CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Savitribai Phule Pune University

(Formerly University of Pune)

Three Year B.Sc. Degree Program in Biotechnology

(Faculty of Science & Technology)

F.Y. B. Sc. (Biotechnology)

Choice Based Credit System Syllabus

To be implemented from Academic Year 2019-2020

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Preamble of the Syllabus:

Biotechnology has expanded and established as an advanced interdisciplinary applied science. The study of Life itself is at the core of it and the interdisciplinary networking potential of biotechnology has given it a separate status in fundamental research as well as in modern industrial enterprise. Global and local focus has slowly shifted to not only current “Century of Knowledge” but also on to technology development and application in life sciences. In the milieu of research and industrialization for economic development and social change, biotechnology is an ideal platform to work. The interdisciplinary nature of biotechnology integrates living systems including animal, plant and microbes and their studies from molecular biology to cell biology, from biochemistry to biophysics, from genetic engineering to stem cell research, from bioinformatics to genomics-proteomics, from environmental biology to biodiversity, from microbiology to bioprocess engineering, from bioremediation to material transformation and so on. The relevance and application of these studies on living organisms and their bioprocesses is extensively covered in this field with the help of technology. Green revolution and white revolution was possible in India thanks to the deeper and intrinsic understanding of biotechnology. Economic and social renaissance is staged on biotechnology especially, since it’ s biomedical and cutting edge technological applications are tremendously powerful in shaping this century and exciting future. Biotechnologists are always in demand as an efficient work force in fundamental research and industries. Education and research sectors require such interdisciplinary trained work force to develop future generations of science leaders. Career opportunities for graduate students are created and expanding at the biotechnology parks and in manufacturing industries, teaching, research institutes and IT industry. The restructures syllabus is a choice based credit system with semester pattern. Biotechnology has grown extensively in last couple of decades. The syllabi till today had been sufficient to cater to the needs of students for building up their careers in industry and research. However, with the changing scenario at local and global level, we feel that the syllabus orientation should be altered to keep pace with developments in the education and industrial sector. The need of the hour is to design appropriate syllabi that emphasize on teaching of technological as well as the economical aspects of modern biology. The proposed credit based curriculum ensures the requirement of academia and industry. Theory supplemented with extensive practical skill

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

sets will help a graduate student to avail the opportunities in the applied fields (research, industry or institutions) without any additional training. Thus, the university /college itself will be developing the trained and skilled man-power. Biotechnology being an interdisciplinary subject, this restructured syllabus will combine the principles of physical, chemical and biological sciences along with developing advanced technology. Biotechnology curricula are operated at two levels viz. undergraduate and postgraduate. The undergraduate curricula are prepared to impart primarily basic knowledge of the respective subject from all possible angles while postgraduate syllabus emphasizes on more applied courses. In addition, students are to be trained to apply this knowledge particularly in day-to-day applications of biotechnology and to get a glimpse of research. The basic aim of the revised course curriculum is to integrate various disciplines of life sciences which will cater the needs of human resources in academia and industry. The Overall objective of the Program is to promote education and research in biotechnology and provide academic and professional excellence for immediate productivity in academics, government organization, biomedical sectors, health and nutrition settings for ultimate benefit of society and sustainable development. The objectives of the course curriculum are: • To introduce the concepts in various allied subjects • To enrich students’ knowledge in basic and applied aspects of life sciences. • To help the students to build interdisciplinary approach in teaching/ learning & in research. • To inculcate the sense of scientific responsibilities and social awareness • To help students build-up a progressive and successful career in academia and industry. The present course curriculum will generate skilled human resource required in academia and Industry. In general, as a result of this program, the student will be able to achieve basic and advance knowledge based proficiency in applied subjects of life sciences, create and develop students with interdisciplinary mind set for learning science, improve problem solving aptitude using scientific methods in biotechnology and allied subjects, will adopt scientific approach for implications of biotechnology in society, environment and education, will demonstrate knowledge and learn various biological processes at cellular and molecular level and get expertise in the different techniques used in the fields of Biotechnology.

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Title of the Course: B.Sc. (Biotechnology) Structure of the course: Semester: I Theory

Course Course Title Credits Number Marks Code of Lectures BBt-101 Fundamentals of 2 Credits 30 50 (35 External +15 Internal) Chemistry-I

BBt-102 Fundamentals of 2 Credits 30 50 (35 External +15 Internal) Physics

BBt-103 Biochemistry I 2 Credits 30 50 (35 External +15 Internal)

BBt-104 Biophysics 2 Credits 30 50 (35 External +15 Internal)

BBt-105 Animal Sciences I 2 Credits 30 50 (35 External +15 Internal)

BBt-106 Plant Sciences I 2 Credits 30 50 (35 External +15 Internal)

BBt-107 Microbiology I 2 Credits 30 50 (35 External +15 Internal)

BBt-108 Biomathematics and 2 Credits 30 50 (35 External +15 Internal) Biostatistics-I

PRACTICAL

BBt-109 Practical In Chemistry and 1.5 15 P 50 (35 External +15 Biochemistry Credits Internal)

BBt-110 Practical In Plant and Animal 1.5 15 P 50 (35 External +15 science Credits Internal)

BBt-111 Practical In Microbiology & 1.5 15 P 50 (35 External +15 Biostatistics-I Credits Internal)

BBt-112 Practical In Physics and 1.5 15 P 50 (35 External +15 Biophysics Credits Internal)

Total Credits (Theory + Practical) 22 Credits

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Semester II Course Course Title Number code Credits of Marks Lectures BBt-201 Fundamentals of Chemistry 2 Credits 30 50 (35 External +15 II Internal)

BBt-202 Biochemistry II 2 Credits 30 50 (35 External +15 Internal)

BBt-203 Bioinstrumentation 2 Credits 30 50 (35 External +15 Internal)

BBt-204 Animal Sciences II 2 Credits 30 50 (35 External +15 Internal)

BBt-205 Plant Sciences II 2 Credits 30 50 (35 External +15 Internal)

BBt-206 Microbiology II 2 Credits 30 50 (35 External +15 Internal)

BBt-207 Biomathematics and 2 Credits 30 50 (35 External +15 Biostatics-II Internal)

BBt-208 Computer in biology 2 Credits 30 50 (35 External +15 Internal)

PRACTICAL

BBt-209 Practical In Chemistry & 1.5 Credits 15 P 50 (35 External +15 Biochemistry II Internal)

BBt-210 Practical In Plant and 1.5 Credits 15 P 50 (35 External +15 Animal science II Internal)

BBt-211 Practical In Microbiology 1.5 Credits 15 P 50 (35 External +15 & Bioinstrumentation Internal)

BBt-212 Practical In Computer & 1.5 Credits 15 P 50 (35 External +15 Biostatistics Internal)

Total Credits (Theory + Practical) 22 Credits

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

B. Sc. Biotechnology (CBCS Semester Pattern) S. Y. B. Sc. Biotechnology Semester III

Course Course Title Credits Number Marks Code of Lectures BBt-301 Cell Biology I 2 Credits 30 50 (35 External +15 Internal

BBt-302 Molecular Biology I 2 Credits 30 50 (35 External +15 Internal

BBt-303 Genetics 2 Credits 30 50 (35 External +15 Internal

BBt-304 Metabolism 2 Credits 30 50 (35 External +15 Internal

BBt-305 Environmental 2 Credits 30 50 (35 External +15 Internal Biotechnology

BBt-306 Bio analytical Techniques 2 Credits 30 50 (35 External +15 Internal

EVS- AECC-I Environment 2 Credits 30 50 (35 External +15 Internal 231 science theory paper 1

LA-231 AECC-II Language theory 2 Credits 30 50 (35 External +15 Internal paper 1

PRACTICAL

BBt-309 Practical in Cell Biology 2 Credits 15 P 50 (35 External +15 Internal and Genetics BBt-310 Practical in Bio analytical 2 Credits 15 P 50 (35 External +15 Internal Techniques BBt-311 Practical in Molecular 2 Credits 15 P 50 (35 External +15 Internal Biology and Environmental Biotechnology

Total Credits (Theory + Practical) 22 Credits

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Semester IV Course Course Title Credits Number Marks code of Lectures BBt-401 Cell Biology II 2 Credits 30 50 (35 External +15 Internal BBt-402 Molecular Biology II 2 Credits 30 50 (35 External +15 Internal

BBt-403 Immunology 2 Credits 30 50 (35 External +15 Internal

BBt-404 Animal Development 2 Credits 30 50 (35 External +15 Internal

BBt-405 Plant Development 2 Credits 30 50 (35 External +15 Internal

BBt-406 Microbial 2 Credits 30 50 (35 External +15 Biotechnology Internal

EVS- 241 AECC-III Environment 2 Credits 30 50 (35 External +15 science theory paper 2 Internal

LA-241 AECC- IV Language 2 Credits 30 50 (35 External +15 theory paper 2 Internal

PRACTICAL

BBt-409 Practical in Molecular 2 Credits 15 P 50 (35 External +15 Biology and Microbial Internal Biotechnology BBt-410 Practical in Animal and 2 Credits 15 P 50 (35 External +15 Plant Development Internal

BBt-411 Practical in Cell biology 2 credit 15 P 50 (35 External +15 and immunology Internal

Total Credits (Theory + Practical) 22 Credits

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

B. Sc. Biotechnology (CBCS Semester Pattern) T. Y. B. Sc. Biotechnology Semester V Course Course Title Credits Numbe Marks code r of Lectur es BBt-501 Industrial Microbiology 2 Credits 30 50 (35 External +15 Internal BBt-502 R- DNA technology 2 Credits 30 50 (35 External +15 Internal

BBt-503 Plant Tissue Culture 2 Credits 30 50 (35 External +15 Internal

BBt-504 Animal Tissue Culture 2 Credits 30 50 (35 External +15 Internal

BBt-505 Applied biotechnology I 2 Credits 30 50 (35 External +15 Internal

BBt-506 Biodiversity and Systematics 2 Credit 30 50 (35 External +15 Internal

BBt-507 SEC – I : Summer Industrial 2 Credits 30 50 (35 External +15 Internship / Review writing/ Internal Start up Design or Case study Report

BBt-508 SEC – II : Project formulation 2 Credits 30 50 (35 External +15 and presentation Internal

PRACTICAL

BBt- Practical in Industrial 2 Credits 15 P 50 (35 External +15 509 Microbiology Internal BBt- Practical in Plant Tissue Culture 2 Credits 15 P 50 (35 External +15 510 and Animal Tissue Culture Internal

BBt- Practical in R- DNA technology 2 Credit 15 P 50 (35 External +15 511 and Biodiversity Internal

Total Credit (Theory + Practical) 22 Credit

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Semester VI

Course Course Title Credits Number of Marks code Lectures BBt-601 Enzyme and Enzyme 2 Credits 30 50 (35 External +15 Technology Internal BBt-602 Agriculture Biotechnology 2 Credits 30 50 (35 External +15 Internal

BBt-603 Applied Biotechnology II 2 Credits 30 50 (35 External +15 Internal

BBt-604 Food and Pharmaceutical 2 Credits 30 50 (35 External +15 Biotechnology Internal

BBt-605 Bioinformatics 2 Credits 30 50 (35 External +15 Internal

BBt-606 Bio safety and Bioethics and 2 Credits 30 50 (35 External +15 IPR Internal

BBt-607 SEC – III & SEC – IV : 4 Credit 60 100 (70 External +30 & 608 Project Internal

PRACTICAL

BBt- Practical in Enzyme Technology 2 Credits 15 P 50 (35 External +15 609 Internal

BBt- Practical in Agriculture 2 Credits 15 P 50 (35 External +15 610 Biotechnology and Internal Bioinformatics

BBt- Practical in Food and 2 Credits 15 P 50 (35 External +15 611 Pharmaceutical Biotechnology Internal

Total Credit(Theory + Practical) 22 Credit

Note: • Each Credit = 15 Lecture • Each credit will be equivalent to 15 clock hours of teaching and each practical credit is equivalent to 30 clock hours of teaching in a semester.

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Equivalence of previous syllabus along with proposed syllabus:

S. Paper Title of Previous Syllabus Equivalent Paper Title of New Syllabus No. 1 Bb- 101 Fundamentals of Chemistry BBt- 101 Fundamentals of Chemistry-I BBt - 201Fundamentals of Chemistry-II 2 Bb- 102 Fundamentals of Physics BBt- 102 Fundamentals of Physics BBt- 203 Bioinstrumentation 3 Bb- 103 Basics of plant and animal BBt- 105 Animal Sciences I sciences BBt - 106Plant Sciences I 4 Bb- 104 Mathematics & Statistical BBt- 108 Biomathematics and Biostatics-I Methods for Biologists BBt- 207 Biomathematics and Biostatics-II 5 Bb- 105 Fundamentals of Biological BBt- 103 Biochemistry I Chemistry BBt- 202 Biochemistry II 6 Bb- 106 Biophysics & BBt- 104 Biophysics Instrumentation BBt- 203 Bioinstrumentation 7 Bb- 107 Microbiology BBt- 107 Microbiology I BBt- 207 Microbiology II 8 Bb- 108 Computers and BBt- 208 Computer in Biology applications BBt- 108 Biomathematics and Biostatics-I 9 BBt- 109 Practical In Chemistry and Bb- 109 Practical in Chemistry & Biochemistry I

Biochemistry BBt- 209 Practical In Chemistry and Biochemistry II BBt- 112Practical In Physics and Biophysics 10 Bb- 110 Techniques in Physics, BBt-211Practical In Microbiology & Biophysics & Instrumentation Bioinstrumentation BBt- 110 Practical In Plant and animal 11 Bb- 111 Laboratory Exercises in science Biosciences BBt- 111 Practical In Microbiology BBt-212 Practical In Computer & Biostatistics 12 Bb- 112 Quantitative Methods in

Biology

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Course Code: BBt-101 Fundamentals of Chemistry-I (2 Credit Course) Total Lectures=30

Unit Topics No. of Lectur es I Atomic Structure 4 Historical background electronic structure of atom, atomic & molecular orbitals, Shapes of atomic orbitals molecular orbital method, selection rules to find electronic configuration of elements. II Molecules 6 Diatomic molecules, Valence bond theory, VSEPR theory, hybridization involving s, p, d, orbitals(sp,sp 2,sp 3,dsp 2,sp 2d,sp 3d,sp 3d2), homo and heteronuclear diatomic molecules, bond order, magnetic properties III Chemical Bonding 6 Types of bond covalent, ionic, hydrogen bonding, inter and intramolecular hydrogen bonding, dipole- dipole, dipole-induced dipole interaction, structure of water molecule, oxidation state. Hydrophobic & hydrophilic interaction, IV Thermodynamics - 8 Types of systems, intensive and extensive properties, equilibrium and non-equilibrium states, reversible and irreversible processes, laws of thermodynamics, internal energy, enthalpy, entropy Endothermic and exothermic reactions, free energy and work, Gibb’s Helmholtz equations, ATP and its role in bioenergetics, biological oxidation reduction reactions(in terms of electrons), Basics of Organic & S tereochemistry -IUPAC nomenclature, V Reactions of functional groups- Alkane, Alkene, alkyne, alcohol, 6 amines, alkyl halides, ether. Organic reactions- oxidation, reduction, elimination, addition, substitution ( electrophilic/ Nucleophilic) Conformations, configurations, isomerism (structural and stereoisomers), Enantiomers ,Chiral centers, Geometric isomers Newman’s & Fisher Projection formulae, epimers, anomers, furanose and pyranose form, free radical reactions.

Recommended Textbooks and References: 1. General Chemistry , 1st edition (2000), C.N. R. Rao, Macmillan Publishers, India. 2. Principles of Physical Chemistry, 4th edition (1965), S.H. Maron and C.F. Prutton, Collier Macmillan Ltd 3. The elements of Physical Chemistry, 5th edition (2009), Atkins P, de Paula J. , W. H. Freeman Publication, USA 3. An Introduction to Electrochemistry, edition reprint, 2011, Samuel Glasstone, biblioBazaar, USA 4. Physical Chemistry for biological sciences, 1st edition, (2005), Chang R., University Science Books, USA 6. Physical Chemistry, 1st edition, (2003) David Ball, Thoson Learning, USA.

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5. Essentials of Physical Chemistry, 24th edition, (2000), B S Bahl, G D Tuli, ArunBahl, S. Chand Limited, India. 6. Concise Inorganic Chemistry. 5th edition (2008), Author: J. D. Lee, John Wiley & Sons, USA. 7. Organic Chemistry, 6 th edition, (1992), Morrison Robert Thornton, Pearson Publication, Dorling Kindersley (India Pvt. Ltd.) 8. Guide book to Mechanism in Organic Chemistry by Peter Sykes, 6 th edition, (1996), Prentice Hall, India.

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Course Code: BBt-102 Fundamentals of Physics (2 Credit Course)

Total Lectures=30

Unit Topics No. of lectures I Measurements: Physical quantities, fundamental and derived units, System of Units, order of magnitude. Length: radius of proton to astronomical distances. Mass: atomic mass unit to mass of Earth. 4 Time: fast elementary particle to age of Earth. Amount of substance. Luminous intensity. Inter-conversion of units.

II Fluid mechanics: Fluids: Definition, Pressure, density. Variation of pressure with depth in a fluid at rest. Measurement of pressure. Various units of pressure and their inter conversion. Streamline and 5 turbulent flow. Equation of continuity. Flow of liquids through capillaries. Viscosity, Newton’s law of viscosity, coefficient of viscosity. Ostwald’s viscometer. Relevance to life sciences. III Surface Tension: Surface tension and surface energy. Cohesive and adhesive forces. Capillary action, angle of contact, wettability. 5 Factors affecting surface tension. Applications. Relevance to life sciences. IV. Waves and oscillations: Difference. Types of waves (transverse and longitudinal). Reflection of waves. Principle of superposition of waves. Standing and travelling waves. Sound waves as pressure 8 waves. Audible, ultrasonic, and infrasonic waves. Characteristics of sound waves. Beats. Doppler Effect. Applications in life sciences.

V Geometrical Optics: Reflection, Refraction (Snell’s Law). Types of lenses, combinational lenses, radius of curvature, focal length, Lens 8 maker equation. Microscopes. Optical power, diopter. Magnification. Mirrors. Aberrations.

Recommended Textbooks and References 1. Concepts of Physics. Volume I and Volume II. (2010). H. C. Verma. 2. Fundamentals of Physics, 9 th edition (2010). David Halliday, Robert Resnick, Jearl Walker. 3. Sears and Zeemansky’s University Physics, 13 th edition (2012). Hugh Young, Roger Freedman, A. Lewis Ford. 4. A Textbook of Optics (2001). Dr. N. Subrahmanyan, BrijLal, Dr. M. N. Avadhanulu. By S. Chand publications.

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Course Code: BBt-103 Biochemistry I (2 Credit Course) Total Lectures=30

Unit Topic s Lectures I Historical perspective : 3 • Origin of life, abiotic production of biomolecules, cellular and chemical foundation of life. II Water : 8 • Properties of water, Hydrogen bonding, ionization of water, interaction of biological molecules in water, osmosis, pH, titration curves, buffers, Biological buffers. • Types of bond, Covalent and noncovalent interactions in biomolecules with suitable example, functional groups and modification of functional group relevant to biomolecules. III Carbohydrates: 10 • Classification of carbohydrates, sugars and nonsugars, Monosaccharides: Oligosaccaharides and Polysaccharide. • Monosaccharides: Structure & properties of Monosaccharides, ketoses and aldoses D and L configuration, mutarotaion, epimers, anomers, chemical and physical properties; glycosidic bond, • Oligosaccharides: reducing and non-reducing sugars inversion of sugar • Polysaccharides and its classification based on function Storage polysaccharide: eg starch, glycogen and inulin Structural polysaccharides: eg. cellulose, chitin • Functions of Carbohydrate IV Lipid: 9 • Classification of lipids: Simple & complex lipids, fatty acids. • Structure & chemical and physical properties, • Complex lipids: Triacylglycerol, Sphingolipids, Phospholipids and Glycolipids. Steroids. • Lipoproteins • Storage and structural lipids. • Function of lipids

Recommended Textbooks and References 1. Outlines of Biochemistry: 5th Edition, (2009), Erice Conn & Paul Stumpf ; John Wiley and Sons, USA 2. Fundamentals of Biochemistry. 3rd Edition, (2008), Donald Voet& Judith Voet , John Wiley and Sons, Inc. USA 3. Principles of Biochemistry, 4th edition (1997), JefforyZubey, McGraw-Hill College, USA

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4. Biochemistry: 7th Edition, (2012), Jeremy Berg, LubertStryer, W.H.Freeman and company, NY 5. Lehninger , Principles of Biochemistry. 5th Edition (2008), David Nelson & Michael Cox, W.H. Freeman and company, NY. 6. Biochemistry. 5th Edition, (copu right 2013), Reginald Garett and Charles Grisham, Brook/Cole, Cengage Learning, Boston, USA. 7. An Introduction to Practical Biochemistry.3rd Edition, (2001), David Plummer, Tata McGraw Hill Edu.Pvt.Ltd. New Delhi, India 8. Biochemical Methods.1st , (1995), S.Sadashivam, A.Manickam, New Age International Publishers, India

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CBCS: 2019-2020 F.Y.B.Sc. Biotechnology

Course Code: BBt-104 Biophysics (2 Credit Course) Total Lectures=30

Unit Topics No. of lectures I Structure: Introduction, Scope and definition of Biophysics. 2 Biophysics at macroscopic, microscopic level and at the molecular level. II Atomic structure: Historical background, Bohr model. Significance 7 of second and third postulate of Bohr’s model. Derivation of radius and energy value. Quantization of energy levels. Vector atom model. Quantum numbers. Selection rules. Pauli’s exclusion principle. Emission spectra with respect to Na atoms to understand selection rules. III Radioactivity: Nucleus, Properties. Nuclear forces. Nuclear models 7 (liquid drop and shell model). Radioactive nucleus. Nuclear radiations and their properties - alpha, beta and gamma. Half life, physical and biological handling of alpha and beta emitting isotopes. GM counter- Principle, construction and working . IV. Cell membrane: Organization of plasma membrane. diffusion- 8 basics. Passive and active transport. Membrane potential, Nernst equation. Passive electrical properties of cell (capacitance, resistance). Active electrical properties. Electrical model (equivalent) of cell membrane. Depolarization, hyperpolarization of membrane (neuronal). Generation of action potential. Biopotentials : types and measurement V Biophysical properties: Surface tension, adsorption, diffusion, 6 osmosis, dialysis and colloids

Recommended Textbooks and References: 1. Biophysics, an introduction. 1st edition. (2002) Cotteril R. John Willey and Sons Ltd., USA 2. Biophysics. 1st edition (2002), Pattabhi V and Gautham N. Kluwer Academic Publisher, USA. 3. Textbook of optics and atomic physics, 8th edition (1989) P.P. Khandelwal, Himlaya Publishing House, India. 4. Instrumentation measurements and analysis – 2nd edition (2003). Nakraand Choudhari, Tata McGraw Hill, India. 5. Nuclear Physics: An Introduction. 2nd edition (2011). S. B. Patel. Anshan Publication, India 6. Skoog & Lerry, Instrumental Methods of Analysis, Saunders College Publications, New York 7. H. H. Willard, Instrumental Methods of Analysis, CBS Publishers. 8. D.C. Harris, Quantitate Chemical Analysis, W. H. Freeman 9. Christian G.D, Analytical Chemistry, John & Sons, Singapore 10. Skoog, West and Holler, Analytical Chemistry, Saunders College Publications, New York

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11 Vogel’s Textbook of Qualitative Chemical Analysis, ELBS 12. J.A. Dean, Analytical Chemistry Notebook, McGraw Hill 13. John H. Kennedy, Analytical Chemistry: Principles, Saunders College Publication 14. W. Kemp, Organic Spectroscopy, ELBS 15. Hand book of Instrumental Techniques for Analytical Chemistry, Frank Settle, editor, Prentice Hall

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Course Code: BBt-105 Animal Sciences I (2 Credit Course) Total Lectures=30

Unit Topics No. of lectures I Introduction to Kingdom Animalia 6 • Outline classification of non-chordates with examples • Kingdom Protista General characters and classification up to classes; Locomotory Organelles and locomotion in Protozoa • Phylum Porifera General characters and classification up to classes; Canal System in Sycon • Phylum Cnidaria General characters and classification up to classes; Polymorphism in Hydrozoa • Phylum Platyhelminthes General characters and classification up to classes • Phylum Nemathelminthes General characters and classification up to classes • Phylum Annelida General characters and classification up to classes • Phylum Arthropoda General characters and classification u p to classes; Metamorphosis in Insects(Drosophila) • Phylum Mollusca General characters and classification up to classes • Phylum Echinodermata General Characters and classification up to classes; Water-vascular system in Asteroidea. II Outline classifica tion of chordates with examples 6 • Protochordates General features and examples • Agnatha General features of Agnatha and classification of cyclostomes • Pisces General features and Classification up to classes • Amphibia General features and Classification up to classes • Reptiles General features and Classification up to classes • Aves General features and Classification up to classes • Mammals General features and Classification up to classes III Animal Tissues:(Histolo gy) 6 • Structure, location, classification and functions of epithelial tissue, connective tissue, muscular tissue and nervous tissue • Bone and Cartilage - Structure and types of bones and cartilages IV Introduction to Invertebrate and vertebrate model system 12 • Type of Invertebrate: i. Hydra ii. celegans iii. Drosophila iv. Honey bee: Apissp. I Morphology ii. Mouthparts, sting apparatus iii.Social organization iv. Communication in Bees Type: • Vertebrate i. Frog/Toad

Recommended Textbooks and References 1. Jordan , E.L. and Verma P.S. 1978, (i) Chordate Zoology S. Chand & Company

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Ltd. Ram Nagar. New Delhi. 2. Jordan , E.L. and Verma P.S. 1978 (ii) Invertebrate Zoology. S. Chand & Company Ltd. Ram Nagar. New Delhi. 3. Modern Text Book of Zoology: Invertebrates .,R.L. Kotpal . Publisher, RastogiPublications, 2012.

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Course Code: BBt-106 Plant Sciences I (2 Credit Course)

Total Lectures=30

Unit Topics No. of lectures I Introduction to plant world & classification 10 • General & Unique features of plants • Principles, aims and objectives of plant classification , outline of the classification with example • A general account of different groups and their characters with oneexample each of Algae, Fungi, Bryophytes, Pteridophytes, Gymnosperms • Angiosperms – Characteristic features of Dicot and Monocot II Structure of Plant organs 8 • Structure of plant Cell, characteristic feature and cell wall • Morphology & modifications of • Vegetative plant organ : Stem , Leaf and Root • Reproductive plant organs – Flower & Types of Inflorescence III Internal structure of plant organs 4 • Plant Tissues and tissue systems, • Meristematic Tissue and its Type - with example • Permanent Tissue - Simple and Complex - with example IV. Internal organization of plant body 8 • Primary structure of shoot, root & leaf. • Secondary growth, growth rings formation: cambium and its activities, periderm- cork cambium, secondary cortex and cork.

Recommended Textbooks and References 1. Dutta A.C. (2000) A Classbook of Botany (Oxford University Press, UK) 2. Ganguli, Das Dutta (2011) – College Botany Vol I, II and III (New Central BookAgency, Kolkata) 3. Esau K. (1977) Anatomy of seed plants (Wiley, USA) 4. Fahn, A. 1974 Plant Anatomy. Pergmon Press, USA and UK.

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Course Code: BBt-107 Microbiology I (2 Credit Course) Total Lectures=30

Unit Topics No. of lectures I Introduction to Microbial World: 8 • History of Microbiology, Abiogenesis vs Biogenesis, Discovery of Microorganisms, Germ theory of diseases, Koch’s postulates, Pre golden era, Golden Era, post golden Era, Contributions of various scientists in path breaking discoveries, inventions and Product Development. • General Characters and their importance of Prokaryotes, Eubacteria, Archaebacteria, Eukaryotic Microorganisms-(Fungi, Algae, protozoa) , Viruses, viroid and prions. • Importance of study of Microbiology and relevance in Biotechnology (Brief discussion of application of Microbiology in various fields) II Classification of Microorganisms: 4 • All 5 major groups of microorganisms, Similarities and dissimilarities in relation to evolution. • Difference between Prokaryotic and Eukaryotic organisms. • Bacterial Classification: Bergey’s Manual of Systemic Bacteriology III Bacterial cell structure: 8 • Ultrastructure of Bacteria- Cell wall (Gram Positive and Gram negative), Cell Membrane, • Capsule, Flagella, Pili, slime layer, Ribosome, Nucleoid, Mesosomes, Endospore, Cell inclusions (Gas vesicles, carboxysomes,magnetosomes, PHB granules, Glycogen bodies, metachromatic granules)

IV. Observation of Microorganisms: 10 • Bright field Microscope, Dark Field Microscope, Magnification, Resolution, Numerical aperture, Sample Preparation • Wet Mount, hanging drop technique • Theory of staining: Classification of stains, Stain (Basic and Acidic), Fixative, Mordant, Decoloriser, Accentuator • Principles and methods of staining techniques for following (Monochrome, Negative, Differential (Gram, Acid fast ), Special staining- Endospore, flagella, cell wall, nucleic acid, capsule)

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Recommended Textbooks and References 1. Ingraham J. L. and Ingraham C.A. (2004). Introduction to Microbiology.3rd Edition. Thomson Brooks / Cole. 2. Madigan M.T., Martinko J.M. (2006). Brock’s Biology of Microorganisms. 11th Edition. Pearson Education Inc. 3. Prescott L.M., Harley J.P., AND Klein D.A. (2005). Microbiology, 6th Edition. MacGraw Hill Companies Inc. 4. Salle A.J. (1971) Fundamental Principles of Bacteriology.7th Edition. Tata MacGraw Publishing Co. 5. Stanier R.Y., Adelberg E.A. and Ingraham J.L. (1987) General Microbiology, 5th Edition. Macmillan Press Ltd. 6. Tortora G.J., Funke B.R., Case C.L. (2006). Microbiology: An Introduction. 8th Edition. Pearson Education Inc.

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Course Code: BBt-108Biomathematics and Biostatics-I

(2 Credit Course) Total Lectures=30

Unit Topics No. of lectures Mathematics I Fundamentals Mathematical Calculations 8 • Exponents & Powers: Definition and Simple Powers with Numbers, Algebraic rules for working with Powers. • Logarithm: Definition, Laws of logarithm and Change of base theorem (without proofs) Examples based on laws. • Permutations & Combinations : Counting Principle, Permutations with Repetitions (like & dislikes), Circular Permutations, Permutations with r-particular things included/excluded. • Co-ordinate geometry – Area of triangle and quadrilateral, equation of straight line – in slope form, intercept form and perpendicular form. Conics (ellipse, parabola, hyperbola). II Matrices: 7 • Definition, types of matrices, (zero, Identity, square, unit, scaler, triangular, diagonal, upper triangular, lower triangular, symmetric) Addition of matrices, multiplication of matrices, determinant (singular, non-singular). Vector spaces • Definition of vector spaces (10 axioms), subspace of vector space, linear combination, linear dependence, Independence of vectors, Dot and Cross product, Applications of vectors spaces in biology. Biostatistics III Introduction to Statistics 7 • Need of Statistics in biology, collection and organisation/classification, summarization and analysis of biological data • Data, Variables, parameters, populations and samples, types of sampling distribution. • Representation of data using frequency distribution diagram, histogram, ogive curves, bar and pie diagrams. IV Descriptive biostatistics 8 • Measures of Central Tendency: Mean, Mode, Median. • Measures of Variability: Standard deviation, standard error, Range, Mean deviation, Quartile deviation and coefficient of variation. Correlation and Regression : • Positive and negative correlation, calculation of correlation coefficient, regression, linear regression and regression equation.

Recommended Textbooks and References

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1. Fundamentals of Mathematical Statistics by S.C. Gupta and V. K. Kapoor. Sultan Chand & Co. 2. Discrete Mathematics By B.S. Verma, Vishwa Prakashan. 3. Mathematics for Biological Science by JagdishArya & Ladner.1979. Prentice Hall 4. Introduction to the Practice of Statistics, by David S. Moore, George P. McCabe, and Bruce A. Craig, 9th Edition, W.H. Freeman and Co., New York (2017). 5. Mathematics for Biological Scientists, M.Aitken, B. Broadhursts, S. Haldky, Garland Science (2009). 6. P.S.S. Sunderrao and J. Richards-An introduction to Biostatistics, Prentice Hall Pvt. Ltd. India 7. Fundamentals of Biostatistics. By Irfan A Khan. 8. Campbell R.C.- Statistics for Biologists, Cambridge University Press, Cambridge.

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Course Code: BBt-109 Practical in Chemistry and Biochemistry - I (1.5 Credit Course) (Total Practical =15) (15x3 hrs.)

Sr.No. Title of Experiment No. of practical Chemistry 1. Titrations 1 • To study Acid base titration based by conductivity measurement. • To determine alkali content in antacid tablet using HCl 2 Chemical Kinetics : To study kinetics of ester hydrolysis 1 3 Thermochemistry 1 To determine enthalpy and entropy change of a reaction 2FeCl 3 + 3Mg 2Fe + 3MgCl 2 4 Hardness of water : To estimate hardness of water by 1 using EDTA 5 Qualitative analysis : To perform qualitative test for – 1 Hydrocarbons, alcohols, aldehyde, ketones, aniline, amide 6 pH-metry: To determine the pKa value of a given weak 2 acid by pH-metry titration with strong base. Biochemistry 1 Biochemical Calculations Preparation of solutions, 1 buffers. 2 Working of Colorimetry and preparation of standard 1 graph Calculate ƛ max foe given sample. 3 Isolation & identification of starch from plant source 1 4 Saponification number : To find out saponification 1 number of given lipid 5 :Qualitative analysis • Qualitative tests for sugars 1 • Qualitative test for Lipids 6 To estimate concentration of reducing 1 sugar in given sample by DNSA method 7 Quantitative Estimations : To estimate concentration of cholesterol in given 1 sample.

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Course Code: BBt-110 Practical in Plant and animal Science

(1.5 Credit Course) Total Practical =15(15x3 hrs.)

Sr. Title of Experiment No. of No. Practical Plant Science

1 Study of Algae, fungi, bryophytes, pteridophytes , gymnosperms 2 with one example each 2 Study on morphological parameters of angiosperms 2 3 Study on anatomy of root, stem & leaf of dicot plant 1

4 Study on anatomy of root, stem & leaf of monocot plant 1 Animal Science 5 Study of Paramecium 1 • Morphology • Reproduction-Binary fission & Conjugation 6 Culturing of Paramecium 1 7 Study of Hydra: Permanent slides 2 • Morphology • Reproduction • Regeneration in Hydra 8 Study of Drosophila : 2 Characters, sexual dimorphism – eye & wing mutations Life cycle 9 Culturing Drosophila using standard methods 1

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Course Code: BBt-111 Practical in Microbiology & Biostatistics (1.5 Credit Course) (Total Practical =15) (15x3 hrs.)

Sr.No. Title of Experiment No. of practical Microbiology 1. Introduction to Microbiology Laboratory and common 2 microbiology laboratory instruments e.g. Incubator, Hot Air Oven, Autoclave, Colorimeter, pH Meter, Distillation Unit, Chemical Balance, Laminar air flow hood, Clinical Centrifuge 2. Handling of Microorganisms and Biosafety measures 1 3. Observation of Microorganisms. 5 • Use and Care of Compound Microscope • Wet Mount- pond water, fungal staining • Monochrome staining • Negative staining • Gram’s staining • Spore staining • Motility- Hanging drop technique Biostati sti cs 1 Introduction to MS Excel and use of spreadsheets for 2 data organization and basic mathematics calculations 2 Data representation using various graphical types 1 3 Hypothesis testing using ‘Data analysis tools’: t-test, 2 Chi square test 4 Analysis of variance 1 5 Correlation and regression analysis of data and 1 graphical representation

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Course Code: BBt-112 Practical in Physics and Biophysics (1.5 Credit Course) Total Practical =13 (13x3 hrs)

Sr.No. Title of Experiment No. of Practical Physics 1 Study of Vernier Callipers and Micrometer Screw Gauge 1 2 To study the components and working of travelling microscope 1 3 Surface–tension measurement: Using Jaeger’s method/, soap 2 bubble Method 4 Viscosity measurement using Ostwald’s viscometer (for known 1 and Unknown viscosity 5 Study the Calibration of Spectrometer. 1 6 To study Plane diffraction grating 1 Biophysics 1 Study the process of Osmosis 1 2 Determine the surface tension of liquid 1 3 Determination of Diffusion Pressure Deficit using potato tubers 1 4 Dialysis 1 5 Working of a G.M. counter 2

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Course Code: BBt-201 Fundamentals of Chemistry-II (2 Credit Course) Total Lectures=30

Unit Topic s Lectures I Ionic equilibria – 10 • pH, buffer, Equilibrium constant, Le Chatelier’s principle, Acid and bases, strength of acid & bases, dissociation constant, pK values, solubility product, Acid–base titrations, indicators used in titrations, Titration curves, Solubility product • Ionic product, Condition for precipitation, • Handerson Hasselbalch equation & related problems, Osmosis, law of osmotic pressure and its measurement, determination of molecular weight from osmotic pressure • Properties of water, water as a reactant, interaction of biomolecules with water II Chemical kinetics – 6 • Rates of reactions, order, zero, first & second order reactions, & molecularity • Differential and integrated rate equation • Half-life periods, Arrhenius equation, collision theory of reaction rate, temperature dependent reaction rates III Electrochemistry - 7 • Electrochemical cell, half cell, reaction, reduction potential, electrochemical series, thermodynamic potential function from cell potential measurement, Liquid junction potential, Huckel theory, overvoltage/overpotential IV Basics of mole concept 7 • Mole concept, Determination of molecular weight by gram molecular volume relationship, problems based on mole concept, Solutions, colligative properties, • Methods of expressing concentrations, strength, Normality, Molarity and Molality, ppm. • Volumetric experiments -acidimetry, alkalimetry, permanganometry, dichrometry, iodometry.

Recommended Textbooks and References 1. University General Chemistry , 1st edition (2000), C.N. R. Rao, Macmillan Publishers, India , 2. Principles of Physical Chemistry, 4th edition (1965), S.H. Maron and C.F. Prutton, Collier Macmillan Ltd 3. The elements of Physical Chemistry, 5th edition (2009), Atkins P, de Paula J. , W. H. Freeman Publication, USA 4. An Introduction to Electrochemistry , edition reprint, 2011, Samuel Glasstone, BiblioBazaar, USA

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5. Physical Chemistry for biological sciences, 1st edition, (2005), Chang R., University Science Books, USA 6. Physical Chemistry, 1st edition, (2003) David Ball, Thoson Learning, USA. 6. Essentials of Physical Chemistry, 24th edition, (2000), B S Bahl, G D Tuli, ArunBahl, S. Chand Limited, India. 7. Concise Inorganic Chemistry.5th edition (2008), Author: J. D. Lee, John Wiley & Sons, USA. 8. Organic Chemistry, 6 th edition, (1992), Morrison Robert Thornton, Pearson Publication, Dorling Kindersley (India Pvt. Ltd.) 9. Guide book to Mechanism in Organic Chemistry by Peter Sykes, 6 th edition, (1996), Prentice Hall, India.

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Course Code: BBt-202 Biochemistry II

(2 Credit Course) Total Lectures=30

Units Topics Lectures I Proteins: 10 • Functions of proteins, • Polymer of amino acids, Classification of amino acids, • Chemistry of amino acids: Ionisation of amino acid side chains, Configuration, zwitterion, reactions of amino acids, titration of amino acid, Isoelectric pH. • Protein structure: ,Primary structure and peptide bond formation , Secondary structure, secondary repeats Tertiary and Quarternary structure (eg. Haemoglobin). • Protein denaturation and renaturation. II Vitamins : 6 • Classification , Structure and Biochemical functions of fat soluble and water soluble Vitamins. • Coenzymes: Thiamine , Riboflavin, Niacin, PlP, Coenzyme A, lipoic acid ,Folic acid and B12. III Enzymes: 8 • General properties & classification of enzymes • Biocatalyst, Active site, Specificity, Energy of activation, Reaction Rate. Rate law for enzyme catalyzed reaction • Enzyme units, specific activity, turnover number. • Lock and key, Induced fit hypothesis. • Parameters affecting enzyme activity(temp, pH, substrate, cofactor, enzyme con.) • Enzyme inhibition IV Nucleic acids : 6 • Purine, Pyrimidines, Nucleosides, Nucleotides, Polynucleotide. • Nucleoproteins • Covalent structure of DNA and RNA • Forces stabilizing nucleic acid structure • Properties of Nucleic Acid. • Denaturation & renaturation of Nucleic Acids. • Different forms of DNA

Recommended Textbooks and References 1. Outlines of Biochemistry: 5th Edition, (2009), Erice Conn & Paul Stumpf ; John Wiley and Sons, USA 2. Fundamentals of Biochemistry. 3rd Edition, (2008), Donald Voet& Judith Voet , John Wiley and Sons, Inc. USA 3. Principles of Biochemistry, 4th edition (1997), JefforyZubey, McGraw-Hill College, USA

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4. Biochemistry:7th Edition, (2012), Jeremy Berg, LubertStryer, W.H.Freeman and company,NY 5. Lehninger , Principles of Biochemistry. 5th Edition (2008), David Nelson & Michael Cox, W.H. Freeman and company, NY. 6. Biochemistry. 5th Edition, (copu right 2013), Reginald Garett and Charles Grisham, Brook/Cole, Cengage Learning, Boston, USA. 7. An Introduction to Practical Biochemistry.3rd Edition, (2001), David Plummer, Tata McGraw Hill Edu.Pvt.Ltd. New Delhi, India 8. Biochemical Methods.1st , (1995), S.Sadashivam, A.Manickam, New Age International Publishers, India

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Course Code: BBt-203 Bioinstrumentation

(2 Credit Course) Total Lectures=30

Unit Topics No. of lectures I Bio instrumentation : 2 Introduction, Concepts- Analytical techniques II Spectroscopy: 8 • Definition. Electromagnetic wave. Electromagnetic spectrum. Applications of each region of electromagnetic spectrum for spectroscopy. • Lambert-Beer’s Law, types of sources, Instrumentation of single beam and double beam instrument. Introduction to molecular energy levels. Excitation. Absorption. Emission. Rotational spectra. Energy levels of rigid diatomic molecules. • Electron spectroscopy. UV-visible spectroscopy. Principle, construction and working of colorimeter, Spectrophotometer. Application to biomolecules (proteins, DNA, Hb, chlorophyll). III Separation methods : Theory of chromatography; instrumentation 2 and applications of Thin layer chromatography (TLC) IV. Bioinstruments: Concepts- Analytical techniques, .Principle 8 construction, working and applications for analysis of biomolecules of following instruments. • pH meter , isoelectric pH. • Centrifuge (RCF, sedimentation concept), different types of centrifuges. different rotors, differential and density gradient centrifugation, analytical ultra-centrifugation, determination of molecular weights and other applications, • Mass spectroscopy (Bainbridge mass spectrometer). • Atomic absorption spectrometer (AAS). V Microscopes: 6 Concepts - Resolving power. Construction and working principles of the following microscopes– Stereo zoom (Dissecting), Compound , Light microscopy, Bright & Dark Field microscopy, Inverted, Phase contrast, Fluorescence. VI Thermoregulation: T hermometric properties and types of 4 thermometers (clinical, thermocouple, bimetallic, platinum resistance, thermistor - thermometers). Body temperature and its regulation. Recommended Textbooks and References 1. Biophysics, an introduction. 1st edition. (2002) Cotteril R. John Willey and SonsLtd., USA 2. Biophysics. 1st edition (2002), Pattabhi V and Gautham N. Kluwer AcademicPublisher, USA.

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3. Textbook of optics and atomic physics, 8th edition (1989) P.P. Khandelwal,Himlaya Publishing House, India. 4. Instrumentation measurements and analysis – 2nd edition (2003). NakraandChoudhari, Tata McGraw Hill, India.

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Course Code: BBt-204 Animal Sciences II (2 Credit Course) Total Lectures=30

Unit Topic s No of lectures I Animal Physiology I 6 • Digestion: Structure and function of digestive glands; Digestion and absorption of carbohydrates, fats and proteins • Respiratory: Physiology, External and internal Respiration, Transport of oxygen and carbon dioxide in blood, Factors affecting transport of gases.

II Animal Physiology II 6 • Functioning of Excitable Tissue (Nerve and Muscle) Structure of neuron, Propagation of nerve impulse (myelinated and non- myelinated nerve fibre); Structure of skeletal muscle, Mechanism of muscle contraction (Sliding filament theory), Neuromuscular junction • Endocrine and Reproductive Physiology Structure and function of endocrine glands (pituitary, thyroid, parathyroid, pancreas, adrenal, ovaries, and testes), Brief account of spermatogenesis and oogenesis III Parasitology 10 • Introduction to Host-parasite Relationship Host, Definitive host, Intermediate host, Parasitism, Symbiosis, Commensalism • Parasitic Protozoa Life history and pathogenicity of Plasmodium vivax • Parasitic Helminthes Life history and pathogenicity of Fasciola hepatica • Parasitic Helminthes Life history and pathogenicity of Taenia sp . IV Economic Zoology 8 • Vermiculture • Aquaculture • Sericulture • Apiculture

Recommended Textbooks and References 1.Economic Zoology , Shukla&Upadhyaya, 4th Edition., Rastogi Publications,2009. 2. Modern Parasitology: A Textbook of Parasitology, 2nd edition, (1993) F. E. G. Cox, Wiley & Sons, USA 3.Guyton, A.C. & Hall, J.E. (2006). Textbook of Medical Physiology.XIEdition.Hercourt Asia PTE Ltd. /W.B. Saunders Company. 4.Tortora, G.J. & Grabowski, S. (2006). Principles of Anatomy & Physiology. XI Edition John Wiley & son

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Course Code: BBt-205 - Plant sciences II

(2 Credit Course) Total Lectures=30

Unit Topics No. of lectures I Plant water relationship and its importance 9 • Definition, significance and mechanism: i. Permeability ii. Diffusion& imbibition iii Osmosis & its types • Relation between osmotic pressure (OP),turgor pressure(TP) and wall pressure (WP) , DPD (Suction pressure) • Absorption and Transport of water • Introduction and mechanism of Ascent of sap - transpiration and guttation, Translocation of mineral elements. (Capillarity, Imbibition, Atmospheric pressure and Cohesion-tension) II Plant Metabolism: 8 • Photosynthesis: - Photosynthesis pigments, concept of two photo systems, photophosphorylation, calvin cycle, CAM plants, photorespiration, compensation point. • Respiration: Mechanism - Glycolysis, Krebs’s cycle and ETS • Nitrogen metabolism- inorganic & molecular nitrogen fixation III Growth and development of plants 8 • Essential nutrients for Plant growth and their role • Plant growth regulators • Introduction to physiology of flowering: a) Photoperiodism b) Vernalisation IV Economic importance of plants : 5 Cereals, Pulses, Oil seeds, Fiber plants, Medicinal Plants,Timber yielding, Beverages with examples

Recommended Textbooks and References 1. Devlin R.M. (1983) - Fundamentals of Plant Physiology (Mac. Millan, New York). 2. Salisbury, F.B. and Ross, C.W. 1991 Plant Physiology, Wadsworth Publishing Co. Ltd. 3. Nelson, D.L., Cox, M.M. 2004 Lehninger Principles of Biochemistry, 4thedition, W.H.Freeman and Company, New York, USA. 4. Economic Botany: Hill, A.W ; McGraw Hill Book Co., New York. 5. Economic Botany: Pandey, B.P. ;S.Chand and Co., New Delhi. 6. Economic Botany: Sen, S. ; New Central Book Agency, Calcutta.

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Course Code: BBt-206 Microbiology- II (2 Credit Course) Total Lectures=30

Unit Topic No. of lectures I Cultivation, growth and isolation of microorganisms: 15 • Basic Nutritional (Macro and micro), and environmental requirements (Hydrogen ion concentration, Temperature and Oxygen and other), Nutritional classification of bacteria • Design of media (Bacterial and Fungal): Types of media and Composition: Liquid, semi-solid and solid media, Selective media, Enrichment media, Enriched media, differential media, selective and differential media, Minimal media and there uses. • Reproduction in microorganisms: Binary Fission and other asexual methods of reproduction, logarithmic representation of bacterial populations, phases of growth, calculation of generation time and specific growth rate. • Cultivation –Concept of Pure culture, co-culture and Mixed culture, Colony characteristics. • Isolation of microorganisms and pure culture techniques: Streak, Spread, Serial Dilution, Pour plate, Enrichment, Single cell isolation Colony • Preservation and Maintenance methods II. Control of microbial growth: 12 • Definition: Sterilization and Disinfection. • Physical Agents – Heat (Dry and Moist heat), pasteurization, Radiation, Filtration • Principle and working of Autoclave and Hot air oven. • Sterilization Efficiency • Chemical Agents and their Mode of Action - Aldehydes, Halogens, Quaternary Ammonium Compounds, Phenol and Phenolic Compounds, Heavy Metals, Alcohol, Dyes, and Detergents • Disinfectant -Characteristics of an Ideal disinfectant , Examples of Disinfectants and Evaluation of Disinfectant • Antibiotics and other chemotherapeutic agents- Examples and mode of action (one example each), Concept of MIC and MBC III . Microbial Interactions (Any 2 examples each) 3 • Microbe-Plant, • Microbe-Animal • Microbe-Microbe interaction • Handling of microorganisms and Biosafety measures.

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Recommended Textbooks and References 1. Ingraham J. L. and Ingraham C.A. (2004). Introduction to Microbiology.3rd Edition.Thomson Brooks / Cole. 2. Madigan M.T., Martinko J.M. (2006). Brock’s Biology of Microorganisms. 11th Edition. Pearson Education Inc. 3. Prescott L.M., Harley J.P., AND Klein D.A. (2005). Microbiology, 6th Edition.MacGraw Hill Companies Inc. 4. Salle A.J. (1971) Fundamental Principles of Bacteriology.7th Edition. Tata MacGraw Publishing Co. 5. Stanier R.Y., Adelberg E.A. and Ingraham J.L. (1987) General Microbiology, 5th Edition. Macmillan Press Ltd. 6. Tortora G.J., Funke B.R., Case C.L. (2006). Microbiology: An Introduction. 8th Edition. Pearson Education Inc.

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Course Code: BBt-207 Biomathematics and Biostatics-II (2 Credit Course) Total Lectures=30 Unit Topics No. of lectures Mathematics I Linear equations 7 • Homogeneous and non-homogeneous linear equation system • Eigen values and Eigen vectors, • Applications of linear equations in biology Differentials equations • Types (ordinary and partial), order and degree of differential equation. • Homogeneous and non-homogeneous differential equation. • Applications: growth and decay, low of cooling.

II Differential Calculus 8 • Derivative and its physical significance, derivative of a function, implicit function, basic rules for differentiation, maxima and minima – their applications in biology (wave equation, heat equation, laplace equation). Integral Calculus • Integration of functions, basic rules for integration, definite and indefinite integrals, geometric meaning of integration, applications in finding area under curves. Applications of integration in biology. Biostatistics III Probability and probability distribution 8 • Probability theory experiments • Discrete random variable, bionomial distribution and the poisson distribution, Normal distribution and application in biosciences IV Hypothesis testing and correlation 7 • Purpose of hypothesis testing, data, assumptions and hypothesis, significance level, types of errors • Test statistics: Testing mean, testing variance, distribution of test statistics (t and z). • Student’s t – test, chi square test, ANOVA (One and Two way)

Recommended Textbooks and References 1. Fundamentals of Mathematical Statistics by S.C. Gupta and V.K.Kapoor. Sultan Chand &Co. 2. Discrete Mathematics By B.S. Verma, VishwaPrakashan. 3. Mathematics for Biological Science by JagdishArya& Ladner.1979. Prentice Hall.

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4. Thomas' Calculus, by George B. Thomas, Joel Hass, Christopher Heil, Maurice D. Weir, 14 th edition,Pearson Publishers (2018). 5. Elementary Differential Equations and Boundary Value Problems, by William E. Boyce and Richard C.DiPrima, 10 th edition, Wiley publication (2012). 6. Introduction to the Practice of Statistics, by David S. Moore, George P. McCabe, and Bruce A. Craig,9th Edition, W.H. Freeman and Co., New York (2017). 7. Mathematics for Biological Scientists, M.Aitken,B.Broadhursts,S. Haldky, Garland Science (2009). 8. Fundamentals of Biostatistics. byIrfan A Khan. 9. P.S.S. Sunderrao and J. Richards-An introduction to Biostatistics, Prentice Hall Pvt. Ltd. India. 10. Differential Calculus by Shanti Narain 11. Integral Calculus by Shanti Narain 12. Differential Equation by A.R.Forsyth

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Course Code: BBt-208 Computers in biology (2 Credit Course) Total Lectures=3 Unit Topics No. of Lectures I History: 2 • Generations of computers (I, II, III, IV, V) • Modern computers:The workstation, The Minicomputer, Mainframe Computers, Parallel processing Computer & The Super Computer. Introduction to computers: 3 • Overview and functions of a computer system • Input and output devices • Storage devices: Hard disk, Diskette, Magnetic tape, RAID, ZIP devices, Digital tape, CD-ROM, DVD (capacity and access time) Introduction to operating system: 2 • Operating system concept-Windows and unix/Linux II Data processing & presentation: 2 • Introduction : MS office (Word, Excel & Power Point) Computer viruses: 3 • An overview of Computer viruses • What is a virus? Virus symptoms, How do they get transmitted? • General Precautions Internet searches: 3 • Concepts in text-based searching, Searching Medline. Pub Med, bibliographic database III Databases 9 Introduction & need of databases, Types of databases Basic concepts in: • Data Abstraction • Data Models • Instances & Schemes • E-R Model (Entity and entity sets; Relations and relationship sets; E-R diagrams; Reducing E-R Diagrams to tables) Network Data Model: Basic concepts Hierarchical Data Model: Basic concepts Multimedia Database: Basic concepts and Applications Indexing and Hashing • B + Tree indexed files • B Tree indexed files • Static Hash functions

• Dynamic Hash functions

Text Databases

Introduction & Overview of Biological database, Types of Biological Database

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IV Bioinforma tics: Introduction to bioinformatics, History, Goals, 6 Relation to other fields.

Recommended Textbooks and References 1. Bioinformatics –Principles and Applications by ZhumurGhosh, BibekanandMallick-Oxford university press 2. Introduction to Bioinformatics by Teresa Attwood and David.J.Parry Smith- Pearson education 3. Computer Fundamentals , 4th edition (2004) P.K. Sinha, BPB publication, India 4. Computer Networks. 4th edition (2008). Tanenbaum. Pearson Education, India 5. Introduction To Database Management Systems, 1st edition, (2004), AtulKahate, Pearson education, India.

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Course Code: BBt-209 Practical in Chemistry and Biochemistry– II

(1.5 Credit Course) (Total Practical =15) (15x3 hrs.)

Sr.No. Title of Experiment No. of Practical Chemistry 1. Viscometer : To determine viscosity of a given liquid 1 by Ostwald’s viscometer 2 Titration : To determine content of acetic acid in 1 vinegar using NaOH 3 Titration : To determine normality/molarity using acid 2 base volumetric titration 4 Stereochemistry : To study different conformations of 1 biomolecules using models 5 Separation techniques : 2 • To study Separation Techniques like Recrystallization, distillation, sublimation, • To separate plant pigments by TLC Biochemistry 6 Estimations : 2 • Estimation of concentration of protein by Biuret method • Estimation of concentration of protein by Lowery’s method 7 Estimation of concentration of cholesterol 1

8 Melting temperature of nucleic acid : To determine T m 1 of DNA 9 Thin layer chromatography : To separate amino acids 2 and sugars by thin layer chromatography (TLC) 10 Enzyme activity : To find out enzyme activity (amylase) 1

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Course Code: BBt-210 Practical in Plant and Animal sciences II (1.5 Credit Course) Total Practical =15(15x3 Hrs.)

Sr.No. Title of Experiment No. ofPractical

Plant Sciences 1 Study the process of Osmosis and Turgor pressure and 1 determination of Diffusion Pressure Deficit 2 Determination of rate of respiration 1

3 Estimation of chlorophyll content in photosynthesizing and non- 1 photosynthesizing leaf

4 Effect of plant growth regulators on germination of seed 1

5 Studies on economically important plants: Students should 2 prepare herbarium specimens with their uses

Animal Sciences

6 Study and Dissection of Honey Bee , Mounting of Mouth parts, 2 pollen basket, Antenna Cleaner, Sting Apparatus , legs and wings 7 Study of Plasmodium sps. 1 8 Study of Fasciola sp. 1 9 Enumeration of red blood cells using haemocytometer. 1 10 Collection ,Classification and preservation of Insects 2

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Course Code: BBt-211: Practical in Microbiology II and Bioinstrumentation (1.5 Credit Course) (12-15 Practical (15x3 hrs.)

Sr. Title of Experiment No. of No. Practical Microbiology 1 Preparation of Media and Glassware 1 • Bacterial growth media- Nutrient broth, Nutrient agar plates, butts and slants, MacConkey’s agar plates. • Fungal growth media- potato dextrose agar plates 2. Aseptic transfer techniques 1 3. Demonstration of microbes in air, on table surface, finger 1 tips on nutrient media. Cultivation of microorganisms: Isolation and purification of bacteria by steak plate 1 4. technique Enumeration of bacteria by using following 4 techniques : • Spread plate • Serial dilution and Pour plate • Neubauer’s chamber (yeast cells) Bioinstrumentation 1 Working and components of various types of Centrifuges 1 2 Microscopy – Components and working of Bright field 1 compound microscope 3 Functioning and Standardization of pH meter and 1 Preparation of buffers and measurement of pH 4 Separation and identification of amino acids by paper 1 chromatography. 5 Separation and identification of sugars by TLC 1 6 Beer and Lambert’s Law – Components and working of 1 Colorimeter, Spectrophotometer 7 Absorption spectra of DNA melting and protein 1 8 To find out isoelectric point of amino acids 1

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Course Code: BBt-212 Practical in Computer and Biostatistics (1.5 Credit Course) Total Practical= 15(15x3 hrs.)

Sr.No. Title of Experiment No of Practical Computer 1 A:Tutorials operating systems: DOS 1 File handling: copy, rename, delete, type Directory structure: make, rename, move directory 2 Word Processing (Microsoft Word): Creating, Saving & 1 Operating a document, Editing, Inserting, Deleting, Formatting, Moving & Copying Text, Find & Replace, Spell Checker & Grammar Check, Document Enhancement (Borders, Shading, Header, Footer), Printing Document (Page Layout, Margins), 3 Introduction to the use of Wizards & Templates, Working with 1 Graphics (Word Art), Working with Tables & Charts, Inserting

Pictures 4 Spreadsheet Applications (Microsoft Excel): Worksheet Basics: 2 Entering information in a Worksheet, Saving & Opening a Worksheet, Editing, Copying & Moving Data, Inserting, Deleting & Moving Columns & Rows, Clearing. 5 Database Applications (Microsoft Access): Fields, Records, 2 Files, Organization of Files. Access Modes: Updating Records, Querying, Reports, Forms & sub forms. Biostati stics 1 Introduction to MS Excel and use of spreadsheets for data 2 organization and basic mathematics calculations

2 Hypothesis testing using ‘Data analysis tools’: t-test, Chi square 2 test. 3 Analysis of variance 1 4 Correlation and regression analysis of data and graphical 2 representation

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Savitribai Phule Pune University B. Sc. Biotechnology (CBCS Semester Pattern) S. Y. B. Sc. Biotechnology Revised Syllabus w.e.f. June 2020 Semester III Theory Subject Name of Subject Credits Total No. Marks Distribution code of Lectures BBt-301 Cell Biology I 2 Credits 30 50 (35 External +15 Internal

BBt-302 Molecular Biology I 2 Credits 30 50 (35 External +15 Internal

BBt-303 Genetics 2 Credits 30 50 (35 External +15 Internal

BBt-304 Metabolism 2 Credits 30 50 (35 External +15 Internal

BBt-305 Environmental Biotechnology 2 Credits 30 50 (35 External +15 Internal

BBt-306 Bio analytical Techniques 2 Credits 30 50 (35 External +15 Internal

BBt-307 AECC-I (Environment) 2 Credits 30 50 (35 External +15 Internal

BBt-308 AECC-II (Language 2 Credits 30 50 (35 External +15 Internal Communication)

PRACTICALS

BBt-309 Practical in Cell Biology and 2 Credits 15 P 50 (35 External +15 Internal Genetics BBt-310 Practical in Bio analytical 2 Credits 15 P 50 (35 External +15 Internal Techniques BBt-311 Practical in Molecular Biology and 2 Credits 15 P 50 (35 External +15 Internal Environmental Biotechnology

Total Credits (Theory + Practical) 22

Semester IV Theory Subject Name of Subject Credits Total no. of Marks code Lectures BBt-401 Cell Biology II 2 Credits 30 50 (35 External +15 Internal

BBt-402 Molecular Biology II 2 Credits 30 50 (35 External +15 Internal BBt-403 Immunology 2 Credits 30 50 (35 External +15 Internal BBt-404 Animal Development 2 Credits 30 50 (35 External +15 Internal BBt-405 Plant Development 2 Credits 30 50 (35 External +15 Internal BBt-406 Microbial Biotechnology 2 Credits 30 50 (35 External +15 Internal BBt-407 AECC-III (Environment) 2 Credits 30 50 (35 External +15 Internal BBt-408 AECC- IV (Language 2 Credits 30 50 (35 External +15 Internal Communication)

PRACTICALS

BBt-409 Practical in Molecular Biology 2 Credits 15 P 50 (35 External +15 Internal and Microbial Biotechnology BBt-410 Practical in Animal and Plant 2 Credits 15 P 50 (35 External +15 Internal Development BBt-411 Practical in Cell biology and 2 credit 15 P 50 (35 External +15 Internal immunology Total Credits (Theory + Practical) 22

Subject Code: BBt- 301 Subject: Cell Biology I (2 Credit Course) Total Lectures=30

Unit Cell Biology I Topic No of lecture (30) I Introduction To Cell 5  Cell Theory  Types of Cell: i. Prokaryote & Eukaryotic Cell ii. Plant & animal cell iii. Cellular Diversity: Cell structure & related functions II Cell Membrane 6 i Chemical components of biological membranes ii. Organization and Fluid Mosaic Model, membrane as a dynamic entity iii. Functions of cell membrane iv Transport – Active and Passive transport with one example Bulk transport: Exocytosis, endocytosis. III Cell Organelle 12  Structure, components and function of : i. Nucleus, ii. Mitochondria iii. Chloroplast iv. Lysosomes and Vacuoles v. ER & SER vi. Golgi Bodies IV  Cell Junctions 7  Extracellular Matrix  Cytoskeleton & Basal Bodies

Reference books: 1. Molecular Cell Biology. 7th Edition, (2012) Lodish H., Berk A, Kaiser C., KReiger M., Bretscher A., Ploegh H., Angelika Amon A., Matthew P. Scott M.P., W.H. Freeman and Co., USA 2. Molecular Biology of the Cell, 5th Edition (2007)BruceAlberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter. Garland Science, USA 3. Cell Biology, 6th edition, (2010) Gerald Karp. John Wiley & Sons., USA 4. The Cell: A Molecular Approach, 6th edition (2013), Geoffrey M. Cooper, Robert E. Hausman, Sinauer Associates, Inc. USA 5. Karp, G. 2010. Cell and Molecular Biology: Concepts and Experiments. 6th Edition. John Wiley & Sons. Inc. 6. De Robertis, E.D.P. and De Robertis, E.M.F. 2006. Cell and Molecular Biology. 8th edition.Lippincott Williams and Wilkins, Philadelphia. 7. Cooper, G.M. and Hausman, R.E. 2009. The Cell: A Molecular Approach. 5th edition. ASMPress& Sunderland, Washington, D.C.; Sinauer Associates, MA. 8. Becker, W.M., Kleinsmith, L.J., Hardin. J. and Bertoni, G. P. 2009. The World of the Cell. 7th edition. Pearson Benjamin Cummings Publishing, San Francisco. Subject Code: BBt- 302 Subject : Molecular Biology I (2 Credit) Total Lectures=30

Unit Molecular Biology I Topic No of lectures (30) 1 Historical and conceptual Background-  Molecular basis of heredity & Central dogma of Molecular Biology 8  Discovery of DNA as genetic material: Griffith’s experiment, Hershy and Chase warring blender experiment, Miescher to Watson and Crick- historic perspective  Nucleic acids- structure, properties and function, Nucleoside and nucleotide  Structure of DNA: DNA forms; A, B & Z  Salient features of double helix, Chargaff’s rule  Types and structure of RNA : tRNA, rRNA , mRNA and non- coding RNA (miRNA, SiRNA) II Concept and Organization of Genome  Chromosomal organization and structure. 8  Chromatin structure: Euchromatin, heterochromatin (nucleosomes)- histone, non-histone proteins  Organization of DNA: Prokaryotes, Viruses  Organelle DNA – mitochondria and chloroplast DNA  Definition of gene – introns/exons, Regulatory sequences, promoters, enhancers and suppressors III Genetic Code 4  Concept of codon, reading frame, frame shift, Major scientific contributions to decipher genetic code  Properties of genetic code IV Replication of DNA  DNA synthesis: general principles, bidirectional replication, Semiconservative nature of DNA replication, Rolling circle 10 replication  The replication complex: Enzymes involved in DNA replication, Unique aspects of eukaryotic & prokaryotic DNA replication, Fidelity of replication.

Reference Books : 1. Genes X, 10th edition (2009), Benjamin Lewin, Publisher - Jones and Barlett Publishers Inc. USA 2. Molecular Biology of the Gene, 6th Edition (2008), James D. Watson, Tania Baker, 3. Stephen P. Bell, Alexander Gann, Michael Levine, Richard Lodwick, Pearson Education, Inc. and Dorling Kindersley Publishing, Inc. USA 4. Molecular Biology, 5th Edition (2011), Weaver R., Publisher-McGrew Hill Science. USA 5. Fundamentals of Molecular Biology, (2009), Pal J.K. and Saroj Ghaskadbi, Oxford University Press. India 6. Karp, G. (2010). Cell and Molecular Biology: Concepts and Experiments. VI Edition. JohnWiley & Sons. Inc. 7. De Robertis, E.D.P. and De Robertis, E.M.F. (2006). Cell and Molecular Biology.VIII Edition. Lippincott Williams and Wilkins, Philadelphia. 8. Molecular Biology of the Gene (VI Edition.). Cold Spring Harbour Lab. Press, Pearson Pub. 9. . Principles of Gene manipulation and Genomics. - S.B. Primrose and R.M. Twyman. Blackwell Publication 10. Biotechnology - Fundamentals and applications. - S.S. Purohit and S.K. Mathur. Agrobotanica publications.Gene Cloning and DNA analysis. - T.A. Brown. Blackwell Publication. 11. Recombinant DNA - Genes and Genomes. - James D. Watson, Any A candy, RichardM.M, Jan A Witkowski. W.H. Freeman and Company Publication. 12 Genomes: T A Brown, John Wiley & Sons

Subject Code: BBt- 303 Subject : Genetics (2 Credit Course) Total Lectures=30

Sr. No Topic Lectures I  Mendalism and Mendalian Genetics : Genetic basis of Inheritance: Variations,Heridity, Pre- Mendelian Concept, Importance of Genetics 8  Mendelian Genetics: Mendel Experiments  Mendel’s Law: Law of Segregation , Mono Hybrid.  Law Of Independent Assortment- Di Hybrid and Tri Hybrid  Deviation From Mendel’s Law- Partial or Incomplete Dominance, Co Dominance, Epistasis  Penetrance and expressivity-Pleiotropism  Gene Interaction-Modified Di Hybrid Ratio, Multiple Allele II  Chromosomal aberrations and Mutations. : 9 i) Variation in chromosome number – types, dosage compensation and barr bodies (Human). ii) Variation in chromosome structure – types, generation of variation, iii) Mutations Classification and types, molecular basis of mutations, iv) Mutagens and their action, hot spot mutations. III  Sex Determination and Recombination: 9  Linkage and Recombination- Discovery of Linkage, Complete and incomplete linkage, crossing over, Cytological Proof Of Crossing Over, three point cross ,Recombination Frequency and Map Distance  Mechanism of Sex Determination- i) Homo and Heterogametic Theory, ii) Coincidence and interference, iii) X-Linked Inheritance iv) Non Mendelian Inheritance v) Pedigree Analysis IV  Genetic Disorders 4 Sickle Cell Anemia, Hemophilia, Colour Blindness, Albinism, Down’s and Kleinfelter’s Syndrome  Genetic Counseling

Reference Books : 1. Genetics, by Strickberger M W (2006) (Prentice Hall, India) 2. Fundamentals of Genetics. B.D Singh 3. Genetics: analysis of genes and genomes by Hartl DL, Jones EW (2001) –(Jones and Bartlett, Massachusetts) 4. Introduction to genetic analysis by Griffiths AJ, Wessler SR, Carroll SB, Doebley J (2012) – (Freeman & Co, New York) tenth edition. 5. Molecular genetics of bacteria (ASM Press, Washington) Snyder L, Champness W (2007) 6. Textbook of Cell Biology, Genetics, molecular biology , Ecology and Evolution.: P.S. Verma and V.KAgarwal (2001) 7. Principals of Genetics: Robert H. Tamarin, 7th Edition. 8. GENES IX (2006): Benjamin Lewin. 9. Concepts of genetics (2011) : Robert Brooker. 10. Genetics: A Mendelian Approach (2006) :Peter J. Russell

Subject Code: BBt- 304 Subject : Metabolism (2 Credit Course) Total Lectures=30 Units Metabolism Topic Lectures (30) 1 Introduction to Metabolism, 4  ATP energy cycle,  Chemistry of Metabolism: Oxidation–reduction reaction, Group transfer reactions etc,  Concept of Bioenergetics, ATP & Phosphoanhydride bond. 2 Lipid Metabolism – 6  Outline of lipid synthesis,  Catabolism of Fatty acid: beta oxidation, Oxidation of unsaturated fatty acids, Oxidation of odd chain fatty acids, Cholesterol, ketone bodies. 3 Carbohydrate Metabolism – 8  Aerobic & Anaerobic glycolysis, sequence of reactions in glycolysis, regulation in glycolysis,  Pyruvate metabolism, citric acid cycle & its regulation,  glycogenesis, glycogenolysis (sequence of reactions & regulation),  Pentose-phosphate pathway (sequence of reactions & regulation), 4 Amino acid Metabolism – 7  Essential & non essential amino acids, Brief outline of amino acid synthesis,  Catabolism of Amino acids, Transamination,  Urea Cycle,  Metabolic breakdown of individual amino acids – glucogenic & ketogenic amino acids), amino acids as biosynthetic precursors, 5 Nucleotide Metabolism – 5  Biosynthesis of purine & pyrimidine (de novo & salvage pathway); Degradation of purine & pyrimidine.

Reference Books : 1. Conn EE and Stump PK. 2010. Outlines of Biochemistry. 5th Ed. John Wiley Publications. 2. Voet D and Voet JG. 2011. Biochemistry. 4th Ed. John Wiley and Sons, Inc. NY, USA 3. Nelson DL and Cox MM. 2012. Lehninger‟s Principles of Biochemisry, 6th Ed . Macmillan Learning, NY, USA. 4. Berg JM, Tymoczko JL, Stryer L and Gatto GJ. 2002. Biochemistry, 7th Ed. W.H. Freeman and Company, NY, USA 5. Stryer, L., “Biochemsitry”, 4th Edition, W.H. Freeman & Co., 2000. 6. Murray, R.K., etal “Harper’s Biochemistry”, 23rd Edition, Prentice Hall International, 1993.

Subject Code: BBt-305 Subject: Environmental Biotechnology (2 Credit Course) Total Lectures=30

Unit Environmental Biotechnology Topic No. of lectures I  Foundations of Environment and Ecology 2 Environment: Definitions, Components - Atmosphere, Hydrosphere, Lithosphere, Biosphere) and Inter‐relationships, Ecology and Ecosystems: Interconnections in nature II  Ecosystem: Principles and its concepts- Introduction. Characteristics, Components of ecosystem and Types- Aquatic and terrestrial ecosystems, Homeostasis  Biotic Community: Types; Characteristics , Structure 7  Ecological succession: Types, General process of succession. Concept of climax  Energy flow: Food chain, food web, Trophic Levels, Energy efficiency, Energy Budget. III  Threats to Environment and Ecosystem Environmental pollution : Types, sources and consequences of : 5 Air, Water, Soil, Radiation Biotechnological approaches for pollution control IV  Biotechnology in Protection and Restoration of Ecosystem i) Bioremediation: Importance of bioremediation, ii) Use of microorganisms for Bioremediation, 4 iii) Phytoremediation. iv) Bioindicators and detectors V  Environmental Priorities in India- i) Environmental Impact Assessment (EIA case study), 2 ii) Red data book iii) TRAFIC VI  Waste and Disaster Management: i) Biomedical waste management 3 ii) Integrated waste management iii) Hazards to the environment VII  Microbial Biodegradation of : i) Plastic 3 ii) Hydrocarbons iii) Dyes, pesticides/ insecticides and herbicides VIII  Current global environmental issues i) Ozone layer depletion (Montreal protocol), El Nino, ii) Acid rain ‐ causes and effects, iii) Green House Effect, 4 iv) Global climate change v) Greenhouse gases and their impact on the environment vii) Global warming – effect on oceans, coastline and marine ecosystem viii) Impact of global warming on India.

Reference Books 1. Ecology and environment (2005) Sharma PD Rastogi Publication, New Delhi 2. Ecology and environmental biology (2011) Saha T K Books & Allied (p) Ltd, Kolkata 3. Ecology science and practice (2001) Faurie et al Oxford & IBH Publ. Co. Pvg. Ltd, New Delhi 4. Ecology: Principles and Applications (1998) J. L. Chapman, M. J. Reiss Cambridge University Press, Cambridge 5. Environmental Biology (2000) Varma&Agarwal S. Chand Limited, New Delhi 6. Environmental biology and toxicology (2011) Sharma PD Rajpal And Sons Publishing, Delhi 7. Environmental biotechnology(2010) Rana Rastogi Publications, New Delhi 8. Environmental Science (2011) Santra S.C. New Central Book Agency, Kolkata 9. Fundamentals of Ecology (2005) Eugene Pleasants Odum, Gary W. Barrett Brooks and Coel, USA 10. Fundamentals of Ecology (2009) Dash 3rd edition, Tata McGraw-Hill Education, New Delhi 11. Introduction to Environmental Biotechnology (2007) Chattergy PHI Learning Pvt. Ltd, Delhi 12. Textbook of environmental studies for undergraduate courses (2005) Erach Bahrucha Universities Press, Hyderabad 13. Evans & Furlong. Environmental Biotechnology.Theory& Applications. 2nd ed 2011. Wiley-Blackwell. 14. Scragg A. Environmental Microbiology Oxford Univ Press. 2005. 15. Bhattacharya & Banerjee. Environmental Biotechnology. Oxford Univ Press 2008.

Subject Code: BBt- 306 Subject: Bio analytical Techniques (2 credit course) Total Lectures=30

Units Bio analytical Techniques Topic Lectures 1 Introduction: 2 Lab safety, Scientific notation & Units, errors & accuracy in experimentation, Biochemical Calculations, Buffer solutions, Measurement of pH, Calibration of pipettes & balance 2 Spectroscopy: 8  The electromagnetic spectrum  Concept &Measurement of transmittance and absorbance  Beers Lamberts law, molar extinction coefficient, limitations of Beers Lamberts law  Types of spectrometers – UV & visible; Principles, Instrumentation and applications

3 Centrifuge: 6  General principle- sedimentation velocity, sedimentation equilibrium  Types of centrifuges: preparative and analytical centrifugation, differential centrifugation, density gradient, ultracentrifuge  Applications

4 Chromatographic Techniques: 8  Introduction to chromatography, General principles Planar Chromatography Partition chromatography: Thin layer chromatography, paper chromatography  Column chromatography–columns, stationary phases. Packing of columns, application of sample, column development, fraction collection and analysis.  Adsorption chromatography: Ion Exchange Chromatography, Size exclusion chromatography

5 Electrophoresis: 6  General principle, factors affecting electrophoresis voltage, current, resistance, buffer, composition, concentration, pH.  Agarose Gel electrophoresis  SDS-PAGE – Native and denaturing gels,  Applications

Reference Books: 1. Wilson K and Goulding K.H., A biologist’s guide to Principles and Techniques of Practical Biochemistry. 2. Willard and Merrit, Instrumental Methods and Analysis 3. Ewing GW, Instrumental Methods of Chemical analysis. 4. Vogel’s, Text Book of Quantitative Chemical Analysis, 6th Edition, 2004. 4. Raymond P. W. Scott, Techniques and Practice of Chromatography –Vol. 70. 6. Sethi P.D, DilipCharegaonkar, Chromatography –2nd Edition. 7. Hanes, Gel Electrophoresis of Proteins- A Practical Approach, 8. Biophysical chemistry by Upadhyay, Upadhyay and Nath, Himalaya publication house.

Subject Code: BBt-309 Subject: Practical in Cell Biology and Genetics (2 Credit Course) Total Practical= 15 P (15x3hrs.) Sr.no. Topic Practical Section I : Cell Biology Study of Prokaryotic and Eukaryotic cell structure. Study of Electron 1 1 Micrographs of all important cell organelles 2 Micrometry- Measurement of cell size taking different types of cells. 2 3 Staining and Observation of human cheek epithelial cells 1 Isolation and characterization of the following subcellular components, using appropriate samples, by differential centrifugation: i. Nuclei : staining and counting ii. Mitochondria : Succinate Dehydrogenase assay iii. Chloroplast : Microscopic Observation iv. Lysosomes: Acid Phosphatase assay 4 4 Methods of cell lysis and confirmation 1 Section II : Genetics 7. Problem Sets of – 3  Mendalian inheritance and Non Mendalian inheritance Monohybrid cross. Dihybrid cross and Trihybrid cross  Incomplete Dominance, Co-dominance.  Epistasis.  Gene interactions 8 Problems set of Linkage and Pedigree analysis 3  2 point cross. 3 point cross and genetic mapping.  Tetrad analysis: Chromosome interference, analysis of ordered and unordered tetrads.  Sex linked inheritance 9 Studies on karyotype analysis 1

References:

1. Cell biology and genetics lab manual Boğaziçi University Department of Molecular Biology and Genetics 2007-2008 2. Cell Biology Laboratory The University of Toledo Department of Biological Sciences/Natural Sciences and Mathematics 3. Principals of Genetics: Robert H. Tamarin, 7th Edition. 4. Genetics, (2006) Strickberger MW - (Prentice Hall, India.)

Subject Code:BBt-310 Subject : Practical in Bio Analytical Technique and Metabolism (2 Credit Course) Total Practical = 15 P(15x3hrs)

Sr. No. Topic Practical Section I – Biochemical & Biophysical Techniques Quantitative determination of free amino acid content from 1 biological sample. 1 2. The separation of amino acids by ion exchange chromatography 2 3 The separation of dyes by using Gel filtration Chromatography 1 4. SDS-polyacrylamide Slab gel electrophoresis of proteins 2 5. Native gel electrophoresis of proteins 1 Determine λ max of DNA, protein, bromophenol blue solutions 6 using spectrophotometer 1 Section II – Metabolism 7. Estimation of glucose by Benedict’s method 1 8 Estimation of amylase activity from given sample. 1 Estimation of reducing sugar by DNSA (dinitrosalicylic acid) 9 method 1 10 Estimation of alkaline phosphates activity from given sample. 1 Estimation of creatinine in urine or Preparation of lactalbumin 11 from milk or Chlorophyll from plant source 1 12 Estimation of cholesterol by ZAK’s method 1

Reference Books : 1. Jayaram T. 1981. Laboratory manual in Biochemistry, Wiley Estern Ltd. New Delhi. 2. Plummer D. 1988. An Introduction to Practical Biochemistry. 3rd ed. Tata McGraw Hill, New Delhi. 3. Nath RL. 1990. Practical Biochemistry in Clinical Medicine. Academic Pub. 4. Sadasivam S and Manickam A. 1996. Biochemical Methods. 2nd ed. New Age International (P) Ltd. Publisher, New Delhi.

Subject Code: BBt-311 Subject : Practical in Molecular Biology and Environmental Biotechnology (2 Credit Course) Total Practical= 15 P (15x3hrs.)

Sr. No Topic Practical Molecular Biology 1 Reagent and buffer preparation 1 1 Estimation of Nucleic acids by UV-Vis spectrophotometry 1 2 Determination of melting temperature of DNA 1 3 Bacterial DNA isolation by alkaline lysis/ lysozyme method and purity 2 check by using A 260/280. 4 Bacterial DNA agarose gel electrohporesis 1 5 Estimation of DNA by diphenylamine method 1 6 Isolation of RNA from Yeast or Yeast Tablets 1

Environmental Biotechnology 1 Study of pollution indicator plants in terms of morphology and anatomy 1 (any 5-7 plants) 2 Community sampling-By Quadrate method for plants : 2 Percentage of frequency, density, abundance . frequency class diagram and comparison with Raunkiaers frequency chart, Simpson’s index of dominance. 3 Microbial (Bacterial, Algal and Fungal) community estimation 1 4 Study of polluted and unpolluted soil by 1 i) Physical properties : Colour, Texture, Water holding capacity ii) Chemical properties: pH, Organic content, chlorides and Alkalinity 2 5 Testing genotoxicity of water sample : Polluted and non Polluted 1

Reference Books : 1 Introduction to Environmental Biotechnology (2007) Chattergy PHI Learning Pvt. Ltd, Delhi 2 Textbook of environmental studies for undergraduate courses (2005) Erach Bahrucha Universities Press, Hyderabad 3 Scragg A. Environmental Microbiology Oxford Univ Press. (2005). 4 Evans & Furlong. Environmental Biotechnology.Theory & Applications 2nded 2011. Wiley-Blackwell. 5. Lab manual on molecular biology January 2016 Edition: First Edition, Media Associates Delhi-53Editor: Ruhi Dixit, KartikayBisen, Ashwani Kumar, Ashim Borah, Chetan KeswaniISBN: 978-81-909182-7-5

Savitribai Phule Pune University B. Sc. Biotechnology (CBCS Semester Pattern) S. Y. B. Sc. Biotechnology Revised Syllabus w.e.f. June 2020 Semester IV Subject Code: BBt-401 Subject : Cell Biology II (2 Credit Course) Total Lectures=30

Unit Topic No of lecture 1 Cell Cycle 4  Introduction to cell cycle  Phases and Check points of cell cycle 2 Cell Division in Plant & Animal 7  Mitosis  Meiosis 3 Cell Signaling 12  Signaling molecules  Signaling receptors: Cell surface receptors  Autocrine, syncrine & paracrine signaling  G-protein signaling (one example)  Calcium Signaling 4 Cell Death 7  Aging, Apoptosis and Necrosis  Neoplasia  Autophagy  Ferroptosis  Pyroptosis

Reference books: 1. Molecular Cell Biology. 7th Edition, (2012) Lodish H., Berk A, Kaiser C., KReiger M., Bretscher A., Ploegh H., Angelika Amon A., Matthew P. Scott M.P., W.H. Freeman and Co., USA 2. Molecular Biology of the Cell, 5th Edition (2007)BruceAlberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter. Garland Science, USA 3. Cell Biology, 6th edition, (2010) Gerald Karp. John Wiley & Sons., USA 4. The Cell: A Molecular Approach, 6th edition (2013), Geoffrey M. Cooper, Robert E. Hausman, Sinauer Associates, Inc. USA 5. Karp, G. 2010. Cell and Molecular Biology: Concepts and Experiments. 6th Edition. John Wiley & Sons. Inc. 6. De Robertis, E.D.P. and De Robertis, E.M.F. 2006. Cell and Molecular Biology. 8th edition.Lippincott Williams and Wilkins, Philadelphia. 7. Cooper, G.M. and Hausman, R.E. 2009. The Cell: A Molecular Approach. 5th edition. ASM Press& Sunderland, Washington, D.C.; Sinauer Associates, MA. 8. Becker, W.M., Kleinsmith, L.J., Hardin. J. and Bertoni, G. P. 2009. The World of the Cell. 7th edition. Pearson Benjamin Cummings Publishing, San Francisco.

Subject Code: BBt-402 Subject: Molecular Biology II (2 Credit Course) Total Lectures=30

Unit Topic No of lectures I Synthesis of RNA: Transcription:  Transcription in prokaryotes: Prokaryotic RNA polymerase, role of sigma factor, promoter, Initiation, elongation and termination 8  Transcription in Eukaryotes: Eukaryotic RNA polymerases, transcription factors, promoters, enhancers, mechanism of transcription initiation, promoter clearance and elongation RNA splicing and processing: processing of pre-mRNA: 5’ cap formation, polyadenylation, splicing.  Splicing mechanisms, Splicing of tRNA precursors, Splicing of rRNA precursors II Synthesis of Protein: Translation  Structure of ribosome and assembly  Protein Synthesis in Prokaryotes: properties of the prokaryotic Initiator tRNA-fMet, Charging of tRNA, amino acyl tRNA synthetases 10  Protein Synthesis in Eukaryotes: Mechanism of initiation, elongation and termination of polypeptides,  Fidelity of translation, Inhibitors of translation.  Posttranslational modifications of proteins III DNA damage and repair 5  Causes and types of DNA damage  Mechanism of DNA repair: Photo reactivation, base excision repair, nucleotide excision repair, mismatch repair, SOS repair, recombination repair IV Regulation of activity of Genes and Gene products in Prokaryotes: a) General aspects of gene Regulation: inducible and repressible system 7 b) The lactose operon : Catabolite repression c) The Arabinose operon: Positive , negative regulation d) The Tryptophan operon : Regulation by attenuation.

Reference Books : 1. Genes X, 10th edition (2009), Benjamin Lewin, Publisher - Jones and Barlett Publishers Inc. USA 2. Molecular Biology of the Gene, 6th Edition (2008), James D. Watson, Tania Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Lodwick, Pearson Education, Inc. and Dorling Kindersley Publishing, Inc. USA 3. Molecular Biology, 5th Edition (2011), Weaver R., Publisher-McGrew Hill Science.USA 4. Fundamentals of Molecular Biology, (2009), Pal J.K. and SarojGhaskadbi, OxfordUniversity Press. India 5. Karp, G. (2010). Cell and Molecular Biology: Concepts and Experiments. VI Edition. JohnWiley & Sons. Inc. 6. De Robertis, E.D.P. and De Robertis, E.M.F. (2006). Cell and Molecular Biology.VIII Edition. Lippincott Williams and Wilkins, Philadelphia. 7. Molecular Biology of the Gene (VI Edition.). Cold Spring Harbour Lab. Press, Pearson Pub. 8. Principles of Gene manipulation and Genomics. - S.B. Primrose and R.M. Twyman.Blackwell Publication

Subject Code: BBt- 403 Subject : Immunology (2 Credit Course) Total Lectures=30

Unit Topics No. of lectures (30) I Immunology: Basic definitions and fundamentals of the immune 07 system  Definitions - Infection, Invasion, Pathogen, Immunity, Antigen, Antibody  Concept of Host pathogen interaction  Organization of Immune system: a) Structure and function of the cells and tissues of immune system. b) Structure and function of Primary and Secondary lymphoid organs  Types of immunity: a) Innate and Acquired immunity b) Cell mediated and Humoral immunity  Immune Response: Primary and Secondary  Phagocytosis II Components of the immune system: 08  Antigens: Types and properties of an antigen. Factors affecting immunogenicity.  Immunoglobulin: Structure and their types. Properties and function of different Immunoglobulin classes.  Complement system: Components, function and pathways.  Major Histocompatibility Complex: Types, structure and function  Cytokines: Types, properties and their function III Antigen-Antibody Interactions 07  General characteristics of Antigen-Antibody reaction  Concept of Lattice hypothesis and Zone phenomenon  Principle and example of different diagnostic tests: i. Precipitation, Agglutination, Immunodiffusion and Complement fixation test ii. Radioimmunoassay, Immunofluorescence, ELISA iii. Western blotting IV Clinical Immunology 8  Hypersensitivity reactions: Types of Hypersensitivity and clinical manifestation.  Autoimmunity: Mechanisms, Types of autoimmune diseases  Concept of Immunotherapy  Vaccine Technology:  Adjuvant- Properties and role with suitable example  Concept with suitable example of Killed and Live attenuated vaccines, Combined vaccines  Modern Techniques: Concept of Subunit vaccines, Recombinant DNA Vaccines, Conjugate vaccines, Polyvalent vaccines, Monoclonal antibodies, Chimeric antibodies with suitable example

Reference Books 1. Ananthanarayan R and Paniker CKJ. Textbook of Microbiology. University Press Publication. 2. Roitt I. Essential Immunology. 10th Ed. Blackwell Science. 3. Kuby. Immunology. 4th edition. W. H. Freeman & company. 4. SudhaGangal and ShubhangiSontakke, Textbook of basic and clinical immunology, 1st edition (2013), University Press, India

Subject Code: BBt- 404 Subject : Animal Development (2 Credit Course) Total Lectures=30

Unit Topics Lectures

I  History of developmental biology, 2  Model organisms in study of developmental biology: frog, chick, mouse, Drosophila, Sea urchin, Zebra Fish , Caenorhabditis elegans II Reproduction and Development: 9  Basics of gametogenesis: Oogenesis, spermatogenesis and spermiogenesis  Detailed structure of gametes  Fertilization process in sea urchin and mammals  Types of eggs, types and patterns of cleavage  Morphogenetic movements III Gastrulation 8  InAmphioxus, frog, chick, Drosophila up to formation of three germinal layers III Basics of neurulation 2 IV Concept of pattern formation 2  Maternal effect genes and their role in Drosophila pattern formation V  Concept of Stem cells, Progenitor cells, cell lineages, 1 determination, commitment and differentiation, re differentiation and trans-differentiation VI Different types of regeneration with one example of each type 2 VII Theories of ageing 1 VIII  Apoptosis during Embryonic development, intrinsic an 2 extrinsic pathways IX Abnormal development and teratogenesis in animals 1

Reference Books: 1. Development Biology, 9th edition, (2010),Gilbert S.F.(Sinauer Associates, USA) 2. Principles of Development, 5thedition (2018), Wolpert L and Tickle C, Publisher: Oxford University Press, USA. 3. An introduction to embryology, 5th edition, B. I. Balinsky, B.C. Fabian (2012) Cengage Learning India

Subject Code: BBt-405 Subject : Plant Development (2 Credit Course) Total Lectures=30

Unit Topic No. of lectures 1 Plant as a living system 3  Principles and Unique features of plant development  Comparison of Plant and animal development, 2 Plant development at:  Cellular, organ and whole-plant levels 2  Whole plant as an interacting dynamic system 3 Major phases of plant development i) Vegetative development: 3  Zygote to seed embryo to seedling till vegetative maturity  Pattern formation in plants- vegetative ii) Reproductive development:  Shift from vegetative to reproductive phase  Structure of flower 4  Induction- perception of inductive stimuli and subsequent changes,  Pattern formation in plants- flowering 4  Microsporogenesis, development of male gametophyte and male gamete  Megasprogenesis, development of female gametophyte and 5 female gamete  Double fertilization and triple fusion  Development of endosperm 5 Concept of  competence,  Determination,  Commitment, 3  Differentiation,  De-differentiation and  Re-differentiation (partial/ terminal) in vivo with one example each 6 Model systems to understand plant development : 6  Arabidopsis Molecular regulation of development in

Arabidopsis 7 Parthenogenesis-  Haploid , Diploid  Parthenocarpy – Natural , Induced 4  Importance of seed and seed dispersal  Applications of Plant development in Biotechnology

Reference Books: 1. Development Biology, 9th edition, (2010), Gilbert S.F.(Sinauer Associates, USA) 2. Principles of Development, 4th edition (2010), Wolpert L and Tickle C, Publisher: Oxford University Press, USA. 3. Bhojwani S.S. and Bhatnagar S.P.(2009) – Embryology of Angiosperms (Vikas Publ House, New Delhi) 4. Burgess J. (1985) An Introduction to Plant Cell Development (Cambridge Univ Press, UK) 5. Taiz L, Zeiger E (2010) – Plant physiology (Sinauer Associates, USA). 6. Sharma HP (2009) – Plant embryology: Classical and experimental (alpha sci) 7. Steeves TA & Sussex IM (2004) – Patterns in plant development. (Cambridge Univ Press, Cambridge, New York) 8 The molecular life of plants by Jones et al Wiley 9. Biochemistry and Molecular Biology of Plants, 2nd Edition - Bob Buchanan et al Wiley 10. Plant Physiology, Taiz and Zeiger Sixth edition Sinaeur

Subject Code: BBt : 406 Subject : Microbial Biotechnology (2 Credit Course) Total Lectures=30

Unit Topic No. of Lectures I History and Scope of Microbial Biotechnology 1 II Food and Dairy Microbiology 7 A) Food Microbiology  Role of microorganisms in food spoilage, Factors affecting growth of microbes in food (intrinsic and extrinsic factors), Spoilage of meat and poultry, Fruits and vegetable, Canned food.  Principles of Food Preservation.  Methods of preservation Chemical and Physical methods. B) Dairy Microbiology  Milk: Definition, Composition of milk, Normal and abnormal microflora of milk, Sources of contamination of milk, International standards of Milk.  Milk Spoilage- Flavour and colour defects, Stormy fermentation, Sweet curdling, Ropiness.  Grading of milk- Direct and Indirect Tests  Preservation of Milk- Pasteurization and efficiency of pasteurization.  Microbial processing of milk- Curd,Yogurt, Butter, Kefir, Cheese.  Food borne diseases- Food infection and intoxication III Medical Microbiology 7  Medical Microbiology: Normal flora,  Diseases of various systems Tuberculosis, Leprosy, Typhoid, Polio, Syphilis, Tetanus, causative agent, symptoms, morphology, pathogenesis, diagnosis and treatment. IV Microbes in Waste treatment Processes 8  Water borne diseases: Indicators of faecal pollution, Routine bacteriological analysis of water for potability: Presumptive, Confirmed, Completed test, Membrane Filter Technique and Eijkman tests.  Bacteriological standards of drinking water.(WHO, BSI)  Sewage and Industrial waste water: Types of wastes, relevance of COD and BOD determination in analysis of waste water  Methods and principles of treatment of sewage (primary, secondary and tertiary treatment methods  Microbial consortium for effluent treatment. V Applications of Microbial Biotechnology  Geomicrobiology-Ore leaching (methods and examples), MEOR.  Bioweapons  Biofertilizers and Biopesticides and Microbial plant growth 7 Promoters( gibberellins and IAA)  GMOs-Norms and applications  Microbial Sweeteners (Thaumatin, Monelin)  Microbial toxins and their applications  Microbial Polysaccharide production: any 2 examples  Concept of Synthetic Biology and Bio metabolite Production

References Books : 1. Food Microbiology, Frazier & Westhoff, 4th edition, Tata McGraw Hill Publications 2. Modern Food Microbiology, James Jay, 7th edition, Springer Publications 3. Advances in Biotechnology, S. N. Jogdand, Himalaya Publishing House 4. Milk & Milk Products, C. Eckles, 4th edition, Tata McGraw Hill Publications 5. Prescott, S.C. and Dunn, C.G., (1983) Industrial Microbiology, Reed G. AVI tech books 6. General Microbiology - Stanier R.Y., 5th edition, ( 1987)Macmillan Publication, UK. 7. Fundamental Principles Of Bacteriology, Salle,A.J.,McGraw Hill Company, New York 8. Tortora, G.J., Funke, B.R., Case, C.L, 1992. Microbiology: An introduction 5th Edition, Benjamin Pub. Co. NY 9. Davis B.D., Delbacco, 1990 Microbiology 4th edition, J.B. Lippincott Co. NY 10. Wolfgang K. Joklik, 1992, Zinsser Microbiology 20th Edition, McGraw-Hill Professional Publishers 11. Dey, N.C and Dey, TK. 1988, Medical Bacteriology, Allied Agency, Calcutta, 17thEdition 12. Ananthnarayana, R. and C.E, Jayaram Panikar, 1996 Text book of microbiology, 5th edition, Orient Longman. .Park and Park, Preventive and Social medicine. 2013, Publisher: Banarsidas Bhanot, Jabalpur 13. Ingraham J.L. and Ingraham C.A. (2004) Introduction to Microbiology. 3nd Edition. Thomson Brooks / Cole. 14. Madigan M.T, Martinko J.M. (2006) Brock’s Biology of Microorganisms. 11th Edition. Pearson Education Inc. 15. Salle A.J. (1971) Fundamental Principles of Bacteriology. 7th Edition. Tata MacGraw Publishing Co. 16. Standard Methods for the Examination of Water and Wastewater (2005) 21st edition, Publication of the American Public Health Association (APHA), the American Water Works Association (AWWA), and the Water Environment Federation (WEF); edited by Andrew D. Eaton, Mary Ann H. Franson.Satyanarayan, U. Biotechnology(2008), Books and Allied Ltd.Kolkata 17. Sing, B. D. Biotechnology,(2010), Kalyani Publishers, New Delhi

Subject Code:BBt-409 Subject : Practicals in Molecular Biology and Microbial Biotechnology (2 Credit Course) Total Practical= 15 P (15x3hrs.)

Sr. No. Title of Experiment No. of Practical Molecular Biology 1 Preparation of Reagents 1 2 Isolation of Eukaryotic( Plant) DNA and analysis by 2 Agarose gel electrophoresis 3 Isolation of Eukaryotic( Animal) DNA and analysis by 2 Agarose gel electrophoresis 4 Estmation of RNA by Orcinol method 1 5 Estimation of proteins by Bradford method 1 Microbial Biotechnology 6 Food and Dairy Microbiology: 3 a. Isolation and identification (Genus level) of spoilage causing microorganisms from spoiled foods b. Grading of raw milk (Dye reduction test, DMC) c. Determination of efficiency of Pasteurization by phosphatase test 7 Study of Normal flora of humans (Skin and oral cavity) 1 8 Assessment of potability of water: 3 a. Presumptive b. Confirmed and c. Completed test. d. Eijkman’s teste. e. IMViC tests 9 Visit to Dairy/ Effluent treatment plant / Sewage Treatment 1 /Biofertilizer plant/ any other relevant industry and report writing.

Reference books : 1 Lab manual on molecular biology January 2016 Edition: First Edition, Media Associates Delhi-53Editor: Ruhi Dixit, KartikayBisen, Ashwani Kumar, Ashim Borah, Chetan KeswaniISBN: 978-81-909182-7-5 2 Modern Food Microbiology, James Jay, 7th edition, Springer Publications 3 Madigan M.T, Martinko J.M. (2006) Brock’s Biology of Microorganisms. 11th Edition. Pearson Education Inc 4 Ananthnarayana, R. and C.E, Jayaram Panikar, 1996 Text book of microbiology, 5th edition, Orient Longman. .Park and Park, Preventive and Social medicine. 2013, Publisher: Banarsidas Bhanot, Jabalpur

Subject Code: BBt-410 Subject : Practicals in Animal & Plant development 2 Credit Course (Total Practical= 15 P (15x3hrs.)

Sr. no. Topic of practical Practical No Animal development 1 Study of frog development, observation of different development 1 stages (Permanent slides or fixed embryos) 2 Study of amphioxus development, observation different development 1 stages (Permanent slides) 3 Study of staging & staining of Chick embryos (24 h, 48h, 72 h) 2 4 Effect of teratogen on development of chick embryo by window 2 technique 5 Demonstration of any one technique of chick embryo culturing 1 6 Demonstration of regeneration in Hydra 1

Plant Development 1 Methods of studying plant development (any suitable plant material) 1 a) Dissection b) Sectioning c) Staining d ) Mounting 2 Study of apices and meristem- 2 RAM, SAM, florally induced meristem 3 Microsporogenesis- anther squash technique 1 4 Development of male and female gametophytes 1 5 Developmental stages during plant embryogenesis in dicots and 1 monocots 6 Dissection of seed and excision of young embryo and endosperm (Two 1 dicotyledon and Two monocotyledon example)

Reference Books: 1. Burgess J. (1985) An Introduction to Plant Cell Development (Cambridge Univ Press, UK) 2. Taiz L, Zeiger E (2010) – Plant physiology (Sinauer Associates, USA). 3. Sharma HP (2009) – Plant embryology: Classical and experimental (alpha sci) 4. Development Biology, 9thedition, (2010), Gilbert S.F.(Sinauer Associates, USA) 5. Principles of Development, 5thedition (2018), Wolpert L and Tickle C, Publisher: Oxford University Press, USA. 6. An introduction to embryology, 5th edition, B. I. Balinsky, B.C. Fabian (2012) Cengage Learning India

Subject Code: BBt-411 Subject :Practical in Cell Biology and Immunology (2 Credit Course) Total Practical= 15 P (15x3hrs.)

Unit Topic Practical Section I : Cell Biology 1 Study of different stages of Mitosis 2 2. Effect of colchicine on mitosis 1 3 Study of different stages of Meiosis in Tradescantia 2 4 Study of polytene chromosomes (Drosophila/Chironomus larva) 2 Section II – Immunology 5. Determination of blood group using slide agglutination 1 Reaction 6 To determine total leukocyte of given blood sample 1 7 Determine Differential count of given blood sample 1 Immunodiffusuion: a) Single Radial immunodiffusion 8 b) Ouchterlony double diffusion technique (pattern of identity) 2 Determination of antibody titer by tube agglutination test (Widal 9 Test) 2 10 Detection of presence of antigen by qualitative ELISA(Dot ELISA) 1

Reference Books : 1 Cell biology and genetics lab manual Boğaziçi University Department of Molecular Biology and Genetics 2007-2008 2 Cell Biology Laboratory The University of Toledo Department of Biological Sciences/Natural Sciences and Mathematics 3 Ananthanarayan R and Paniker CKJ. Textbook of Microbiology. University Press Publication. 4 Roitt I. Essential Immunology. 10th Ed. Blackwell Science. 5 Kuby. Immunology. 4th edition. W. H. Freeman & company.

University of Pune

Three Year B. Sc. Degree Course in

BIOTECHNOLOGY

T.Y.B.S C. BIOTECHNOLOGY

Syllabus

(To be implemented from Academic Year 2015-16)

Course structure: First Year B.Sc. Biotechnology

Course Code and Course Name Theory/ Marks Lecture/ Practical Practical Bb- 101 Fundamentals of Chemistry Theory 100 90L

Bb- 102 Fundamentals of Physics Theory 100 90L

Bb- 103 Basics of plant and animal sciences Theory 100 90L

Bb- 104 Mathematics & Statistical Methods for Biologists Theory 100 90L

Bb- 105 Fundamentals of Biological Chemistry Theory 100 90L

Bb- 106 Biophysics & Instrumentation Theory 100 90L

Bb- 107 Microbiology Theory 100 90L

Bb- 108 Computers and application Theory 100 90L

Bb- 109 Practicals in Chemistry and Biochemistry Practical 100 30 P

Bb- 110 Practicals in Physics, Biophysics and Instrumentation Practical 100 30 P

Bb- 111 Practicals in Biosciences Practical 100 30 P

Bb- 112 Quantitative Methods in Biology Practical 100 30 P

Course structure: Second Year B.Sc. Biotechnology

Course Code and Course Name Theory/ Marks Lecture/ Practical Practical

Semester I

Bb- 211 A Genetics & Theory 75 45L B Immunology 25 15L Bb- 212 Cell Biology Theory 100 60L Bb- 213 Environmental Biology and Biotechnology Theory 100 60L Bb- 214 Practicals in Environmental Biotechnology Practical 100 30P Bb- 215 Practicals in Cell Biology & Genetics Practical 100 30P

Semester II

Bb- 221 Molecular biology Theory 100 60L Bb- 222 Animal and Plant development Theory 100 60 Bb- 223 Scientific writing and communication Theory 50 30L Bb- 224 Metabolic Pathways Theory 50 30L Bb- 225 Practicals in Molecular biology Practical 100 30 P Bb-226 Practicals in Developmental biology Practical 100 30 P

Course structure: Third Year B.Sc. Biotechnology

Course Code and Course Name Theory/ Marks Lecture/ Practical Practical

Semester I

Bb-331 Microbial Biotechnology Theory 100 60L Bb-332 Plant and animal tissue culture Theory 100 60L Bb- 333 Biodiversity & Systematics Theory 100 60L Bb-334 Practicals in Tissue culture Practical 100 30P Bb- 335 A Practicals in Microbial biotechnology Practical 75 30P B Practicals in Field studies and report writing 25

Semester II

Bb-341 Large scale Manufacturing process Theory 100 60L Bb - 342 Biochemical and biophysical techniques Theory 100 60L Bb - 343 Practicals in Recombinant DNA Technology Theory 100 60L Bb -344 Techniques in Genetic Engineering Practical 100 30P Bb- 345 A Practicals of large scale manufacturing process Practical 50 30P B Practicals in biochemical and Biophysical techniques 50

Bb-331: Microbial biotechnology (60L)

Sr. No. Topic Lecture

1 Microbial Biotechnology - History and Scope 1

2 a. Microbial Growth Kinetics: Batch (Monod’s equation), Fed Batch 8 and continuous culture. b. Yield Coefficients: (Definition and Concept) Yx/s, Yp/s, Y p/x, Y ATP , Respiratory quotient (RQ)

c. Grow Growth in relation to product formation (Growth linked and non- growthlinked products) d. Classification of microorganisms on the basis of their environmental requirements such as: pH, Temperature, oxygen, salt , sugar, moisture and their molecular adaptations to extreme environments. 3 Immobilization of enzymes : Methods, Properties, Applications , Advantages and 4 Disadvantages of Immobilization, Biosensors and Biochips-Types and applications

4 Medical Microbiology : No rmal flora, diseases of various 8 systems(Tuberculosis,SARS,Typhoid,Polio,Syphilis,Tetanus,Anthrax,Leprosy) ,causative agent, symptoms, morphology, pathogenesis, diagnosis & treatment

5 Food and Dairy Microbiology 20

A) Food Microbiology : a. Food as a substrate (Intrinsic and extrinsic factors) b. Microbiological spoilages and sources of microorganisms, Spoilage of foods- Meat and poultry products, bread, fruits and vegetables, eggs, canned foods. c. Food Preservation: d. General principles and methods of food preservation ,Use of Chemicals (Added and Developed Preservatives) Canning, Radiations, Low and High Temperature e. Concept of TDP, TDT, D, F and Z values. f. HACCP (Hazard Analysis and Critical Control Points) g. Different types of fermented foods produced from microorganisms- Idli, Dhokla, Soysauce, Sauerkraut h. B) Dairy Microbiology : a. Definitions of milk and milk products, composition of milk and factors affecting composition b. Sources of contamination of milk c. Flavour and Colour defects, Sweet curdling, and Stormy fermentation, Ropiness d. Preservation- Pasteurization (LTH, HTST, UHT), phosphatase test. e. Grading of milk (Direct and indirect tests), Brucella ring and Mastitis tes ts f. Fermented dairy foods-Curd, yoghurt, kefir, butter and cheese and their spoilages

C) Food sanitation and Food borne diseases: Intoxications and Infections (Staphylococcus aureus, Clostridium botulinum Salmonella , pathogenic

E. coli, Aspergillus flavus )

6 Water and Waste water: 15

i) Water : Indicators of faecal pollution, Routine bacteriological analysis of water for potability: Presumptive, Confirmed, Completed test, Membrane Filter Technique and Eijkman tests. Bacteriological standards of drinking water.(WHO, BSI) ii) Drinking Water purification methods: Sedimentation, coagulation, flocculation, Filtration (Slow sand and Rapid Sand),disinfection.

ii) Sewage and Industrial waste water : Types of wastes, relevance of COD and BOD determination in analysis of waste water,

iii) Methods and principles of treatment of sewage (primary, secondary and tertiary treatment methods- Effluent treatment (Distillery and Textile) Microbial consortium for effluent treatment.

6. Applications of microorganisms: 12

i) Geomicrobiology-Ore leaching (methods and examples), MEOR, Microorganisms in extraterrestrial life studies ii) Alcoholic beverages: Wine, Beer iii) Biofertilizers and Biopesticides and Microbial plant growth Promoters( gibbe rellins and IAA) iv) GMOs-Norms and applications v) Microbial Sweeteners (Thaumatin, Monelin) , Flavour enhancers and microbial toxin production and their applications vi) Microbial Polysaccharide production: Xanthan, Dextran, Alginate, Scleroglucan, Gellan, Pullulan, Curdlan

vii) Bioplastic-Biopol, Microbial rubber and adhesive polymers

viii ) Biotransfrmations-Indigo and glycerol to dihydroxy acetone

ix) Biotechnology biosafety –Norms and measures

References:

1. Microbiology – 5th Edition (1993), Pelczar M.J., Chan E.C.S., Krieg N.R., The McGraw Hill Companies Inc. NY, USA 2. General Microbiology - Stanier R.Y., 5th edition, ( 1987)Macmillan Publication, UK. 3. Food Microbiology –Frazier W. C., 4 th edition (2008) The McGraw Hill Companies Inc. NY, USA

Bb-332 Plant and Animal Tissue Culture (60L)

Sr. No. Topic Lecture A. Plant Tissue Culture:

1 Con cepts of Cell th eory & Ce llular totip otency, Landmarks in plant tissue 1 culture. 2 Infrastructure & Organization of plant tissue culture laboratory – General & 2 ase ptic labo ratory, di ff erent wo rk areas , equipm ents & in struments requi red. 3 Aseptic techniques – Washing & preparation of glassware, packing & 2 sterilization, media sterilization, surface sterilization, aseptic work station, precaut ions to maint ain aseptic cond ition s. 4 Culture Media – Nutritional requirements of the explants, PGRs and their in 3 vitro rol es , media p reparatio n. 5 ‘Explant’ for plant tissue culture 4 Response of explants in vitro– Dedifferentiation and redifferentiation a) callus formation b) organogenesis ( direct and indirect ) c) embryogenesis ( di rect and indi rect ) 6 Callus culture technique – Introduction, principle, , factors affecting, 2 Morphology & int ernal structu re 7 Suspension culture technique – Introduction, principle, 2 types, synchronization 8 Organ culture technique – Introduction, principle, factors affecting w.r.t. 2 root tip cul ture, leaf cultu re, sho ot tip & meristem cultu re, 9 Anther & pollen culture – Introduction, 2 principle, , factors affecting, 10 Ovary, ovule, embryo and endosperm culture. 2 11 Pr ot opl as t –isol ation , cultu re and fusion 3 12 Parameters to assess growth and development in vitro 1 13 Som aclonal variation – Introdu ction, terminology, origin 1 14 Applications of plant tissue culture 3 B. Animal Tissue culture

1 a. Introduction: Comparison with bacterial culture 5 b. In vivo verses in vitro growth conditions for cells of multicellular organisms c. Concept of monolayer, suspension, histotypic/ organotypic, organ culture d. Maintenance of aseptic conditions 2 Equipment and infrastructure 4 a. Laboratory design b. Instruments used in ATC c. Labware: TC flasks . 3 Nutrition & Physiology 4 a. Rationale behind medium formulation with examples b. Advantages and disadvantages of serum. Serum free media c. Balanced salt solutions, 4 Primary cell culture 3 a. Source selection, different methods of establishing primary cell culture b. Special reference to fibroblast culture and lymphocyte culture 5 Cell lines 6 a. Evolution of cell line b. Finite and transformed cell lines c. Mammalian and insect cell line growth conditions d. Subculture 6 Characterization of cell lines 4 a. Need for characterization b. Karyotyping, biochemical & genetic characterization of cell lines. 7 Cell storage and distribution 2 a. Cryopreservation b. Cell repositories 8 Application of Animal cell cultures. 2

Reference Books:

1. R. Ian Freshney. Culture of animal cells, 6th Edition, 2010. A John Wiley & Sons, Inc., USA 2. R.W.Masters. Animal Cell Culture- Practical Approach, 3 rd Edithion,2000, Oxford University Press. USA 3. Principles And Practice Of Animals Tissue Culture, Sudha Gangal, 2 nd edition, ( ), University Press, India 4. Razdan M.K. (2009) - Introduction to Plant Tissue culture (Oxford & IBH Publ, New Delhi) 5. Bhojwani S.S. & Razdan M.K. (1996) - Plant Tissue Culture : Theory & Practice (Elsevier, New Delhi) 6. Jha TB & Ghosh B (2007) – Plant tissue culture: Basic and applied (Universities Press, Hyderabad)

Bb-333 Biodiversity and Systematics (60L)

Sr. No. Topic Lectures I Biodiversity 45 1 Understanding Biodiversity 13 Concept of Biodiversity, 7 1.1 Definitions, Taxonomic, ecological and genetic perspectives of biodiversity, Change in Biodiversity over time and space, Magnitude. Ecosystem diversity, 6 Species diversity, 1.2 Genetic diversity, Indices of biodiversity analysis. ( Plant, Animal and Microbial) 2 Biodiversity in Ecosystems 6 2.1 Biomes of the world 2 2.2 Biodiversity in India: Habitats, Niche 2 2.3 Behaviour patterns of animals- Habits 2 3 Population Interactions 10 3.1 Population growth forms, age class distribution and carrying capacity 2 3.2 Population density, abundance and richness 3 3.3 Population Structure and interactions 2 Mathematical modeling- of Logistic growth, competition and prey- 3 3.4 predator dynamics 4 Conservation of Biodiversity 9 4.1 Status of biodiversity and need for conservations 2 4.2 Strategies for Conservation, methods for conservation- Ex situ and In situ 4 4.3 Conservation policies, laws and organization- 3 Rio Conference, Earth Summit, Conservation efforts in India- Governmental and NGOs 5 Biodiversity Utilization 7 5.1 Management, documentation and databases of biodiversity 2 ( Biodiversity Informatics) 5.2 Domesticated animal and agricultural diversity 3 5.3 Socio- economic importance of biodiversity 2 II Systematics 15 6 Biological Systematics 7 6.1 Concept of species and variation 4 6.2 Need for taxonomy and nomenclature 2 6.3 Introduction to classification systems 1 7 Important Tools and techniques in Systematics 8 7.1 Techniques in morphological, histological, embryology and anatomical 4 analysis 7.2 Molecular tools in taxonomy 4

Reference Books:

1. A Text Book of the Plant Geography Of India (1983) Bharucha F R OUP India 2. An Advanced Text Book On- Biodiversity- Principle And Practices (2004) Krishnamurthy K V Oxford and IBH Publishing, Delhi 3. Biological Systematics: Principles And Applications (2002) Randall T. Schuh Cornell University Press, USA 4. Biotechnology Applications (2009) C S K Mishra I K Interntional Pvt Ltd, New Delhi 5. Communities And Ecosystems (1975) Whittaker R H Macmillan Pvt Ltd, NewYork 6. Ecology: Principles and Applications (1998) J. L. Chapman, M. J. Reiss Cambridge University Press, Cambridge 7. Environmental biotechnology(2010) Rana Rastogi Publications, Meerut

8. Environmental Science (2011) Santra S.C. New Central Book Agency, Kolkata

9. Evolution (2005) Douglas J. Futuyma Sinauer Associates, Inc. Publishers, Sunderland 10. Fundamentals of Ecology (2009) Dash 3rd edition, Tata McGraw-Hill Education, New Delhi 11. Fundamentals of Molecular Biology (2009) Pal & Ghaskadbi Oxford University Press, New Delhi 12. Fundamentals of Plant Systematics (1986) Radford A E Harper and Row, New York 13. Genetic Engineering: Principles And Practice (1996) Sandhya Mitra Macmillan Pvt Ltd India, Bangalore 14. Genetics Of Populations (2011) Philip Hedrick Jones & Bartlett Learning, Burlington, MA 15. Global Biodiversity Strategies (1992) Courrier Kathleen (Editor) World Resource Institute,USA 16. Introduction To Microbiology (2004) John and Catherin Ingraham Brooks/Cole Pub, USA 17. Living In The Environment (2012) G. Tyler Miller, Jr., Scott E. Spoolman Brooks and Coel, CengageBrain learning, USA 18. Mathematical Biology (1989) Murray J D Springer, New York 19. Modern Text Book of Zoology-Vertebrates (2010) Kotpal R E Rastogi Publication, New Delhi 20. Phylogenetic Systematics (1999) W Hennings, D Dwight Davis, R Zangerl University of Illinois Press, Champaign, IL

21. Plant Systematics (2010) Michael G. Simpson Academic Press, Salt lake city, UT, USA 22. Plant Systematics- A Phylogenetic Approach (2008) Walter S Judd Sinauer Associates, Sunderland 23. Population Genetics (2011) Hamilton M Wiley Publisher, New Delhi 24. Principles Of Gene Manipulation And Genomics (2009) S. Primrose and R. Twyman Blackwell Publishing House, New Jersey 25. Systematics And Biogeography (2010) David M. Williams , Malte C. Ebach Springer, New York 26. Systematics And The Origin Of Species, From The Viewpoint Of A Zoologist (1942) Meyer E Harvard University Press, Cambridge, MA 27. Systematics: A Course Of Lectures (2012) Ward C. Wheeler Wiley-Blackwell Publishing, New Jersey 28. Text Book of Biodiversity (2003) Krishnamurthy K V Science Publishers, Jodhpur 29. http://www.earthsummit.info/ 30. http://www.un.org/geninfo/bp/enviro.html

Bb-334 Practicals in Tissue Culture (30P)

Sr. No. Topic Practical (Total 30 P) 1 ATC laboratory design and equipment used in ATC 1 2 Familiarity to Aseptic conditions 2 3 Animal cell culture media preparation, sterilization, washing, packing 2 4 Observation of cells in culture – Principles & practice 1 5 Isolation of Lymphocyte for culture: Ficoll -hypaque density gradient separation 2 6. Maintenance of cell lines (Sp2O) 3 7 Cell staining methods viz. Giemsa 1 8 Viable cell count and growth studies 2 9 PTC Laboratory : organization of facility and equipment 1 10 Asept ic manipul ati on – was hin g, ca pp ing, packing & 2 sterilization, laminar flow operation and safety precautions 11 Stock solutions & media preparation 2 12 Callus culture technique-Initiation of culture, callus morphology & internal 2 structure 13 Suspension culture technique–Initiation of culture, sub culture and growth 2 measurement 14 Effect of plant growth regulators on in vitro response of explants. 2 15 Initiation of shoot tip & axillary bud culture 2 16 Anther and/ embryo culture 2

BT 335 a Practicals in Microbial Biotechnology

Sr. No. Practical Title Practicals (23P) 1 Study of Growth Curve and Generation time of Bacteria/ Yeast using 1 turbidometry 2 Effect of Environmental factors on growth of bacteria (pH, Temperature, 2 salt and Sugar) 3 Immobilization of whole yeast cells/ enzyme by suitable method and 2 determination of stability of immobilized enzyme. 4 Isolation and identification (Genus level) of spoilage causing 2 microorganisms from spoiled foods. 5 Detection of Aflatoxin in foods 1 6 Isolation and identification of starter organisms from Idli batter/ Dahi 2 7 Grading of raw milk (Dye reduction test, DMC) 2 8 Determination of efficiency of Pasteurization by quantitative phosphatase 1 test. 9 Assessment of potability of water 3 a.Presumptive b.Confirmed and c.Completed test. d. Eijkman’s test e. IMViC tests

10 Preparation and Efficiency testing of Biofertilizer/ Biopesticide. 2 11 Production of microbial Polysaccharide. 3 12 Visit to Dairy/ Effluent treatment plant / Sewage Treatment plant. 2

Bb-335 b Practicals in F ield studies (7P)

One day field visit to local forest ecosystem to conduct following Practicals-

Quadrate/transact methods for plant diversity analysis Point count for bird/butterfly/insect diversity Calculation of species diversity, richness and abundance from the field visit data Report writing of the field visit with photo documentation.

Bb341 Large Scale Manufacturing Process (60L)

Sr.No. Topic Lectures 1 a. Fermentation - Definition, Historical perspective, Lay out of a typical fermentation unit. 4 b. Definition and Concept of Bioprocess Engineering, Various components of Bioprocess. c. Types of fermentations: Submerged, Surface, Solid State, Dual, Batch, Continuous, Fed Batch. 2 a. Screening - Definition and Objectives: 5 Primary and Secondary Screening b. Strain Improvement : Objectives, Methods for strain improvement with examples (mutant selection, mutants with altered permeability, auxotrophic mutants, analogue resistant DNA technology) c. Microbes of industrial importance, Culture collection centers of industrially important microorganisms. d. Inoculum build up for Industrial fermentations : Bacteria and Fungi 3 a. Bioreactor Design : Characteristics of an ideal Fermenter, 8 Construction material used, surface treatment of material Design of a typical Batch Fermenter Aerator and Agitator- types, Baffles, Seals and valves used, steam traps. Additional accessories and peripherals. b. Different designs of bioreactors : Mechanically agitated and non-mechanically agitated • Bubble column • Bubble Cap • Air Lift (internal and external loop) • Packed Bed reactor • Fluidized bed reactor • Pressure cycle • Animal and Plant cell Bioreactors 4 Media components and optimization : 5 Media used for large scale production: Carbon sources: Cane and Beet molasses, Malt, Corn, Starch, oils, hydrocarbons, alcohols. Nitrogen sources : Corn steep liquor, Soybean meal, peanut meal Buffers Chelators Water Precursors, Inhibitors, Inducers Antifoams- types, mode of action, advantages and disadvantages. Inoculum and Production media Media for animal cell culture. Medium Optimization • Classical Approach • Plackett and Burman design • Response Surface Methodology (RSM) 5 Air and Media Sterilization : Concept of Aseptic Operations and 4 Containment. Air sterilization : Principles, Mechanism of capture of particles in air, Fixed (absolute) and non-fixed pore (depth) filters, Filter sterilization of air, Theory of depth filter, Validation of air filters.

Media Sterilization : Principles, Thermal Death time, Decimal reduction time, Del factor, Indicator organism, Designing of sterilization cycle using thermal death of microbes, loss of nutrient quality during sterilization, Equipments used in sterilization: Batch and Continuous, Use of Non sterilized media. 6 a. Measurement and Control of different Bioprocess parameters : 10 (Physical and Chemical Parameters): Temperature, pH, Dissolved oxygen, Microbial biomass, Fluid flow, Pressure, Weight, In let and exit gas, foam, CO2, Use of computers in Bioprocess b. Oxygen Uptake rate, Oxygen transfer rate, Concept and importance of KLa, Determination of KLa values, Different rheologies of fermentation media, Factors affecting KLa values c. Scale Up and Scale down. 7 Methods and equipments used in Downstream processing: 8 a. Definition: Unit operations and downstream processing, General strategy of product recovery. b. Precipitation (Agents used :Salts, Organic solvents, polyelectrolytes, acids and bases) c. Filtration (Plate Frame. Rotary Vacuum, Filter Aids, Flocculating agents) d. Centrifugation (types used in Industry: basket, tubular bowl, Scroll, multichamber, disc bowl) e. Cell Disruption (Physico – mechanical and chemical methods). f. Liquid- Liquid extraction(Principle, Co and counter current extraction) g. Chromatography ( one example each of use of Adsorption, Ion exchange, Gel and Affinity in product recovery can be explained along with manufacturing process of antibiotics, enzymes and vaccines). h. Membrane Processes (Ultra filtration, Reverse Osmosis) i. Drying (Drum and Spray Drying) j. Whole broth Processing. 8 Large Scale Manufacturing Process of: 10 a. Biomass based Products: Baker’s Yeast, Single cell Protein b. Enzymes: Amylase, Restriction Enzymes c. Antibiotics: Penicillin, Streptomycin d. Vitamins: B12, Riboflavin e. Amino acids: Glutamic acid, Lysine f. Vaccines: DPT, Polio g. Biotransformation Products : Steroids, Ascorbic acid 9 a. Concept of Good Manufacturing Practices(GMP),Standard Operating 4 Practices(SOP) b. Quality Control and Quality Assurance (Definition, Functions and Responsibilities) c. Tests Used for Quality Assurance of finished product: i. Sterility Testing ii. Pyrogen testing iii. Bacterial endotoxin (LAL test) iv. Ames Test. 10 Bioprocess Economics : Basic objectives in developing economically 2 viable process, Market Potential, Fixed and Variable costs, Depreciation, Amortization, and Selection of Pricing.

Reference Books:

1. Principles of Fermentation Technology, 2 nd edition, (2003), Whittaker & Stan bury, Butterworth-Heinemann, An imprint of Elsevier Science, UK 2. Practical fermentation technology, 1 st edition, (2008), BRIAN MCNEIL & LINDA M. HARVEY, John Wiley & Sons, USA 3. Industrial Microbiology: An Introduction, 1 st edition, (2007), Waits and Morgan, Blackwell Science Ltd USA. 4. Morden Industrial Microbiology and biotechnology, 1st edition, (2007), Nduka Okafor, Science Publishers, USA 5. Industrial Biotechnology, 1 st edition, (2009), Abilasha Mathuriya, Ane books Pvt.Ltd, India

Bb-342 Biochemical & Biophysical Techniques

Sr. No. Topic Lecture 1 Introduction, Lab safety, Scientific notation & Units, errors & 10 accuracy in experimentation, understanding of concentration of solutions, Strong acids and bases, weak acids and bases, polyprotic acids, buffers, biological buffers, pH metry. 2 Microscop y: Introduction to different types of microscopy, con 10 focal microscopy, phase contrast, fluorescence microscopy, inverted microscopy. preparation of specimens for different types of microscopy 3 Spectrophotometry: Electromagmantic radiations(dual natur e) 10 wavelength, frequency, properties of Electromagnetic radiation, electromagnetic spectra, light absorption and excitations of electrons. Beer-Lambert’s Law, UV-visible spectroscopy (chromophores in proteins), instrumentation(spectrophotometer and colorimeter), molecular extinction coefficient, fluorescence spectroscopy 4 Centrifugation: Introduction, basic principle of sedimatation, 10 angular velocity & centrifugal field, g & RPM conversion - preparative & analytical centrifugation, [ultracentrifuge], density gradient centrifugation, rotor types , care maintenance & safety. 5 Chromatography: Introduction, principles - distribution 10 coefficient, RF value Types of chromatographs a) Thin layer, HPTLC, paper chromatography b) Column chromatography – gel filtration, ion-exchange, affinity chromatography, c) adsorption chromatography 6 Electrophoresis: Introduction , Theory, principles, supporting 10 matrices, capillary electrophoresis. Electrophoresis of proteins- SDS, native, activity staining Nucleic acids – Agarose, Pulse field gel electrophoresis.

Reference Books:

1. Biophysics, an introduction. 1 st edition. (2002) Cotteril R. John Willey and Sons Ltd., USA 2. Biophysics. 1 st edition (2002), Pattabhi V and Gautham N. Kluwer Academic Publisher, USA. 3. Textbook of optics and atomic physics – P.P. Khandelwal (Himlaya Publishing House.) 4. Instrumentation measurements and analysis – 2nd edition (2003). Nakra and Choudhari, Tata Mc Graw Hill, India. 5. Nuclear Physics: An Introduction. 2 nd edition (2011). S. B. Patel. Anshan Publication, India

Bb 343: Recombinant DNA Technology (60L)

Sr. No Topic Lecture 1 Milestones of genetic engineering- Historical perspective. 2 Recombinant DNA Technology- Introduction 2 Molecular tools and applications -restriction enzymes, 5 ligases, polymerases, alkaline phosphatase. 3 Gene cloning Vehicles- vector: plasmids, cosmids, phage vectors- λ and M13, 10 YACs, BACs, expression vectors, Agrobacterial vectors ho st – propert ies of ho st 4 Transformation- techniques of introducing DNA in bacteria, animal and plant 8 cells Selection of transformants & characterization 5 Nucleic acid purification, yield, yield analysis, plasmid characterization, 5 isolation strategies. 6 DNA sequencing techniques– Maxam-Gilbert’s method, Sanger’s Dideoxy 4 method, Automated DNA sequencing, Next generation sequencing 7 Restriction enzyme digestion and restriction mapping 4 Southern and northern analyses. 8 Genomic library-screening of recombinants 4 9 Gene manipulations by site-directed mutagenesis -PCR 7 Technology cDNA library, reverse transcription, comparison between genomic an d cDN A library 10 Genome mapping, DNA fingerprinting 5 11 Applications of Genetic Engineering, Recombinant DNA guidelines 6

Reference Books:

1. Molecular Biology of the Gene, 6th Edition (2008), James D. Watson, Tania Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Lodwick, Pearson Education, Inc. and Dorling Kindersley Publishing, Inc. USA 2. Molecular Biotechnology: 4 th edition. (2010), Glick B.R., Pasternak J.J., Patten C. L., ASM press, USA 3. Principles of Gene Manipulation & Genomics, 7 th Edition (2006), Primrose and Twyman, Blackwell Publishing, USA. 4. Molecular cloning – a laboratory manual – (Vol. 1-3), 4 rd edition, (2012), Green and Sambrook, Cold Spring Harbor Laboratory Press, USA

Bb-344 Practicals in Recombinant DNA Technology (30P)

Sr. No. Topic Practical (30P) 1 Isolation of plasmid DNA & Gel electrophoresis 3 2 Genomic (Plant andAnimal) DNA- Isolation and 4 3 Genomic (bacterial) DNA- Isolation and quantitation 3 4 DNA Ligation 2 5 Preparation of competent Cells 1 6 Transformation of E. coli and selection of recombinants. 4 7 Colony PCR of recombinant and analysis 2 8 Restriction mapping of recombinant DNA 4 9 Southern blotting techniques 4 10 Western blotting technique 3

Bb-345 A Practicals in large scale manufacturing process Bb-345 B Practicals in Biochemistry & Biophysical Techniques

Sr. No. Topic Practicals (30P) Bb - 345 A Practicals in large scale manufacturing process (15P)

1 a. Screening and isolation of antibiotic producing organism 3 from soil (Crowded plate/ Giant colony method) b. Isolation of auxotrophic mutants by Gradient plate technique. 2 Production, Recovery (Filtration, Precipitation) and 3 estimation (Titrimetric or colorimetric) a of Primary metabolite (Organic acid) Production, Recovery (Filtration, Solvent extraction) and 3 estimation (Bioassay) a of Secondary metabolite (Antibiotic) 4 Preparation of wine 2 5 Laboratory Scale Production, Recovery and estimation of 2 Ethanol 6 Determination of Minimum inhibitory Concentration (MIC) 1 of antibacterial compound 7 Sterility testing of injectables/autoclave 1 8 Visit to a Fermentation Units

Bb -345 B Biochemistry & Biophysical Techniques (15P)

9 Preparation of buffer. 1 10 Laboratory safety, preparation of solutions, calibration of 1 pipette. 11 Thin layer chromatography – sugar , amino acids 2 12 Paper chromatography – amino acids 1 13 Estimation of cholesterol 1 14 Spectrophotometry – Estimation of ascorbic acid – DCPIP 1 method 15 Spectrophotometry – A spectra of Protein, nucleic acid. 2 1 Chromatography – Ion -exchange –separation of 2 compounds 17 Electrophoresis – separation of mixture of proteins – Native 2 PAGE and activity staining 18 Demonstration of HPLC and GC 2

M. Sc. [I] Biotechnology

Savitribai Phule Pune University

(Formerly University of Pune)

Two Year Degree Program in Biotechnology

(Faculty of Science & Technology)

Revised Syllabi for

M.Sc. (Biotechnology) Part-I

(For Colleges Affiliated to Savitribai Phule Pune University)

Choice Based Credit System Syllabus

To be implemented from Academic Year 2019-2020

Savitribai Phule Pune University 1

M. Sc. [I] Biotechnology

Title of the course: M.Sc. (Biotechnology)

Preamble:

Biotechnology has grown, extensively in last couple of decades. This advanced ‘interdisciplinary’ life science branch encompasses areas viz. molecular biology, genetics, biochemistry, microbiology, immunology, virology, plant and animal tissue culture, chemistry and engineering.It is a fast emerging “cutting edge” science with distinctive advantages as it finds applications in practically all aspects of life. The subject offers exciting opportunities in various fields from basic research to industry oriented career. Global and local focus has slowly shifted to using knowledge of life Science for innovative technology development that is being used for betterment of human life.Many fundamental research fields from cell biology to molecular biology, from biochemistry to biophysics, from genetic engineering to stem cell research, from bioinformatics to genomics-proteomics, from environmental biology and to biodiversity, from microbiology to bioprocess engineering, from bioremediation to Insilco drug discovery etc. comes under the umbrella of Biotechnology.

The proposed choice based credit curriculum and grading system will cater to the existing interdisciplinary nature of biotechnology can also offer many courses to the other branches of life science. The generative power of biological data is effectively harnessed by biotechnology like no other field. Economic and social renaissance is staged on biotechnology especially, since it’s biomedical and cutting edge technological applications are tremendously powerful in shaping this century and exciting biofuture. Keeping in view the expanse and applications of Biotechnology in every field, there is going to be a perpetual demand for resource personnel with Biotechnology specialization. The post graduate program is aimed to cater to this ever increasing demand and to groom the students to excel in their future career. Education and research sectors require such interdisciplinary trained workforce to develop future generations of science leaders.

Introduction:

Master’s in Biotechnology course syllabus is revised to cater to the needs of credit basedsemester and grading system. The changing scenario of higher education in India and abroad is taken into consideration while restructuring this syllabus and more oriented towards current need of modern research and industrial sectors. The syllabus encompasses the fundamental academics at one end and latest technologies in life science at the other. Theory courses will help students develop their knowledge sets on various topics of biotechnology, to which, they are introduced at the undergraduate

Savitribai Phule Pune University 2

M. Sc. [I] Biotechnology level. Extensive practical courses are designed to supplement the theory courses with hands on experimentation in wet-lab and on fields. Empowerment of students to face research and industrial outlets is at the centre of this syllabus. Students having to select their own courses will develop the depth in specialization and also make them ready to face the upcoming scientific advances in the world without any further training. M.Sc. syllabus has been prepared keeping in vision the undergraduate curriculum. At the undergraduate level, students were introduced to many fundamental topics in life sciences such as molecular biology, developmental biology, fermentation technology, biodiversity, bioinformatics and tissue culture etc. At the post graduate level they will be also be acquainted with the thrust/new areas of biotechnology like bioinformatics, clinical research, data base management, IPR, Food Technology etc. to give the students the advantage of not only learning these subjects but also give them the edge over others in their employability. A research project/ industrial training modules are incorporated to provide a buffer zone for budding biotechnologists eager to enter the life science sector.

Objectives to be achieved:

• To help the students to build interdisciplinary approach • To empower students to excel in various research fields of Life Sciences • To inculcate sense of scientific responsibilities for social and environment awareness.  To acquaint the students with thrust areas of biotechnology  To adapt the internationally acknowledged Choice Based Credit System (CBCS) that offers opportunities to learn core subjects and to explore additional avenues of learning beyond the core subjects for complete development of an individual.

Savitribai Phule Pune University 3

M. Sc. [I] Biotechnology Course Structure: Semester I Course code Course Title Credits Core Compulsory Theory Papers (CCTP) MBT- 101 Advanced Biological Chemistry 4 MBT- 102 Cell & Molecular Biology 4 MBT- 103 Genetics & Immunology 4 Core Compulsory Practical Paper: CCPP-1 MBT- 104 Laboratory Course I - Advanced Biological 4 Chemistry, Cell & Molecular Biology, Immunology Choice Based Optional Papers: CBOP (any One) MBT -105 Environmental Biotechnology 4 ( 2T + 2P) MBT -106 Food Biotechnology 4 (T) Total 20 Credits

Semester II CourseCode Course Title Credits

Core Compulsory Theory Papers (CCTP)

MBT- 201 Genetic Engineering 4 Credits

MBT- 202 Bacteriology and Virology 4 Credits

MBT- 203 Plant Biotechnology 4 Credits

Core Compulsory Practical Paper : CCPP-1

MBT- 204 Laboratory Course II - Genetic Engineering, 4 Credits Bacteriology and Virology, Plant Biotechnology

Choice Based Optional Papers: CBOP (any One)

MBT -205 Clinical Research, Data Base management, & IPR 4 Credits

MBT -206 Medical Biotechnology 4 Credits

Total 20 Credits

Savitribai Phule Pune University 4

M. Sc. [I] Biotechnology

Semester III Course code Course Title Credits Core Compulsory Theory Papers (CCTP) MBT- 301 Animal & Stem Cell technology 4 Credits MBT- 302 Bioprocess engineering 4 Credits MBT- 303 Bioinformatics & Biostatistics 4 Credits Core Compulsory Practical Course : CCPP-1 MBT - 304 Laboratory Course IV- Animal Biotechnology, 4 Credits Bioprocess engineering &Bioinformatics & Biostatistics Choice Based Optional Papers: CBOP (any One)

MBT - 305 Nano Biotechnology 4Credits (2T + 2P) MBT - 306 Agricultural Biotechnology 4 Credits (2T + 2P) Total 20 Credits

Semester IV Course code Course Title Credits Core Compulsory Theory Papers (CCTP) MBT- 401 Genomics and Proteomics 4 Credits MBT- 402 Advanced Bio analytical Techniques 4 Credits Core Compulsory Practical Paper : CCPP-1 MBT- 403 Research Project 4 Credits Choice Based Optional Papers: CBOP (any Two) MBT - 404 Bio entrepreneurship & Start up Designing 4Credits MBT - 405 Pharmaceutical Biotechnology & Drug 4 Credits Designing MBT - 406 Research Methodology & Scientific 4 Credits Communication MBT - 407 Quality Control, Bio safety & Bioethics 4 Credits Total 20 Credits

Savitribai Phule Pune University 5

M. Sc. [I] Biotechnology

Equivalence of previous syllabus along with proposed syllabus

Paper Title of Previous Syllabus Equivalent Paper Title of New Syllabus BT 101 Advanced Biological Chemistry MBT 101 Advanced Biological Chemistry MBT – 102 Cell & Molecular Biology BT 102 Molecular Biology BT 103 Environmental Biotechnology MBT- 105 Environmental Biotechnology (CBOP) BT 104 Cell Biology MBT -102 Cell & Molecular Biology BT 105 Exercises in Advanced Biological MBT – 104 Laboratory Course I - Advanced Chemistry Biological Chemistry, Cell & Molecular Biology MBT – 104 Laboratory Course I - Advanced BT 106 Exercises in Molecular and Cell Biology Biological Chemistry, Cell & Molecular Biology BT 107 Exercises in Environmental MBT – 105 Environmental Biotechnology Biotechnology (CBOP) BT 201 Genetic Engineering MBT – 201 Genetic Engineering BT 202 Immunology MBT – 103 Genetics & Immunology BT 203 Principles of Bacteriology and Virology MBT – 202 Bacteriology and Virology BT 204 Plant Biotechnology MBT – 203 Plant Biotechnology BT 205 Exercises in Genetic Engineering MBT – 204 Laboratory Course II - Genetic Engineering, animal & Plant Biotechnology BT 206 Exercises in Immunology MBT – 104 Laboratory Course I - Advanced Biological Chemistry, Cell & Molecular Biology BT 207 Exercises in Plant Biotechnology MBT – 204 Laboratory Course II - Genetic Engineering, animal & Plant Biotechnology BT 208 Exercises in Bacteriology and Virology MBT 204 Laboratory Course II - Genetic Engineering, animal & Plant Biotechnology

Savitribai Phule Pune University 6

M. Sc. [I] Biotechnology

Semester I Course Code: MBT-101: Advanced Biological Chemistry:4 Credits

60 lectures Units Topics No. of Lectures Protein Chemistry:  Structure of Proteins: Primary, Secondary, Tertiary, 15 I quaternary. Study of protein motifs and protein families.  Protein folding mechanisms and Pathways. Factors affecting stability- Molten globule, energy funnel, chaperons.  Protein misfolding and diseases  Protein –protein interaction and protein –DNA interaction  Structure –function relationship  Protein Engineering and its applications  Peptides and Therapeutic Proteins Enzymes: II  Enzyme – Concept of active site, binding sites, 15 Stereospecificity of enzyme and ES complex formation  Enzyme Activity,Various factors influencing enzyme activity and Enzyme inhibition  Mechanism of enzyme action and Enzyme regulation.Multienzyme complexes  Enzyme kinetics, Rate of reactions, steady state enzyme kinetics, Michaelis-Menten Equation - form and derivation. Significance of Vmax and Km, K/cat. Bisubstrate reactions. Graphical procedures in enzymology.Lineweaver Burke’s Plot, EdieeHofstee plot  Clinical and Industrial Applications of enzymes Enzymes :Diagnostics and therapeutic enzymes used in a Biosensors (glucose oxidase, Cholesterol Oxidase),  .Enzyme Engineering and III Metabolomics: 15  Overview of metabolism, Integration of Metabolism  The Metabolome – Metabolic flux, Metabolic flux analysis  Metabolic engineering – 2 eg. Polyketides Synthesis, Xenobiotics IV Phytochemistry: 15  Introduction to secondary Metabolism, primary metabolite as precursors of secondary Metabolite  Pathways for secondary Metabolite 1. Mevalonate pathways 2.Shikimate Pathway 3.Isoprene Unit Pathways (IPP) Savitribai Phule Pune University 7

M. Sc. [I] Biotechnology  Study of secondary Metabolite 1. Alkaloids 2. Phenolics 3. Terpenoids  Extraction methods & Qualitative & Quantitative Analysis

Reference Books: 1. Proteins: Biotechnology and Biochemistry, 1st edition (2001), Gary Walsch, Wiley, USA 2. Phytochemical Method, 3rd edition (1998), A.J. Harborne, Springer, UK. 3. Pharmacognosy, 14th edition, (2008), Dr. C. K. Kokate, A. P. Purohit, S. B. Gokhale, NiraliPrakashan, India. 4. Trease and Evans' Pharmacognosy, 16th edition (2009), William Charles Evans, Saunders Ltd. USA. 5. Introduction to Practical Biochemistry, (2000), S. K. Sawhney, Randhir SinghNarosa, 2000. Practical Enzymology, 2nd edition (2011), HansBissWanger, Wiley-Blackwell, USA. 6. Biochemical Calculations, 2nd Ed., (1997) Segel Irvin H., Publisher: John Wiley and Sons, New York. 7. Enzymes: Biochemistry, Biotechnology & Clinical chemistry, (2001) Palmer Trevor, Publisher: Horwood Pub. Co., England. 8. Metabolic Engineering: Principles and Methodologies. (1998). Gregory N Stephanopoulos, Aristos A Aristidou, Jens Nielsen. Publisher: Academic Press, San Diego, US 9. Outlines of Biochemistry: 5th Edition, Erice Conn & Paul Stumpf ; John Wiley and Sons, USA 10. Fundamentals of Biochemistry. 3rd Edition (2008), Donald Voet& Judith Voet , John Wiley and Sons, Inc. USA 11. Lehninger, Principles of Biochemistry. 5th Edition (2008), David Nelson& Michael Cox, W.H. Freeman and company, NY. 12. Outlines of Biochemistry: 5th Edition, (2009), Erice Conn & Paul Stumpf ; John Wiley and Sons, USA 13. Biochemistry: 7th Edition, (2012), Jeremy Berg, LubertStryer, W.H.Freeman and company, NY 14. An Introduction to Practical Biochemistry.3rd Edition, (2001), David Plummer, Tata McGraw Hill Edu.Pvt.Ltd. India 15. Biochemical Methods.1st , (1995), S.Sadashivam, A.Manickam, New Age International Publishers, India

Savitribai Phule Pune University 8

M. Sc. [I] Biotechnology

4 Credits Semester I 60 Course Code: MBt-102- Cell & Molecular Biology: lectures

Unit Topics No. of lectures I Cell structure and transport 8  Specialized Cells: Muscle & Nerve cells, Structure & functions  Molecular basis of muscle contraction.  Mechanism of nerve transmission- Resting and action potential, electrical and chemical transmission, Neurotransmitters and their receptors.  Plasma membrane types (animal, plant and bacterial)  Transport across plasma membrane and intra-cellular transport (vesicular and membrane transport) at molecular level II Cell communication 12  Organelles and membrane trafficking  Cell signalling: communication between cells and environment  Extracellular matrix and cell junctions- relevance to tissue structure and function  Signalling at cell surface, signalling molecules, hormones and receptors  Signalling pathways that control gene activity, signal transduction and second messengers III Cell Cycle and Cell Death Pathway 10  Cell differentiation, , cell transformation in plants and animals  Cell Cycle and its regulation: An over view of mechanics of Cell Division  Assembly and disassembly of cytoskeletal elements, role in cell division  Regulation of cell cycle events- Cyclins, Cyclin dependent kinases, inhibitors.  Cell death Role of hormones and growth factors Programmed cell death Cell transformation and etiology of cancer IV Information flow in biological systems: 8  Central dogma, Properties of DNA: UV absorption, Denaturation and renaturation kinetics thermodynamics of melting of the double helix, kinetics of unwinding of the double helix, Interaction with small ions. Genome Structure and Gene family:  Chromatin organization and remodeling, chromosome, centromere, telomere.  Gene families, clusters, Pseudogenes, super-families  Organelle genomes. C-value paradox and genome size, Cot curves, repetitive and non-repetitive DNA sequences, Cot ½ and Rot ½ values, satellite DNA, DNA melting and buoyant density.

Savitribai Phule Pune University 9

M. Sc. [I] Biotechnology  Mobile genetic elements:Transposable elements in bacteria, IS elements composite transposons, replicative and non-replicative transposons, Mu transposition, Controlling elements in TnA and Tn 10 transposition.  Transposable elements of Eukaryotes: Maize, Drosophila and Yeast. SINES andLINES, retrotransposons V Mechanism of Replication: 10  Mechanism of prokaryotic DNA replication, models of replications in prokaryotes.Eukaryotic DNA polymerases and mechanism of replication. Telomere synthesis-telomerases. Replication of viral DNA, rolling circle model. Inhibitors of replication.  Recombination Homologous and site-specific recombination,  Models for homologous recombination-Holliday junction, NHEJ, Proteins involved in recombination- RecA, RuvA, B, C, Gene conversion  DNA damage and Repair: DNA damage- alkylation, deamination, oxidation, UV radiation. Repair mechanisms- photoreactivation, excision repair, post replication repair, mismatch repair and SOS repair VI Gene Expression in Prokaryotes and Eukaryotes 12  Mechanism of Transcription: Mechanism of transcription and regulation function of bacterial RNA polymerases. Eukaryotic RNA polymerases-transcription factors, mechanism of transcription andregulation.  Post transcriptional modifications of mRNA :Caping, poly adenylation, mechanism of splicing, Group I, II and III, splicesome assembly, splicing editing, Group IV splicing Processing of tRNA and rRNA. Inhibitors of transcription.  Regulation of Gene expression in prokaryotes:Operon model- Inducible and repressible systems. Attenuation, positive and negative regulation with respect to tryptophan and arabinose operon.role of cAMP and CRP in the expression of lac genes, catabolite repression with respect to lactose operon.  Regulation of gene expression in eukaryotes: transcriptional control, cis control elements, promoters, enhancers, transacting factors, homeobox in the control of developments in insects and vertebrates. DNA binding motifs of transcription factors, posttranscriptional control.  Gene Silencing: concept,transcriptional and post transcriptional gene silencing, RNAi pathway (si RNA and mi RNA).  Co- and post-translational modifications of proteins: Control of translation in eukaryotes (Antisense RNA, Heme and interferon).

Savitribai Phule Pune University 10

M. Sc. [I] Biotechnology

Reference Books 1. Molecular Cell Biology. 7th Edition, (2012) Lodish H., Berk A, Kaiser C., KReiger M., Bretscher A., Ploegh H., Angelika Amon A., Matthew P. Scott M.P., W.H. Freeman and Co., USA 2. Molecular Biology of the Cell, 5th Edition (2007) Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter. Garland Science, USA 3. Cell Biology, 6th edition, (2010) Gerald Karp. John Wiley & Sons., USA 4. The Cell: A Molecular Approach, 6th edition (2013), Geoffrey M. Cooper, Robert E. Hausman, Sinauer Associates, Inc. USA 5. Genes XI, 11th edition (2012), Benjamin Lewin, Publisher - Jones and Barlett Inc. USA 6. Molecular Biology of the Gene, 6th Edition (2008), James D. Watson, Tania Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Lodwick. Pearson Education, Inc. and Dorling Kindersley Publishing, Inc. USA 7. Molecular Biology, 5th Edition (2011), Weaver R., McGrew Hill Science. USA 8. Fundamentals of Molecular Biology, (2009), Pal J.K. and SarojGhaskadbi, Oxford University Press. India 5. Molecular Biology: genes to proteins, 4th edition (2011), Burton E Tropp, Jones & Bartlett Learning, USA

Savitribai Phule Pune University 11

M. Sc. [I] Biotechnology

Semester I Course Code: MBT-103 Genetics and Immunology: 4 Credits

Total Lectures=60

Unit Topics No. of lectures

I  Overview of Mendelian genetics, Laws of segregation in plant 08 crosses, inbreeding, selfing, heterosis, maintenance of genetic purity.  Drosophila genetics as a model of higher eukaryotes Monohybrid &dihybrid crosses, back-crosses, test- crosses,analyses of autosomal and sex linkages, screening of mutations based on phenotypes and mapping the same, hypomorphy, genetic mosaics, genetic epistasis in context of developmental mechanism.  Arabidopsis as model organism for genetic studies

II Population genetics and genetics of evolution 08  Introduction to the elements of population genetics: genetic variation, genetic drift, neutral evolution; mutation selection, balancing selection, Fishers theorem,  Hardy Weinberg equilibrium, factors affecting Hardy Weinberg equilibrium (selection, mutation, migrations and genetic drift )  In-breeding depression & mating systems; population bottlenecks, , Bayesian statistics; adaptive landscape, spatial variation & genetic fitness. III Human genetics and methodologies 08  Clinical genetics, diagnostic tools and techniques for human genetic disorder Genetic approaches to complex genetic diseases- hypertension, diabetes and Alzheimer’s

Savitribai Phule Pune University 12

M. Sc. [I] Biotechnology IV Genetic Mapping 06  Genetic recombination and linkage  Genetic mapping and physical mapping  Molecular markers & marker based genetic linkage maps  Linkage Disequilibrium  Genome-wide association study and haplotype mapping  Applications of genetic maps

V Immunology: fundamental concepts and overview of the 06 immune system Components of innate and acquired immunity; phagocytosis; complement and inflammatory responses; pathogen recognition receptors (PRR) and pathogen associated molecular pattern (PAMP); innate immune response; mucosal immunity; antigens: immunogens, haptens; Major Histocompatibility Complex: MHC genes, MHC and immune responsiveness and disease susceptibility, Organs of immune system, primary and secondary lymphoid organs. VI Immune responses generated by B and T lymphocytes 12 Immunoglobulins - basic structure, classes & subclasses of immunoglobulins, antigenic determinants; multigene organization of immunoglobulin genes; B-cell receptor; Immunoglobulin super family; principles of cell signaling; basis of self & non-self discrimination; kinetics of immune response, memory; B cell maturation, activation and differentiation; generation of antibody diversity; T-cell maturation, activation and differentiation and T-cell receptors; functional T Cell subsets; cell-mediated immune responses, ADCC; cytokines: properties, receptors and therapeutic uses; antigen processing and presentation- endogenous antigens, exogenous antigens.

VII. Antigen-antibody interactions 06 Precipitation, agglutination and complement mediated immune reactions Advanced immunological techniques: RIA, ELISA, Western blotting, ELISPOT assay, immune fluorescence microscopy, flow cytometry and immunoelectron microscopy; surface plasmon resonance. Biosensor assays for assessing ligand –receptor interaction; CMI techniques: lympho proliferation assay, mixed lymphocyte reaction.

Savitribai Phule Pune University 13

M. Sc. [I] Biotechnology VIII Vaccinology 6  Active and passive immunization; live, killed, attenuated, subunit vaccines;  Vaccine technology: role and properties of adjuvants, recombinant DNA and protein based vaccines, plant-based vaccines, peptide vaccines, conjugate vaccines; T cell based vaccine, chimeric, generation of monoclonal antibodies, hybrid monoclonal antibodies; and generation of immunoglobulin gene libraries.

Reference Books: 1. Hartl, D. L., & Jones, E. W. (1998). Genetics: Principles and Analysis. Sudbury, MA: Jones and Bartlett. 2. Pierce, B. A. (2005). Genetics: a Conceptual Approach. New York: W.H. Freeman. 3. Tamarin, R. H., & Leavitt, R. W. (1991). Principles of Genetics. Dubuque,IA: Wm. C. Brown. 4. Smith, J. M. (1998). Evolutionary Genetics. Oxford: Oxford University Press 5. Kindt, T. J., Goldsby, R. A., Osborne, B. A., &Kuby, J. (2006). Kuby Immunology.New York: W.H. Freeman. 6. Brostoff, J., Seaddin, J. K., Male, D., &Roitt, I. M. (2002). Clinical Immunology.London: Gower Medical Pub. 7. Murphy, K., Travers, P., Walport, M., &Janeway, C. (2012). Janeway’sImmunobiology. New York: Garland Science. 8. Paul, W. E. (2012). Fundamental Immunology. New York: Raven Press. 9. Goding, J. W. (1996). Monoclonal Antibodies: Principles and Practice: Productionand Application of Monoclonal Antibodies in Cell Biology, Biochemistry, andImmunology. London: Academic Press. 10. Parham, P. (2005). The Immune System. New York: Garland Science. 11. Principles of Genetics 5th Edition by D. Peter Snustad (Author), Michael J. Simmons (Author) 12. Genetics Author B. D. Singh Edition 2, reprint Publisher Kalyani Publishers 13. Genetic Mapping and DNA Sequencing edited by Terry Speed, Michael Waterman

Savitribai Phule Pune University 14

M. Sc. [I] Biotechnology

Semester I

Course Code: MBT 104 Laboratory Course I

(Advanced Biological Chemistry, Genetics and Immunology, Cell and Molecular Biology)

S.No. Practical Number of Practicals 1 Extraction, purification and characterization of protein : Beta 5 galactosidase  Extraction and assay of enzyme activity  Isolation, precipitation and Dialysis  Enzyme Purification by using Column Chromatography- Ion exchange/ Gel filtration  Characterization by Native / SDS PAGE 2 Study of Enzyme Kinetics of beta Galactosidase: 3 • Effect of substrate concentrations on the rate of enzymatic reaction using Line Weaver Burk double reciprocal plot. • Determination of Km, Vmax and Kcat. 3 Extraction and Qualitative/Quantitative estimation of 1 phytoconstituents 4 Double diffusion, Immuno-electrophoresis and 2 RadialImmuno diffusion 5 Complement fixation test. 1 6 Antibody titre by ELISA method 1 7 SDS-PAGE, Immunoblotting, Dot blot assays 1 8 Separation of mononuclear cells by Ficoll-Hypaque and their 1 cryopreservation 9 Separation of leucocytes by dextran method. 1 10 Isolation of nuclei and chromatin 2 Mononucleosome size determination by agarose gel electrophoresis 11 Extraction and Analysis of Histones 2 12 Isolation of RNA and analysis by agarose gel 1 13 Demonstration of PCR/RT-PCR using suitable genes 2 14 Restriction digestion of DNA using suitable RE and 1 resolution on agarose gel. 15 Isolation of mitochondria and lysosomes and assay of SDH 1 and acid phosphatase activity respectively 16 Programmed cell death during limb development In Chick 1 17 Staining of animal cells (Histone by Fast green; DNA by 1 Fuelgen; RNA by Methyl green Pyronin).

Savitribai Phule Pune University 15

M. Sc. [I] Biotechnology 18 Karyotyping and Ideogram construction in onion roots using 2 Colchicine treatment 19 Visit to animal house, or any National Research Institute and Industry Report writing.

Savitribai Phule Pune University 16

M. Sc. [I] Biotechnology

Semester I

Course Code: MBT-105 Environmental Biotechnology 4 credits(2 T + 2P Credit Course) Total Lectures=30

Unit Topics No. of lectures I Energy and Environment 2  Introduction to environmental Science  Natural energy resources and their exploitation (Conventional) II Pollution and Environment  Introduction to environmental components, future scenarios 1 of the global environment  Impact on environment (biotic & abiotic), transport and 2 diffusion, monitoring, quality standards, carbon foot prints  causes and consequences of climate change (global warming, Ozone hole, Sea level rise), 2 III Waste management  Waste water technology, Activated sludge process, 3 Removal of organic and inorganic pollutants  Solid waste management: Sources and types, Impact of solid waste disposal, 3 Recycle, Reuse and Recovery solutions IV Bioremediation Removing Pollutants from Environments  Introduction to use of biological agents in pollution control, 6 Advantages, limitations and applications Principle, types of Bioremediation and Factors affecting: Natural, Engineered, Ex-situ and in-situ  Xenobiotic degradation,: Biomining, Biomethanation, Bioleaching, Bio plastic technology  Biological Fertilizer and pesticides.  Principles and methods in: Bioaugmentation, Biostimulation, Phytoremediation

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M. Sc. [I] Biotechnology V Environment monitoring 2  Remote sensing and GIS : Principal, and objectives, Energy sources for remote sensing, Types of remote sensing, Applications- Agricultural, Forestry, Water Resource Urban Planning, Wildlife Ecology, Environmental Informatics 2  Environmental Impact Assessment: Introduction, Objectives, Classification, Guidelines. Case Study. 2  Environmental Audit: Introduction, Types, General Methodology, International and Indian Eco-standards ISO14000 series overview. IV Environmental Laws and Policies 6  International: in the view of global concerns, objectives of laws/regulations, importance Stockholm conference, Nairobi declaration, Rio conference,  India: Environmental Policy , Anti Pollution Acts: The water Act. 1974, The Air Act 1981, The Environment Protection Act 1986- Their important objectives

Reference Books: 1. Alternative Energy: S. Vandana; APH Publishing Corporation 2. Bio-Energy Resources: Chaturvedi; Concept Pub. 3. Renewable Energy – Environment and Development: M. Dayal; KonarkPub.Pvt. Ltd. 4. Water Sheds, Cambridge University Press, 2004. Wiley & Sons Limited, 2004. 5. William J. Deutsch, Groundwater Geochemistry: Fundamentals and Applications to Contamination, Lewis Publishers, 1997. 6. Advanced Renewable Energy Sources (2012) GopalNathTiwari and R K Mishra, RSC Publishing 7. Agenda 21: Guidelines for Stakeholders Patwardhan&Gunale 8. An Introduction To Geographic Information Technology (2009) Suchandra Choudhury I K International Pvt Ltd. 9. Bioremediation (1994) Baker, K.H and Herson, D.S.McGraw Hill, Inc. New York 10. Biotreatment of Industrial & Hazardous Waste (1993) M.V.Levin and Gealt, M.A McGraw Hill. Inc 11. Concepts and Techniques of Geographic Information Systems (2009) C.P.Lo.Albert and K.W.Yeung 2nd 12. Ecology and environmental biology (2011) Saha T K Books & Allied (p) Ltd edition, Prentice Hall, Inc. 13. Environment Impact Assessment (1996) Larry W. Canter McGraw-Hill Book Company 14. Environmental Audit (2002) Mhaskar A.K. Enviro Media Publications 15. Environmental Biology (2000) Varma&Agarwal S. Chand Limited 16. Environmental biotechnology(2010) RanaRastogi Publications 17. Environmental Protection and Laws (1995) Jadhav and BhosaleV.M.Himalaya publishing House. Savitribai Phule Pune University 18

M. Sc. [I] Biotechnology 18. Environmental risks and hazards (1994) Susan Cutter Prentice Hall, Inc. 19. Environmental Science (2011) Santra S.C. New Central Book Agency 20. Remote sensing of the environment (2000) John R. Jensen Dorling Kindersley India Pvt. Ltd 21. Soil and Water Conservation Engineering (1981) G. O. Schwab, Richard K. Frevert, Talcott W. Edminster, and Kenneth K. Barnes 22. Textbook of Remote sensing and GIS (2006) M. Anji Reddy 3rd 23. Waste Water Engineering: Treatment and Reuse (2002) Met Calf & Eddy INC, Tata mc Graw Hill edition, Prentice-Hall 24. http://envfor.nic.in/index.php 25. http://www.earthsummit2012.org/

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M. Sc. [I] Biotechnology

Semester I Course code: MBT-105, Practical Course in Environmental Biotechnology

2 Credit Course Total Practical =15

Sr.No. Topic No. of practical

1 Removal and estimation of pollutant from soil/water samples by 2 biostimulation/ phytoremediation 2 Genotoxicity assay on polluted water- Onion root tip and pollen 2 germination assay. 3 Qualitative and quantitative estimation of biodegradation of 2 pesticide/ insecticide/fungicide. 4 Estimation of Total suspended solids of waste water 1 5 Determination of dissolved oxygen concentration of water sample 1 6 Determination of chemical oxygen demand (COD) of sewage 1 sample. 7 Determination of biological oxygen demand of sewage sample 1 8 Acquisition of “Google Earth” images for the known and 2 unknown area for land use - land cover mapping.

9 Review on EIA case study. 2

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M. Sc. [I] Biotechnology

Semester I CourseCode: MBt- 106 Food Biotechnology Elective 4 Credits Course Total Lectures=60

Unit Topic No. of lectures I Microbes in Food Spoilage & Control  Types of micro-organism normally associated with food- mold, yeast, and bacteria, Microbial growth pattern, physical and chemical factors, influencing destruction of micro- organisms. 8  Micro-organisms in natural food products and their control. Biochemical changes caused by micro-organisms, deterioration and spoilage of various types of food products.  Food poisoning and microbial toxins, standards for different foods. Food borneintoxicants and mycotoxins. II Microbial biotechnology  Genetically modified microorganisms  Fermentation Technology- Use of microbes in the production of alcohols (Beer, Wine), bread, Yogurt, Organic acids (Acetic 5 acid, Lactic acid, Citric acid), Vitamins  Pigments, Flavors, sweeteners Enzyme in Food Technology  Production of food related enzymes- Amylases, Proteases, Lipases, Cellulases, Pectinases. Applications of these 5 enzymes in food processing  Applications of Biotechnology in food waste management and development of value added products III Nanobiotechnology  Use of nanoparticles for delivery of bioactive constituents, nanoencapsulation, nanopackaging, nanosensors for detection of pesticides & pathogens 7  Applications of Nutrigenomics in the food industry  Ethical Concerns, Safety and Regulatory Issues of biotechnological products IV. Prebioticsand Probiotics  Food Sources- Prebiotics [Dietary fibre, Oligosaccharides (Galacto-oligosaccharides, Fructo-oligosaccharides), Resistant Starch, Sugar alcohols],  Traditional Fermented Foods as sources of Probiotics 10

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M. Sc. [I] Biotechnology

 Strains of microorganisms used as probiotics  Role in Health and Disease, Mechanism of Action, Levels of Probiotics required for therapeutic efficacy V Nutraceuticals  Concept of Neutraceuticals and functional foods  Major nutraceuticals and their health applications- Bioactive peptides, Curcumin, Conjugated Linoleic acid, Glucosamine, Carnitine, Creatine 9  Safety and adverse effects associated with the consumption of functional foods and nutraceuticals  Recent trends in food formulation; antioxidant rich food products; concepts for formulation of foods for drought and disaster afflicted; defense services, sportsmen, space food VI  Role of QC and QA Quality: Quality Control, Quality Assurance, Concepts of quality control and quality assurance functions in food industries.  Quality Improvement Total Quality management: Quality 8 evolution, quality gurus, defining TQM, principals of TQM, stages in implementation, TQM road map. Quality improvement tools, customer focus, cost of quality VII  Food Laws Food Laws and Standards: National and International food laws, Mandatory and voluntary food laws.  FSSAI Indian Food Regulations and Certifications: Food Safety and 8 Standards Act, FSSAIRules, food adulteration, misbranding, common adulterants in foods, Duties and responsibilities of Food Safety Authorities

Reference Books: 1. Anthony Pometto (2005). Food Biotechnology, 2nd Edition. CRC Press 2. Byong H Lee (2014). Fundamentals of Food Biotechnology, 2nd Edition, Wiley- Blackwell 3. Goldberg, I 1994. Functional Foods: Designer Foods, Pharma foods, Nutraceuticals Chapman & Hall 4. Gibson, GR and William, CM. 2000. Functional foods - Concept to Product. Woodhead publishing. 5. Aluko, R.E. (2012). Functional Foods and Nutraceuticals. Springer 6. InteazAlli. 2004. Food Quality Assurance: Principles and Practices. CRC Press, Boca Raton, FL,USA. 7.Ronald H. Schmidt and Gary E Rodrick. 2003. Food Safety Handbook. John Wiley & Sons, Inc.,Hoboken. New Jersey, USA.

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M. Sc. [I] Biotechnology 8. R.E. Hester and R.M.Harrison. 2001. Food Safety and Food Quality. Royal Society of Chemistry,Cambridge, UK. 9. Branen A.L. and Davidson, P.M. 1983. Antimicrobials in Foods. Marcel Dekker, Newyork. 10. Jay J.M. 1986. Modern Food Microbiology. 3rd Edn. VNR, New York. 11. Robinson, R.K. Ed. 1983. Dairy Microbiology. Applied Science, London.

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M. Sc. [I] Biotechnology

Semester II Course Code: MBT-201 Genetic Engineering

4 Credits Course Total Lectures=60

Unit Topic No. of lectures

I Introduction and tools for genetic engineering 12 Impact of genetic engineering in modern society; general requirements for performing a genetic engineering experiment; restriction endonucleases and methylases; DNA ligase, Klenow enzyme, T4 DNA polymerase, polynucleotide kinase, alkaline phosphatase; cohesive and blunt end ligation; linkers; adaptors; homopolymeric tailing; labelling of DNA: nick translation, random priming, radioactive and non-radioactive probes, hybridization techniques: northern, southern, south-western and far-western and colony hybridization, fluorescence in situ hybridization.

II. Different types of vectors 12 Plasmids; Bacteriophages; M13 mp vectors; PUC19 and Bluescript vectors, phagemids; Lambda vectors; Insertion and Replacement vectors; Cosmids; Artificial chromosome vectors (YACs; BACs); Expression vectors: pMal; GST; pET-based vectors; mammalian expression and replicating vectors; Baculovirus and Pichia vectors system, yeast vectors, shuttle vectors, Intein-based vectors

III. Different types of PCR techniques 12 Principles of PCR: primer design; fidelity of thermostable enzymes; DNA polymerases; types of PCR – multiplex, nested; reverse- transcription PCR, real time PCR, touchdown PCR, hot start PCR, colony PCR, asymmetric PCR, cloning of PCR products; PCR based site specific mutagenesis; PCR in molecular diagnostics for viral and bacterial detection;

Sequencing methods: enzymatic DNA sequencing; chemical sequencing of DNA; automated DNA sequencing; RNA sequencing; chemical synthesis of oligonucleotides; mutation detection: SSCP, DGGE, RFLP.

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M. Sc. [I] Biotechnology IV Gene manipulation and protein-DNA interaction 12 Insertion of foreign DNA into host cells; transformation, electroporation, transfection; construction of libraries; isolation of mRNA and total RNA; reverse transcriptase and cDNA synthesis; cDNA and genomic libraries; construction of microarrays – genomic arrays, cDNA arrays and oligo arrays; study of protein-DNA interactions: electrophoretic mobility shift assay; DNasefootprinting; methyl interference assay, chromatin immunoprecipitation.

IV Gene silencing and genome editing technologies 12 Gene silencing techniques; introduction to siRNA; siRNA technology; Micro RNA; construction of siRNA vectors; principle and application of gene silencing; gene knockouts, Genome editing by CRISPR-CAS with examples

Genetic diseases-Detection and Diagnosis, Gene therapy – ex vivo, in vivo, gene delivery systems, viral and non viral. DNA marker technology in plants, DNA fingerprinting, Genetically engineered biotherapeutics and vaccines and their manufacturing, Transgenic animals and Bio-pharming.

Reference Books:

1. Old, R. W., Primrose, S. B., &Twyman, R. M. (2001). Principles of Gene Manipulation: an Introduction to Genetic Engineering. Oxford: Blackwell Scientific Publications. 2. Green, M. R., &Sambrook, J. (2012). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. 3. Brown, T. A. (2006). Genomes(3rd ed.). New York: Garland Science Pub. 4. Selected papers from scientific journals, particularly Nature & Science. 5. Technical Literature from Stratagene, Promega, Novagen, New England Biolabetc.

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M. Sc. [I] Biotechnology

Semester II

Course Code: MBT-202: Bacteriology and Virology 4Credits Course, Total Lectures = 60

Unit BACTERIOLOGY No. of Lectures I Taxonomy and Diversity of Bacteria: 8 Taxonomy, binomial nomenclature, types of bacterial classification systems, new approaches to bacterial taxonomy (numerical taxonomy, ribotyping, rRNA sequencing, fatty acid profile) ribosomal RNA analyses for tracing microbial evolution, genetic basis of evolution, evolution of physiological diversity.  Concept of ‘unculturable’ bacterial diversity. · Strategies for culture of ‘unculturable’ bacteria  The measurement of microbial diversity, Measures and indices of diversity.  Metabolic Diversity in Bacteria II Ultrastructure of Bacteria : 10  Cell wall (Gram positive, Gram negative and Archea),  Cell membrane (Gram positive, Gram negative and Archea),  Spore (endospore formation, germination, genetic basis and structure),  Flagella (Assembly, Chemotaxis mechanism)  Capsule, Fimbriae and Pilli ,  Cell inclusions  Siderophores – Structure, Function and Significance III Extremophiles: 4 Archaea, adaptations in extremophiles, applications in biotechnology IV Applied Bacteriology: 8  Bacteriology and Public health: Mycobacteria, Enteric bacteria (One example each, Pathogenicity, Virulence and methods of identification), Quorum Sensing (Concept and significance in Biofilm and pathogenicity of Bacteria)  Bacteriology and Agriculture:Biofertlizers, Biopesticides, Mass production of biofertilizers and quality control,Role of Agrobacterium  Pre and Probiotics  Bacteriology and environment: Bioremediation (Petroleum and Xenobiotic)  Microbial Fuel Cells  Bioluminescence  Bio surfactants Savitribai Phule PuneCurrent University topics/ recent developments of importance can discussed 26

M. Sc. [I] Biotechnology VIROLOGY V Introduction to viruses: General properties of viruses Morphology and 4 ultrastructure of Viruses, Virus related structures – Viroids and Prions Classification of viruses: ICTV system, Baltimore system VI Replication of viruses: 8  Mechanism of virus adsorption and entry into host cell  Genome replication  Post transcriptional processing  Translation of viral proteins  Protein nucleic acid interactions and genome packaging  Assembly, exit and maturation of progeny virions VII Bacteriophages: 3  Morphology, Genome organization and Life cycle of lamdaphage, M13 VIII Cultivation of viruses: 5  In ovo: using embryonated chicken eggs  In vivo: using experimental animals  Ex vivo / In vitro: using various cell cultures - primary and secondary cell lines, suspension cell cultures and monolayercell culture  In plants and plant cell cultures IX Viral Diagnosis: 7  Microscopy, Cultivation, Serological and Molecular methods, Infectivity assays, immunodiagnosis Antivirals:  Physical and Chemical agents, Therapeutic agents, Vaccines  Viral Interference and Interferons. Nature and source of interferons, Classification of interferons. X Animal, Plant and Poultry viruses: 3  Diseases and Importance with examples  Re-emerging and New emerging viral diseases with example (Influenza, H1N1,SARS,Nipah and Marburg), Current outbreaks

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M. Sc. [I] Biotechnology

Reference Books: 1. Ingraham J. L. and Ingraham C.A. (2004). Introduction to Microbiology. 3rd Edition. Thomson Brooks / Cole. 2. Madigan M.T., Martinko J.M. (2006). Brock’s Biology of Microorganisms. 11th Edition. PearsonEducation Inc. 3. Prescott L.M., Harley J.P., AND Klein D.A. (2005). Microbiology, 6th Edition. MacGraw Hill Companies Inc. 4. Salle A.J. (1971) Fundamental Principles of Bacteriology. 7th Edition. Tata MacGraw Publishing Co. 5. Stanier R.Y., Adelberg E.A. and Ingraham J.L. (1987) General Microbiology, 5th Edition.Macmillan Press Ltd. 6. Tortora G.J., Funke B.R., Case C.L. (2006). Microbiology: An Introduction. 8th Edition. Pearson Education Inc. 7. Wilson K. and Walker J.M. (2005) Principles and Techniques of Biochemistry and Molecular 8. Flint Jane. S. (1999), Principles of Virology 3rd edition, ASM (American Society of Microbiology) Press Publisher, 2 volumes. USA. 9. Bernard.N. Fields, Lippincott and Williams Wilkins, USA Field’s Virology - 2 volumes, 5th edition, (2006),

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M. Sc. [I] Biotechnology Semester II Course Code: MBT-203 Plant Biotechnology

4Credits Total Lectures=60

Unit Topic No. of lectures I In vitro propagation methods 12  Micropropagation - Advantages over conventional methods, Stages of micropropagation (stage 0 to stage 4),  Commercial application of micro propagation.  Organogenesis,  Commercial application of micro propagation.  Somatic embryogenesis and artificial seeds.  In vitro androgenesis and its applications,  Protoplast: isolation, fusion somatic hybridization, cybridization and their applications  Production of bio active secondary metabolites by plant tissue culture.  Suspension culture: initiation, growth and application II Cryopreservation : 7  Concept, theory and various methods and techniques of cryopreservation of plant culture till its revive back  Applications and Disadvantages of cryopreservation III Genetic transformationMethods: 14  Ti plasmid &Ri Plasmid vectors. Mechanism of T-DNA transfer to plants, Agro infection, Plant viral vectors.  Physical Methods: electroporation, microinjection and particle bombardment and selection of transformants and regeneration of transgenic plants.  Selectable markers, Reporter genes and Promoters used in plant vectors and their role in genetic transformation. IV Genetic manipulation : Introduction, 13  Transgenic plantsfor biotic and abiotic stress,  Production of secondary metabolites  Concept of Synthetic Biology for production of bioactive secondary metabolites  Increase in productivity by manipulation of photosynthesis and nitrogen fixation,  molecular farming (improvement in protein, lipids, carbohydrates),vaccines, antibodies, therapeutic proteins, Approaches to marker-free transgenics Savitribai Phule Pune University 29  Debate over GM crops

M. Sc. [I] Biotechnology V Marker assisted plant breeding and QTL mapping 14  Introduction  Concept and types of markers  Gene vs marker  QTL mapping and marker- assisted selection (MAS)  QTL mapping techniques  Important properties of ideal markers for MAS  Selection for major genes linked to markers  Potential of marker-assisted selection for Crop improvement  Practical applications of MAS.  MAS for major genes or improvement of qualitative and quantitative traits  Marker-assisted backcrossing : MABC procedure and theoretical and practical considerations  Marker-assisted gene pyramiding

Reference Books: 1. Chawla HC (2004) – Introduction to plant biotechnology (Science Publ) 2. Davies K (Ed) (2004) – Plant pigments and their manipulation – Annual plant reviews, vol 14 (Blackwell Publ) 3. Altman A, Hasegawa PM (Ed) (2012) – Plant Biotechnology and agriculture. Prospects for the 21st century (Academic press). 4. Bhojwani SS. &Razdan MK (1996). - Plant Tissue Culture: Theory & Practice(Elsevier). 5. Slater A, Scott NW, Fowler MR (2008) – Plant Biotechnology: the Genetic Manipulation of plants (Oxford Press) 6. Vasil IK, Thorpe TA (1994) – Plant cell and tissue culture (Springer) 7. H K Das Textbook of Biotechnology 4th edition 8.Plant Cell and Tissue Culture. A Laboratory manual 1994. Reinert J and Yeoman MM Springer 9. Biotechnology in Crop Improvement, HSChawla. International BookDistributing Company 1998 10. Practical Application of Plant Molecular Biology. RJ Henry. Chapman andHall 1997 11. Elements of Biotechnology, P.K. Gupta. Rastogi and Co., Meerut 1996

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M. Sc. [I] Biotechnology 12. A Text Book of Biotechnology, HD Kumar (WE pub.) 13.Gene transfer to Plants 1995, Polykus I and Spongernberg, G.Ed. Springer Scam. 14.Molecular Approaches to Crop Improvement1991. Dennis Liwelly Eds. PP 16 15. Plant Biotechnology 1994, Prakash and Perk, Oxford & IBH Publishers Co 16.Plant Cell and Tissue Culture. A Laboratory manual 1994. Reinert J and Yeoman MM Springer. 17. Plant Biotechnology: An Introduction to Genetic Engineering by Adrian Slater, Nigel W. Scott, Mark R. Fowler. Oxford University Press, 2008. 18. Anderson, J.A., S. Chao, and S. Liu, 2007: Molecular breeding using a major QTL forFusarium head blight resistance in wheat. Crop Sci. 4. 19. Heffner, E.L., M.E. Sorrells, and Jannink, J.-L. 2009. Genomic selection for crop improvement. Crop Sc. 49: 1-12.

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M. Sc. [I] Biotechnology

Semester II Course Code: MBt-204 Lab Course II (Genetic Engineering, Bacteriology and Virology, Plant Biotechnology) 4 Credits Course

Sr .No List of Practical No. of Practical 1. Plasmid DNA isolation and DNA quantitation 1

2. Restriction Enzyme digestion of plasmid DNA 1

3. Genetic Transfer-Conjugation, gene mapping 2

4. Polymerase Chain Reaction and analysis by agarose 1 gel electrophoresis 5. Preparation of competent cells 1

6. Transformation of E.coliwith standard plasmids, 2 Calculation of transformation efficiency.

7. Vector and Insert Ligation 1

8. Southern hybridization 1

9. Cleanliness, Good laboratory practices, media preparation, 1 Sterilization of media and glassware

10. Isolation of the following types of bacteria from natural 3 samples. Identification of the bacteria to at least the Genus level using the Bergey’s Manuals: Mesophilic bacteria /Thermophiles The identification key must be designed for each isolated and identified bacterium. Students are expected to isolate at least one Genus from each group. 11. Cultivation of Anaerobes (any one method) 1

12. Propagation of viruses in animals/tissue clture /embryonated 2 eggs.

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M. Sc. [I] Biotechnology

13. Qualitative and quantitative detection of bacteriophages 1

14. Animal virus titration by Hemagglutination test 1

15. Electron microscopic observations of ultrastrucutre of animal 1 viruses( Pox, Influenza, Rabies and TMV

16. Chlorella or Spirulinaculture establishments and study of its 1 growth using suitable parameters 17. In vitro induction of somatic embryogenesis and preparation 1 of artificial seeds 18. Induction of Androgenesisin vitro 1 19. Protoplast isolation and Fusion from plant material 1 20. Micropropagation : initiations , multiplication and subculture 2 21. Initiation of suspension culture and identification of common 2 secondary metabolites production 22. Preservation of in vitro cultures—use of slow growth and low 2 temperature 23. Visit to tissue culture laboratory and report writing

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M. Sc. [I] Biotechnology Semester II Course Code MBT 205:Clinical Research, Data Management and IPR 4Credits Course Total Lecture: 60 Unit Topic Number of Lectures CLINICAL RESEARCH AND DATA MANAGEMENT I Introduction to Clinical Research 1 Drug Development Process  Overview of Drug Development Process including clinical trials phases

II Protocol Designing: 5  Definition of protocol, its importance and purpose  Protocol format: Chapters (Headings) and broad contents of protocol  Important scientific and administrative aspect included in protocol  Protocol writing team and role of each member  Clinical trial design: Types of study designs  Sampling, sample size, randomization, Inclusion & Exclusion criteria  Phases of clinical trial & Types of trials

III Good Clinical Practice (GCP)-ICH E6: 5  Ethical Principles and their origin  Ethics in clinical research: As per ICMR & GCP  Ethics committees: Roles & responsibility of IEC and IRB  Ethics in relation to vulnerable groups & special situations  Responsibilities of Sponsors, Investigators & Regulators  ICH: Purpose, regulations & guidelines  Informed consent and Informed consent form  Essential Documents

IV Drug Regulatory Affairs (Clinical Trial) 4  Regulatory Authority in India (DCGI & CDSCO)  Schedule Y of Drugs & Cosmetics Act  International Scenario of Regulatory Aspects: FDA, CFR,

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M. Sc. [I] Biotechnology V Clinical Safety &Pharmacovigilance: 3  Definitions of AE, ADR, SAE,  Recording & reporting: Objectives & Importance  Pharmacovigilance: International procedures  Pharmacovigilance in India VI Monitoring of Clinical Trials 2  Monitoring and its role in clinical trials  CRF and other source documents relevant to monitoring

Concept of Database and Clinical Data Management VII  Concept and designing of Database, 10  Data management & IT in clinical research  CRF designing  Query raising and query resolution  EDC System and 21 CFR Part 11 compliance  Practical for Protocol Design, CRF Design and source documentation

INTELLECTUAL PROPERTY RIGHTS VIII  General Regime of Intellectual Property Rights: Overview 6 and Historical Perspectives;  Intellectual Property as an Instrument of Development;  Need for Protecting Intellectual Property- Policy Consideration- National Perspectives and International demands;  TRIPS (Trade Related Intellectual Property Rights) Agreement and International Treaties related to IPR IX  Patents: Criteria of Patentability; types of patent 8 applications: provisional and complete specifications.  Procedure for Filing Patent Applications, Patent Granting Procedure;  Revocation, Patent Infringement and Remedies;  Relevant Provisions of the Biological Diversity Act, 2002;  Commercialization of patented innovations; licensing – outright sale, licensing, royalty;

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M. Sc. [I] Biotechnology X  Copyright and Neighboring Rights - Conceptual 12 Framework, Copyright works, Ownership, transfer and duration of Copyright, Renewal and Termination of Copyright, Neighbouring Rights, Infringement of copyrights and remedies; Examples and Case study;  Protection of Plant Varieties and Plant Breeders’ Rights - Protection of Plant Varieties and Farmers' Rights, Authority and Registry, Registration of Plant Varieties and Essentially derived variety, Duration, Effect of Registration and Benefit Sharing; Examples and Case study; XI Patent Specification Drafting Exercise 4

Reference Books: 1. Katzung, B.G. Basic and Clinical Pharmacology, (2010) Prentice hall,International 2. National Ethical Guidelines for Biomedical and Health Research Involving Human Participants (2017) 3. E6 Good Clinical Practice. Code, Document Title, Previously coded. E6(R2) Good Clinical Practice(GCP). Finalised Integrated Addendum: November 2016. 4. New Drugs and Clinical Trials Rules 2019 5. Website: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm 6.Karki, M S, Intellectual property rights: basic concepts (2009) M Atlantic Publishers & Distributors, New Delhi 7. Wadehra, B.L. Law Relating To Intellectual Property, (2011), Fifth Edition, Universal Law Publishing Co.Pvt. Ltd. 8. TIFAC 2002 Some questions and answers on Patents an d Copyrights th 9. Das, H K ,Text book of Biotechnology,( 2010), 4 edition, Wiley India Pvt. Ltd, New Delhi rd 10. Chawala, H .S., Introduction to Plant Biotechnology, 3 edition, Science Publishers 11. Hirvani R, Patents in Plant Breeding: Guarding the Green Gold-,Biotech News, (2009),vol 4., 12. GanguliPrabuddh, Intellectual Property Rights , (2001), Tata McGraw-Hill Publishing Company Ltd. 13. Narayanan,P, Law of copyright and Industrial Designs,(2010), Eastern Law House, Delhi 14. Office of the Controller General Of Patents, Designs & Trade,(CGPDTM): Manual of Patents/Manual of Industrial Design/Draft Manual of Trademarks 15. Website: https://www.wipo.int / www.ipindia.nic.in

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M. Sc. [I] Biotechnology

Semester II Course Code: 206 Medical Biotechnology 4 Credits Course Total Lectures= 60 Unit Topics No. of Lectures I Introduction to molecular basis of Disease : 15  Introduction, Worldwide market in medical biotechnology, Revolution in diagnostics and therapy.  Introduction to Chromosomal Disorders and Structural Disorders with examples  Classifications of Genetic diseases  Single Gene disorders Sickle cell anaemia and Thalassemia, polygenic diseases eg Type I diabetes, Alzhimer Disease  Infectious disorders Diagnosis: 15 II  Diagnosis using protein and enzyme markers: Enzyme probes Glucose oxidase, Monoamine oxidase.  Diagnosis using Monoclonal antibodies – hormonal disorders & infectious diseases  DNA/RNA based Diagnosis: PCR based &Use of Nucleic acid probes  Biosensors in clinical diagnosis  Microarray Technology for disease diagnosis  Genetic Counselling III Therapies: 15  Gene Therapy: ex vivo & in vivo gene therapy  Strategies of Gene therapy:Gene augmentation, antisense therapy, ribozymes.  Vectors used in gene therapy and synthetic vectors  Gene therapy trials: ADA deficiency, Cystic fibrosis, HIV  Enzyme therapy: Gauchers disease,  Hormone replacement therapy: Diabetes  DNA based Vaccines: Subunit Vaccines and Attenuated Vaccines IV Stem Cell Therapy and Nanotechnology: 15  Stem cells in therapy -embryonic & adult stem cells, Characteristics & properties of stem cells. Potential use of stem cells  Cell & Tissue engineering  Bio-artificial organs (liver, Blood cells, skin)  Nanotechnology in diagnosis

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M. Sc. [I] Biotechnology

Reference Books: 1) Introduction to Human Molecular genetics- J J Pasternak, John willey Publications 2) Human Molecular genetics – McConkey 3) Medical Biotechnology-PratibhaNallari V Venugopal Rao Oxford Press 4) Medical Biotechnology-1st edition- Juditpongracz,Mary Keen 5) Medical Biotechnology-by Bernald Glick, Terry L Delovitch, Cheryl L Pattern ASM press 2014. 6) Molecular Biotechnology- Principles and Applications of Recombinant DNA, 4thEdition by Bernald Glick Cheryl L Pattern 7) Medical Biotechnology first edition by Trivedi P C Avishkar Publisher 8) Medical Biotechnology Principle and Applications by Kun L Y world Science Publications. 9) Methods of Biotechnology and Bioengineering by Vyas CBS publications 2004 10) Stem Cell technology by Marshak et al CSHL publications

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Savitribai Phule Pune University M.Sc. II Year Biotechnology (CBCS Semester Pattern) Semester III Revised syllabus w.e.f. June 2020

Semester III

Course code Course Title Credits

Core Compulsory Theory Papers (CCTP)

MBT- 301 Animal & Stem Cell technology 4 Credits

MBT- 302 Bioprocess engineering 4 Credits

MBT- 303 Bioinformatics & Biostatistics 4 Credits

Core Compulsory Practical Course : CCPP-1 MBT - 304 Laboratory Course IV- Animal 4 Credits Biotechnology, Bioprocess engineering & Bioinformatics & Biostatistics

Choice Based Optional Papers: CBOP (any One)

MBT - 305 Nano Biotechnology 4 Credits (2T + 2P)

MBT - 306 Agricultural Biotechnology 4 Credits (2T + 2P)

Total 20 Credits

Savitribai Phule Pune University M.Sc. II Biotechnology (CBCS Semester Pattern) Semester III Revised syllabus w.e.f. June 2020 Subject Code: MBT- 301 Subject : Animal and Stem Cell Technology 4 Credit course (Total Lectures:60)

Unit Topic Lecture (Total 60L) I Introduction to tissue culture: 5  History, basics of animal tissue culture  Importance of maintenance of sterility and use of antibiotics  Detection of Mycoplasma and viral contaminants  Prevention of Cross contamination, eradication of contaminants  Logic of formulation of tissue culture media: natural, synthetic media, sera and substitutes  Introduction to the balanced salt solutions and simple growth medium.  Role of carbon dioxide in animal cell culture  Cell senescence. II Various systems of tissue cultures: 5 Distinguishing features, advantages and limitations.  Methodology: i. Primary culture, ii. Explant culture, iii. Suspension culture. Behavior of cells, properties, utility with different examples  Cell lines: Definition, establishment and maintenance, Finite and Continuous Cell line. Normal, Transformed and established cell lines: characteristic features, Contact inhibition, anchorage (in) dependence, Cell and tissue response to various factors III Organ culture: 5  Methods, behavior of organ explant, and applications of organ culture.  Histotypic and organotypic cultures: methods and applications  Introduction to organ transplants, tissue engineering, bio-artificial organs IV Growth studies: 5  Cell proliferation, cell cycle, mitosis in growing cells  Cryopreservation of cultured cells  Measurement of viability and cytotoxicity, microscopic examination ofcultures, subculture of cells (monolayer and suspension cells), passage number  Cell cloning and types, cell synchronization, Cell transformation  Cell Separation: Various method- advantages and limitations; Scaling up, Cell hybridization V Application of animal cell culture: 5  For in vitro testing of drugs, production of viral vaccines and pharmaceutical proteins, monoclonal antibodies.  Mass production of biologically important compounds.  Propagation of viruses (viral sensitivity of cell lines).  Harvesting of products, purification and assays. VI Stem cells technology – 15

 Concept, characteristics of adult stem cells, embryonic stem cells, embryonic carcinoma cells, induced pluripotent stem cells  Identification, purifications, assessment of proliferation  Long term maintenance and characterization.  Stem cell self-renewal and pluripotency: molecular mechanisms  Cell cycle regulation in stem cells  Concept of Stem cell niche with examples Neural stem cells, Hematopoietic stem cells, mesenchymal stem cells  Applications of stem cells in therapeutics VII Transgenic animals: 12  Overview of different methods of introduction of a transgene viz. micronuclear injection method, transduction with recombinant viruses, REMI etc.  Targeted gene insertion, gene silencing by RNAi,:  Cre-LoxP recombination for genetic modification  CRISPR/Cas9 for targeted genome editing  Transgenic animals: fish, Xenopus, mammals,  Concept of Knockout mice, methods and application  Mouse models for human genetic disorders, neurodegenerative disorders VIII Animal husbandry and reproductive biotechnology: 5  Overview of livestock breed and their productivity in India  Artificial breeding :-Various methods of semen collection, artificial insemination, estrous synchronization, cryopreservation of germ cells,  In vitro fertilization and embryo transfer technology,  Animal cloning: concept and application in conservation

IX Biosafety issues and Bioethics associated with Animal Tissue culture, developing 3 transgenic animals and human cloning References:

1. R. Ian Freshney. Culture of Animal cells, 5rd Edition, 2010. A John Wiley & Sons, Inc., Publications, USA 2. R.W.Masters. Animal Cell Culture- Practical Approach, 3rd Edithion,2000, Oxford University Press. USA 3. Robert Lanza et al. Essentials of Stem Cell Biology”, Academic Press, 2nd edition, 2006.USA 4. Text book of Animal Husbandary, 8th edition, ( 1998 ) G.C. Banerjee,Oxford and IBH Publishin co.Pvt. Ltd. India 5. Molecular Biotechnology: 4th edition. (2010), Glick B.R., Pasternak J.J., Patten C. L., ASM press, USA 6. Gene Transfer to Animal Cells, 1st edition (2005), R. M. Twyman, Taylor & Francis USA.

Savitribai Phule Pune University M.Sc. II Biotechnology (CBCS Semester Pattern) Semester III Revised syllabus w.e.f. June 2020 Subject Code: MBT- 302 Subject : Bioprocess Engineering 4 Credit course (Total Lectures:60)

Sr No Topic No. of lectures 60

 Bioprocess development: An interdisciplinary challenge, 15 Biotechnology & Bioprocess Engineering, Definition of Bioprocess and I bioprocess Engineering, over view of bioprocesses with their various components. Aseptic operations and Containment  Types of Fermentations : Solid state fermentation, Dual/Multiple, Aerobic, Anaerobic, batch, fed-batch, continuous  Design of Fermenter/ bioreactors: Overview of types of Bioreactors, Novel Designs of Bioreactors.  Kinetics of operation of bioreactors: Batch, Fed Batch and Continuous processes., Growth Linked and Non growth Linked Products, Kinetic modelling, Model structures, Material balances and energy balances  Isolation, screening and maintenance of industrially important microbes  Strain Improvement: Product formation and inhibition pathways and their regulations, Strain improvement by: Mutation, Protoplast fusion, parasexual cycle and genetic engineering  Inoculum Development: Inoculum Development for bacterial, yeast and mycelial processes, aseptic method of inoculation, achievement and maintenance of aseptic conditions.

II  Media for industrial fermentations: 10 Medium requirements for fermentation processes, carbon, nitrogen, minerals, vitamins and other complex nutrients, oxygen requirements, Medium formulation (Statistical design) of optimal growth and product formation, Ingredients for mammalian cell culture and plant cell culture.  Sterilization of media and air: Thermal death kinetics of microorganisms, Del factor, design organism, Design of sterilization process (batch and continuous), sterilization of bioreactor, feed and liquid waste, sterilization of air, exhaust air, theory of depth filter, designing of depth filters. Monitoring of process variables:  Types of sensors, Measurement and control of various parameters (pH, Temperature, dissolved oxygen, microbial biomass, inlet and exit gases, fluid flow, Pressure, Foam) P.I. D. control, Computer control of variables.  Scale Up and Scale Down : Importance, parameters involved III Mass transfer, Aeration and agitation of fermentation broth: 12  Mass transfer: Concept of mass transfer, Molecular diffusion and role in bioprocess, Two–film theory, Convective mass transfer, volumetric mass transfer, Liquid-Solid, Liquid-liquid and Gas- liquid mass transfer equations and significance in bioprocess.  Aeration : Oxygen Uptake in cell cultures, Oxygen transfer from Gas bubble to Cell. Gas hold up, KLa importance, Measurement of KLa, Determination of KLa, Factors affecting KLa.  Agitation: Design of impellors and their flow patterns. Fermentation Broth rheology–Newtonian and Non Newtonian fluids, Factors affecting broth rheology, Power requirement for mixing Power number, Reynolds number, Flow regimes in fermentation tank (Laminar, turbulent and transition),Correlation between mass transfer coefficient and operating variables.

IV Downstream Processing: 8  Bio separation :- filtration, centrifugation, sedimentation, flocculation; Cell disruption (Physical , Chemical and enzymatic methods);  Extraction(Liquid-liquid, Aqueous two phase, Supercritical fluid); Distillation,  Purification by chromatographic techniques; Reverse osmosis and ultra- filtration; Drying; Crystallization, Whole Broth Processing V Industrial Production and Recovery process of: 10  Vitamins (Vitamin C), Amino acids (Glutamic acid), Enzymes (Extra and Intra cellular one example each), Antibiotics (Rifamycin), Organic acids (Lactic acid), Recombinant Vaccines,  Biotransformation product(Steroids),Brewing (Beer), Cheese, Exopolysaccharides, Biodiesel. VI Quality Control (QC) and Quality assurance(QA) : 5  Roles and responsibilities of QC and QA departments, Common Quality control tests,  Standard Operating Procedures (SOP) & Good Manufacturing Practices (GMP) ,Regulations on use and distribution of Biotechnology products.

References:

1. Stanbury, P. F., Whittaker, A. and Hall, S., (2016) Principles of Fermentation technology, Springer, Third edition 2. Peppler, H. J.,D. Perlman (1979), Microbial Technology, Vol I and II, Academic Press, Second edition (E book by Elsevier) 3. Casida, L. E., (1984), Industrial Microbiology, Wiley Easterbs, New Delhi 4. Casida, L. E., (2019), Industrial Microbiology, New age International, New Delhi, Second Edition. 5. Prescott. S.C and Dunn, C. G., (2004) Industrial Microbiology, CBS Publishers and Distributors, Fourth Edition. 6. A.H. Patel. (2011), Industrial Microbiology, Macmillan India Ltd., Second Edition. 7. Crueger, W. and Crueger, A. (2005) A Text Book of Industrial Biotechnology, Panima, New Delhi. 8. Satyanarayan U, (2008) Biotechnology, Arunabha Sen Books allied Publishers. 9. Schuler,M. and Kargi,F.Bioprocess Engineering -Basic Concept, Prentice Hall of India, New Delhi. 10. Pauline Doran, (2012), Bioprocess Engineering Principles - Academic Press, second Edition 11. Operational Modes of Bioreactors, BIOTOL series - Butter worth, Heinemann 1992 12. Bioreactor Design & Product Yield, BIOTOL series - Butter worth Heinemann 1992 13. Lydersen B., N. a. D’ Elia and K. M. Nelson (Eds.) (1993) Bioprocess Engineering: Systems, Equipment and Facilities, John Wiley and SonsInc. 14. Harrison,R, Todd, P(2006), Bioseparations science and Engineering,Oxford University Press 15. Aydin Berenjian, (2019) Essentials in Fermentation Technology Springer; Kindle edition

Savitribai Phule Pune University M.Sc. IInd Year Biotechnology (CBCS Semester Pattern) Semester III Revised syllabus w.e.f. June 2020 Subject Code: MBT- 303 Subject: Bioinformatics and Biostatistics 4 Credit course (Total Lectures:60)

Unit Topic No. of lectures 60

I Major Bioinformatics Resources and Biological databases 4

 Computers in Biology and medicine, Database concept  NCBI/EBI/EXPASY  Biological literature databases (PubMed)  Nucleic acid sequence databases (NCBI’s GenBank + the European Nucleotide Archive [ENA] + the DNA Data Bank of Japan [DDBJ],)  Protein sequence databases (UniProtKb,SwissPort, TrEMBL).

II Basic Concepts in Biological sequence Analysis : 8

 Biomolecular sequence analysis: Overview and Concepts  Pairwise sequence alignment algorithms (Needleman &Wunsch, Smith & Waterman)  Scoring matrices for Protein and Nucleotide sequences (PAM series and BLOSUM series), Gap Penalty and Penalty Scheme  Database Similarity Searches (BLAST, FASTA)  Multiple sequence alignment algorithms, Methods of MSA (Progressive, Iterative, Block-Based Alignment) (CLUSTALW and CLUSTALX,T-Coffee)  Protein profiles and Hidden Markov Model (HMM)  Application of Multiple sequence alignment (Phylogenetic analysis) III Structural Bioinformatics 8

 Major Structural Resources (PDB and PMDB)  PDB File Format  Basic Structure Visualization o Visualization of major secondary structure (helices, beta sheets) and their role in protein structure o Visualization of various interactions : Polar (Hydrogen Bonds), Apolar (Hydrophobic, van der Waals, Pi stacking), Other (Salt Bridges, Coordination with ions) in protein structures and their role.  Protein Structure Classification (SCOP and CATH)  Protein Structure Prediction o Need and Concept of protein structure prediction, protein folding and model generation o protein secondary structure prediction methods (Alignment- based and Single sequence-based secondary structure predictions o Tertiary structure prediction (Homology modeling and Fold Recognition, ab initio methods) o Ramchandran Plot

IV Pharmacophore modelling and Chemoinformatics 5  Chemoinformatics  Chemical Structure representation: 1D, 2D and 3D structures  Molecular file formats (SMILES, WLN, SDF, MOL,PDB etc)  Compound library formatting and filtering (Physicochemical and substructure filters)  Pharmacophore modelling  Pharmocophore: Definition and classes (HBA, HBD, Aromatic etc.)  Identification of pharmacophore features V Molecular Modeling 5  Introduction to modelling protein ligand interactions  Pose Prediction Strategies in molecular Docking: Rigid body docking flexible ligand docking (Conformational search method, Fragmentation method, Database method)  Scoring Functions: Force field-based, Empirical, Knowledge-based  Application in Structure Based Drug Designing Biostatistics

I. Introduction: 4  Biological variables, parameters of statistical data display.  Types of scales: linear, power, log, circular (with biological examples)  Curves and Equations: Linear, saturating, sigmoid, exponential, logistic, power, multinomial, algebraic, differential, partial differential

II Sampling, distribution and presentation 7  Sampling methods; Types of sampling; random sampling, Probability and non-probability sampling, stratified sampling, etc.  Power analysis and sample size calculations  Statistical data distribution, normal and skewed distribution, coefficient of skewness, moments and Kurtosis  Data presentation models; covariance models, spatial statistical model, multivariate spatial model, Gaussian and non-gaussian random process models, etc. III Hypothesis Testing (with biological examples) 5  Principles of hypothesis testing, significance level, null hypothesis  Type I and Type II errors  Examples of hypothesis testing: comparison of means, t-test, Chi- square test

IV Design, correlation and regression analysis 8  Statistical design of experiments, single and multifactorial designs, fractional factorial designs.  Principles of experimental designs; randomization, replication and local control; Complete, incomplete and randomized block designs;  Covariance and correlation, Pearson’s, Kendal’s and Spearman’s correlations, use of correlation and regression in biological analyses  Univariate, Bivariate and Multivariate data; linear, multilinear, and non- linear regression, generalized linear model and other models of regression analysis (nonparametric regression, Bayesian linear regression, etc.) V Statistical Methods: 6  Analysis of variance table (ANOVA),  Post hoc Tests-  Tukey’s test for pairwise comparison of treatments  Dunnet’s test for comparison of treatment means with control  Duncan’s multiple range test  Mann–Whitney U test

Reference Books:

1. Mount David W.. Bioinformatics: Sequence and Genome Analysis. Publisher: Cold Spring Harbor Laboratory Press; Latest Edition 2. Baxevanis Andreas D. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Latest Edition. Publisher: New York, John Wiley & Sons, Inc. 3. Teresa Attwood, Parry-Smith David J. Introduction to Bioinformatics. Publisher: Pearson Education (Singapore) Pte.Ltd., Latest Edition 4. Gibas Cynthia, JambeckPer. Developing Bioinformatics Computer Skills. Publisher: Shroff Publishers and distributors O'Reilly Media, Inc., Latest Edition 5. Bourne Philip E., WeissigHelge. Structural Bioinformatics (Methods of Biochemical Analysis, V. 44), 2003. Publisher: Wiley-Liss. ISBN: 0471202002. 6. Forbes Burkowski. Structural bioinformatics: An algorithmic approach. Publisher: CRC Press, 2009. ISBN: 9781584886839. 7. Leach, Andrew. Molecular Modelling: Principles and Applications. Publisher: Prentice Hall. 2001. ISBN: 0582239338 8. Branden ,Tooze John. Introduction to Protein Structure. Publisher: New York, Garland Publishing Inc. 1999. ISBN: 0815323050. 9. Sternberg Michael J. E. Protein Structure Prediction: A Practical Approach. Publisher: USA, Oxford University Press. 1997. ISBN: 0199634953. 10. Gasteiger Johann, Engel Thomas. Chemoinformatics: A Textbook. Publisher: Wiley-VCH; 1st edition. 2003. ISBN: 3527306811. 11. Gasteiger Johann, Handbook of Chemoinformatics: From Data to Knowledge (4 Volumes). Publisher: Wiley-VCH. 2003. ISBN:3527306803. 12. MuthukumarasamyKarthikeyan, Renu Vyas. Practical Chemoinformatics. Publisher: Springer. 2014. ISBN: 9788132217794 13. Lesk, A. M. (2002). Introduction to Bioinformatics . Oxford: Oxford University Press. 14. Lesk, A. M. (2004). Introduction to Protein Science: Architecture, Function, and Genomics. Oxford: Oxford University Press. 15. Billingsley, P. (1986). Probability and Measure. New York: Wiley. 16. Rosner, B. (2000). Fundamentals of Biostatistics . Boston, MA: Duxbury Press 17. Daniel, W. W. (1987). Biostatistics, a Foundation for Analysis in the Health Sciences. New York: Wiley. 18. P.S.S. Sunderrao and J. Richards-An introduction to Biostatistics, Prentice Hall Pvt. Ltd. India 19. Campbell R.C.- Statistics for Biologists, Cambridge University Press, Cambridge.

Savitribai Phule Pune University M.Sc. IInd Year Biotechnology (CBCS Semester Pattern) Semester III Revised syllabus w.e.f. June 2020 Subject Code: MBT- 304 Subject: Laboratory Course IV (4 Credit course) (Laboratory course in Animal Biotechnology, Bioprocess Engineering, Bioinformatics and Statistics) Sr. Animal Biotechnology Practical No. Of No. Practical

1. Initiation of primary culture from chick embryo 1

2. Subculture and establishment of cell line 2

3. Growth curve analysis of cell line 1

4. Demonstration of cryopreservation of cell 1

5. Chromosome spread preparation from cell line 1

Sr No Bioprocess Engineering Practical

1. Screening and identification (Genus Level) of a production strain (enzyme 2 /antibiotic) from soil samples. Maintenance of the isolated production organism (Agar slants/ glycerol stocks /soil culture/ lyophilization) at least two methods.

2. Medium optimization for laboratory scale production of 1 enzyme/antibiotics.

3. Study of Working of lab bench fermenter ( with production of enzyme or 1 antibiotic using screened organism)

4. Recovery and Assay of product formed (Bioassay or Enzyme assay). 1

5. Solid state fermentation : Lab scale production of a product. 1

6. Visit to fermentation industry and Report writing 1

Sr. Bioinformatics and Biostatistics Practical No.

1. Using online resources like NCBI, PubMed(GenBank, UniProtKB, PDB) 1

2. Sequence alignment using BLAST/ Database Similarity searching using 1 BLAST

3. Phylogenetic analysis using Phylip or Mega 1 4. Basic Structure visualization using DeepView (Performing basic tasks like 1 Selecting and Displaying structures, Colouring, Measuring distances and labeling)

5. Prediction of protein tertiary structure using any method (CPH, 1 MODELLER, SWISS Model, EasyModeler)

6. Molecular Docking using AutoDock and Molecular visualization of docked 1 complexes (using Pymol or Chimera)

7. Biostatistics practical based on theory course : 4

i. Determination of Karl-Pearson’s coefficient of correlation/ Spearman’s rank correlation coefficient from the given grouped and ungrouped data. ii. Examples based on t – test , Chi-square test for goodness of fit and independent attributes. iii. Analysis of variance on the given data (ANOVA) iv. Measures of skewness and measures of Kurtosis (grouped and ungrouped data).

Savitribai Phule Pune University M.Sc. II Biotechnology (CBCS Semester Pattern) Semester III Revised syllabus w.e.f. June 2020 Subject Code: MBT- 305 Subject: Nanobiotechnology (4 Credit Course: 2 Credit Theory + 2 Credit Practical)

Units Topic Lectures(30)

I Introduction to Nanobiotechnology: 4  History of nanotechnology and its emergence, Concept of Nano- biotechnology,  Types of nanoparticles and Their Properties: Quantum dots, Polymeric nanoparticles,  Metal nanoparticles, metal oxide nanoparticles, Dendrimers, Composites. II Methods for synthesis of Nanomaterials: 9  Physical, Chemical, biological methods: Chemical precipitation and co- precipitation, polyol, and borohydrate reduction methods, Sol-Gel synthesis; Microemulsions synthesis, Hydrothermal, Solvothermal synthesis methods, Microwave assisted synthesis; Sonochemical assisted synthesis, Core-Shell nanostructure, Organic-Inorganic hybrid nanocomposites, Quantum dot (QDs) synthesis.  Microbial/plant mediated Nanoparticle Production: Overview and concept of microbial/plant mediated nano-particle production; Methods of microbial/plant mediated nano-particle production

III Physiochemical characterization of Nanomaterials: 5  Optical (UV-Vis/Fluorescence), X-ray diffraction, Imaging and size (Electron microscopy- TEM, SEM; light scattering- DLS, NTA; Zeta potential), IV A. Applications of Nanomaterials in: 10  Proteins - Lipids - RNA and DNA;  Protein Targeting - Small Molecule/Nanomaterial - Protein Interactions; Nanomaterial-Cell interactions-Manifestations of Surface Modification (Polyvalency). Nanomaterials and Diagnostics/Drug Delivery and Therapeutics:  Peptide/DNA Coupled Nanoparticles; Lipid Nanoparticles For Drug Delivery; Inorganic Nanoparticles For Drug Delivery; Metal/Metal Oxide Nanoparticles (antibacterial/anti fungal/anti viral activities); Anisotropic and Magnetic Particles (Hyperthermia). MRI, Imaging Surface Modified Nanoparticles; MEMS/NEMS based on Nanomaterials; B. Applications of Nanobiotechnology:  Nanomedicines  Nanoparticles for diagnostics and imaging  Food Science ( Food Processing, Food Packaging, detection of pathogens)  Nanosensors  Nanotechnology for water remediation and purification,  Nanotechnology in agriculture.  Green Nanotechnology V Concerns of Nanomaterials/Nanobiotechnology:: 2  Fate of nanomaterials, environmental and health impact of nanomaterials, Genotoxicity and cytotoxicity evaluation of Nanomaterials ,eco- toxicology

Reference Books:

1. The Chemistry of Nanomaterials: Synthesis, Properties and Applications, 2 Volume Set C. N. R. Rao (Editor), Achim Müller (Editor), Anthony K. Cheetham (Editor), 2004. Wiley Publisher. 2. Nanobiotechnology: Concepts, Applications and Perspectives, Christof M. Niemeyer (Editor), Chad A. Mirkin (Editor) , Wiley Publishers, April 2004. 3. Nanotechnology: A Gentle Introduction to Next Big Idea, Mark Ratner and Daniel Ratner, Low Price edition, Third Impression, Pearson Education. 4. Nanoparticles: From theory to applications – G. Schmidt, Wiley Weinheim , 2004 5. Nanochemistry: A Chemical Approach to Nanomaterials – Royal Society of Chemistry, Cambridge UK 2005.

Subject Code: MBT- 305 Subject: Nanobiotechnology (2 Credit Practical Course)

Sr. Laboratory Course - Nanobiotechnology No. Of No. Practical 1. Synthesis of metal/metal oxide Nanoparticles by: 3 a. Chemical b. Microbial and c. Plant based method 2. Characterization of nano-materials by spectroscopic method: 2 i. Analysis of absorption spectra of thin films of Nanomaterials ii. Determination of absorption coefficient for different wavelength 3. Biological activities of nanoparticles: 2 1. Antimicrobial activities of synthesized nanoparticles (MIC/MBC determination) 2. Cytotoxicity testing of nanoparticles using MTT/Tryphan blue assay

Savitribai Phule Pune University M.Sc. IInd Year Biotechnology (CBCS Semester Pattern) Semester III Revised syllabus w.e.f. June 2020 Subject Code: MBT- 306 Subject : Agricultural Biotechnology

(2 Credit Course)

Unit Topics Lectures 30L)  Introduction to agricultural Biotechnology 10 L  Importance of Agriculture at national economy  Advantages of biotechnological methods over conventional methods of crop I improvement.  In-Vitro Plant propagation- a) Virus indexing, virus free plants, b) fruit crop c) flower crops d) Cereals and e) oil seeds plants  Endosperm culture & production of triploids for production of seedless plant varieties with examples  Use of bioreactors in plant production & Scale-up for Commercialization  Beneficial microorganisms in Agriculture: Biofertilizer (Bacterial Cyanobacterial and Fungal), microbial Bio insecticides  Major pest and diseases of horticultural crops and their control by Biotechnological methods Crop improvement – 3L  Improvement of crop quality (FlavrSavr tomato, Golden rice) II  Chloroplast manipulations for production of therapeutic proteins, vaccines, antibodies and increased production, III Recent advances – 8L  Plant genotyping by different methods PCR, Plant fingerprinting, Microsatellite, Nanotechnology.  Homogenous assays – Qualitative Real Time PCR assays, applications  CRISPR based technology: Introduction, techniques, and its application in plants  Plant DNA Barcoding- Introduction, Barcoding Markers (matK, rbcl, ITS, tm HpsbA), Recent advances in plant bar coding Benefits, Limitations

 Development and formulation (with various carrier materials) of 8L bioinoculants, for better Agricultural productivity, using: i. Growth promoting , IV ii. Nitrogen fixing, iii. Phosphate solubilizing, iv. Metal chelating, (siderophores) v. Growth hormone producing microorganisms  Agricultural biotechnology and agribusiness  Opportunities in the Agriculture Biotechnology

References :

1. Plant molecular breeding, (2009), Newbury HJ, John Wiley and Sons.,USA. 2. Ashwani Kumar, Shekhawat NS (2009) – Plant tissue culture and molecular a. Markers :their role in improving crop productivity (IK International) 3. Biotechnology, 4th edition, (2010), H K Das, Wiley India Pvt. Limited, India 4. Chawla HC (2004) – Introduction to plant biotechnology (SciencePubl) 5. Plant Biotechnology: the genetic manipulation of plants (Oxford Press) (2008) – Slater A,Scott NW, 6. Fowler MR Green MR &Sambrook J. (2014) Molecular Cloning: A Laboratory Manual. 4th Ed. Vol. I, II & III. Cold Spring Harbor Laboratory Press. 7. Plant Genetic Engineering (2012) Grierson D Springer Netherlands. 8. Principles of Gene Manipulation and Genomics (2006) Primose SB &Twyman RM. 7th Ed. Blackwell Publishing. 9. Molecular Cloning: A Laboratory Manual (2001)Sambrook J. and Russel D, 3rd Ed Cold Spring Harbor Laboratory Press. 10. Plant cell tissue and organ culture: fundamental methods by C. L. G. C. Philips and L.R.Wetter 1995. National Research council, Canada, PRL, Saskatoon. 11. Plant Biotechnologyand Agriculture (2011) : Arie Altman and Paul Hasegawa Elsevier Pblications (1st Ed) 12. Agriculture A.K. 2006. Flower crops: Cultivation and Management. New India Publishing Agency, IPA. . 13. Shanmugavelu, K. G. Production Technology of Fruit Crops. 14. Kunte, Y.N., Kawthalkar, M. P. And Yawalkar, K .S. 1997. Principles of Horticulture and Fruit Growing. 3rd Edn. 15. Textbook of Agricultural Biotechnology Paperback – 2008 by Nag and Ahindra 16. Handbook on Agriculture, Biotechnology and Development(2014) : By Daved Castle 17. Biocatalysis and Agricultural Biotechnology: Fundamentals, Advances, and ...By Anjali Priyadarshini, Prerna Pandey (2017). 18. Agricultural Biotechnology (2006) By Varun Metha )Book by Varun Mehta 19. Agricultural Biotechnology (2016) :Vivian Laura Savitribai Phule Pune University M.Sc. IInd Year Biotechnology (CBCS Semester Pattern) Semester III Revised syllabus w.e.f. June 2020 Subject Code: MBT- 306 Subject : Agricultural Biotechnology

(2 Credit Practical Course)

Sr. Laboratory Course - Agricultural Biotechnology No. Of No. Practical 1. Production of virus free plants 2 Virus indexing- ELISA and PCR, (Demonstration) 2. Suspension culture and study the parameters to scale-up the 2 production of in-vitro plants Monitoring of growth and differentiation of cells, 3. Endosperm culture for regeneration of seedless plants 2 Hardening /Acclimatization of regenerated plants, Transfer to soil 4. Non gel techniques for plant genotyping and CRISPR based 1 technology (Demonstration using web resources) 5. Preparation, formulation (using suitable carrier material) and 1 application (pot trials) of bio inoculants (Nitrogen fixing and Phosphate solubilising Microorganisms)

Savitribai Phule Pune University

M. Sc. Biotechnology IInd Year, Semester IV (CBCS Semester Pattern) Revised syllabus w.e.f. June 2020

Semester IV Course code Course Title Credits

Core Compulsory Theory Papers (CCTP)

MBT- 401 Genomics and Proteomics 4 Credits

MBT- 402 Advanced Bio analytical Techniques 4 Credits

Core Compulsory Practical Paper : CCPP-1 MBT- 403 Research Project 4 Credits

Choice Based Optional Papers: CBOP (any Two)

MBT - 404 Bio entrepreneurship & Start up Designing 4 Credits

MBT - 405 Pharmaceutical Biotechnology & Drug 4 Credits Designing

MBT - 406 Research Methodology & Scientific 4 Credits Communication

MBT - 407 Quality Control, Bio safety & Bioethics 4 Credits

Total 20 Credits

Savitribai Phule Pune University M. Sc. Biotechnology IInd Year, Semester IV (CBCS Semester Pattern) Revised syllabus w.e.f. June 2020 Subject code : MBT-401 Subject – Genomics and Proteomics (4 Credit Course) Total Lectures=60 (4 C)

Units Topic Lectures Genomics I  Genomics and Proteomics overview, omes and omics, 8L  Concepts and applications Genome overview with model organisms example  Whole Genome sequencing – Methods, Assembly and Analysis, NGS Platforms  Comparative genomics - Goals, bioinformatics of genome annotation, methods and limitations.  Structural genomics –Goals, methods, applications.  Functional genomics –Goals, methods, applications. II Transcriptomics and Microarray 10 L  Introduction to transcriptomics and expression profiling DNA and RNA Microarray –Preparation, working and analysis  Investigative techniques –EST, SAGE, SNP, MPRAs  DNA and RNA Microarray –Preparation, working and analysis. Microarray databases and bioinformatics tools. III Applications of genomics 12L  Metagenomics  Toxicogenomics  Pharmacogenomics  Basic research  Medical Genetics Proteomics IV Introduction & concept of proteomics, Protein structure-function 5 L relationship, Types of Proteomics:  Protein expression proteomics  Structural Proteomics,  Functional Proteomics V Techniques in Proteomics: 12L  Protein Isolation and Separation techniques  Structural analysis of proteins- X-ray crystallography and NMR spectroscopy  2 D electrophoresis  Peptide mapping & sequencing  Protein structure prediction- homology modelling  Mass Spectrometry: MALDI_TOF, ESI Tandem, Ion Trap, Peptide mass fingerprinting  LC-MS, (SILAC) - Chemical tagging, fluorescence, radio- labeling VI Applications of Proteomics 8  Protein expression profiling  Protein-protein & Protein-DNA interaction (Chip Technique)  Methods for detection of protein-protein interactions - Yeast 1, 2 and 3 `hybrid systems – Phage display –  Proteomics and Protein microarrays, databases and allied bioinformatics tools. VII Applications 5  Health care, Biomarkers in disease diagnosis, -Biomarker, drug development and their target identification  Identification and characterization of novel proteins

Reference Books: 1. Daniel C. Liebler, Introduction to Proteomics. Humana Press. 2. Twyman RM, Principle of Proteomics. BIOS Scientific Publishers. (2004). 3. Kamp RM, Methods 4. in Functional Genomics: Protein Structure Analysis. 5. Birkhauser (2000). 6. Hubert Rehn. (2006). Protein Biochemistry and Proteomics, Acadamic Press. 7. Liebler Humana. (2002). Introduction to proteomics: Tools for new Biology, W.CBS Pub., 8. Apweiler R. (2000). Protein sequence databases, Adv. Protein Chem. 54: 31-71 9. Pearson WR. (1996). Effective protein sequence comparison, Methods Enzymol., 266: 227-258. 10. Spang R and Vingron M. (1998). Statistics of large scale sequence searching. Bioinofrmatics. in Proteome and Proteome Analysis. Springer. (2004). 11. Baker D and Sali A. (2001). Protein structure prediction and structural genomics, Science, 294: 93-96. 12. Stekel D. (2003). Microarray bioinformatics, Cambridge University Press, Cambridge, UK. 13. Huynen MA, Snel B, Mering C and Bork P. (2003). Function prediction and protein Networks, Curr. Opin. Cell Biol., 15: 191-198. 14. Bioinformatics - From Genomes to Drugs (2001) (editor) WileyVCH; 1st edition 15. Bioinformatics-Sequence and Genome Analysis (2004) David W Mount Cold Spring Harbor Laboratory Press; 2nd edition 16. Comparative Genomics Webb Miller et al Annu. Rev .Genomics Hum. Genet 2004, 5, 15-56. 17. P Baldi and G W Hatfield DNA microarrays and gene expression (2002) Cambridg University Press 16 Functional Genomics : Methods and Protocols (2003) M J Brownstein, A B Khodursky Humana Press 17 Genome analysis and bioinformatics (2009) Sharma T R I.K. International Publishing House Pvt. Limited

Savitribai Phule Pune University M. Sc. II Biotechnology (CBCS Semester Pattern) Semester IV Revised syllabus wef. June 2020 Subject Code: MBT- 402 Subject: Advanced Bio-analytical Techniques (4 Credit Course) Total Lectures=60 Units Topic Lectures I Microscopic Techniques: 13  Staining and Visualization of cells and subcellular components.  Cryotomy, Scanning and Transmission microscopes, different fixation and staining techniques for EM  Freeze-etch and freeze- fracture methods for EM, Image processing methods in microscopy, confocal microscopy, single cell imaging. I Histochemical and Immunotechniques 12  Antibody generation, Detection of antigen using ELISA, RIA, Western blot  Immunoprecipitation, Flow cytometry and FACS  Detection of antigens in living cells (Stem Cell Markers)  in situ localization by techniques such as FISH and GISH. II Advanced Application of Spectroscopy 15  UV visible spectrophotometer, Fluorescence spectroscopy, Circular dichroism, NMR , IR and ESR spectroscopy ,  Molecular structure determination using X-ray diffraction and X ray crystallography  Molecular analysis using light scattering, Mass spectrometry and LC-MS and surface plasma resonance methods. IV Advanced Chromatography and Electrophoretic technique: 12  Introduction, principle and applications of HPTLC, HPLC, GLC,GC  Affinity chromatography: Principle, types, Application,  IF and 2 D electrophoresis, Capillary Electrophoresis, DGGE ( Denaturing gradient gel electrophoresis) V  Advanced Bio-analytical Techniques and Automated 08 Systems  Advances in PCR technology & its applications (modifications),  Next Generations Sequencing (NGS): Principles and instrumentation, NGS data procession tools,  Automated microbial identification system, Automated DNA/RNA Microarry systems.

Reference Books : 1. Principles and Techniques of Biochemistry and Molecular Biology,7th edition, (2010), Wilson K.M., Walker J.M., Cambridge University Press, UK 2. Biophysics. 1st edition (2002), Pattabhi V and Gautham N. Kluwer Academic Publisher, USA. 3. Biochemical spectroscopy. Vol 46 of Methods in Enzymology. (1995) Kenneth Sauer. Academic Press, USA 4. Modern experimental biochemistry. 3rd edition. (2000) Rodney Boyer. Prentice Hall Publisher, USA. 5. Analytical Biochemistry, 3rd edition, (1998), David Holmes, H.Peck , Prentice Hall, UK. 6. Willard and Merrit, Instrumental Methods and Analysis 7. Ewing GW, Instrumental Methods of Chemical analysis. 8. Vogel’s, Text Book of Quantitative Chemical Analysis, 6th Edition, 2004. 9. Raymond P. W. Scott, Techniques and Practice of Chromatography –Vol. 70. 10. Sethi P.D, DilipCharegaonkar, Chromatography –2nd Edition. 11. Hanes, Gel Electrophoresis of Proteins- A Practical Approach, 12. Biophysical chemistry by Upadhyay, Upadhyay and Nath, Himalaya publication house. 13. Next Generation Sequencing Methods and Protocols: Editors: Head, Steven R., Ordoukhanian, Phillip, Salomon, Daniel R. (Eds.) 2018. 14. Statistical Analysis of Next Generation Sequencing Data: Editors Somnath DattaDan Nettleton. 15. Next-Generation Sequencing Data Analysis 1st Edition by Xinkun Wang. CRC Press 2020. 16. Google search for Unit V contents

Savitribai Phule Pune University M. Sc. II Biotechnology (CBCS Semester Pattern) Semester IV Revised syllabus wef. June 2020 Subject Code: MBT- 403 Subject : Research Projects (4 Credit Course)

Project work , Thesis Submission & presentation

 Project work / Thesis / Dissertation shall be carried out under the supervision of a qualified teacher in the concerned Department./Research Institute/Industry

 Project work / Thesis / Dissertation shall be pursued for a minimum of 12 weeks during the final semester, following the preliminary plan of work carried out in during the previous semester.

 The Project Report/Thesis / Dissertation report is to be prepared as per standard scientific research methodology and duly signed by the supervisor(s) and the Head of the Department shall be submitted to the concerned department.

 The assessment (Internal and external) of the project work will be as per SPPU guidelines.

Savitribai Phule Pune University M. Sc. II Biotechnology (CBCS Semester Pattern) Semester IV Revised syllabus wef. June 2020 Subject Code: MBT - 404 Subject : Bio-entrepreneurship & Start up Designing (4 Credit Course) Total Lectures=60 Unit Title Lectures 60 I Introduction to Entrepreneurship Lectures  Meaning Knowledge and concept of entrepreneurship, 10  Need and Importance of entrepreneurship  The history of entrepreneurship development,  Skills and characteristic of successful entrepreneurs;  Entrepreneurship process;  Factors impacting emergence of entrepreneurship  Role of entrepreneurship in economic development,  Evolution and Growth of Entrepreneurship in India II An Entrepreneur and an Entrepreneurship Journey  Types of Entrepreneurs 11  Ethical Entrepreneurship  Entrepreneurial Value: Values, Attitudes and Motivation.  The entrepreneurial decision process, and role models,  Self Assessment of Qualities,  Skills, Resources and Dreams.  Role of Society and Family in the growth of an entrepreneur. Activity : Motivational games to boost the decision power, accuracy and Attitude of the students III Starting the venture: 11 Generating business idea –  Sources of new ideas,  Methods of generating ideas,  Creative problem solving,  Opportunity recognition and assessment  Environmental scanning,  Competitor and industry analysis;  Feasibility study : - Market feasibility:-Marketing plan: marketing research for the new venture, Steps in preparing marketing plan, - Technical/operational feasibility, - Financial feasibility. Activity : 1. Organization of ‘Brain Storming’ session for generating Creative Business idea 2. Market survey/Marketing Strategy IV Preparing a Business Plan: 11  Introduction to Business and its Environment  Components of a business plan,  Meaning and significance of a business plan  Challenges of New Venture Strategies  Start-up Policy Framework and Incentives  drawing business plan  Preparing project report;  Business Plan Preparation  Presenting business plan to investors  Execution of Business Plan  Business Incubation Centres Activity : Presentation on Business plan /Start-up business plan V Entrepreneurship as Problem Solving 6  Entrepreneurs- as problem solvers.  Risk taking-Concept; types of business risks.  Barriers to Entrepreneurship.  Support structure for promoting entrepreneurship (various government schemes). VI Dimensions of Entrepreneurship 6  Entrepreneurial Culture  Entrepreneurial Society  Women Entrepreneurship  Rural Entrepreneurship VII Strategic Frameworks for Decision 5  Vision, Mission, Objective and Goal  Porter’s 5-Forces Model  SWOT Analysis  Competitive Strategies  Value Chain Analysis

Reference Books: 1. Entrepreneurship, Hisrich, Robert D., Michael Peters and Dean Shepherded, , Tata McGraw Hill, ND 2. Entrepreneurship, , Brace R., and R., Duane Ireland, , Pearson Prentice Hall, New Jersy (USA). 3. Entrepreneurship, Lall, Madhurima, and ShikhaSahai, , Excel Book, New Delhi. 4. Entrepreneurship Development and Small Business Enterprises, Charantimath, Poornima, Pearson Education, New Delhi. 5. Entrepreneurship : New Venture Creation – David H. Holt 6. Entrepreneurship : Hisrich Peters 7. The Culture of Entrepreneurship- Brigitter Berger 8. Dynamics of Entrepreneurship development and Management: Entrepreneurship, Project Management, Finances, Programmes, and Problems – Vasant Desai (2009) 9. Entrepreneurship Development – Dr. P.C. Shejwalkar 10. Thought Leader : Shrinevas Pandit 11. Leadership and new Science : Margrat wheatly 12. Handbook of Entrepreneurship Research: An Interdisciplinary Survey and Introduction (International handbook series on Entrepreneurship) (2003) : Zolten J ACs, David B. Audretch 13. Knowledge-Driven Entrepreneurship ( 2009) : The Key to Social and Economic Transformation By Martin Curley, Piero Formica and Thomas Anderson 14. Entrepreneurship (3rd ed) Steven Brandt 15. The Entrepreneurial Connection – Gurmit Narula 16. Business Guru Speak –S.N. Cnary 17. Dhirubhai Ambani: Against All Odds: A Story of Courage, Perseverance and Hope Paperback – 1 July 2017 : by A G Krishnamurthy 18. Mythbreaker: Kiran Mazumdar-Shaw and the Story of Indian Biotech Hardcover – 29 April 2016 by Seema Singh 19. The Entrepreneur's Guide to a Biotech Startup: Peter Kolchinsky 20. The Anotomy of your Creativity : Chris Grady Savitribai Phule Pune University M. Sc. II Biotechnology (CBCS Semester Pattern) Semester IV Revised syllabus w e f June 2020 Subject Code: MBT - 405 Subject : Pharmaceutical Biotechnology & Drug Designing (4 Credit Course) Total Lectures=60 Units Topic Lectures I Introduction : 8L  Introduction to Pharmaceutical Biotechnology and Drug discovery.  Drug targets: Structure and functions; Physiochemical properties of drugs; drugs from natural sources.  Pharmacodynamics, pharmacokinetics and drug metabolism, Drug tolerance & intolerance, drug allergy, drug induced side effects with examples.  Screening and isolation of bioactive compounds , II Drug action and Resistance 8L  Mechanism of action of anti-diabetic, anticancer, anti- inflammatory and antibiotics (any two drugs of each)  Mechanisms of drug resistance to antibiotics and anticancer drugs with examples  MDR, XDR or PDR  Assay of drug potency- bioassay and immunoassay III Process of Drug Development 8L  Target identification and validation.  Pre-clinical studies- -Toxicity (Cytotoxicity, Genotoxicity, Reproductive toxicity, Carcinogenicity, Mutagenicity, and other tests)  Animal models for in vivo activity of drugs testing  Clinical trials: Phase I,II,III and IV IV Biopharmaceuticals : 10 L  Introduction and scope of Biopharmaceutical industry  Biotherapeutics: Various categories of therapeutics like Vitamins, Antibiotics, Hormones, Enzymes, Hematopoietic Growth Factors and Coagulation Factors, Interferon’s and Cytokines for Anti-infective and Cancer Therapy.  Biopharmaceuticals Manufacturing: Overview of upstream & downstream processing  Production of Biopharmaceuticals using Synthetic Biology Approach (eg. Artemisinin) V Computer aided drug design (CADD) 18 L  Introduction to CADD  Identification drug targets using molecular modeling, combinatorial libraries and high-throughput screening (HTS)  Methods of drug designing: 1. Structure based drug design  Molecular docking: Types and principles, Semi-flexible docking, Flexible docking; Ligand and protein preparation, Macromolecule and ligand optimization,  Analysis of docking results and validation with known information.  Use of Small-molecule libraries, Natural compound libraries for virtual high throughput screenings.  Commonly used docking software 2. Ligand based drug design  Quantitative structure activity relationships; Introduction to chemical descriptors like 2D, 3D and Group-based  Pharmacophore modeling, Pharmacophore-based screenings of compound library, analysis and experimental validation.  Concept of quantitative drug design using Quantitative structure-activity relationship models (QSAR models)  Types of molecular modelling for proteins VI Role of Regulatory Authorities in Drug Approvals 8L  The Food and Drug Administration (FDA), Investigational new drug application, New drug application;  European regulations National regulatory, authorities, European medicines agency and the new EU drug approval system, Centralized procedure, Mutual  Indian drug regulations, & pharmacopeia  Market issues of drug patenting and licencing in Pharma industry

Reference Books: 1. Olive Kaiser ,Rainer Muller, Pharmaceutical Biotechnology: Drug Discovery and Clinical Application, Wiley VCH publisher, 2004 2. Vyas and Dixit Pharmaceutical Biotechnology, 1 st CBS Publisher New Delhi, 1991 3. P. K. Gupta, Elements Of Biotechnology, Rastogi Publication, 10 th edition, 2004 4. S.S. Purohit, Biotechnology Fundamentals and Applications Student edition Agrobios Publisher;2002 5. K. Sambamurthy, Ashutosh Kar, Pharmaceutical Biotechnology, 2nd edition New AGE International (LP) Limited, 2007 6. Hermann Dugas, Bioorganic Chemistry: A chemical Approach to Enzyme action by Springer New York, 1999. 7. Kerns, E.H.; Di, L. Drug-Like Properties: Concepts, Structure Design and Methods:from ADME to Toxicity Optimization, Academic Press, Oxford, 2008 8. M. E. Wolff, John Wiley & Sons Burger’s Medicinal Chemistry and Drug Discovery, 7th Edition, Vol. 1-6. Principles and Practice, edited by: New York, 2010. 9. Foye’s Principles of Medicinal Chemistry, 7th Edition, edited by T.L. Lemke, D. A.Williams, V. F. Roche, and S.W. Zito, Williams and Wilkins: Philadelphia, 2013. 10. Edward C. Olson, Christoffersen Editor, Ralph E. Computer-assisted drug design / 2009, American Chemical Society. 11. Martin YC, Marcel Deckker Quantitative Drug Design - A Critical Introduction by Inc. New York. 12. Veerapandian, “Structure Based Drug Design”. Taylor and Francis, 1997. 13. Drug Design, V.M. Kulkarni, K.G. Bothara, Nirali Prakashan 14. Graham L. Patrick An Introduction to Medicinal Chemistry, ,Oxford University Press1995 15. Richard B. Silverman The Organic Chemistry of Drug Design & Drug Action, , Elsevier Academic Press, 2014. 16. Natanya Civjan, Chemical Biology: Approaches to Drug Discovery and Development to Targeting Disease, Edited by Wiley (2012). 17. Biology For Engineers 2019 Edition by SINGAL R, CBS Publishers and Distributors

Savitribai Phule Pune University M. Sc. II Biotechnology (CBCS Semester Pattern) Semester IV Revised syllabus wef. June 2020 Subject Code: MBT - 406 Subject: Research Methodology & Scientific Communication (4 Credit Course) Total Lectures=60 Sr Topic No. of No lectures 1. Introduction to Research Methods: 5  Types of research philosophies (positivist, interpretivist, pragmatist and realistic), various steps in scientific research, Scientific temper and attitude, Experimental Design, Defining Controls, deductive and inductive reasoning; reductionist and holistic approaches of scientific research. 2 Scientific Methodology: 5  Problem identification, Critical thinking, hypothesis formulation and hypothesis testing (Power analysis)  Difference between hypothesis, reasoning, theory and scientific law 3 Data Collection and analysis: 20  Types of Data, Methods and Techniques of data collection  Methods of primary data collection (observation/ experimentation/ questionnaire/ interviewing/ case/ pilot study) Methods of secondary data collection (internal/ external), schedule method  Research data organization:  Creating, Analyzing, Formatting Data & Content using Spreadsheets Insert, View, Edit etc.  Managing Lab Work books, Data tabulation, Calculations, Equations and analyzing biological Data using statistical tools. Data Analysis:  Data distributions, Statistical tests for comparison of sample means and sample variance-t-test, non-parametric tests, Correlation and Regression, F, t and Z distribution; goodness of fit, chi-square.  Introduction to multivariate analysis Mathematical models Simulation as a tool to test these models.  Software for data processing: Multidimensional Use of Excel; Sigmastat; GraphPad Prism; SPSS, SAS, R software. 4 Research in Practice: 5  Literature review, Journals, Conference Proceedings, Journal Impact factor, Citation Index, h, g, h-g index, Reading a scientific paper. 5 Research Ethics: 5  Social implications of research, bio-safety issues Animal experimentation ethics, wild-life ethics and human experimentation ethics  Data fudging and plagiarism: Use of URKUND, Turnitin and iThenticate software 6 Scientific Communication: 20  Importance of scientific communication, Types of scientific communications, Logical organization of scientific data and documentation Different modes of scientific communication:  Scientific Writing: Characteristic of good scientific writing, Structure and content, Style, Literature references,  Report Writing: Types of research reports, guidelines for writing a report, report format, Details of research Proposal writing, Research paper writing, Thesis writing(Introduction, Literature review, Materials and Methods, Results, Discussion, Conclusion and Implications, conflict of interest)  Oral forms of scientific Communication-Popular and Scientific talks, Poster presentations, Organizing Presentation Material , Use of audio visual aids in presentation elements of presentation preparation: objective, subject, audience, Length of talk Managing & Delivering Presentations  Legal forms of communication in science: Plagiarism and scientific misconduct, Ethics in scientific communication, patent submissions.  Internal examination of this paper should be based on following activities 1. Review writing/ Report writing 2. Scientific presentation of research paper from reputed journal. 3. Research Data collection and analysis

References: 1. H. Hofmann, Scientific Writing and Communication Papers, Proposals, and Presentations. New York: Oxford UniversityPress, 2010, pp. xv–xvi. 2. T. L. J. Ferris, E. Sitnikova, and A. H. Duff, “Building graduate capabilities to communicate research and planssuccessfully,” Int. J. Eng. Educ., vol. 26, no. 4, pp. 891–899, 2010 3. Michael Alley, The Craft of Scientific Writing, fourth edition, Springer,2018. 4. Stephen B. Heard, The Scientists Guide To Writing, Princeton University Press, 2018. 5. Anthony M. Graziano, Michael L. Raulin, Research Methods: A Process Of Inquiry(2012) 8th Edition, , Pearson Publication, Delhi2. Barass Robert, Scientists Must Write: A Guide to Better Writing for Scientists,Engineers and Students (2002), Routledge Publication, UK3. 6. David B. Resnik, The Ethics of Science: An Introduction (1998), Routledge Publication,UK5. 7. Fisher R A, TheDesign of Scientific Experiment (1971) 9th edition, Collier MacmillanPublishers, London 8. GanguliPrabuddh, Intellectual Property Rights (2001), Tata McGraw-Hill PublishingCompany Ltd., Delhi7. 9. John D'Angelo, Ethics in Science: Ethical Misconduct in Scientific Research (2012),CRC Press, USA 10. Kuhn Thomas, The Structure of Scientific Revolution (2012) 50th anniversary edition,Chicago University Press, USA 11. Martha Davis, Scientific Papers And Presentations 2nd edition (2004), Academic Press 12. Medawar, P. B. And Medawar, J. S., The Life Science: Current Ideas of Biology(1977), Wildwood House, London 13. Peter Raven et al, Biology 9th edition (2010), McGraw-Hill Education, Singapore 14. Popper Karl, The Logic of Scientific Discovery (2004), Routledge Publication, UK 15. Richard P. Feynman, The Meaning Of It All: Thoughts Of A Citizen-Scientist (2005),Basic Books, New York 16. Richard P. Feynman, The Pleasure of Finding Things Out: The Best Short Works OfRichard P. Feynman (1999), Edited By Jeffrey Robbins, Perseus Books, USA

Savitribai Phule Pune University M. Sc. Biotechnology (CBCS Semester Pattern) Revised syllabus w.e.f. June 2019 Subject code: MBT- 407 Subject – Quality Control, Biosafety & Bioethics (4 Credit Course) Total Lectures=60 (4 C)

Units Topic Lectures Quality Control I  Quality Standard & Quality assurances: 10 Concept of quality Assurance & Quality control their function and adventage, Quality assurance and quality management in Biotech Industy  Critical quality point in different stages of production including raw materials & processing material  Types of validation in pharma industry, Importance of validation Elements of validation (Q,OQ, PQ,DQ) Toxicity, clinical trials, studies, clinical research & clinical data management,  Export, Import of product, Rules & Regulations for start up companies GMP , cGMP II Essential Documents & Regulatory Submission, Compliance And 10 Audits –  Preparation, production and quality control of regulatory documents, creating editorial timelines and work flow specifications, SOP  Scheduling and tracking documents, writing and proofreading.  Development and updates on specifications for the design, tracking of regulatory documents and artwork used in regulatory document  Regulatory requirements for Biotech/pharma product development Bioethics

III Introduction 10  Introduction to Ethics and Bioethics, Framework for ethical Decision Making  National Ethical Guidelines for biomedical and health research.  Bioethical issues related to Healthcare & medicine Food & agriculture Genetic engineering IV Ethical Issues: 10  Animal cloning & human cloning  Human genome project, biopiracy, biowarfare  Public education of producing transgenic organism  Legal & socioeconomic impacts of Biotechnology  Hazardous materials used in biotechnology: Handling & disposal  Experimenting on Animals: Animal right activities Blue cross in India- society for prevention of cruelty against Animals. CPCSEA committee, Ethical limits of Animal use.  Publication ethics and regulations  Biodiversity Biosafety

V Biosafety 14  Introduction, Biosafety in Laboratory & Institution, Laboratory associated infections & other hazards.  Introduction to Biological Safety Cabinets, Primary Containment for Biohazards  Biosafety Levels, Biosafety Levels of Specific Microorganisms, Recommended Biosafety Levels for Infectious Agents and Infected animals  Safety & hazards: Chemical & radiation hazards Control of exposure to radiation, Fire prevention methods  Industrial Hygiene & toxicology: Introduction , evaluation & control, Personal protective equipment  Risk Analysis, Risk Assessment, Risk management and communication VI Biosafety guidelines – 6  Guideline & regulations( National & International)  GMOs & LMOs Guidelines of India  Environmental release issues of GMOs,  Risk Analysis, assessment, risk management and communication  Roles of Institutional Biosafety Committee RCGM, GEAC etc

Reference Books:

1. Deepa Goel & Shomni Parashar IPR, Biosafety and Bioethics, , published by Pearson Education India 2. M K Sateesh Bioethics and Biosafety. Jeffrey M. Gimble, Academia to Biotechno logy, Elsevier Academic Press. 3. Rajmohan Joshi (Ed.). 2006. Biosafety and Bioethics. Isha Books, Delhi. 4. Sasson A, Biotechnologies and Development, UNESCO Publications. 5. Senthil Kumar Sadasivam and Mohammed Jaabir M. S. (2008). IPR, Biosafety and Biotechnology Management, Jasen Publications, Ind