamentals of Biostatistics, Bernard Rosner, Duxbury Press; 6th Ed., 2005. 4 Epidemiology and Biostatistics: An Introduction to Clinical Research, Bryan Kestenbaum, 1st Ed., Publisher: Springer, 2009. 5 Adaptive Design Methods in Clinical Trials, Shein-Chung Chow, CRC, 2006. 6 Introduction to Randomized Controlled Clinical Trials, 2nd Ed., John N.S. Matthews, CRC, 2006. 7 The Oxford Textbook of Clinical Research Ethics, Ezekiel J. Emanuel, Oxford University press, 2008.

34 MBS 407: ADVANCED IMMUNOLOGY

Immunoglobulins Introduction, Overview of Immunoglobulin, V Gene Assembly and recombination, three Immunoglobulin gene Expression, Chromosomal Translocation involving Immunoglobulin loci.

Major Histocompatibility Complex Detailed Structure and Molecular Interaction of MHC Molecules, Chemistry of peptide, Binding and Presentation, MHC and Transplantation, MHC and Diseases, Pathogen Interface with Antigen Presentation, TCR Genes, Chromosomal Translocations associated with Disease and Molecular Mechanism of T-Cell Activation.

Complement Complement: Location, Regulation and Activation, Biological Consequences of Complement Activation. Complement as Pathogenic Factor in Disease.

Hybridoma Technology, Utilising Transgenic and Knockout Mice in understanding immune mechanisms, Mucosal Immunity, Aging and Immune Functions, Cytotoxic T-Lymphocytes, Inflammation, Systemic Autoimmunity, Pathogensis of Allergic Diseases, Transplantation Immunology, Tumor Immunology, Immune Response to Infectious Disease-Viral, bacterial and Protozoans, Vaccines, immuno Deficiency Diseases, Immunotherapy, signal Transduction in Innate Immunity, Microbial evasion strategies.

Student Seminar

Reading List

1 Kuby Immunology by Thomas Kindt and Richard A. Goldsby and Barbara A. Osborne; Ed.6th; W.H. Freeman and Company, New York; 2007 2 Cellular and molecular immunology by Abul K. Abbas and Andrew H. Lichtman and Shiv Pillai; Ed. 6th; Sounders; 2007. 3 Immunology; Ed.7th by David Male and Jonathan Brastoff and David B. Both and Ivan Roitt; Mosby Elsevier; 2006. 4 Immuno biology: the immune system in health and disease by Charles A. Janeway and Paul Travers and Mark Walport and Mark J. Shlomchik; Ed. 7th; Garland Science; 2008. 5 Immunology of infection diseases by Stefan H. E. Kaufmann and Alan Sher and Rafi Ahmed; ASM Press, Washington; 2002 6 Essentials of immunology & serology by Jacqueline H. Stanley; DELMAR; Australia; 2002.

35 MBS 408: ADVANCED TOXICOLOGY & PHARMACOLOGY

Environmental and Pesticide Toxicology Metallic Pollutants: Mercury, lead, arsenic, cadmium, fluoride; Source, exposure, absorption, target site interactions and health hazards.

Pesticides Brief classification with examples, residual and non-residual pesticides. Mode of entry and mode of action of pesticides in target and non-target organisms; metabolism of pesticides, phase I and phase II reaction, elimination. Ecotoxicology: Impact of pesticides residues on ecosystems, non-target organisms; Pesticide beioaccoumlation, biomagnification through food chain. Environmental alteration of pesticides - microbial and solar, fate and dissipation of pesticides residue under tropical and temperature conditions.

Pesticide hazards to man Accidental and occupational exposure, entry through air, food and water, Main routes of entry and factors affecting intake, distribution, biotransformation and elimination dynamics. Residue levels in man: Indian experience Vs developed countries; Residues in tissues and organs distribution and redistribution; Pregnancy and transfer to fetus. Health hazards: Nonfatal subtle levels, biochemical and physiological effects; Parameters used in carcinogenic risk assessment of pesticide residues; Animal experiments carcinogenic, teratogenic and mutagenic tests; Organochlorine insecticide residues as carcinogens- parent status Carcinogens phenoxyherbicides, arsenicals and HCB; Organochloro residue burden in newborn babies in developing countries and potential hazards. Pharmacokinetics and Pharmacodynamics: General mechanism of drug action and the factors, which modify drug action.

Pharmacological classification of drugs; the discussion of drugs should emphasize the following aspects:

Drugs acting on the central nervous system : General anesthetics, adjunction to anesthesia, intravenous anesthetics. Analgesic and non-steroidal anti-inflammatory drugs, narcotic analgesics, antirheumatic and antigout remedies, sedatives and hypnotics, pshychopharmacological agents, anti-convulsants, analeptics. Centrally acting muscle relaxants and anti-parkinsonism agents, anti-Alzheimers drugs. Local anesthetics.

Drugs acting on the eye, mydriatics, drugs used in glaucoma. Drugs acting on the respiratory system- bronchodilators, expectorants and antitussive agents. Antacids, histamine and anti-histamines, prostaglandins. Cardiovascular drugs, cardiotonics, antianginal agents, antihypertensive agents, peripheral vasodilators and drugs used in atherosclerosis. Drugs acting on the blood and blood forming organs, haematinics, coagulants and anticoagulants, haemostatics, blood substitutes and plasma expanders. Drugs affecting renal function- diuretics and antidiuretics. Hormones and hormone antagonists- hypoglycemic agents, antithyroid drugs, sex hormones and oral contraceptives, corticosteroids. Drugs acting on the digestive system- carminatives, digestants, bitters, antacids and drugs used in peptic ulcer, purgatives and laxtives, antidiarrhoeals, emetics, antiemetics.

Chemotherapy of microbial diseases, urinary antiseptics, sulfonamides, penicillins, streptomycin, tetracyclines and other antibiotics; antitubercular drugs, antifungal agents, antiviral drugs, antileprotic drugs.

Chemotherapy of protozoal diseases , Drugs used in cancer, Disinfectants and antiseptics.

Reading List

1 Essential of medical pharmacology; 5th Ed. By K.D. Tripathi; Jaypee Brothers; New Delhi; 2003. 2 Goodman & Gilmans the pharmacological basis of therapeutics by Joel G. Hardman and Lee E. Limbird; 9th Ed.; 1995.

36 3 Pharmacology H. P. Rang and M.M. Dale and J.M. Ritter and P.K. Moore; Ed.5th; Churchill Livingstone, 2003. 4 Integrated pharmacology by Clive P. Page and M.J. Curtis and M.C. Sutter and M.J. Walker and B.B. Hoffman; Mosby; 1997.

5 Principles of toxicology by Karen E. Stine and Thomas M. Brown; Ed.2nd; CRC Press; 2006 6 Lus basic toxicology: fundamentals, target organs and risk assessment by Frank C. Lu and Sam Kacew; Ed.4th; Taylor & Francis; 2002 7 Casarett and Dulls toxicology: the basic science of poisons by Curties D. Klaassen; Ed.7th; McGraw Hill; New York; 2007 8 Toxicology by Hans Marquradt and S.G. Schafer and R.D. McClellah and Academic Press; 1999 9 Principles and practice of toxicology in public health by Ira R. Richards; Jones and Bartlett Publishers; 2007 10 Handbook of human toxicology by E.J. Massaro; CRC Press; 1997

37 PRACTICALS (9 hrs per week) MBS 106: PRACTICALS

9GENETICS

Experiments in Concepts in genetics:

1. Estimation of colony forming units in E.coli and its application in isolation of pure mutant strains from mixtures. 2. To set up and analyze results of crosses between mutants and wild type Drosophila to understand Mendelian genetic principles using Drosophila: Dominant and recessive inheritance; sex linked inheritance. 3. Using balancer stock to localize recessive mutations on chromosomes in Drosophila. 4. Preparation of polytene chromosomes and immunostaining for a chromatin interacting protein. 5. Analysis of chromatin organization in mouse tissue for specific sequences through Micrococcal nuclease sensitivity followed by PCR. 6. Detection and analysis of Variable number of tandem repeats (VNTR) in human genome by PCR: mapping the VNTR sequence on the human genome using Bioinformatics tools.

9BIOCHEMISTRY

1. Salting in and salting out of proteins. 2. Desalting of proteins by dialysis and Sephadex G-25. 3. Protein estimation by Loorys & Bradford methods. 4. Ion-exchange chromatography. 5. Affinity chromatography for protein purification. 6. To check purity of protein & subunit structure by SDS page & silver staining. 7. Western blot analysis to check special proteins. 8. Isolation of genomic & plasmid DNA. 9. Protein & Nucleic Acid blasts, Clustal W and sequence alignment etc.

9MEDICAL MICROBIOLOGY

Bacteriology

1. Preparation and sterilization of different culture media (e.g. Blood agar, chocolate agar, nutrient agar, nutrient broth, Mac Conkey agar) and to obtain pure cultures. 2. To carry out different types of staining such as Gram staining, Acid fast staining, Spore staining, Alberts staining of the given bacterial culture. 3. To determine the antibiotic sensitivity profile of the given microbial culture using Kirby-Bauer method. 4. To carry out the following biochemical tests for given bacterial cultures: Catalase test, Urease set, Indole test, Methyl red test Voges-Prauskauer test, Citrate test, Lysine iron agar, Triple sugar iron, Sugar fermentation tests (glucose, maltose, sucrose).

Mycology

1. To prepare temporary mounts from cultures/clinical specimens and observe permanent slides of the following: Rhizopus, Mucor, Aspergillus fumigatus, Aspergillus flavus, Candida albicans, Blastomyces dermatidis, Penicillium marneffei, Nocardia, Histoplasma capsulatum. 2. To demonstrate the presence of Candida albicans in the given clinical specimen using the germ tube test.

MBS 206: PRACTICALS

9ORGANIC CHEMISTRY

1. Crystallization 2. TLC, Column chromatography 3. Interpretation of IR spectra and functional groups. 4. Preparations involving examples of reactive intermediates (any six): Cannizaro reaction, Dibenzal, benzalacetone, Benzophenone, photochemical reaction, NBS-reaction, Reimer-Tieman reaction, Oxidation of an alcohol, Enamine reaction, Glucose phenylhydrazone, Protection of amino acids, Synthesis of dipeptide, Any example of enzymes catalyzed organic synthesis

9IMMUNOLOGY

1. Collection of blood: Retro -orbital bleeding, tail vein puncture 2. Separation and preservation of serum and plasma 3. Various routes of immunization: Intraperitoneal, Subcutaneous and Intra muscular 4. Immunization of animal (BALB/C) intraperitoneally with BSA 10% and adjuvant Immunodiffusion techniques 5. Circulating Immune complex level estimation by PEG method 6. Separation of mononuclear cells from blood 7. Separation of lymphocytes from solid organs, spleen and bone marrow by nylon wool method, Isolation of peritoneal macrophages 8. Functional assay for macrophages using, Nitroblue tetrazolium test (NBT), Cell adhesion assay, Phagocytosis assay. 9. Indirect haemagglutination, demonstration of ELISA technique and FACS

9MOLECULAR BIOLOGY AND BIOTECHNOLOGY

1. Preparation of competent cells and Transformation of E.coli with given plasmid. 2. Restriction digestion of isolated plasmids or RFLP analysis of given DNA of PCR diagnostic. 3. Ligation of a DNA fragment in an expression vector. 4. Screening of positive clones. 5. Induction of proteins cloned in expression vectors. 6. PCR of 16 S rRNA gene for phylogenetics analysis. 7. DNA protein interactions by electrophoretic mobility shift assay. 8. Mammalian cell culture & transformation of recombinant vector containing GFP. 9. Expression of proteins in mammalian cells using fluorescence microscopy.

39 MBS 306: PRACTICALS

9ADVANCED HUMAN PHYSIOLOGY

Hematology 1. To measure inspiratory and expiratory parameters 2. To record the conduction velocity of ulnar nerve 3. To prepare a stained blood smear to identify the different leukocytes in the blood smear and to do a differential leukocyte count. 4. To determine the total RBC counts per cubic millimeter of blood and to show the effect of hypotonic, isotonic, salt solutions on red blood cells 5. To determine the bleeding time by Duke method, clotting time by capillary tube method, osmotic fragility of a given sample blood. 6. To estimate the total amount of hemoglobin in human blood 7. Ergometry 8. Reticulocyte count, Eosinophil count, Platelet count

Experiment On Animal Heart (Rat/Frog) 9. Measurement of Heart Rate and to study the effect of temperature, ions on Heart Rate 10. Study of autorhythmicity of Heart 11. To measure Muscle Twitch and Tetany

9ANALYTICAL & BIOMEDICAL TECHNIQUES AND INSTRUMENTATION

1. To verify Lambert Beers law . 2. To study interaction of intercalating agents like ethidium bromide and porphyrin with DNA using: a. UV visible spectroscopy. b. Fluorescence spectroscopy. 3. Studying the Conformation change of Biomolecule using CD spectroscopy. 4. Biomolecular Interaction studies using Yeast 2 Hybrid System. DNA protein interactions by EMSA. 5. Infra red Spectroscopy. Recording and interpretation of IR of a biological fluid. 6. HPLC: Analysis of 5-hydroxy tryptamine from blood, HPLC analysis of Nucleobases from Calf thymus DNA. 7. Gas Chromatography. Analysis of opium alkaloids from opium, Analysis of Cortisol from blood. 8. Mass Spectroscopy: Identification of a biopolymer using MALDI/ LC-MS. 9. NMR: 1H and 31P spectroscopy of muscle physiology during exercise and calculation of pH change from spectra. 10. Spectral Identification of a simple organic compound/metabolite/drug.

9PHARMACOLOGY & TOXICOLOGY

1. Animal handling and precautions, and study the routes of administration 2. Topical application of Atropine and Pilocarpine on rabbit eye 3. Analgesic effect of diclofenac on mice/rat 4. Study the effects of acetylcholine (Ach) and plot the dose-response curve. 5. Study the effect of general anaesthesia with ketamine 6. To determine the effect of promethazine on phenobarbitone induced sleeping time in mice. 7. To determine the acute toxicity of a given drug and calculate the LD50 value. 8. Detection of organophosphorous pesticides in biological sample. 9. To test the presence of paracetamol in the given biological sample. 10. To study the effect of organophosphate Malathion on the specific activity of the enzyme acetylcholinestrase in rat brain homogenate.

Dr. B R Ambedkar Center for Biomedical Research Faculty of Science University of Delhi

SYLLABUS FOR Ph.D. COURSE WORK

The center in keeping with its inter-disciplinary nature offers the following syllabus for the Ph.D. Course work. There are a total of four papers that each student has to clear. Paper I (Research Methodology), Paper II (Tools and Techniques in Biomedical Research) and Paper III (Writing a Research proposal) are compulsory. In Paper IV a student can opt for any two modules.

Overview of the Papers:

The Research Methodology paper has been designed to inculcate a scientific temperament in the student and introduce the basic requirements for being a good and motivated researcher. Emphasis is laid on the need to identify a challenging research topic following an extensive literature survey. Learning how to design simple and complicated experiments, the need for reproducibility, analyses of the data obtained and its significance in moving forward follows this. In parallel, the student is also trained to follow ethical guidelines, display scientific integrity; identify conflict of interest and plagiarism issues while writing scientific documents.

The Paper on Tools and Techniques in Biomedical Research focuses on the principles, scope and applications of routine and advanced techniques the student is likely to use in his/her research. This will prepare the student to keep in mind the scope and limitations of each technique that will be useful in designing experiments and interpreting the data.

The Paper on Writing a Research Proposal, prepares the students for writing grant proposals that will be extremely useful following the successful completion of the Ph.D. With a number of post-doctoral fellowships now being offered by leading National and International funding agencies this paper will be beneficial to him/her.

The Advanced Modules Paper with an array of modules is in keeping with the inter-disciplinary nature of ACBR. A student can opt for any two. Any student is welcome to attend the courses of other modules as well but will be evaluated on his/her choice of the modules opted at the start of the semester.

Course structure and evaluation criteria:

All the papers will be evaluated at the end of each semester and include internal assessment. The individual teachers as per their chosen criteria will decide the internal assessment. A written exam will be held for Papers I, II and IV. For Paper III (Writing a Research Proposal) the student will have to submit a project proposal and defend the same in the form of power-point presentation.

The student has to score at least 50% marks in each paper to qualify the same.

Program Structure

PAPER NO. Paper Title End-semester Internal Assessment Examination PHBS-I Research Methodology 50 Marks 50 Marks (July-December) (July-December) PHBS-II Tools and Techniques in 70 Marks 30 Marks Biomedical Research (July-December) (July-December) PHBS-III Writing a Research 70 Marks 30 Marks Proposal (January-June) (January-June) PHBS-IV Advanced Modules 70 Marks 30 Marks (any two) (January-June) (January-June)

PHBS-I: Research Methodology

Research Methodology: An Introduction

Objectives and motivation in research, Approaches to scientific research- Issues and concerns related to scientific investigation; lack of exclusivity of methods of research; Merging of various approaches in practice of scientific research

Literature Search and managing research outcomes

Introduction to peer-reviewed and open access journals, E-journals and E-books. Citation of papers; Search of research articles via subject and author index. Common search engines for literature- NCBI, Scopus, Google Scholar, Scirus, SciFinder. Systematic literature search. The importance of reliability of retrieved data; source evaluation. Formulating key word(s)based query to retrieve appropriate data, Managing personal reference database.

Defining a Research Problem

Identifying gaps in knowledge through literature mining, identifying area of societal need like health/technology/anticipated crisis such as epidemic, energy, water. Elements for outlining a research problem. Developing an approach strategy, feasibility testing.

This unit will have extensive classroom discussion, and students’ participation through formulation of pilot projects to illustrate identification of research problems.

Designing of Experiment: Strategies, Planning and Analysis

Selection of research topic and its national and international scenario. Techniques involved in research plan using an illustration, Defining Standard Operating Protocols (SOPs), Research Conditions, Repeatability, reproducibility and reliability of results, Accuracy and Precision, Significant figures with reference to numerical data, Errors and uncertainty analysis. Types of errors: Gross error, systematic error, random error, Statistical analysis of data.

Methods in Biomedical Research

To illustratively discuss Clinical Research, Ethical issues in clinical research, Epidemiology: (classical examples of epidemiological studies such as leprosy, twin studies), Good clinical research methodology

Laboratory and Safety Practices

Biosafety; Introduction to occupational health and safety (chemical, biological and radiation), awareness about handling toxic laboratory chemicals, pathogenic microorganisms, and their safe disposal. Idea about labels and Material Safety Data Sheet (MSDS), safety equipment and procedures, Fire extinguishers, First aid kit.

Research Ethics and Intellectual Property

Research and scientific writing ethics, plagiarism, concept of peer-review, conflict of interest, research misconduct. Illustrations of violation of ethical conduct. Introduction to IPR (Patent, trademarks, copyright, trade secrets), Importance of academia-industry interaction, Marketing of research outcome.

Scientific Documentation

Significance of report writing, steps in report writing, Types of report: Decision-oriented (Technical) and Survey-based report. Guidelines for reviewing draft report format, typing instructions, citing references with examples. Writing a scientific paper; structuring a manuscript, data representation for effective communication. Discussions on Journals relevant to Biomedical research and their paper writing patterns could be discussed.

SUGGESTED READINGS

1. Robbins and Cotran Pathologic Basis of Disease, 8th edition (2009), Vinay Kumar, Abul K.Abbas, Jon C. Aster, Nelson Fausto; Saunders Publishers, ISBN-13: 978-1416031215. 2. General and Systematic Pathology, 2nd edition (1996), J., Ed. Underwood and J. C. E. Underwood; Churchill Livingstone, ISBN-13: 978-0443052828. 3. Robbins Basic Pathology, 9th edition (2012), Kumar, Abbas, Fausto and Mitchell; Saunders Publication, ISBN-13: 978-1437717815. 4. Medical Laboratory Technology Methods and Interpretations Volume 1 and 2, 6th edition (2009), Ramnik Sood; Jaypee Brothers Medical Publishers, ISBN-13: 978-8184484496. 5. Pathophysiology, 3rd edition (2012), Lee-Ellen C. Copstead-Kirkhorn and Publisher Saunders, ISBN-13: 978-1455726509.

B.Sc (Hons) Biomedical Science

Semester VI

BMS 602: Toxicology Preamble: Different types of poisons have been known to humans since ages. Even in early times when science was in its infancy, curious people such as “Paracelsus” could predict “Every substance is a poison and, it is the right dose of the substance which differentiates remedy from poisons”. This thought is fundamental even to modern toxicology and pharmacology. There is an increasing use of chemicals in the modern society and hence, toxicology is becoming a more important subject to study with the passage of time. Modern toxicology is a vast, multidisciplinary subject encompassing various other basic fields of science. The present course content is designed to provide the basics of toxicology. Relevant importance has been given to those topics which can build a strong foundation in the subject, based on which, facts can be assimilated during subsequent higher studies. THEORY Total Lectures 48 Unit I: Introduction (2 Lectures)

Brief history, Different areas of modern toxicology, classification of toxic substances, various definitions of toxicological significance.

Unit II: Toxic exposure and response (5 Lectures)

Unit III: Evaluation of toxicity (2 Lectures)

Various types of dose response relationships, assumptions in deriving dose response, LD50, LC50, TD50 and therapeutic index.

Unit IV: Mechanism of toxicity (10 Lectures)

Delivery of the toxicant, mechanisms involved in formation of ultimate toxicant, detoxification of ultimate toxicant.

Unit V: Fate of xenobiotics in human body (10 Lectures)

B.Sc (Hons) Biomedical Science

Unit VI: Toxic agents (8 Lectures) Human exposure, mechanism of action and resultant toxicities of the following xenobiotics: Metals: lead, arsenic, Pesticides: organophosphtes, carbamates, organochlorine, bipyridyl compounds and anticoagulant pesticides.

Unit VII: Eco-toxicology (7 Lectures)

Unit VIII: Clinical toxicology (4 Lectures)

Management of poisoned patients, clinical methods to decrease absorption and enhance excretion of toxicants from the body use of antidotes.

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. Separation of a mixture of benzoic acid, beta- napthol and napthelene by solvent extraction and identification of their functional Groups. 2. Determination of Dissolved oxygen (DO) using Winkler‟s method. 3. Determination of Biological oxygen demand (BOD) of water. 4. To perform quantitative estimation of residual chlorine in water samples. 5. To determine the total hardness of water by complexo-metric method using EDTA. 6. To determine acid value of the given oil sample. 7. To estimate formaldehyde content of given sample. 8. Calculation of LD50 value of an insecticide from the data provided. 9. Determination of COD (chemical oxygen demand) of the given water sample.

SUGGESTED READINGS 1. Cassarett and Doull‟s Toxicology “The Basic Science of The Poisons” 7th edition (2008), Curtis D. Klaassen Editor, McGrawHill Medical. ISBN: 9780071470513. 2. Cassarett and Doull‟s “Essentials of Toxicology” 2nd edition (2010), Klaassen and Whatkins, McGraw Hill Publisher. ISBN-13: 978-0071622400. 3. Introduction to Toxicology, 3rd edition (2001), John Timbrell, Taylor and Francis Publishers. ISBN 13: 9780415247627. 4. Principles of Toxicology, 2nd edition (2006), Stine Karen and Thomas M Brown, CRC press. ISBN-13: 978-0849328565. 5. Lu‟s basic toxicology: Fundamentals target organ and risk assessment, 5th edition (2009), Frank C Lu and Sam Kacow, Informa Health care. ISBN: 9781420093117.

B.Sc (Hons) Biomedical Science

Skill Enhancement Courses (SEC)

B.Sc (Hons) Course in Biomedical Science

B.Sc (Hons) Biomedical Science

SEC: Skill Enhancement Courses

BMS-S1: Methods in Epidemiological Data Analysis (EDA) BMS-S2: Medical Laboratory Diagnostics (MLD) BMS-S3: Techniques for Forensic Science BMS-S4: Tools in Modern Biology In alphabetical order

(Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.)

B.Sc (Hons) Biomedical Science

BMS-S1: Methods for Epidemiological Data Analysis

Preamble: In public health work, one may be concerned with planning of experiments and the analysis of their results. Therefore, one has to deal with statistical data analyses that come from no deliberate experiment but that arise because of the data collected from the population in the course of public health study and survey. This course therefore provides training to the students on how to conduct epidemiological surveys, design questionnaire and analyze the data. The students will get hands-on-training on „R‟, a free software environment for statistical computing and graphics. Total sessions: 12 (Each session of 2/4 Lectures)

Unit I: Understanding Epidemiological Data (1 session) 1. Analysis of data from National Cancer Registry Program (NCRP) 2. Understanding incidence, mortality (rates, ratios and proportions) Components of epidemiology: disease frequency, distribution of disease and determinants of disease. Epidemiological approach and measurements- vital statistics (rates, ratios and proportions), measurements of health indicators (morbidity, mortality and fertility rates).

Unit II: Epidemiologic Methods and Survey (4 sessions) 1. Designing a questionnaire for survey of prevalence diabetes/ hypertension/ allergy/ respiratory disorders/etc. 2. Defining the parameters for ethical issues in a study 3. Determining the target and control populations 4. Surveying the population for the diseases mentioned above Data collection: observational (descriptive and analytical) and experimental studies. Epidemiology study designs- case control and cohort studies (prospective and retrospective), techniques of sampling and matching, sources of bias.

Unit III: Data Organization and Presentation (2 sessions) 1. Introduction to „R‟ software 2. Analysis of data from NCRP data and survey conducted by the students Basic principles of „R‟ software for tabulation and graphical representations (bar diagrams, histograms, pie charts, box plot, etc.), measures of central tendency (mean, mode, median and partition values), dispersion (range, standard deviation, coefficient of variance and covariance) and skewness.

Unit IV: Statistical Modeling and Analysis using ‘R’ on NCRP data and survey conducted by the students (5 sessions) 1. Correlation studies 2. Regression studies 3. Probabilistic distribution studies 4. Comparison of groups and ascertaining statistical significance of differences Correlation analysis (scatter diagrams and Karl Pearsons coefficient of determination, standard and probable errors) and regression analysis. Inferential statistics: sampling distributions and 48

B.Sc (Hons) Biomedical Science

standard error, null and alternate hypothesis, basic concept and illustrations of type I and type II errors, concept of confidence interval estimation, large sample tests for single mean and difference of means, single proportion and difference of proportions, students t-distribution (test for single mean, difference of means and paired t-test), chi-square distribution, F-distribution, one-way and two-way ANOVA, non parametric analysis (sign and rank tests), p-value.

SUGGESTED READINGS 1. Park‟s Textbook of Preventive and Social Medicine, 21st edition (2011), K. Park, M/s Banarsi Das Bhanot Publishers. 2. Primer of Biostatistics, 7th edition (2011), Stanton Glantz, McGraw-Hill Medical. ISBN-13: 978-0071781503. 3. Basic epidemiology,2nd edition (2006), R. Bonita, R. Beaglehole, TordKjellstrèom, Contributor; World Health Organization, illustrated, Publisher: World Health Organization, ISBN-13: 978-9241547079. 4. Biostatistics: A Foundation for Analysis in the Health Sciences,10th edition (2013), Wayne W Daniel and Chad L. Cross, Wiley. ISBN-13: 978-1118302798. 5. Principles of Biostatistics,2nd edition (2000), Marcello Pagano and KimberleeGauvrean, Thompson learning. ISBN-13: 978-0534229023. 6. Biostatistical Analysis, 5th edition (2009), Jerrold H. Zar, Pearson. ISBN-13: 978- 0131008465. Website for ‘R’: www.r-project.org Website for NCRP: http://www.ncrpindia.org/

B.Sc (Hons) Biomedical Science

BMS-S2: Medical Lab Diagnostics (MLD)

Number of Sessions: 12 (Each session has 2/4 Lectures)

Unit I: Fundamentals of Clinical Diagnostics (2 sessions)

Laboratory 1: Sterilization Techniques: Physical methods and Chemical methods. Laboratory 2: General overview of blood banking, blood typing, blood screening in transfusion medical lab.

Introduction to clinical laboratory principles and procedures. Concept of GLP and ISO labs, quality control and laboratory safety. Regulation of diagnostic labs and accreditation methods. Guidelines for collection transport, preservation processing and analysis of specimen. Overview of phlebotomy, urinalysis, basic hematology, clinical biochemistry, immune-serology and clinical microbiology. Guidelines for proper discard of biological waste and chemical wastes.

Unit II: Approaches to diagnosis of infectious diseases: (4 sessions)

Laboratory 3: Isolation of bacteria from mixed culture. Study of morphological, cultural, biochemical characteristics of common bacterial pathogen Laboratory 4: To study composition and use of important differential media for identification of pathogenic bacteria EMB agar, McConkey agar, TCBS agar and Salmonella-Shigella agar and blood culture media (any two) Laboratory 5 and 6: Enumerate the microbial load on the selected fresh produce from major outlets. Isolate and identify the common microorganisms present on their surface using microbiological, biochemical and PCR techniques. Classification of culture media and quality control of culture media. Innoculation, incubation and purification methods in bacteriology. Preservation of bacterial culture. Rapid identification system, Continuous monitoring culture systems: BacT/ESP/BACTEC

B.Sc (Hons) Biomedical Science

Use of conventional microbiological tools supplemented by most modern analytical techniques including PCR for enumeration, isolation and identification of microbes (mainly on fresh produce).

Setting up “Gold Standard” method, concepts of accuracy (efficiency), Precision, sensitivity, specificity, Prevalence positive predictive value and negative predictive value.

Unit III: Immunoserology: Principles and Application. (3 sessions)

Laboratory 7, 8 and 9:Antigen-antibody interaction and its use in diagnosis: Detection and diagnosis of common diseases: Widal and typhi dot for typhoid, Acylatedhaemoglobin in Diabetes, TSH levels in Thyroid condition, Malaria antigen in Malaria, NS1 antigen in Dengue (any three immune diagnostic tests).

Concepts of Immune response to be explained. Techniques to be discussed: ELISA - direct, indirect, competitive and sandwich ELISA, Co-immunoprecipitation for protein-protein interaction studies.

Unit IV: Medical Cytogenetics (3 sessions)

Human cytogenetics and its application to medicine, cell culture and harvest, chromosome banding and staining, chromosome identification, cytogenetics nomenclature, chromosome abnormalities and aberrations, chromosomal syndromes, classification of genetic disorders, Disciplines within Clinical Genetics and integration of genetic diagnostic services with other healthcare services (Clinical Genetics, Prenatal Diagnosis, Infertility, Cancer Cytogenetics)

Skills that are developed at the end of this course:

1. The student will demonstrate knowledge of how to obtain reliable information from a variety of sources (e.g. web, popular media, and scientific publications). 2. Practical training to work in diagnostic setting increased. 3. The student will demonstrate knowledge of how to communicate the results of a scientific investigation.

B.Sc (Hons) Biomedical Science

SUGGESTED READINGS 1. Bailey and Scott‟s Diagnostic Microbiology, 12th edition (2007), Betty A. Forbes, Daniel F. Sahm and Alice S. Weissfeld; Mosby Elsevier Publishers, ISBN-13: 978-0808923640. 2. Medical Laboratory Technology Methods and Interpretations Volume 1 and 2, 6th edition (2009), Ramnik Sood; Jaypee Brothers Medical Publishers, ISBN-13: 978-8184484496. 3. Current Protocols in Human Genetics, 1st edition (1994), Dracopoli and Nicolas C. Dracopoli; John Wiley and Sons, Inc., ISBN-13: 978-0471034209. 4. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Michael R. Green and Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978-1936113422. 5. Microbiology: A Laboratory Manual, 10th edition (2013), James Cappuccino and Natalie Sherman, Benjamin Cummings, ISBN-13: 978-0321840226.

B.Sc (Hons) Biomedical Science

BMS-S3 Techniques for Forensic Science

Preamble: Forensic science is the application of scientific knowledge to questions of civil and criminal law. Interest in forensic science has grown considerably in recent years. Keeping this in view, the present forensic science course is designed for students to explore how forensic scientist‟s work, the tools and techniques they use and how they reach the conclusions they present in court. This engage students in using a creative, problem solving and inquiry based approach to investigate the crime scene. It also explains the characteristics of a fingerprint collect, process, and analyze fingerprint evidence and explain DNA analysis.

Number of Sessions: 12 (Each session has 2/4 Lectures)

Unit I: Crime Scene Investigation (2 Sessions)

Laboratory 1: Documentation of crime scene by photography, sketching and field notes. Laboratory 2a: Simulation of a crime scene for training. Laboratory 2b: To lift footprints from crime scene.

Unit 2: Types of injuries and death (1 session)

Laboratory 3: Case studies to depict different types of injuries and death.

Classification of injuries and their medico-legal aspects, method of assessing various types of deaths.

Unit 3: Forensic chemistry and Ballistics (2 sessions)

Classification of fire arms and explosives, introduction to internal, external and terminal ballistics. Chemical evidence for explosives.

Unit 4: Forensic Graphology (2 sessions)

Laboratory 6: Identification and comparison of handwriting characters Laboratory 7: To perform thin layer chromatography of ink samples.

B.Sc (Hons) Biomedical Science

General and individual characteristics of handwriting, examination and comparison of handwritings and analysis of ink various samples.

Unit 5: Forensic Toxicology (1 session)

Laboratory 8: Identification techniques of common toxins, drugs, pesticides, Volatile poisons, vegetable poisons etc. in given biological samples and crime scene.

Role of the toxicologist, significance of toxicological findings

Unit 6: Fingerprint analysis (1 session)

Laboratory 9a: Investigate method for developing fingerprints by Iodine crystals. Laboratory 9b: To observe the effects of surface temperature on fingerprints.

Fundamental principles of fingerprinting, classification of fingerprints, development of finger print as science for personal identification.

Unit 7: DNA Fingerprinting (2 sessions)

Laboratory 10: DNA isolation in minimal available biological samples Laboratory 11: PCR amplification on target DNA and DNA profiling

Principle of DNA fingerprinting, application of DNA profiling in forensic medicine.

Unit 8: Cyber Forensic Investigation (1 session)

Laboratory 12a: Digital Evidence Collection Laboratory 12b:E-Mail Investigation, E-Mail Tracking, IP Tracking, E-Mail Recovery, Recovering deleted evidences, Password Cracking

Investigation Tools, eDiscovery, Evidence Preservation, Search and Seizure of Computers, Introduction to Cyber Security.

B.Sc (Hons) Biomedical Science

SUGGESTED READINGS 1. Forensic Science – An introduction to Scientific and Investigative Techniques, 3rd edition (2009), James SH, Nordby JJ and Bell S; CRC Press, ISBN-13: 978-1420064933. 2. Practical Forensic Microscopy: A laboratory manual, 1st edition (2008), Barbara Wheeler and Lori J Wilson; Bios Scientific Publisher, ISBN-13: 978-0470031766. 3. Forensic Handwriting Identification: Fundamentals, Concepts and Principals 1st edition (2000) Ronald N. Morris, Academic press ISBN-13: 978-0125076401 4. Handbook of Firearms and Ballistics: Examining Interpreting Forensic Science by Brian J Heard 2nd edition (2008), John Wiley and Sons ISBN-13: 978-0470694602. 5. Principles of Forensic Medicine and Toxicology, 1st edition (2011) Rajesh Bardale; Jaypee Brothers Medical Pub, ISBN-13: 978-9350254936. 6. Practical Crime Scene Processing and Investigation, 2nd edition (2011), Ross M Gardner, CRC press ISBN-13: 978-1439853023. 7. Forensic Medicine and Toxicology: Oral, Practical And Mcq, 3rd edition (2006), Karmakar,Jaypee Brothers, ISBN-13:978-8171797350. 8. Fundamentals of Forensic Science, 2nd edition (2010), Houck, M.M. and Siegel, JA; Academic Press, ISBN-13: 978-0123749895. 9. Criminalistics- An Introduction of Forensic Science, 10th edition (2010), Prentice Hall Inc; ISBN-13: 978-0135045206.

B.Sc (Hons) Biomedical Science

BMS-S4: Tools in Modern Biology

Unit I: Plasmids and Biotechnology (3 sessions) 1. Isolation of Plasmid (mini-prep) from E. coli culture 2. Restriction digestion of plasmid and its analysis 3. Extraction of DNA from agarose gel 4. Construction of restriction maps from the data provided

Significance of plasmids in biotechnology; different methods of plasmid isolation; types and relevance of restriction sites and their potential in mapping.

Unit II: Amplification and Analysis of DNA sequences (3 sessions) 1. Primer designing 2. Optimization of PCR conditions for temperature (gradient PCR) and Mg2+ concentration 3. Detection of bacteria specific genes using colony PCR 4. Analysis of DNA sequences with electropherograms

Principle, applications and modifications of PCR; essentials for a primer; concept of DNA sequencing and analysis of electropherograms.

Unit III: Purification and Analysis of Proteins (4 sessions) 1. Comparative analysis of protein on native and denaturing gels 2. Protein purification by affinity chromatography 3. Separation of proteins by ion exchange chromatography

Concept of protein structure and denaturation with relevance to its resolution on gel; principle of chromatography and its application in purification and studying interactions

Unit IV: Cell culture and Imaging (2 sessions) 1. Preparation of media and culturing of cells 2. Fluorescence imaging demonstration in E coli with GFP and mammalian cells with PI/DAPI.

Essentials of cell culture, composition of media and the variations therein, analysis of the status within using fluorescence microscopy.

B.Sc (Hons) Biomedical Science

SUGGESTED READINGS 1. Gene cloning and DNA analysis, 6th edition (2010), T.A. Brown. Wiley-Blackwell ISBN- 13: 978-1405181730. 2. Human Molecular Genetics, 3rd edition (2003), Tom Strachan and Andrew Read; Garland Science Publishers, ISBN -13:978-0815341826. 3. Physical Biochemistry: Applications to Biochemistry and Molecular Biology, 2nd edition (1982), David Freifelder, W.H. Freeman and Company. ISBN-13: 978-0716714446. 4. Principles and Techniques of Biochemistry and Molecular Biology 7th edition (2010), Wilson K and Walker J. Cambridge University Press, 2010. ISBN-13: 9780521516358. 5. Principles of Gene Manipulation and Genomics, 7th edition (2006), S.B. Primrose and R.M. Twyman. Blackwell Scientific ISBN-13: 978-1405135443. 6. Molecular Biotechnology: Principles and Applications of Recombinant DNA, 4th edition (2009), Bernard R. Glick, Jack J. Paternack, Cheryl I. Patten. ASM press, ISBN- 13:9781555814984. 7. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Three-volume set by Michael R. Green, Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978- 1936113422. 8. Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications, 6th edition (2010), ISBN-13: 978-0470528129.

B.Sc (Hons) Biomedical Science

Discipline Specific Elective (DSE) Courses

B.Sc (Hons.) Course in Biomedical Science

B.Sc (Hons) Biomedical Science

DSE: Discipline Specific Elective (Theory + Practical*)

BMS-A: Computational Biology and Drug Discovery BMS-B: Genome Organization and Function BMS-C: Human Genetics BMS-D: Medical Biochemistry BMS-E: Medical Biotechnology BMS-F: Project Work In alphabetical order

(Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.)

B.Sc (Hons) Biomedical Science

BMS-A: Computational Biology and Drug Design

Preamble: This course will introduce the discipline of computational biology and drug design. It has been designed to explain the different aspects of nucleotide and protein sequence analyses, sequence alignments and their applications in understanding biology. The course will also emphasize on the strategic issues in drug discovery and development, principles of computational methods involved in lead generation virtual screening, quantitative structure- activity relationship and molecular docking.

THEORY Total Lectures: 48 Unit I: Introduction to computational biology (2 Lectures) What is computational biology and bioinformatics, internet and bioinformatics, chemoinformatics. Introduction to linux and common terminal commands.

Unit II: Biological databases and genome browsers (10 Lectures) Introduction to various databases and their classification (primary and secondary databases) e.g. NCBI, DDBJ, EMBL, ENSEMBL, UCSC and their use in laboratories: literature, sequence, structure, medical, enzymes and metabolic pathways databases.

Unit III: Sequence alignment and visualization (8 Lectures) Local and global sequence alignments (Needleman-Wunsch and Smith-Waterman algorithms), pair-wise (BLAST and FASTA algorithms) and multiple sequence alignment (Clustal W) and its importance. Theory behind BLAST- how Hidden Markov Model (HMM) can be used to model a family of unaligned sequences or a common motif within a set of unaligned sequences and further be used for discrimination and multiple alignment, BLAST score, amino acid substitution matrices, s-value and e-value, calculating the alignment score and significance of e and p value.

Unit IV: Phylogenetic analysis (4 Lectures) Basics and tools for phylogenetic analysis, cladistics, tree-building methods (character and distance based methods), construction of phylogenetic trees (PHYLIP) and identifying homologs.

Unit V: Microarray analysis (3 Lectures) Introduction and use of DNA microarray to assay gene expression, designing of the experiment, analysis and biological interpretation, principle and applications of protein microarray.

Unit VI: Drug discovery pipeline (3 Lectures) Drug life cycle, stages of drug discovery and strategic issues in drug discovery.

B.Sc (Hons) Biomedical Science

Unit VII: Lead generation (6 Lectures) 2D and 3D molecular structures, molecular descriptors and fingerprints, molecular similarity and diversity, topological descriptors, quantitative structure-property relationships.

Unit VIII: Overview of drug development (12 Lectures) HTS, clinical trials, applications of chemoinformatics in drug research (chemical libraries, protein 3D modeling, characterization of binding site, virtual screening, protein-ligand interactions, prediction of pharmacological properties, Introduction to drug databases, PubChem and their use in drug development, Lipinski‟s rule of five, concept of energy minimization and force fields, introduction to rational drug design using example.

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. Retrieval of information from databases. 2. Sequence alignment using BLAST and Clustal W. 3. Phylogenetic analysis using PHYLIP. 4. Microarray analysis using Bioconductor. 5. Molecular format conversion and hands-on molecular visualization program for displaying, animating and analyzing large bio-molecular systems using 3-D graphics. 6. Homology Modeling using SPDBV, model structure refinement using SPDBV and model validation using What Check and Pro Check. 7. Comparing structures, mutations, studying interactions creating electrostatic potential diagrams. 8. Virtual screening and molecular docking using AUTODOCK. SUGGESTED READINGS 1. Bioinformatics: Sequence and Genome analysis, 2nd edition (2004), David W. Mount, Cold Spring Harbour Laboratory Press. ISBN-13: 978-0879697129. 2. Bioinformatics: A practical guide to the analysis of genes and proteins, 3rd edition (2004), Andreas D. Baxevanis and B.F. Francis Ouellette, John Wiley and Sons. ISBN-13: 978- 0471478782. 3. Introduction to Medicinal Chemistry, 4th edition (2009), Graham l. Patrick, Oxford University Press. ISBN-13: 978-0199234479. 4. The Process of New Drug Discovery and Development, 2nd edition (2006), C.G. Smith and J.T. O‟Donnell, Informa Healthcare, ISBN-13: 978-0849327797. 5. Cheminformatics (2003), J. Gasteiger, Thomas Engel; Wiley-VCH. ISBN: 9783527618279. 6. Molecular modeling - Principles and Applications, 2nd edition (2003), A. R. Leach, Pearson Education Limited, UK. ISBN 13: 9780582382107. 7. Cheminformatics in Drug Discovery (2006), edited by. T.I. Opera; Wiley Publishers, ISBN: 9783527604203. 8. Molecular dynamics simulation: elementary methods (1992), J. M. Haile, Wiley- Interscience, New York. ISBN-13: 978-0471184393.

B.Sc (Hons) Biomedical Science

BMS B: Genome Organization and Function

Preamble: The paper Genome Organization and Function deals with the more intriguing concepts of gene regulation (transcriptional, translation and genomic), gene silencing, RNAi and forms and mechanisms of regulatory RNAs. The organization of the genome from overlapping gens in bacteria and DNA of cell organelles to the abundance of repetitive DNA in higher organisms will be discussed. The paper concludes with an introduction to the Human genome project, its goals and features.

THEORY Total Lectures: 48

Unit I: Gene Regulation in Prokaryotes and Eukaryotes (20 Lectures) a) Transcriptional regulation in prokaryotes: Principles of Transcriptional regulation, Bacterial gene regulation with reference to lactose, tryptophan and arabinose operon. Role of sigma factors in gene expression. b) Eukaryotic gene regulation: Transcriptional control - Conserved mechanism of regulation, activators, signal integration, combinatorial control, transcriptional repressors, signal transduction and control of transcriptional regulators, examples of steroid receptors, MAP kinase and STATs pathways, c) Eukaryotic gene regulation: Post-transcriptional control - Regulation of translation, translation-dependent regulation of mRNA and protein stability, post translational control and role of ubiquitin. d) Eukaryotic gene regulation: Genomic control – gene amplification and deletions, DNA rearrangements, chromosome puffs, DNA methylation, changes in histone and chromosome remodeling proteins.

Unit II: Regulatory RNAs (08 Lectures)

Riboswitches, RNA interference, miRNA, siRNA, Regulatory RNA and X-inactivation (reference of calico cats), RNA editing

Unit III: Human Genome Project (8 Lectures)

B.Sc (Hons) Biomedical Science

Unit IV: Organization of the Human Genome (12 Lectures)

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. Preparation of various stock solutions for mentioned experiments. 2. Comparative analysis of genomic DNA and plasmid DNA by restriction enzyme digestion and estimation of size of a DNA fragment after electrophoresis using DNA markers 3. Quantification of unknown DNA using Lambda-HindIII marker 4. Preparation of human metaphase chromosome and Giemsa Staining 5. Perform Southern Hybridization. 6. SDS-Polyacrylamide Gel Electrophoresis for proteins 7. Demonstration of Western Blotting

SUGGESTED READINGS 1. Molecular Biology of the Gene, 6th edition (2007), Watson, J. D., Baker T.A., Bell, S. P., Gann, A., Levine, M., and Losick, R; Benjamin Cummings Publishers, ISBN-13: 978- 0805395921. 2. Principles of Genetics, 6th edition (2011), D. Peter Snustad, Michael J. Simmons; John Wiley and Sons, ISBN-13: 978-0470903599. 3. The World of the Cell, 7th edition (2008), Becker, Kleinsmith, Hardin and Bertoni. Benjamin Cummings, ISBN-13: 978-0805393934. 4. Human Molecular Genetics, 3rd edition (2003), Tom Strachan and Andrew Read; Garland Science Publishers, ISBN -13: 978-0815341826. 5. The Cell: A Molecular Approach, 6th edition (2013), Cooper and Hausman; Sinauer Associates, Inc. ISBN-13: 978-1605351551. 6. DNA Replication, 2nd edition (2005), Arthur Kornberg; University Science Books ISBN-13: 978-1891389443. 7. Cell and Molecular Biology: Concepts and Experiments, 7th edition (2013), Gerald Karp; Wiley Publishers, ISBN-13: 978-1118206737. 8. Genomics: The Science and Technology behind the Human Genome Project, 1st edition (1999), Cantor and Smith; John Wiley and Sons, ISBN-13: 978-0471599081. 9. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Michael R. Green and Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978-1936113422. 10. Concepts of Genetics, 10th edition, (2012). William S. Klug, Michael R. Cummings, Charlotte A. Spencer, Michael A. Palladino. ISBN-13: 978-0321724120.

B.Sc (Hons) Biomedical Science

BMS-C: Human Genetics

Preamble: This course is designed to develop an appreciation for the groundwork carried out so far in order to gain an insight into mechanisms of human genetic diseases, relate to how it has been built on the numerous genetic studies carried out over decades to contribute to the understanding of relationship between genotype and phenotype. The time is poised for understanding human as a model organism. The course will also introduce the methods for whole genome analysis and the genome sequencing.

THEORY Total Lectures: 48

Unit I: History of Human Genetics (1 Lecture) Early Greek concepts about inheritance, Cytogenetics history (the works of Winiwater, Painter and Tjio and Levan), Landmark achievements of Galton, Garrod etc. Unit II: Patterns of Inheritance for Monogenic Traits (5 Lectures) Recapitulation of principles of human deciphering inheritance pattern through pedigree analysis: Autosomal inheritance-dominant, recessive, sex-linked inheritance, sex-limited and sex- influenced traits and mitochondrial inheritance. Deviations from the basic pedigree patterns- nonpenetrance, variable expressivity, pleiotropy, late onset, dominance problems, anticipation, genetic heterogeneity and uniparental disomy, mosaicism and chimerism, consanguinity and its effects, epigenetic modifications and imprinting Unit III: Human Genome Project (4 Lectures) History, organization and goals of human genome project, Tools (Vectors- BAC, PAC, YAC and sequencing techniques) and approaches (Hierarchical and shotgun sequencing), outcomes ethical issues and applications in human diseases Unit IV: Organization of the Human Genome (3 Lectures) General features: Gene density, CpG islands, RNA-encoding genes. Gene clusters, diversity in size and organization of genes, types of repetitive DNA, pseudogenes, gene families, genetic markers and their applications Unit V: Techniques for Genomics (6 Lectures) DNA sequencing (Maxam-Gilbert and Sanger Method, introduction to NGS), DNA fingerprinting, polymorphism screening (genotyping of SNPs and microsatellite markers), expression and proteome analysis (microarray, 2-D analysis, pull down assays) Unit VI: Population Genetics (3 Lectures) Genotypic and allelic frequencies, linkage disequilibrium, haplotype construction (two loci using SNPs and/or microsatellites) Unit VII: Mapping strategies (3 Lectures) Physical maps (different types- restriction, cytogenetic maps, use of FISH in physical mapping, radiation hybrids and clone libraries in STS mapping) and genetic maps

B.Sc (Hons) Biomedical Science

Unit VIII: Identification of Genetic Basis of Disease (3 Lectures) Principles and strategies, positional and candidate gene approaches, positional- cloning approach (examples- HD, CFTR), concept of twin and adoption studies Unit IX: Prenatal Diagnosis (2 Lectures) Brief introduction, methods of prenatal diagnosis Unit X: Clinical Genetics: (4 Lectures) Inborn errors of metabolism and their genetic basis (example- phenylketonuria), genetic disorders of haemopoietic systems (examples- sickle cell anemia and thalassemia), genetic basis of color blindness, genetic basis of familial cancers (example- retinoblastoma), genetics of mental retardation Unit XI: Implications of Genome Research: (4 Lectures) Diagnosis and screening of genetic disorders, prenatal genotyping for mutations in β- globin gene and sickle cell anemia, DNA profiling: establishing identity and relationships, applications in personalized medicine (genetic polymorphism in drug metabolism genes e.g. cytP450 and GST and their effect on drug metabolism and drug response), genetic counseling Unit XII: Guided short project (10 Lectures) Short project involving, data analysis/in silico analysis of genomes/ literature based project; guiding the students through identification of the project, discussions on approach and methodology, and strategies for data analysis

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. PTC testing to prove monogenic inheritance. 2. Demonstration of DNA fingerprinting. 3. Polymorphism analysis using PCR. 4. Mapping of clones/STS on plasmids or BACs. 5. Video based demonstration of tools for prenatal diagnosis. 6. Haplotype construction. 7. Web based analysis: retrieval of a desired human sequence from NCBI database and sequence alignment using BLAST.

B.Sc (Hons) Biomedical Science

SUGGESTED READINGS 1. Strachan and Read. Human Molecular Genetics.4th Edition. Garland Science, 2010. ISBN: 978-0815341499. 2. Cantor and Smith. Genomics, 2002, John Wiley and Sons, Inc. ISBN: 9780471599081. 3. J.N. Pasternak. An introduction to Human Molecular Genetics, 2nd Edition, Wiley-Liss, 2005. ISBN: 978-0-471-47426-5. 4. G.N. Wilson. Clinical Genetics: A short Course. Wiley-Liss, 2000. ISBN: 978-0471298069. 5. Vogel and Motulsky, Human Genetics: Problems and Approaches, 3rd Edition, Springer Verlag, 1997. ISBN: 978-3-540-37653-8. 6. T.A. Brown. Genomes, 2nd edition, Oxford: Wiley-Liss; 2002. ISBN-10: 0-471-25046-5.

B.Sc (Hons) Biomedical Science

BMS D: Medical Biochemistry

Preamble: The Medical Biochemistry course has been formulated to impart medically relevant information on clinical biochemistry. Students would learn the principle and applications of the diagnostic enzymology, interplay of hormones in the metabolism and details of various biomolecules of diagnostic significance. These topics are included to educate students on the clinical significance of biochemistry. This course will also focus on the contemporary methods and practical approaches that are used in the clinical laboratories for the investigation of the diseased state.

THEORY Total Lectures: 48

Unit I: Basic Concepts and Scope (02 Lectures)

Unit II: Enzymes: Distribution and diagnostic significance (10 Lectures)

Unit III: Hormones (08 Lectures)

Unit 4: Structural complexities and diseases associated with carbohydrates and lipids (10 Lectures)

Carbohydrates: Sugars as information molecules; detailed account on Lectins: their role in physiological functions and their potential as drug targets in various infectious diseases. Dietary fibers. Lipids: Types of Lipoproteins (chylomicrons, VLDL, LDL, HDL); disorders associated with lipoprotein metabolism (hypercholesterolemia, Atherosclerosis). Metabolism of ketone bodies in diabetic patients. Prostaglandins- classification, biosynthesis, role of COX-1, COX-2, NSAIDS in synthesis; functions Steroids-Cholesterol- biosynthesis and regulation, inhibitors of cholesterol biosynthesis (Statins-structure and mechanism of action).

B.Sc (Hons) Biomedical Science

Unit 5: Vitamins (06 Lectures)

Unit 6: An overview of integrative metabolism (12 Lectures)

Local and global regulation in tissue specific metabolism, interplay of insulin and glucagon integration of various metabolic pathways of proteins, lipids, carbohydrates and nucleic acids, obesity role of leptin, ghrelin and other hormones in regulation of body mass, electron transport chain and inhibitors, oxidative phosphorylation, role of uncouplers and ionophores.

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. Preparation of serum and plasma from whole blood. 2. Quantitative determination of the following in the whole blood/plasma/serum: a) LFT: i) SGPT and SGOT ii) Creatine kinase iii) Albumin/total protein b) KFT: i) Urea ii) Uric acid c) Metabolites: i) HDL/LDL and triglycerides ii) Serum protein A: G ratio. iii) Serum glucose. 3. Five case studies based on above quantitative estimations performed.

B.Sc (Hons) Biomedical Science

SUGGESTED READINGS 1. Tietz Fundamentals of Clinical Chemistry, 6th edition (2007), Carl A. Burtis, Edward R. Ashwood, and David E. Bruns;WB Saunders Co, ISBN-13: 978-0721638652 2. Harpers Illustrated Biochemistry, 29th edition (2012), Robert Murray, David Bender, Kathleen M. Botham Peter J. Kennelly, Victor Rodwell, P. Anthony Weil; McGraw-Hill Medical, ISBN-13: 978-0071765763 3. Lehninger‟s Principles of Biochemistry, David L. Nelson and Michael M. Cox, 5th edition(2008), ISBN-13: 978-0716771081 4. Textbook of Medical Biochemistry, 7thedition (2007), Chatterjea&Shinde, Jaypee Publications, ISBN: 81-8448-134-9. 5. Biochemistry, J. M. Berg, J. L. Tymoczko and L. Stryer, 6th edition (2006), W. H. Freeman and Co. ISBN-13: 978-0716787242 6. Fundamentals of Biochemistry: Life at the Molecular Level, 4th edition (2012), Donald Voet, Judith G. Voet, Charlotte W. Pratt; Wiley, ISBN-13: 978-0470547847

B.Sc (Hons) Biomedical Science

BMS E: Medical Biotechnology

THEORY Total Lectures: 48

Unit I: Introduction to Biotechnology (1 Lecture)

Brief history and Importance

Unit II: Basic techniques (4 Lectures) Agarose gel electrophoresis, Southern, Northern and Western blotting and hybridization, use of enzymatic and chemiluminiscent methods for detection of proteins, detection of nuclei acids by radioactive and fluorescent probes.

Unit III: Manipulation of DNA (5 Lectures)

Unit IV: Cloning Vectors (8 Lectures)

Unit V: Cloning and expression of cloned genes in prokaryotic and eukaryotic Cells (6 Lectures)

B.Sc (Hons) Biomedical Science

Unit VI: Polymerase chain reaction (PCR) (4 Lectures)

Principle and applications, primer-design, detailed understanding of PCR and RT- (Reverse transcription) PCR.

Unit VII. Construction of genomic and cDNA libraries, screening and selection of recombinants (6 Lectures)

Unit VIII. Random and site-directed mutagenesis (4 Lectures)

Unit IX:Application of Medical Biotechnology (8 Lectures)

Unit X: Biosafety and ethical issues in biotechnology (2 Lectures)

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. To understand the method of digesting DNA with different restriction enzymes. 2. To maintain and store the E.coli DH5 alpha cells. 3. Preparation of Competent Cell (Calcium Chloride Treatment). 4. To prepare insert and vector for ligation. 5. To perform ligation reaction using T4 DNA ligase. 6. Transform competent bacterial cells with foreign DNA. 7. To identify recombinants by blue-white screening and PCR.

B.Sc (Hons) Biomedical Science

SUGGESTED READINGS

1. Gene cloning and DNA analysis, 6th edition (2010), T.A. Brown. Wiley-Blackwell ISBN-13: 978-1405181730. 2. Principles of Gene Manipulation and Genomics, 7th edition (2006), S.B. Primrose and R.M. Twyman. Blackwell Scientific ISBN: 978-1405135443. 3. Molecular Biotechnology: Principles and Applications of Recombinant DNA, 4th edition (2009),Bernard R. Glick, Jack J. Paternack, Cheryl I. Patten. ASM press, ISBN- 13:9781555814984. 4. DNA Replication, 2nd edition (1992), Arthur Kornberg; University Science Books, ISBN - 13:978- 0716720034. 5. Genomics: The Science and Technology behind the Human Genome Project, 1st edition (1999), Cantor and Smith; John Wiley and Sons, ISBN-13:978-0471599081. 6. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Three-volume set by Michael R. Green, Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978-1936113422.

B.Sc (Hons) Biomedical Science

Generic Elective (GE) Courses

B.Sc (Hons.) Course in Biomedical Science

B.Sc (Hons) Biomedical Science

GE: Generic Elective Courses

BMS-G1: Biosafety and Bioethics

BMS-G2: Biostatistics

BMS-G3: Bridging Information Technology and Biotechnology

BMS-G4: Concepts in Medicinal Chemistry and Drug Development

BMS-G5: Intellectual Property Rights (IPR) for Biologists

BMS-G6: Pathological Basis of Diseases

BMS-G7: Pharmacology and Toxicology

BMS-G8: Tools and Model organisms in Biomedical Research

In alphabetical order

(Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.)

B.Sc (Hons) Biomedical Science

BMS-G1: Biosafety and Bioethics Preamble: The recent advances in the field of biotechnology have brought into focus several safety and ethical issues. The inventions in the field of genetic engineering and related fields of molecular biology will affect not only us but the plants, microorganisms, animals and the entire environment and the way we practice agriculture, medicine and food processing. An increase in our ability to change life forms in recent years has given rise to the new science of bioethics. The present course focus on the biosafety and bioethical issues the modern society confronts. Topics such as biosafety levels, GM food debate, impact of biotechnology on biosafety, biotech products and ethical issues, governance of biosafety, environmentally responsible use of biotechnology, clinical ethics will be discussed in the curriculum.

THEORY Total Lectures: 48

Unit I: Introduction (03 Lectures)

Unit II: Biosafety guidelines (10 Lectures)

Unit III: Handling and transportation of GM, infectious and radioactive materials (05 Lectures)

Risk analysis, risk assessment, risk management and communication, overview of national regulations and relevant international agreements including Cartagena Protocol.

Unit IV: Biosafety management (06 Lectures)

Key to the environmentally responsible use of biotechnology, ethical implications of biotechnological products and techniques, social and ethical implications of biological weapons.

B.Sc (Hons) Biomedical Science

Unit V: Concept of social science (02 Lectures)

Reason to apply its principles to study cause of health problems and suggest appropriate intervention/ solution to problem.

Unit VI: Foundation of Bioethics (02Lectures)

Definition, historic evolution, codes and guidelines, universal principles.

Unit VII: Codes, Covenants, Declarations and Guidelines (05 Lectures)

Define the term “Bioethics” in relation to profession, society, and biomedicine, learn about gradation of moral and ethical norms from simpler to higher levels for initiating right actions to „first do no harm‟ and learn about prayers, oaths, covenants, declarations, guidelines and codes which have relevance to bioethics.

Unit VIII: Clinical ethics (02 Lectures)

Describe the sanctity of human life and the need to preserve human life, explain about issues related to prenatal screening, clinical trials (Phase I/II/III/IV) studies.

Unit IX: Women health ethics (03Lectures)

Vulnerability of women with respect to health care, examination and screening of women for disease, social issues like domestic violence and female genital mutilation and abortion.

Unit X: Medical errors and Negligence (03 Lectures)

Medical error and medical negligence difference, remedies against medical negligence, protection and compensation related to it.

Unit XI: Critical care ethics (04 Lectures)

Unit XII: Care in HIV and AIDS (02 Lectures)

Basics of HIV infection,identify ethical issues in clinical practice of HIV medicine and its prevention, research ethics related to HIV.

Unit XIII: Ethical use of animals in the laboratory (01 Lecture)

B.Sc (Hons) Biomedical Science

PRACTICALS

(Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.)

1. A case study based on genetic modified organism (Bt-Cotton). 2. A case study based on genetic modified organism (Bt-Brinjal). 3. A case study based on terminator seeds. 4. A case study based on removal of selective marker in a DNA vaccine. 5. A case study on clinical trials of drugs in India with emphasis on ethical issues. 6. A case study on women health ethics. 7. A case study on medical errors and negligence. 8. A case study on critical care ethics. 9. A case study on ethical issues in clinical practice of AIDS. 10. A case study on handling and disposal of radioactive waste.

SUGGESTED READINGS 1. Bioethics and Biosafety, 1st edition (2008), M. K Sateesh, I K International Pvt Ltd, ISBN- 13: 978-8190675703. 2. The Cambridge Textbook of Bioethics, 1st edition (2008), Peter A. Singer and A. M. Viens; Cambridge University Press, ISBN-13: 978-0511545566. 3. Foundation of Bioethics, 2nd edition (1996), E. H Tristram; Oxford University Press, ISBN- 13: 9780195057362. 4. Social science: An introduction to the study of society, 14th edition (2010), Hunt, E. F.,and Colander, D. C. ; Peason/Allyn and Bacon, Boston, ISBN-13: 978-020570271. 5. Principles of Biomedical Ethics, 6th edition (2011), Beauchamp Tl, Childress JF; Oxford University Press, 2001. ISBN-13: 978-0195143317. 6. A Companion to Bioethics, 2nd edition (2012), Helga Kuhse, Peter Singer; John Wiley and Sons, ISBN-13: 978-1444350845. 7. Bioethics: An Introduction to the History, Methods, and Practice, 1st edition (1997), Nancy Ann Silbergeld Jecker, Albert R. Jonsen, Robert A. Pearlman; Jones and Bartlett Learning, ISBN-13: 978-0763702281. 8. Genetically Modified Organisms and biosafety, 1st edition (2004), Tomme Young. ISBN- 13: 978-2831707983. 9. Environmental Safety of Genetically Engineered Crops, 1st edition (2011), Rebecca Grumet, James F. Hancock, Karim M. Maredia, CholaniWeebadde, Michigan State University Press ISBN-13: 978-1611860085. 10. Biosafety and Bioethics, 1st edition (2006), Rajmohan Joshi; Isha Books ISBN-13: 978- 8182053779. 11. Bioethics and biosafety in biotechnology, 1st edition (2007), V. Sreekrishna; New Age International (P) Ltd., ISBN-13: 978-8122420852.

B.Sc (Hons) Biomedical Science

BMS-G2: Biostatistics

Preamble: The objective of this course is to acknowledge, appreciate and effectively incorporate the basic statistical concepts indispensable for carrying out and understanding biological hypothesis, experimentation as well as validations. It is aimed at creating awareness about the applications of statistics in biological sciences along with building confidence in students to logically test their experimental data with an appropriate set of test of significance. Use of open source software and web material is encouraged as the course intends to give wings to the students and not just the height for their soaring potentials!

THEORY Total Lectures: 48

Unit I: Descriptive Statistics (13 lectures) a) Data in Biology: Development in biostatistics, samples and populations, techniques of sampling (random and stratified), sampling and non-sampling errors, variables in biology, accuracy, precision, univariate and bivariate frequency distributions and their graphical representations. b) Measures of Central Tendency: Arithmetic, geometric and harmonic means, mode, median and partition values. c) Measures of Dispersion: Range, standard deviation, coefficient of variance and covariance. d) Moments: Raw and central moments and their relationships. e) Measures of Skewness: Pearson‟s, Bowley‟s and Kelly‟s coefficients of skewness; coefficient of skewness using moments. f) Measures of Kurtosis.

Unit II: Probability and Probability Distributions (15 lectures) a) Probability: Basic concepts, addition and multiplication rules of probability, conditional probability, Bayes‟ theorem and its applications in biostatistics. b) Random variables: discrete and continuous. c) Mathematical Expectation and Variance: definition and properties. d) Probability Distributions: Probability mass function, probability density function and distribution function. Binomial distribution, Poisson distribution, normal distribution and exponential distribution along with their properties and relationships.

Unit III: Correlation and Linear Regression (05 lectures) a) Correlation Analysis: Scatter diagrams, Pearson‟s and Spearman‟s coefficients of correlation, coefficient of determination, standard and probable errors. b) Regression Analysis: Method of least squares, equations of lines of regression and their applications in biostatistics.

Unit IV: Hypothesis Testing: (15 lectures) a) Sampling distributions and standard error, null and alternate hypothesis, basic concept and illustrations of type I and type II errors, concept of confidence interval estimation. b) Large sample tests for single mean and difference of means, single proportion and difference of proportions. 78

B.Sc (Hons) Biomedical Science

c) Student‟s t-distribution: test for single mean, difference of means and paired t- test, chi- square distribution: tests for goodness of fit, independence of attributes and homogeneity, F-distribution, one-way and two-way analysis of variance (ANOVA). d) Non-parametric analysis: Sign and run tests.

PRACTICALS

Computer-based practicals using any statistical software like 'R'. MATLAB, SPSS, Spreadsheets, etc. to understand the following concepts:

1. Graphical data representation 2. Measures of central tendency and dispersion 3. Probability and probability distributions: binomial, Poisson and normal distribution 4. Correlation and linear regression analysis 5. Student‟s t- test 6. Chi-square test 7. ANOVA

SUGGESTED READINGS

1. Primer of Biostatistics, 7th edition (2011), Stanton Glantz, McGraw-Hill Medical. ISBN- 13: 978-0071781503. 2. Biostatistics: A Foundation for Analysis in the Health Sciences,10th edition (2013), Wayne W Daniel and Chad L. Cross, Wiley. ISBN-13: 978-1118302798. 3. Principles of Biostatistics, 2nd edition (2000), Marcello Pagano and KimberleeGauvrean, Thompson learning. ISBN-13: 978-0534229023. 4. Biostatistical Analysis, 5th edition (2009), Jerrold H. Zar, Pearson. ISBN-13: 978- 0131008465.

B.Sc (Hons) Biomedical Science

BMS-G3: Bridging Information Technology and Biotechnology

Preamble: This course has been designed to reflect how information technology synergizes biotechnology. The course will focus on information retrieval from various databases, the basis of sequence data analysis, use of Hidden Markov Model to solve various sequence analysis problems, such as pairwise and multiple sequence alignments, gene annotation etc. THEORY Total Lectures: 48 Unit I: Convergence of biotechnology and information technology (02 Lectures) Introduction to bioinformatics and its applications, Internet and bioinformatics.

Unit II: Databases and genome browsers (08 Lectures) Introduction to various databases and their classification (primary and secondary databases) e.g. NCBI, DDBJ, EMBL, ENSEMBL, UCSC and their use in laboratories: literature, sequence, structure, medical, enzymes and metabolic pathways databases.

Unit III: Sequence alignment and visualization (08 Lectures) Local and global sequence alignments (Needleman-Wunsch and Smith-Waterman algorithms), pair-wise (BLAST and FASTA algorithms) and multiple sequence alignment (Clustal W) and its importance.

Unit IV: Theory behind BLAST (04 Lectures) How Hidden Markov Model (HMM) can be used to model a family of unaligned sequences or a common motif within a set of unaligned sequences and further be used for discrimination and multiple alignment.

Unit V: Phylogenetic analysis (05 Lectures) Basics and tools for phylogenetic analysis, cladistics and its assumptions, tree-building methods (Character and distance based methods), construction of phylogenetic trees (PHYLIP).

Unit VI: Gene ontology (03 Lectures) The Ontologies: cellular component, biological process and molecular function.

Unit VII: Genome analysis (05 Lectures) Features of DNA sequence analysis, gene prediction methods, SNP analysis (dbSNP), sequence assembly and genome annotation.

Unit VIII: Restriction site mapping and primer design (06 Lectures) In silicorestriction mapping, cloning and expression, identification of cDNA from databases, design of primers for standard and real time PCR, e-PCR.

B.Sc (Hons) Biomedical Science

Unit IX: Introduction to machine learning (04 Lectures) Learning from data, how can we extract knowledge from data to take decisions, and program the computer to be able to learn from examples and adapt systems dynamically to enable better user experiences.

Unit X: Application of bioinformatics in biotechnology (03 Lectures) PCR diagnostic design, design strategy for over-expression of a therapeutic protein using specific examples to illustrate the strategy.

PRACTICALS

(Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.)

1. Retrieval of information from nucleotide databases. 2. Sequence alignment using BLAST. 3. Multiple sequence alignment using Clustal W. 4. Phylogenetic analysis using PHYLIP 5. Gene Ontology 6. Gene prediction and ORF finding. 7. In silico primer designing for standard and real time PCR and performing e-PCR.

SUGGESTED READINGS 1. Bioinformatics: Sequence and Genome analysis, 2nd edition (2004), David W. Mount, Cold Spring Harbour Laboratory Press. ISBN-13: 978-0879697129. 2. Bioinformatics: A practical guide to the analysis of genes and proteins, 3rd edition (2004), Andreas D. Baxevanis and B.F. Francis Ouellette, John Wiley and Sons. ISBN: 978- 0471478782.

B.Sc (Hons) Biomedical Science

BMS-G4: Concepts in Medicinal Chemistry and Drug Development Preamble: The course emphasizes on various drug targets in the body and highlights the importance of drug-receptor interactions, lead discovery, drug design and drug development strategies.

THEORY Total Lectures: 48

Unit I: General Introduction (02 Lectures)

Definition and scope of drug design.

Unit II: Drug target classification (08 Lectures)

Unit III: Physicochemical principles of drug action (08 Lectures)

Partitioncoefficient,drugdissolution,acidbaseproperties,surfaceactivity,bioavailablity,stereochemi calaspectsofdrugaction.

Unit IV: Drug receptor interactions (08 Lectures)

Kinetic analysis of ligand receptor interactions using scatchard plot, double reciprocal plot, Hill plot, forces involved, relationship between dose and effect (graded and quantal response).

Unit V: Principles of drug design (08 Lectures)

Introduction to SAR, strategies in the search for new lead compounds, analogue synthesis versus rational drug design, concept of prodrugs.

Unit VI: Drug discovery and pharmainformatics (14 Lectures)

Drug discovery pipeline, drug target identification and validation for microbial pathogen, selection of gene unique to the pathogen, screening for its presence in other microbes and human host, Drug Databases, PubChem, Calculating drug-like properties, introduction to rational drug design methods, optimization of lead compounds, protein 3D structure and binding site analysis, similarity based virtual screening using online tools.

B.Sc (Hons) Biomedical Science

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. Preparation of Benzocaine. 2. Preparation of Aspirin and determination of partition coefficient in octanol-water system. 3. Preparation of Paracetamol. 4. Preparation of Phenacetin. 5. Visualization and analysis of 3D structures of proteins. 6. Finding the active sites in a receptor. 7. Molecular docking using AutoDock or HEX. 8. Searching databases for drug like compounds and computing drug like properties of small molecules.

B.Sc (Hons) Biomedical Science

BMS-G5: Intellectual Property Rights for Biologists

Preamble: Developments in the recent years has increased the knowledge acquisition process which is considered to have commercial value as well. The knowledge pool so generated can be considered as intellectual property which has grown tremendously in academic community and society at large. The pace with which our modern science is progressing today, various new and useful inventions take place. Through this paper, students are made aware to understand the need for creation, protection, and commercialization of intellectual property in the area. Various forms of Intellectual Property Rights are also explained. Paper also deals with the entire process of patent filling, taking some case studies.

THEORY Total Lectures: 48

1. Introduction to IPR (02 lectures) Importance of IPR, advantages of IP protection, relationship with trade, Product / design patent and Terminologies.

2. Types of IPRs (08 lectures) Copyrights, trademarks, Trade Secrets, Patents, and Geographical indicators, IC layout design, plant variety protection.  Copyrights - Nature of Copyright, Author & ownership of Copyright, Rights Conferred by Copyright, Assignment, Transmission, Licensing of Copyrights, Copyright Societies, Office, Board, Registration of Copyrights & Appeals, International Conventions, Copyright pertaining to Software/Internet, Database, Copyright Protection/Database Protection, IP issues in cyber space, Legal Position in USA/Indian Law/WIPO Copyright Treaty  Trademarks- Meaning of Trademarks, Different kinds of marks (brand names, logos, signatures, symbols), Use of a Mark, Registration of Trademarks- Procedure, Opposition to Registration-Procedure, What Marks are Registrable/Not Registrable, Concurrent Registration, Similarity of Marks, Assignment/Transmission/Licensing of Trademarks, Infringement of Trademarks, Passing off Action.  Patents- i. General Introduction: Definition, Product / Process /Design Patents Claims, Dates Associated with patent, Patent Life and Geographical Boundaries, Patent Infringement, Utilization of Intellectual Assets, Ownership of Patents. ii. Patent Search, Patent Databases & Library (USPTO, WIPO, EPO), Practical Search Training. iii. Patent Terminology: (Abstract, Summary, Background, Drawings, Description, Claims)

B.Sc (Hons) Biomedical Science

 Geographical Indicators- Nature of Geographical Indicators, Conditions & Procedure for Registration, Offences, Penalties.

3. Biotechnology and the expanding boundaries of IP protection (02 lectures) Biotechnology and Life Science Industries, Commercial importance of biogenetic resources.

4. Highlights of Indian patent Law (as amended in 2005) (04 lectures) Elements of patentability - Patentable subject matter, Utility, novelty and non- obviousness, Patentability of biotechnological inventions –, biochemical and software.

5. Worldwide patent protection (04 lectures) Paris Convention, World Trade Organization, World Intellectual Property organization, TRIPS Agreement, PCT, UPOV convention, Convention on Biological Diversity, Biopiracy, Traditional knowledge and benefit sharing.

6. Patents filing (05 lectures) Patent filing in India and abroad, Building patent databases and library generation, Preparation of patent documents, Process for examination of patents, Patent Evaluation and Economics of patenting.

7. Intellectual property exploitation and management, Licensing and Technology transfer. (02 lectures) 8. Case studies (06 lectures) (a) Infringement cases; (b) Biopiracy cases (Hoodia case, the Quinoa case, the Enola bean case, The neem patents); (c) Traditional knowledge and IP system; (d) Patents as assets; (e) Trade secrets; (f) Drug pricing as a result of patent filing. (f) Patenting of genetically-engineered micro-organism (Diamond Vs Chakravarthy); (g) Recent cases related to the provisions of Section 3(d) of The Patents Act (Novartis vs Generic Manufacturers, Roche vs Cipla, Astra Zeneca Vs Natco Pharma).

9. Forums, Processes and Initiatives (05 lectures) (a) International: Conference of the parties to the convention on Biological diversity. (b) INDIA: Biodiversity conservation, trade and development, India‟s bio-scientific and technological capacities, implementing TRIPS, Regulatory Framework in Biotech Industry and Pharma setup in India, Clinical trials.

10. Key Business concerns in commercializing Intellectual Property Rights (10 lectures) Competition and Confidentiality issues, Antitrust Laws; Employee Confidentiality; Assignment of Intellectual Property Rights; Technology Transfer Agreements; Intellectual Property Issues in the Sale of Business. Future Developments of Intellectual Property Rights–Indian Traditional Medicine & IP Protection, Folklore, Patenting of Life Forms, International-Traditional Medicines & Health Foods

B.Sc (Hons) Biomedical Science

SUGGESTED READINGS

1. Prabuddha Ganguli – Intellectual property rights : unleashing the knowledge economy, Tata McGraw Hill Publishing. 2. Wadhera, Intellectual property Rights. 3. Patent law / by P Narayanan (Highly Recommended) 4. Selected Reading from Landis 5. The Patents Act (1970), with latest Amendments. 6. Manual of patent practice and procedure: Indian patent office website.

B.Sc (Hons) Biomedical Science

BMS-G6: Pathological basis of diseases

Preamble: Claude Bernad said “Effects vary with the conditions which bring them to pass, but laws do not vary. Physiology and pathology states are ruled by the same forces; they differ only because of the special conditions under which the vital laws manifest themselves” Thus the syllabi of Pathology compliments and supplements the necessary knowledge students have gained in Physiology. Consequently it incorporates topics like cellular adaptations, inflammation, neoplasia, cellular ageing and other infectious diseases. Pathology also provides the necessary inputs for the other disciplines like Pharmacology, social and preventive medicine, medicinal biochemistry etc. All the topics and experiments are introductory in nature and lay stress on introducing Students with basic concepts of pathology

THEORY Total Lectures: 48

Unit I: Introduction (2 Lectures)

History of pathology, Basic definitions and common terms used in pathology, Survival mechanism and disease, microscopic and cellular pathology, scope and techniques used.

Unit II: Cell Injury and responses of cells: Cellular Adaptations, and Cell Death (4 Lectures) An overview of cellular adaptation: Hyperplasia, Hypertrophy, Atrophy, Metaplasia; Causes and mechanisms of cell injury, reversible and irreversible injury, Necrosis, Apoptosis, Types of apoptosis, Intracellular accumulations, Cellular ageing

Unit III: Role of Inflammation in disease (with suitable examples) (7 Lectures)

Unit IV: Role of Tissue repair Healing and Fibrosis (with suitable examples) (5 Lectures)

Basic mechanism of tissue regeneration, and repair by healing, scar formation and fibrosis

Unit V: Common Hemodynamic Disorders in diseases (with suitable examples) (6Lectures)

An overview of Edema, hyperemia, congestion, hemorrhage, hemostasis and thrombosis, Embolism, Infarction and shock with suitable examples

Unit VI: Nutritional diseases (5 Lectures)

Protein energy malnutrition, deficiency diseases of vitamins, minerals, nutritional excess and imbalances.Role and effect of metals .

B.Sc (Hons) Biomedical Science

Unit VII: Cancer (7 Lectures)

Unit VIII: Infectious diseases epidemiology (12 Lectures)

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. Urine analysis for abnormal constituents: protein, fats and glucose 2. Measuring Erythrocyte sedimentation rate. 3. Tissue Processing, embedding and sectioning. 4. Staining and preparation of permanent histological slide. 5. Diagnostic tests for detection of various Diseases – CRP, VDRL, RA, Pregnancy, Dengue and HIV (any four) 6. PCR based diagnostics (for any one disease)

SUGGESTED READINGS 1. Robbins and Cotran Pathologic Basis of Disease, 8th edition (2009), Vinay Kumar, Abul. K. Abbas, Jon C. Aster, Nelson Fausto; Saunders Publishers, ISBN-13: 978-1416031215 2. Robbins Basic Pathology, 9th edition (2012), Kumar, Abbas, Fausto and Mitchell; Saunders Publication, ISBN-13: 978-1437717815 3. General And Systematic Pathology, 2nd edition (1996) J.,Ed. Underwood and J. C. E. Underwood; Churchill Livingstone, ISBN-13: 978-0443052828 4. Textbook of preventive and social medicine, 20th edition, J. E Park; Banarsi Das Bhanot. Publishers. ASIN B0007CBHKI. 5. Medical Laboratory Technology Methods and Interpretations, 6th edition (2009), Ramnik. Sood; Jaypee Brothers Medical Publishers, ISBN-13: 978-8184484496. 6. Pathophysiology, 3rd edition (2012), Lee-Ellen C. Copstead-Kirkhorn and Publisher. Saunders. ISBN-13: 978-1455726509.

B.Sc (Hons) Biomedical Science

BMS-G7: Pharmacology and Toxicology Preamble: The course provides basic insight into principles of pharmacology and toxicology. It also highlights the pharmacodynamics and pharmacokinetics aspect of drugs in general. The emphasis will be on evaluation of toxicity and mechanism of toxicity of xenobiotics.

THEORY Total Lectures: 48 Unit I: General pharmacology and toxicology (6 Lectures)

Nature and source of drugs, routes of drug administration and their advantages, definitions and scope of toxicology.Introduction to ecotoxicology.

Unit II: Mechanism of toxicity (6 Lectures) Formation of ultimate toxicant of xenobiotics and its interaction with target molecules.

Unit III: Pharmacokinetics (6 Lectures) Membrane transport, absorption, distribution of xenobiotics. Brief introduction to biotransformation, Phase- I reactions including oxidations, hydrolysis, reductions and phase II conjugation reactions and excretion of drugs.

Unit IV: Pharmacodynamics (6 Lectures) Mechanism of drug action, receptors and receptors subtypes, Dose response relationship and combined effect of drugs. Concept of LD50, LC50, TD50 and therapeutic index.

Unit V: Introduction and classification of the drugs acting on: a. Central and autonomic nervous system, neurotoxic agents. (6 Lectures) b. Cardiovascular system and cardiotoxic agents. (6 Lectures) c. Kidney and nephrotoxic agents. (4 Lectures)

Unit VI: Introduction and classification a. Anti-inflammatory and analgesic drugs and their related toxicity. (4 Lectures) b. Endocrine drugs (2 Lectures) c. Antimicrobial chemotherapeutic drugs (2 Lectures)

B.Sc (Hons) Biomedical Science

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. Handling of laboratory animals and various routes of drug administration. 2. To study presence of paracetamol/aspirin in the given sample. 3. Separation of a mixture of benzoic acid, beta- napthol and napthelene by solvent extraction and identification of their functional groups. 4. Determination of Dissolved water (DO) using Winkler‟s method. 5. To determine the total hardness of water by complexometric method Using EDTA. 6. To determine Acid value of the given oil sample. 7. Calculation of LD50 value of an insecticide from the data provided.

SUGGESTED READINGS 1. Essentials of Medical Pharmacology, 7th edition (2010), K.D. Tripathi, Jaypee Brothers, ISBN-13: 978-8184480856. 2. Pharmacology, 7th edition (2011), H.P. Rang, M.M. Dale, J.M. Ritter and P.K. Moore, Churchill Livingstone, ISBN-13: 978-0702045042 3. Cassarett and Doull‟s Toxicology “The Basic Science of The Poisons” 7th edition (2008), Curtis D. Klaassen Editor, McGrawHill Medical. ISBN-13: 978-0071470513. 4. Introduction to Toxicology, 3rd edition (2001), John Timbrell, Taylor and Francis Publishers. ISBN-13: 978-0415247627. 5. Cassarett and Doull‟s “Essentials of Toxicology”,2nd edition (2010), Klaassen and Whatkins, McGraw Hill Publisher. ISBN-13: 978-0071622400. 6. Principles of Toxicology, 2nd edition (2006), Stine Karen and Thomas M Brown, CRC Press. ISBN-13: 978-0849328565. 7. Lu‟s basic toxicology: Fundamentals target organ and risk assessment,5th edition (2009), Frank C Lu and Sam kacow, Informa Health care. ISBN: 9781420093117.

B.Sc (Hons) Biomedical Science

BMS-G8: Tools and Model Organisms in Biomedical Research

Preamble: This course has been designed to introduce the various tools and techniques in modern era of biology. It focuses on the principles of microscopy, spectroscopy, chromatography, various molecular biology and immunological techniques. This course also aims to give the students an introduction to different model organisms, what they are used for, which techniques that can be applied to modify their genome, and how the students may use these organisms employing modern technological approaches for research and understanding of biology. It‟s a motley collection of creatures: They fly, swim, wiggle, scurry, or just blow in the wind. But to the scientific community, this compilation has been elevated above all other species. They are the model organisms.-The Scientist, June 2, 2003 THEORY Total Lectures: 48

Unit I: Spectroscopy (5 Lectures) Principles and biological applications of UV, visible spectroscopy, Fluorescence spectroscopy, Infrared spectroscopy, NMR and Mass spectroscopy

Unit II: Microscopy (3 Lectures) Principles of Light microscopy, Phase contrast microscopy, Electron microscopy (EM)- scanning EM, transmission EM and scanning transmission EM (STEM); Fluorescence microscopy.

Unit III: Analytical methods (5 Lectures) Chromatography: Principle and applications of affinity, gel filtration and ion exchange chromatography, HPLC Centrifugation: Principle and different types of centrifugation- differential, density gradient and equilibrium. Flow cytometry: Flurochromes, fluorescent probe and principle, application in biomedical science.

Unit IV: Molecular Biology Methods (8 Lectures) Isolation, purification and quantification of nucleic acids; Agarose and PAGE; Hybridization techniques- Southern, Northern and Western; Restriction enzymes, Gene cloning and RFLP; Principles of PCR, RT PCR, Real time PCR;DNA sequencing- Maxam Gilbert and Sanger methods Unit V: Immunological methods (3 Lectures) Monoclonal antibody generation, isolation of various immune cells and their functional assays, generation and applications of nude mice. ELISA - direct, indirect, competitive and sandwich ELISA, Co-immuno-precipitation for protein-protein interaction studies.

B.Sc (Hons) Biomedical Science

Unit VI: Introduction to model organisms (2 Lectures) What are model organisms? Why there is a need to study model organisms? How to choose a model organism? Unit VII: Different model organisms The following aspects will be discussed under each model organism listed below. Brief history of model organisms, life cycle, culture conditions/maintenance, advantages and disadvantages of the organism as a model, fundamental discoveries made so far using these organisms, discussion on suitability of each for genetic, developmental biology and as disease models: Escherichia coli (2 Lectures) Utilization in discovery of fundamental metabolic pathways. Saccharomyces cerevisiae (Baker’s yeast) (6 Lectures) Mating types and their inheritance. Discovery of cell division cycle genes-cdc mutants,Yeast two hybrid system for protein-protein interactions. Overview of saccharomyces genome database (SGD), commonly used yeast assays, the 'Yeast Genome Deletion Collection'. Caenorhabditis elegans (Nematode worm) (2 Lectures) Insights into the role of proteases (ced genes) in Coursed cell death, cell-fate mapping and lineage studies. Discovery of RNAi in C. elegans, Overview of Wormbase database Drosophila melanogaster (Fruit fly) (4 Lectures) Insights into forms of cancer and neurodegenerative diseases. Flybase, the Gene disruption project, transgenic flies. Mus musculus (Mouse) (4 Lectures) “Premier” model organism for studying complex physiological processes. Generation and application of knock out and transgenic mice as disease models. Knockout database. Introduction to other model organisms (4 Lectures) Dictyostelium discoideum (Social amoeba) as a model for induced multicellularity and differentiation. Daniorerio (Zebra fish) as a model for human disease (any 2).Introduction to tools for Standard mutagenesis and Genetic screening. Daphnia (Water flea) as a model for ecotoxicological studies.

B.Sc (Hons) Biomedical Science

PRACTICALS (Wherever wet lab experiments are not possible the principles and concepts can be demonstrated through any other material or medium including videos/virtual labs etc.) 1. Isolation and spectroscopic quantification of genomic DNA from blood/tissue/ E.coli, determination of melting temperature of DNA. 2. Optimization of PCR conditions for temperature (gradient PCR) and Mg2+ concentration. 3. Restriction digestion of DNA for RFLP and DNA fingerprinting. 4. To perform Southern hybridization. 5. Protein purification by affinity/ion exchange/gel filtration chromatography. 6. To perform sandwich ELISA. 7. Preparation of culture media for Drosophila and study different stages of life cycle of Drosophila. 8. Study of life cycle of Dictyostelium discoideum.

SUGGESTED READINGS 1. Physical Biochemistry: Principles and Applications, 2nd edition (2009), David Sheehan, John Wiley. ISBN-13: 978-0470856031. 2. Cell and Molecular Biology: Concepts and Experiments, 6th edition (2009), Gerald Karp, Wiley. ISBN-978-0470483374. 3. Gene cloning and DNA analysis, 6th edition (2010), T.A. Brown. Wiley-Blackwell ISBN- 13: 978-1405181730. 4. Principles of Gene Manipulation and Genomics, 7th edition (2006), S.B. Primrose and R.M. Twyman. Blackwell Scientific ISBN: 978-1405135443. 5. Human Molecular Genetics, 3rd edition (2003), Tom Strachan and Andrew Read; Garland Science Publishers, ISBN -13:978-0815341826. 6. Immunology, 6th edition, (2006), J. Kuby, W.H. Freeman and Company, New York. ISBN- 13: 978-1429202114. 7. Genetics: A Conceptual Approach, 4th edition (2010), Benjamin A. Pierce, W. H. Freeman, ISBN-13: 978-1429232524. 8. Molecular Cloning: A Laboratory Manual, 4th edition (2012), Three-volume set by Michael R. Green, Joseph Sambrook; Cold Spring Harbor Laboratory Press, ISBN-13: 978- 1936113422. 9. Concepts of Genetics, 10th edition, (2012). William S. Klug, Michael R. Cummings, Charlotte A. Spencer, Michael A. Palladino. ISBN-13: 978-0321724120. 10. Physical Biochemistry: Applications to Biochemistry and Molecular Biology, 2nd edition (1982), David Freifelder, W.H. Freeman and Company. ISBN-13: 978-0716714446. 11. Principles and Techniques of Biochemistry and Molecular Biology, 7th edition (2010), Wilson K and Walker J., Cambridge University Press, 2010. ISBN-13: 978-0521516358. 12. Emerging Model Organisms: A Laboratory Manual, Volume 2, Lab manual edition (2010), Cold Spring Harbor Laboratory Press, ISBN-13: 978-0879698652.