sardar patel university vallabh vidyanagar, gujarat ......lipid biosynthesis: biosynthesis of...

SARDAR PATEL UNIVERSITY Vallabh Vidyanagar, Gujarat

(Reaccredited with ‘A’ Grade by NAAC (CGPA 3.25) Syllabus with effect from the Academic Year 2021-2022

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Master of Science (Biotechnology) M.Sc. (Biotechnology) Semester (I)

Course Code PS01BIT51 Title of the Course Molecular Biology

Total Credits of the Course 04 Hours per

Week 04

Course Objectives:

1. To gain deeper understanding about DNA structure and function. 2. To learn about organization of chromosomal DNA in both prokaryotes

and Eukaryotes as well as its replication. 3. Togain insights into gene expression processes in both prokaryotes and

eukaryotes including its regulation. 4. To inculcate research insights and inquisitiveness amongst students in the

field of molecular biology.

Course Content

Unit Description Weightage* (%)

1. DNA structure DNA structure: Chemistry of DNA, DNA structure, Different conformations of DNA (B, A and Z), Denaturation and Renaturation (Cot curves) of DNA. DNA topology: Supercoiling, Biology of Supercoiled DNA, DNA topoisomerases and their mechanism of action. DNA- protein interactions: General features, Sequence specific DNA binding protein motifs, ss DNA binding proteins.

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2. Organization of genome and its replication Organization of DNA into chromosomes: Packaging of DNA and organization of chromosome in bacterial cells; Packaging of DNA in eukaryotic nucleosome and chromatin condensation, assembly of nucleosomes upon replication, chromatin modification. DNA replication: Mechanism of DNA polymerase catalyzed synthesis of DNA, Types of DNA polymerases in bacteria, Initiation of DNA replication and its regulation in prokaryotes, assembly of replisome and progress of replication fork, termination of replication. DNA replication in eukaryotes and archaea. Inhibitors of DNA replication.

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3. Gene expression in prokaryotes and eukaryotes Transcription: RNA polymerases, features of prokaryotic and eukaryotic promoters, assembly of transcription initiation complex in prokaryotes and eukaryotes, and its regulation; synthesis and processing of prokaryotic and eukaryotic transcripts. Translation: structure and role of t-RNA in protein synthesis, ribosome structure,basic features of genetic code and its deciphering, translation

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(initiation, elongation and termination in detail in prokaryotes as well as eukaryotes).

4. Regulation of gene expression Regulation of gene expression in prokaryotes: Operon concept, positive and negative regulation. Examples of lac (including mutational analysis), ara, and trp operon regulation; global regulatory responses. Regulation of gene expression in eukaryotes: Transcriptional, translational and processing level control mechanisms.

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...

Teaching-Learning Methodology

Topics will be taught and discussed in interactive sessions using conventional black board and chalk as well as ICT tools such as power point presentations and videos. Practical sessions will be conducted in a suitably equipped laboratory either individually or in groups depending on the nature of exercise as well as availability of infrastructure. Course materials will be provided from primary and secondary sources of information.

Evaluation Pattern

Sr. No.

Details of the Evaluation Weightage

1. Internal Written / Practical Examination (As per CBCS R.6.8.3) 15%

2. Internal Continuous Assessment in the form of Practical, Viva-voce, Quizzes, Seminars, Assignments, Attendance (As per CBCS R.6.8.3)

15%

3. University Examination 70%

Course Outcomes: Having completed this course, the learnerwill be able to

1. correlate the structural features of DNA with its function

2 explain DNA-protein interactions in detail

3. describe how genome is organized in prokaryotes and eukaryotes and how

4. explain the molecular details of DNA replication in both prokaryotes and eukaryotes as well as the molecular basis of its fidelity.



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5. Discuss the molecular mechanism of gene expression and its regulation at transcriptional as well as translational levels in all three domains of life.

6 explain experimental insights for gaining molecular level details of gene structure and function

Suggested References: • Lewin’s Genes XII • Molecular Biology of the Gene: Watson et al • Molecular Genetic of Bacteria: Snyder and Champness • Molecular Biology, 4th Edition: Burton E Tropp • Principles of Genetics: Snustad and Simmons

On-line resources to be used if available as reference material

On-line Resources

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Course Code PS01CBIT52 Title of the Course Intermediary Metabolism


Week 03

Course Objectives:

Students should be able to : (1) Understand reactions and importance of cellular metabolism and connection to physiology (2) Understand some of the clinical pathology like starvation, Diabetes, etc.

Course Content


1. Important Bioenergetics concepts: Cells Require Sources of Free Energy

Actual Free-Energy Changes Depend on Reactant and Product

Concentrations

Concept of standard free energy and its relation to free energy and

equilibrium constants

Calculation of standard free energy of biochemical reactions and

membrane transport

Standard Free-Energy Changes Are Additive

The central axis of Intermediary metabolism: Glycolysis, Oxidative

decarboxylation of Pyruvate, Citric acid cycle & oxidative

phosphorylation & their regulation,

Un-couplers and inhibitors of energy transfer.

The role of TCA cycle intermediates to generate biosynthetic intermediates: Generation of Acetyl-CoA in cytosol by citrate, roles of Oxaloacetate and α- ketoglutarate to generate amino acids. The central role of Acetyl-CoA in Carbohydrate, Fat and Protein metabolism.

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2. Regulation of blood glucose homeostasis

Adaptation of Carbohydrate metabolism in starvation: Gluconeogenesis, Metabolic cooperation between Liver and muscle: Glycogenolysis, Cori’s cycle, metabolism in brain, liver, adipose tissue; synthesis &

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utilization of ketone bodies Adaptation of Carbohydrate metabolism in hyperglycemia: Glycogenesis, Pentose phosphate pathway A brief overview of Cellular uptake of fatty acids α,β , ὡ oxidation of fatty acids and lipid peroxidation. Fatty acid biosynthesis: Acetyl CoA carboxylase, Fatty acid synthase, desaturase and elongase. Lipid biosynthesis: Biosynthesis of triacylglycerol, phosphoglycerides, sphingolipids. Biosynthesispathways for steroids and prostaglandins.

3. Degradation of amino acid and their regulation, oxidative deamination, Urea cycle and its regulation. Linkage between urea cycle and citric acid cycle Biosynthesis of amino acids and regulation. Biosynthesis of aminolevulinate and Biosynthesis of heme from aminolevulinate and degradation of heme to bilirubin. Biosynthesis of creatine and phosphocreatine. Biosynthesis of purines and pyrimidines and regulation, Degradation of purines and pyrimidines, and regulation Biosynthesis, Structure and regulation of ribonucleotide reductase, biosynthesis of ribonucleotides, deoxyribonucleotides and polynucleotides

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4. ROS as inevitable by-products of aerobic metabolism Role of NADPH and glutathione in protecting cells against highly reactive oxygen derivatives. Glutathione metabolism Metabolic dysfunction in human diseases: hypertension, hyperlipidemia, atherosclerosis and metabolic syndrome Inborn errors of metabolism: Glycogen storage diseases, phenylketonuria, albinism, Homocystinuria, Maple-syrup urine disease, Gaucher disease, Fabry disease, Lesch-Nyhan syndrome, Gout

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Evaluation Pattern

Sr. No.




15%


Course Outcomes: Having completed this course, the learner will be able to

1. Student should know normal blood metabolites and should be able to relate to abnormal metabolic conditions and understand diagnosis of metabolic disorders.

Suggested References:

Sr. No.

References

1. Nelson David L. and Cox Michael M. (2017). Lehninger Principles of Biochemistry (7thEdn). W.H.Freeman& Co Ltd, Macmillan Publishers,United States of America.

2. Victor Rodwell, David Bender, et al. (2018). Harper's Illustrated Biochemistry(31stEdn). McGraw-Hill Education,Ahmedabad.

3. Jeremy Berg, John L. Tymoczko and Gregory J. GattoJr andLubert Stryer(9thEd.) (2019). Biochemistry. MacmillanPublishers, United States.

https://en.wikipedia.org/wiki/Jeremy_M._Berg



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4. Thomas M. Devlin(2010). Textbook of Biochemistry With Clinical Correlations. (7thEdn.) Wiley-Liss, Inc., New York.


On-line Resources

Related review articles and research papers

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Course Code PS01CBIT53 Title of the Course Cell Biology


Week 04

Course Objectives:

To expose the students to various microscopy techniques used for cell studies with details understanding of the structure and function of various cell organelles, their organization and interaction with the environment. This will also enlighten them on the regulation of cell cycle and programmed cell death explaining the bases of cancer.

Course Content


1. Microscopy in cell studies:

Principle of working and applications of bright field microscopy, dark field microscopy, phase contrast microscopy, fluorescence microscopy, confocal microscopy, scanning and transmission electron microscopy, scanning tunnelling microscopy, atomic force microscopy. Principle and applications of cytophotometry and flow cytometry. Principles of ultra resolved fluorescence microscope.

25%

2. Cell walls and extracellular matrix.

Nucleus, Nuclear pore complex and transport across nuclear envelope.

Structure and functions of Endoplasmic reticulum, Golgi complex and lysosomes (Protein sorting and transport, Types of vesicular transport and their functions). Structure and function of Mitochondria, Chloroplasts and Peroxisomes. Cell-Cell interactions (Cell adhesion proteins, Tight junctions, gap junctions, plant cell adhesion and plasmodesmata).

25%

3. Structure of Plasma membrane, Transport across plasma membrane.

Endocytosis (Phagocytosis, Receptor mediated endocytosis)

Cytoskeleton and cell movement (Structure and organization of actin filaments; Actin, myosin and cell movement; Intermediate filaments; Microtubules and microtubule motors and movements); cilia and

25%



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flagella: structure and function.

Cell signalling: Signalling molecules and their receptors, Functions of cell surface receptors, pathways of intracellular signal transduction, signal transduction and cytoskeleton, signalling in development and differentiation.

4. Cell division cycle (phases of CDC; Regulation by cell growth and extracellular signals; cell cycle check points; regulators of cell cycle progression-MPF, cyclins and CDKs, Inhibitors of cell cycle progression; M-phase and cytokinesis.

Programmed Cell Death: Difference between necrosis, apoptosis and necroptosis, Caspases, Central regulators of apoptosis (Bcl-2 family), signalling pathways that regulate apoptosis.

Cancer: Types of cancer, development and causes of cancer, properties of transformed cells, oncogenes and tumor suppressor genes.

25%



Evaluation Pattern

Sr. No.




15%



1. Understand various techniques for observing cells, cell organelles and the functioning of the cell.

2. Explain various cell organelles with their function and importance for the cell in its



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physiology.

3. Understand how cell interacts with outside environment especially for its energy need, energy generation and interaction with the environment and other cells.

4 Understand how growth of the cell is regulated, factors and process leading to its death and generation of cancerous condition upon failure of cell cycle regulation.


1. 2. 3. 4.

The cell: A molecular approach-Geoffrey M Cooper and Robert E. Hausman Cell Biology-Karp Molecular Biology of the cell- Alberts Molecular Cell Biology-Lodish et al.


Relevant review articles / research papers / handouts of latest development in the subject.

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Course Objectives:

1. To learn preparation of various types of solutions with precise concentration

2. To learn fundamental Biochemistry and Molecular biology practicals. 3. To learn about chemistry of biomolecules and their qualitative analysis. 4. To learn to estimate various biomolecules using spectrophotometric

techniques.

PS01CBIT54 (Lab 1)

1. Orientation to laboratory instruments: pH meter, visible spectrophotometer, centrifuge, water bath, incubator/shaker, autoclave, hot air oven. General laboratory safety instructions and good laboratory practices. Arrangements of lab chemicals.

2. Biochemical calculations, Preparation of molar, normal solutions 3. Preparation of Buffer 4. Microbial culture transfer techniques and isolation and maintenance of pure cultures. 5. To isolate the genomic DNA from E. coli cells. 6. Quantification of given nucleic acid solution and determination of its purity,

concentration spectrophotometrically. 7. To separate nucleic acid fragments using agarose gel electrophoresis. 8. To estimate DNA by DPA method in unknown sample. 9. RNA estimation by orcinol method 10. Quantitative estimation of total carbohydrates. 11. Quantitative estimation of reducing and nonreducing sugars 12. Extraction and Estimation of total proteins. 13. Determination of acid value, iodine number and Saponification number

Evaluation Pattern

Sr. No.


1. Internal Practical Examination (As per CBCS R.6.8.3) 15%


15%


Course Code PS01CBIT54 Title of the Course

LAB-I


Week 04



Page 2 of 2


1. Carry out basic biochemistry experiments.

2 Isolate and estimate DNA and RNA.

3 Learn spectrophotometric estimation of all biomolecules.

References:

1 2

Thimmaiah S. K. (2012). Standad Methods of Biochemical Analysis. Kalyani Publishes, New Delhi, India. An introduction to practical Biochemistry. David T. Plummer. McGraw Hill book company



Page 1 of 2

Course Objectives:

1. To learn qualitative analysis of carbohydrates, amino acids. 2. To learn fundamentals of mitosis and meiosis. 3. To learn operate standard microscope and understand working of

Fluorescence and Phase contrast microscopy.

PS01CBIT55 (Lab 2 A)

1. Qualitative analysis of carbohydrates 2. Qualitative analysis of amino acids 3. Titration of amino acids and determination of pKa value. 4. Quantitative estimation of amino acids 5. To study various stages of mitosis and meiosis in plant cells. 6. To study different cell organelles (Mitochondria, chloroplasts, lysosomes). 7. Growth curve of yeast cells. 8. Cell counting and Viability assay using Trypan blue. 9. Demonstration of various types of Microscopy (Fluorescence, Phase-contrast)

PS01CBIT55 (Lab 2B)

Practicals related to elective papers

Evaluation Pattern

Sr. No.




15%



1. Carry out fundamental Cell Biology and Biochemistry experiments.

2. Culture and maintain various types of microbes in the lab.


LAB-I


Week 04



Page 2 of 2

, carry out cellular analysis.

3 Do biochemical estimations using uv/visible spectroscopy.

References:

1 2

Thimmaiah S. K. (2012). Standad Methods of Biochemical Analysis. Kalyani Publishes, New Delhi, India. Biochemical Calculations: How to Solve Mathematical Problems in General Biochemistry, 2nd Edition Irwin H. Segel

https://www.wiley.com/en-us/search?pq=%7Crelevance%7Cauthor%3AIrwin+H.+Segel



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Course Code PS01EBIT51 Title of the Course

Phytoresource utilization and conservation


Week 04

Course Objectives:

By the end of this course students will have: 1. Clear understanding on extant of diversified local, regional and global

phytoresources available for mankind. 2. Fair understanding about various kinds of little known phytoresources 3. Greater concern towards the exploration and utilization of traditional or

local varieties of crop plants. 4. 4. Greater concern to recognize and appreciate the knowledge of tribal

and traditional societies on phytoresources, and conservation of such knowledge.

Course Content


1. Concept and extant of plant diversity in wild and cultivation. Innovations meeting for world food demands. Origin and history of plant of domestication and agriculture; centers of crop plant origin and diversity; geographical distribution of crops of Indian origin. Plant genetic resources, their importance in crop improvement, collection and managing genetic resources. Role of biotechnology in germplasm conservation.

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2. A brief account on the following major and minor crops of Indian origin, their products and uses. (i) food grains (ii) oil yielding crops (iii) medicinal and aromatic plants. A brief account on the sources, active principles and uses of (i) alcoholic and non-alcoholic beverages (ii) coloring agents (iii) spices (vi) sweetening agents (iv) petrocrops and biofuels.

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3. Ethnomedicobotany: Scope and potential applications; collection methods of ethnomedicobotanical data; field methods and scrutiny of Herbarium specimens and folklore; verification of data; collection of materials for voucher specimen and for phytochemical screening; Avenue trees: concept, role, site specific selection criteria for urban habitations, industrial zones, and highways.

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Indoor plants: different kinds of indoor plants and their significance; site specific selection and care of indoor plants.

4. Forest products: Important timber yielding plants, timber identification/diagnostic features. Non-timber forest products: bamboos, rattans, gums, resins, tannins. Plants as sources of drugs and pharmaceuticals. Drugs of botanical origin: Structure and physical properties; chemistry of secondary metabolites: phenols, phenolic glycosides, saponins, steroids, alkaloids, vitamins and hormones and natural antibiotics.

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Evaluation Pattern

Sr. No.




15%



1. Appreciate the extant and significance of different wild and domesticated plants.

2. Recognize the extant of traditional knowledge and importance of documenting such knowledge.

3. Develop the spirit of exploring uses unconventional plants and unconventional uses of popular plants.




Page 3 of 3

Sr. No.

References

1. Arora, R., K., Nayar, E., R.,(1984). Wild Relatives of Crop Plants in India. National Bureau of Plant Genetic Resources Science Monograph, New Delhi

2. Bole, P., V., Vaghani, Y., (1986). Field Guide to Common Indian Trees. Oxford University Press, Mumbai.

3. Chandel, K., P., S., Shukla, G., Sharma, N., (1986). Biodiversity in Medicinal and Aromatic Plants in India: Conservation and Utilization. National Bureau of Plant Genetic Resources, New Delhi.

4. Ambasta, S., P., (1986). Council of Scientific & Industrial Research. The Useful Plants of India. Publications and Information Directorate, CSIR, New Delhi.

5. Jain, S., K., (2004). A Manual of Ethnobotany. 2ndEdn. Scientific Publishers Journals Department, Jodhpur.

6. Jain, S., K., Sinha, B., K., Gupta, R., C., (1991). Notable plants in Ethnomedicine of India. Deep Publications, New Delhi.

7. Jain, S., K., (2015). Dictionary of Indian Folk medicine and Ethnobotany. S K Jain Publications, New Delhi.


On-line Resources

Relevant review articles/research papers/handouts of latest development in the subject

*****



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Course Code PS01EBIT52 Title of the Course Biomolecules and Bioenergetics


Week 03

Course Objectives:

Students should be able to : (1) Understand the chemistry of biomolecules (2) Understand the importance of Biomolecules n Biotechnology industries.

Course Content


1. Carbohydrates Introduction, natural occurrence, Physiological importance Classification: aldose and ketoses, Mono, oligo and polysaccharides, Structure of monosaccharide Physical properties of carbohydrates: Isomerism, Asymmetric carbon atom, Stereoisomerism, Optical isomerism and measurement of optical activity, enantiomers, diaterioisomers, epimers, anomers, anomeric carbon atom. Configuration in sugars, Reference carbohydrate, Fischer’s projection formula and representation of various sugars, Haworth’s representation of cyclic structure. Furanose and pyranose structures and representation of various sugars, Mutarotation, Conformation in sugars: boat and chair forms. Chemical properties of carbohydrate due to aldehyde and keto groups: Oxidation of sugars, Reduction of sugars, Lobry de Bruyn-von Ekenstein reaction, Reducing action of sugars in alkaline medium, Action of mineral acids, Action of hydroxylamine, Action of hydrogen cyanide, Action of hydrazine Chemical properties of carbohydrate due to hydroxyal groups: Formation of esters, ethers and glycosides, Importance of glycosides. Transformation of sugars: aldo and keto conversions, Sugars to uronic acids, Sugars to vitamin C.

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2. Amino acids Introduction, structure and classification of: standard amino acids, introduction to rare amino acids, non-protein amino acids, essential Vs Non-essential amino

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acids. Physical properties of amino acids: Stereoisomerism, Optical activity, Acid base properties or Ampholytic Nature of amino acids, Titration curve of Alanine. Chemical reactions of amino acids due to carboxyl group: Decarboxylation, Amide formation. Chemical reactions of amino acids due to amino groups: Sanger’s reaction, Edman’s reaction, Dansyl chloride reaction, Oxidative deamination by Ninhydrin. Protein sequencing and alignment Acid-Base Equilibrium & Henderson and Hassebach equation, Buffers and their importance, pKa of amino acid and their relevance, Common reaction mechanism in biological reaction: Peptide bond formation, oligonucleotide and oligosaccharide synthesis, disulphide bond, group-specific chemical modification for amino acid

3. Introduction, classification & functions of lipids, classification & structure of fatty acids, saturated, unsaturated, hydroxyl, cyclic, branched chain, PUFA, MUFA Physical properties, isomerism, geometrical (cis-trans) isomers, positional isomers, melting point, boiling point, solubility, absorption spectra. Chemical properties: salt formation, detergent, esterification, hydrogenation,halogenations, oxidation, Triglycerides:chemical properties, chemical composition, hydrolysis, saponification, hydrogenation, detergents (action and importance). Chemical constants of fat: saponification value, iodine number, reichertMeissl number, acetyl number, acid number. Rancidity of fats: Hydrolytic, oxidative and lipolytic. Prevention of rancidity Waxes: natural waxes, properties, importance Nucleic acids: Structure of major species of RNA - mRNA, tRNA and rRNA. Nucleic acid chemistry – UV absorption, effect of acid and alkali on DNA.

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4. Bioenergetics: The laws of thermodynamics, concept of entropy and free energy; ATP synthesis and hydrolysis, Biological oxidations-–oxygenases ,hydrolases ,dehydrogenases, free energy changes and redox potentials, Gibbs energy, The mitochondrial respiratory chain, order and organization of carriers, proton gradient, iron sulphur proteins, cytochromes and their characterization (Animals, Plants, and Bacteria),

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ATP- synthetase complex, Chemiosmotic theory of Energy Coupling, Inhibitors of ETC,



Evaluation Pattern

Sr. No.




15%



1. Student should be able to carry out laboratory experiments using biomolecules.


Sr. No.

References

1. S. P. Bhutani. Edition 2nd Edition. First Published 2019. eBook Published 4 October 2019. Pub. Location Boca Raton. Imprint CRC Press

2. D. L. Nelson and M. M. Cox, Lehninger’s Principles of Biochemistry (6th Edition), Macmillan, Worth, Pub. Inc., NY.



Page 4 of 4

3. Jeremy M. Berg, LubertStryer, John Tymoczko, Gregory Gatto, Biochemistry (9th Edition). Publisher: WH Freeman

4. Harper's biochemistry 24th edition by R K Murray, D K Granner, P A Mayes and V W Rodwell. pp 868. Appleton & Lange, Stamford, CT.

5. Thomas M. Devlin,Textbook of Biochemistry With Clinical Correlations. Fourth Edition Edited. Wiley-Liss, Inc., New York. 1997


On-line Resources


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Course Code PS04EBIT53 Title of the Course Microbial Physiology


Week 04

Course Objectives:

1. The primary objective of the course is to build a strong foundation in the area of bacterial cell structure, division, survival and propagation.

2. To provide conceptual information into the understanding of signal transduction in bacteria, adaptation to stress and differentiation of microbial systems.

3. Understand the various physiological aspects of bacterial systems like quorum sensing, ion acquisition, Bioluminescence, Host Parasite interactions and Prokaryotic Immune response.

Course Content


1. Two component signal transduction in prokaryotes Bacterial Cell Structure and its type, BacterialCell surfaces, Bacterial Cell wall structure function and synthesis, Membrane transport in bacteria-simple, group translocation, ABC transporters, Protein export in bacteria–Type 1,2,3,4, Protein export pathways. Bacterial capsules structure and importance. Bacterial organs for locomotion: Flagella: structure, types, synthesis, function and mechanism of locomotion, Swarming motility, Motility in spirochetes, Gliding motility, Twitching. Chemotaxis: Molecular mechanism and physiological significance.

25%

2. Bacterial differentiation: endospore formation, physiological and genetic aspects of sporulation, Sporulation inducing signals and events in sporulation Bacterial cell division: molecular mechanisms involved in formation of Z-ring, Cell division machinery. Yeast cell division: Growth and cell division coordination, Cell division events, molecular basis of cell cycle and control. Microbial stress responses: Oxygen toxicity, pH, Heat shock, Osmotic pressure, Osmolarityregulation in E.coli (Omp system), Phosphate assimilation in E.coli (Pho system), Nitrogen fixation in Klebsiella& Rhizobium (Ntr system). Gut microbiome and human health.

25%

3. Bioluminescence: process, biochemistry, genetics and significance. 25%



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Mechanism of action of antibiotics and mechanisms of drug resistance. Bacteriocins: Structure, Classification and physiological significance of it. Siderophores; structure, function and significance Bacterial biofilm: formation steps, dispersion and control strategies Microbial fuel cells: Energy generation principle and application.

4. Quorum sensing process in gram positive and gram negative bacteria and quorum quenching and its use in developing antimicrobial tools. Microbial production of Hydrogen. Host Parasite interactions: Structures and functions involved in Host-parasite interactions, Bacterial damages to host upon infection. Structure and Mechanism of action of Endotoxin, Exotoxin and Exoenzymes formed by bacteria. The prokaryotic “immune system”, CRISPR/Cas

25%

...



Evaluation Pattern

Sr. No.




15%



1. Students will understand thedetails of bacterial cell structure, their organelles in terms of structure and functions. They will be knowingdifferent secretion systems existing in bacteria for secretion of biomolecules and their role in bacterial survival.



Page 3 of 3

2. Students will have detailed information on bacterial and yeast cell division and bacterial endospore formation.

3. They will be made conversant withsignallingsystem in bacteria in response to various nutritional and physiological stresses.

4. Students will be gaining in-depth knowledge about density-based signal transduction in bacteria and its significance in competence, sporulation and antibiotic resistance; would know about quorum quenching and its use in developing antimicrobial tools.


Sr. No. References

1. Bacterial Signalling, Kramar and Jung

2. Microbial Physiology, Moat, Foster and Spector

3. The Physiology and Biochemistry of prokaryotes, David White

4. Bacterial physiology: A molecular approach, W. E. Sharoud

5. Modern Microbial Genetics, Uldis N. Streips& Ronald E. Yasbin

6. The desk encyclopedia of Microbiology, M. Schaechter

7. Topic related latest review articles.


https://www.nature.com/nrmicro/

https://academic.oup.com/femsre

https://www.swayamprabha.gov.in/index.php/home

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Course Code PS01EBIT54 Title of the Course Fundamentals of microbiology


Week 04

Course Objectives:

1. To introduce students to the world of microbes, their evolution and classification 2.Understanding of the bacterial cell structure and various organelles 3. Introducing students to various methods of studying and cultivating microorganisms 4. Learning the handling and control of microorganisms

Course Content


1. (a) Evolution of microorganisms and microbiology

● Members of the microbial world ● Microbial evolution ● Microbiology and its organisms ● Microbiology today

(b) Introduction to microbial taxonomy and the concept of microbial species.

• Introduction to microbial taxonomy • Taxonomic ranks • Exploring microbial taxonomy • Evolutionary processes and the concept of a microbial species • Bergey’s manual of systematic bacteriology

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2. Understanding a bacterial cell and its characteristics

● The “prokaryote” controversy ● A typical bacterial cell ● Bacterial plasma membranes ● Bacterial cell walls ● Cell envelope ● Bacterial cytoplasm ● External structures of a bacterial cell ● Bacterial motility and chemotaxis

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● Bacterial endospores

3. Methods for studying microbes

(a) Microscopy

• Introduction to principles of microscopy • Various types of Microscopes • Preparation and staining of specimens • Differential and special staining methods

(b) Cultivation of microbes

● Microbial growth and reproductive strategies ● Bacterial cell cycle ● Influence of environmental factors on growth ● Microbial growth in natural environments ● Laboratory culture of cellular microbes ● Growth curve ● Measurement of microbial population size ● Continuous culture of microorganisms

25

4. Control of microorganisms

● Principles of microbial control ● The pattern of microbial death ● Mechanical removal methods ● Physical control methods ● Chemical control agents ● Evaluation of antimicrobial agent effectiveness ● Biological control of microorganisms.

25

...


Evaluation Pattern

Sr. Details of the Evaluation Weightage



Page 3 of 3

No.



15%



1. Recognize the importance of microorganisms and their various forms

2. Understand and appreciate the details of bacterial cell structure.

3. Learn various methods of observation and cultivation of microorganisms

4. Use various methods and control agents for control of microorganisms

5. Appreciate and be capable of handling, using and controlling microorganism


Sr. No.

References

1. Prescott’s Microbiology, Ninth Edition.

2. Fundamentals of Microbiology, Pelczar and Chain

3. Microbiology an introduction: G Totatora, Funke and Case

4. Brock Biology of Microorganisms, Madigan, Martinko, Brock


On-line Resources

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Master of Science (Biotechnology) M.Sc. (Biotechnology) Semester (II)

Course Code PS02CBIT51 Title of the Course Animal Biotechnology


Week 04

Course Objectives:

Students should be able to : (1) Maintain subculture and cell lines (2) Understand the pharmaceutical importance and toxicological aspects of cell culture

Course Content


1. Introduction to animal tissue culture (Background, Advantages and limitations of tissue culture, major differences between in vivo and in vitro, types of tissue culture) Biology of cultured cells (Brief description on cell adhesion, cell proliferation, energy metabolism and origin of cultured cells) General out-line of cell types (epithelial tissue, connective tissue, muscular tissue and nervous tissue) Stem cells, germ cells and amniocytes (Culture of embryonic stem cells, culture of amniocytes, applications of stem cells) Aseptic Techniques (Objectives of aseptic techniques, elements of aseptic environment, sterile handling) Sterilization (Different types- dry heat (hot air oven, wet heat (autoclaving), various chemical agents used in sterilization, irradiation techniques (UV and Gamma Ray) Culture of specialized cells (liver, epidermal, astrocytes, testis and ovary)

25

2. Defined media and supplements (Physicochemical properties, balanced salt solutions, serum, selection of medium and serum) Serum- Free Media (Disadvantages of serum, advantages of Serum-free media, Preparation of serum free media, Animal protein free media) Primary culture (Initiation of primary cell culture, isolation of tissue, types of primary culture, mechanical and enzymatic disaggregation) Sub culture and cell lines (Subculture and propagation, routine maintenance, subculture of monolayer and suspension cultures) Monitoring for contamination- Visible microbial contamination, mycoplasma, Viral contamination, Eradication of contamination

25

3. Cell cloning and selection (Feeder layer, suspension cloning, separation of clones)

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Cell separation (Centrifugation, Antibody based techniques, FACS) Cell differentiation (Stem cell plasticity, markers of differentiation, induction of differentiation, differentiation and malignancy) Transformation and Immortalization (Immortalization with viral genes, Immortalization of human fibroblasts, telomerase induced immortalization, Aberrant growth control, tumerogenicity) Characterization (Need for characterization, characterization based on cell morphology, DNA and RNA content, enzyme activity and antigenic markers)

4. Animal reproductive biotechnology: artificial insemination, super ovulation, embryo recovery and in vitro fertilization, ISCI, ZIFT, GIFT, 3 D culture and Idmoc, culture and cryopreservation of embryos, applications of transgenic animal biotechnology; animal cloning- basic concept, cloning for conservation of endangered species. Vaccinology: conventional methods of animal vaccine production, recombinant approaches to vaccine production, modern vaccines.

25



Evaluation Pattern

Sr. No.




15%



1. Student should be able to maintain and work in animal cell culture as well as vaccine production lab



Page 3 of 3


Sr. No.

References

1. Freshney, R. I. (2015). Culture of Animal cells: a manual of basic technique and specialized applications (6thEdn). John Wiley & Sons, Chicago.

2. Masters, J. R. (2000). Animal Cell Culture: a practical approach (3rdEdn). Oxford University Press, UK.

3. Davis, J. M. (Ed.) (2000). Animal Cell Culture: essential methods. John Wiley and Sons, UK.

4. Gilbert, S. F. (2020). Developmental biology. (12thEdn.) Sunderland, Mass: Sinauer Associates.


On-line Resources


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Master of Science M Sc Microbiology Semester III

Course Code PS02CBIT52 Title of the

Course Enzyme Technology


Week 04

Course Objectives:

1.Understanding of basics properties of enzymes 2.Understand factors influencing enzymes and their reaction kinetics 3. Understand the Industrial applications of enzymes and their engineering and computational methods to understand properties and working of enzymes

Course Content


1. Introduction to Enzymology&Practical Enzymology Introduction and historical developments in enzymology Protein Structure: Primary, secondary, tertiary and quaternary structure, techniques used in enzyme characterization Enzyme nomenclature and classification, Characteristics, chemical nature and properties of enzymes, enzyme specificity and rate enhancement. Enzyme Activity, assay methods, factors affecting enzyme activity, progress curve, enzyme activators, coenzyme and cofactors. Enzyme purification: Objectives and strategy, separation techniques, test of purity, case study

25

2. Enzyme Kinetics (Single substrate and Multi-substrate) Chemical reaction kinetics and catalysis Single substrate kinetics: Equilibrium and Steady state kinetics, significance of Km, Vmax&Kcat, enzyme efficiency. Multisubstrate kinetics: General rate equation, compulsory order, random order and ping-pong mechanisms and their primary and secondary plots. Oligomeric enzymes and sigmoidal kinetics Enzyme inhibition and its kinetics: Reversible and irreversible inhibition, competitive, non-competitive and uncompetitive, mixed, partial, substrate inhibition. Thermal kinetics: Effect of temperature on reaction rate, enzyme stability, Arrhenius equation and activation energy.

25

3. Enzyme technology I Industrial enzymes:Production strategies and downstream processing of industrial enzymes.

25



Page 2 of 4

Enzyme Immobilization, Immobilized enzyme reactors Applications of enzymes in diagnostics, as analytical agents, as therapeutic agents, Industrial applications of various enzymes. Business of enzymes in India and world

4. Enzymes Technology II Enzyme engineering: Structure function relationship, Methods of enzyme alterations, examples of engineered proteins. Enzymes in non conventional media, Isoenzymes and its physiological significance, Ribozymes and Abzymes enzyme sensors Design and Construction of novel enzymes Enzyme Computational Biology: Databases and tools for viewing and analysis of structures, comparing structures, locating active site and understanding mechanisms.

25



Evaluation Pattern

Sr. No.




15%




Page 3 of 4


1. Appreciate the versatility of enzymes in the living systems, their properties and working

2. Handle and work with enzymes to understand in depth their kinetics, mechanisms and their regulatory roles.

3. Understand The market potential and economics of enzyme production.

4 Get trained and work with the applications of enzymes in industries, therapeutics and other sectors and also the role of engineered enzymes Appreciate the significance of isoenzymes, abzymes and ribozymes


Sr. No.

References

1. The chemical kinetics of enzyme action: K. J. Laider and P. S. Bunting, Oxford UniversityPress, London.

2. Enzyme Structure and mechanism: Alan Fersht, Reading, USA.

Understanding Enzymes: Trevor Palmer

Fundamentals of Enzymology: Nicholes C. Price and Lewis Stevens, Oxford Univ. Press.

Enzymes: M. Dixon, E. C. Webb, CJR Thorne and K. F. Tipton, Longmans, London

Enzyme Technology: Anusha Bhaskar and V.G. Vidhya, MJP Publishers, Chennai, India.

Enzymes:, Catalysis, Kinetics and Mechanisms, By N.S. Punekar. Springer nature publications, Singapore

ENZYME KINETICS A Modern Approach by Alejandro G. Marangoni. John Wiley & Sons, Inc., Hoboken, New Jersey.

Proteins: Thomas Creighton

Biochemistry: Lubert Stryer.



Page 4 of 4

Enzymology, T Devasena, Oxford Publication


On-line Resources:

https://www.expasy.org/

https://www.ncbi.nlm.nih.gov/

*****



Page 1 of 3


Course Code PS02CBIT53 Title of the Course Immunology


Week 04

Course Objectives:

1. To understand various components of immune system of host fighting against diseases and their structure, organization and function in the defense.

2. To make the students understand the underlying mechanisms leading to malfunctioning of the system and causes and treatment measures for conditions like allergy, autoimmunity and organ transplantation.

Course Content


1. Introduction to immune system: Fundamental concepts; Specificity, memory, diversity and discrimination of self from non-self Cells and organs of the immune system involved in innate and adaptive immunity: cells of the immune system, primary and secondary lymphoid organs – structure and function. Innate immunity: Barriers to entry of pathogens, receptors of the innate immunity (TLR and sensing of PAMPs, CLR, RLR and CLR); Phagocytosis; inflammatory responses. Antigens: antigenicity, immunogenicity and haptens. B and T cell epitopes.

25%

2. Antibody: Structure of immunoglobulin; classes of immunoglobulins, Antibody mediated effector functions. The Organization and Expression of Lymphocyte Receptor Genes: Hozumi and Tonegawa’s Experiment, Multigene organization of Ig Gene, Mechanism of V(D)J recombination, B cell receptor expression, allelic exclusion,B cell isotype switching and somatic hypermutation; expression of membrane bound and soluble immunoglobulin; T cell receptor genes and expression. Complement system: Classical, alternative and lectin pathways, role and regulation of complement system, complement deficiencies. Antigen-antibody interactions: Agglutination, precipitation, RIA and ELISA.

25%

3. The Major Histocompatibility Complex and Antigen Presentation: The structure and function of MHC molecules, general organization and

25%



Page 2 of 3

inheritance of MHC, self – MHC restriction, endogenous and exogenous pathway of antigen processing and presentation; cross presentation of exogenous antigen, presentation of non peptide antigens Cytokines: Properties, receptors, associated diseases, therapeutic applications, cytokine signalling pathways: JAK-STAT and FAS-FASL signalling pathways. Tolerance and autoimmunity: Central and peripheral tolerance; Mechanism of autoimmunity; Autoimmune concepts of systemic and organ specific autoimmune diseases.

4. Cell mediated effector response (Generation of effector CTL’s, Granzyme and Perforin Mediated Cytolysis, Fas-FasL Mediated Cytolysis, NK cell mediated cytolysis. Hypersensitivity and Transplantation: Comparative study of Type I-V hypersensitivities with examples. Grafts and graft rejection mechanism, prevention and control. Tumor immunology and vaccines: Tumor antigens, immune response to tumors and immunotherapy of tumors. Types of vaccines and recent developments.

25%



Evaluation Pattern

Sr. No.




15%



1. To understand the fundamental basis of immune system and immune responses generated against pathogens.



Page 3 of 3

2. To understand the genetic organization for antibody molecules and role of various signalling processes in development and functioning of the immune system.

3. To understand various disorders related to immune system resulting from genetic deficiencies or over response of the system.


Sr. No. References

1. Owen, J. A., Punt, J., &Stranford, S. A. (2013). Kuby immunology (7thEdn). New York: WH Freeman.

2. Murphy, K., & Weaver, C. (2016). Janeway'sImmunobiology (9thEdn) Garland Science.

3. Male, D., Brostoff, J., Roth, D., &Roitt, I. (2012). Immunology (8thEdn) With STUDENT CONSULT Online Access. Elsevier Health Sciences.

4. Abbas, A. K., Lichtman, A. H., & Pillai, S. (2014). Cellular and molecular immunology (6thEdn) Elsevier Health Sciences.

5. W. E. Paul (2013). Fundamental of Immunology (7th Ed.) Lippincott Williams and Wilkins.


Relevant review articles / research papers / handouts of latest development in the subject.

*****



Page 1 of 2

Course Objectives:

1. To learn lay out and working conditions of animal cell culture laboratory. 2. To learn carry out viability assay and maintain cell line by subculturing

using specific media at appropriate conditions. 3. To learn enayme assays. 4. To learn kinetic analysis of enzymes.

PS02CBIT54 (Lab 1) 1. Lab instruments (CO2 incubator, biosafety, inverted microscope) 2. Viable count (trypan blue) 3. MTT assay 4. Primary and secondary culture of animal cells 5. Invertase Assay 5. Progress curve 6. Enzyme curve 7. Substrate saturation curve 8. Optimization of pH for invertase activity 9. Analysis of Substrate saturation data by various plots 10. Inhibition kinetics 11. Optimization of Temperature for invertase activity 12. Effect of temperature on Rate of reaction and determination of activation energy 13. Effect of temperature on enzyme stability 14. Enzymology workshop: kinetics, plots and numericals

Evaluation Pattern

Sr. No.




15%




LAB-I


Week 04



Page 2 of 2

1. Carry out design and carry out experiments in animal cell culture facilty.

2. Carry out enzyme assays and determine kinetic constants.

References:

1 2

Renee Alexander et al.Basic Biochemical methods. John Wiley and sons. Thimmaiah S. K. (2012). Standad Methods of Biochemical Analysis. Kalyani Publishes, New Delhi, India.

SARDAR PATEL UNIVERSITY VallabhVidyanagar, Gujarat


Page 1 of 2

Course Objectives:

1. To learn differentiate and count blood cells. 2. To learn fundamental Immunological tests like immune electrophoresis,

ELISA, Rocket Immuno electrophoresis, etc. 3. To learn separation of proteins by electrophoresis and western blotting.

PS02CBIT55 (Lab 2A)

1. Total count of RBC and WBC. 2. Differential count of WBC. 3. To determine Blood group of given sample 4. To study the technique of immune-electrophoresis for determination of the

concentration of antigen in unknown sample. 5. To study the immuno-diffusion technique by single radial immuno-diffusion. 6. To learn the technique of Dot ELISA for the detection of an antigen. 7. Latex agglutination test 8. RA —Rheumatoid Arthritis test 9. RPR —Rapid Plasma Ragine Test 10. Ouchterlony Double Diffusion test 11. Rocket Immuno-electrophoresis test 12. Counter current Immuno-electrophoresis test 13. Immuno-electrophoresis test (SDS-PAGE) 14. Western blotting test (SDS-PAGE)

PS02CBIT55 (Lab 2B)

Practicals related to elective papers

Evaluation Pattern

Sr. No.




15%



LAB-I


Week 04

SARDAR PATEL UNIVERSITY VallabhVidyanagar, Gujarat


Page 2 of 2


1. Carry out experiments with blood samples.

2. Carry out fundaments immunology testing.

References:

1 Thimmaiah S. K.(2012). Standad Methods of Biochemical Analysis. Kalyani Publishes, New Delhi, India.



Page 1 of 3


Course Code PS02EBIT51 Title of the Course Principles of Ecology


Week 04

Course Objectives:

(i) To understand the ecological aspects of biotic and abiotic mechanisms.

(ii) To learn about distribution, growth and maintenance at population level

(iii) To appreciate about the natural resources and their diversity

Course Content


1. Basic Concepts of Ecology and Environment. Ecosystem concept; Structure and functions of biotic and abiotic components; Energy in ecosystems; Energy exchange and productivity: food chains and food webs, ecological pyramids, nutrient cycles and recycle pathways. Evolution of human settlement, Influence of human activities including various developmental activities on natural ecosystems and on environment.

25

2. Autecology, synecology, habitat ecology, systems ecology. Population - Density, Natality, Mortality, Dispersal, Age distribution, Population distribution; Population growth – Factors affecting biotic potential, Carrying capacity; Population regulation. Community organisation: concept of habitat and niche; population dynamics, species and individuals in the ecosystem. Ecological interactions between different species. Concepts of Habitat, Ecological niche. Keystone species, Dominant species. Types of forest, characteristic features, structure and function of forest, grassland, plantation, desert; Aquatic and agro-ecosystem. Ecological succession-types and causes.

25

3. Climate change: Global warming and greenhouse effect, sources and sinks of green house gases, major GHGs, monitoring greenhouse gases in atmosphere. Impact of climate change on agriculture, forestry, water resources, human health and overall ecological processes. Carbon sequestration; Types of renewable sources of energy; Solar energy, wind energy Geothermal and tidal energy; Biogas, Bio

25



Page 2 of 3

fuels from petrocrops, Energy plantation crops

4. Natural resources of India: land, soil, water, forest including wildlife. Effects of deforestation on soil erosion; Land degradation. Restoration of degraded ecosystems: Soil and water conservation, rain water harvesting and watershed management. Controlling desertification, floods and biological invasions. Impact of green revolution on the environments.

25



Evaluation Pattern

Sr. No.




15%



By the end of this course students will have:

1. An overview of various ecological components of local, regional and global level and their significance.

2. Clear understanding about linkages between biotic and abiotic components

3. Greater sensibility towards the natural world that is still surrounding them.

4. Correlating relationships and conflicts between socioeconomic development and conservation of ecosystems

5. An encouragement to appreciate the ecological services provided by different wild



Page 3 of 3

species.


Sr. No.

References

1. Begon, M., Harper, J. L., Townsend, C. R., (1996), Ecology.4th Edn. Blackwell Science, Cambridge, USA.

2. Odum, E. P., Barrett, G. W. (2005). Fundamentals of ecology. 5thEdn. Thomson Brooks/Cole, Belmont, CA.

3. Ambasht, R. S., Ambasht, N. K. (2017). Textbook of Plant Ecology.15thEdn. Students Friends Publishers, Varanasi

4. Mahendran P., P., Rajan, P., M., (2008). A Textbook on Ecology & Environmental Science. Agrotech Publishing Academy, Rajasthan

5. Sharma, P. D., (2001). Ecology and Environment. Rastogi Publications, Meerut.


On-line Resources

*****



Page 1 of 4


Course Code PS02EBIT52 Title of the Course Biostatistics


Week 04

Course Objectives:

1. Recognize the importance of data collection and its role in determining scope of inference.

2. Understanding of interval estimation and hypothesis testing. 3. Choose and apply appropriate statistical methods for analyzing one

or two variables. 4. Use technology to perform descriptive and inferential data analysis

for one or two variables. 5. Interpret statistical results correctly, effectively, and in context. 6. Appreciate the power of data. 7. To learn explain how statistical techniques are incorporated in the

analysis of biological research data and its presentation. 8. Able to create graphs using Stata to communicate important

information about data, and interpret these graphs. 9. Produce a statistical summary of continuous, categorical or censored

survival data in a single sample using Stata, and interpret it. 10. Explain fundamental concepts in the design and analysis of medical

studies, including the difference between observational and experimental studies, the unit of randomization in randomized studies, the outcome measure of a study, the comparability of the control group or control population, and adjustment for confounding.

11. Explain the concept of a random, representative sample from a population.

12. Explain the logic behind statistical confidence intervals and hypothesis tests.

13. Explain the logic behind parametric tests, permutation tests, (bootstrap estimates of variability and bootstrap confidence intervals); compute them and interpret them.

Course Content


1. Elementary concepts of Biostatistics: Definitions, Importance and Scope of Statistics; Types of Survey Methods; Importance of Data Collection & Data Collecting methods; Concept of a statistical population and sample from a population; Methods of drawing sample from the population: Simple Random Sampling (SRS), Stratified Random Sampling, Cluster Sampling; Experimental Method; Types of Biological Data: Qualitative (Categorical ) Data: Nominal and Ordinal Data Quantitative (Numerical) Data: Individual, Discrete and



Page 2 of 4

Continuous Data; Presentation of Data: Construction of frequency distribution (Simple or Discrete and Grouped): Rules for constructing Grouped frequency distribution; Diagrammatic Presentation: Bar Diagram (Chart), Simple, Sub – divided (Component), Percentage, Multiple, Pie Chart; Graphical Presentation: Stem-and-Leaf Plots, Line Graph, Histogram, Frequency Polygon, Frequency Curve, Ogives or Cumulative Frequency Curves. Descriptive Statistics: Measures of Central Tendency: Mean or Arithmetic Mean, Median, Mode, Partition Values: Quartiles, Deciles, Percentile; Measures of Dispersion (Variation): Range, Quartile Deviation (Q.D), Inter Quartile Range (IQR), Mean Deviation (MD), Standard Deviation (SD) and Variance, Coefficient of Variation (C.V), Box and Whisker Plot. Measures of Skewness and Kurtosis: Absolute and Relative Skewness; Karl – Pearson’s Coeff. of Skewness, Bowley’s Coeff. of Skewness, Skewness based on moments; Moments, Kurtosis.

2. Correlation and Regression Analysis: Correlation: Meaning, Applicaions & Types of Correlation; Positive, Negative, Non–Sense or Spurious; Methods of studying correlation: Scatter Plot (diagram) method, Karl-Pearson’s Correlation Coefficient (Product Moment) Method; Properties of Correlation Coefficient Coefficient of determination and its meaning: Spearman’s Rank Correlation Coefficient; Properties of Rank Correlation Coefficient Regression: Meaning, Properties and Application of Regression Analysis and Regression Coefficients;

3. Concepts of Probability and Probability Distributions: Elements of Probability theory; Classical definition of Probability; Types of Experiments and Events; Theorems/Laws of Probabilities; Conditional Probability; Bayes’ Theorem; Importance and Properties of Probability Distributions: Binomial Distribution, Poisson Distribution, Normal Distribution. Testing of Hypothesis: Procedure of testing hypothesis; Standard Error and Sampling distribution;

4. Different tests of Significance: Large Sample Test: Z - test for (Single) population proportion; Z - test for difference between two population proportions; Z - test for (Single) population mean; Z - test



Page 3 of 4

for difference between two population means; Small Sample Test: t – test for (Single) Population Mean, t – test for difference between two population means (Unpaired t-test), t – test for difference between two population means (Paired t-test); Chi (χ2) test and Goodness of fit; F-test and Analysis Of Variance (ANOVA): Techniques of Analysis of Variance; One–Way Classification, Two–Way Classification model;


Online / Offline / Presentation / Videos

Evaluation Pattern

Sr. No.




15%



1. Develop the ability to apply the methods while working on a research project work.

2. Describe the appropriate statistical methods required for a particular research design.

3. Choose the appropriate research design and develop appropriate research hypothesis for a research project.

4. Develop a appropriate framework for biological research studies.


Sr. No.

References

1. Gupta S.C. and Kapoor V.K. (1986): Fundamental of Mathematical Statistics Sultan Chand and Sons Publishers.

2. Statistical Methods by S. C. Gupta Sultan Chand & Sons publishers.



Page 4 of 4

3. Principles of Biostatistics by Marcello Pagano and Kimberlee Gaurea, Chapman and Hall/CRC publisher.

4. Biostatistics: A Foundation For Analysis in the Health Sciences by Daniel, Wayne (Seventh Edition), Wiley India Pub.


On-line Resources

*****



Page 1 of 3


Course Code PS02EBIT53 Title of the Course Medical Microbiology


Week 04

Course Objectives:

1. To train students in the field of Medical Microbiology with details on representative infections caused by Bacteria, Viruses, Parasites, andfungi.

2. Exposure of students toroutine and advanced molecular diagnosis techniques for the detection of medically important human microbial pathogens and commonly employed prevention and treatment processed

3. Training of the students to work as laboratory technicians and assistpathologist.

Course Content


1. Basics in Medical Microbiology Sources of infection, Modes of transmission,carriers andtheir types – investigation of epidemic diseases.Types of infectious diseases, Prevention and Control of Hospital acquired infections. Immunoprophylaxis.Vaccines: Types and their mode of action. Recent advances in diagnostic microbiology: Automation, Nucleic acid based detection methods. Epidemiology: General account, Principle, Scope and application.

25%

2. Bacteriology Morphology, Cultural Characteristics, Antigenic structures, Pathogenesis, Laboratory Diagnosis, Epidemiology of following bacteria: Staphylococcus, Streptococcus including Pneumococcus, Corynebacterium, Clostridium, Mycobacteria,Vibrios, E. coli, Salmonella, Brucella and Neisseria

25%

3. Virology The Nature and classification of viruses, Morphology: Virus structure

and Virus replication. General properties, diseases caused, lab diagnosis, epidemiology and

prevention of:Pox, Hepatitis (HAV & HAB), Orthomyxo (Influenza), Rabdo (Rabies), SARS, MARS, SARS-CoV-2 and HIV virus

Antiviral compounds [chemicaland natural products] and their mode of action.

25%



Page 2 of 3

4. Parasitology & Mycology Parasitology: Laboratory techniques in parasitology. Morphology, life cycle, laboratory diagnosis, epidemiology of following parasites: Parasites: Entamoeba, Giardia, Leishmania, Plasmodium, Helminths: Taenia, Ascaris, Wuchereriabancrofti, Schistosomes Mycology: Morphology, diseases caused, epidemiology and lab diagnosis of:- Opportunistic fungi - Cryptococcus, Candida, AspergillusMucormycosis Fungi causing Cutaneous mycoses- Dermatophytes Subcutaneous mycoses - Mycetoma, Systemic mycoses-Histoplasma

25%

...



Evaluation Pattern

Sr. No.




15%



1. Students will learn basis of virulence factors and pathogenesis of different bacterial, parasitological, viral and mycological diseases and the laboratory diagnosis techniques. They would also understand epidemiological aspects and social impact of some dreadful as well as emerging infections like HIV,MARS, SARS-CoV-2, Mucormycosisetc.

2. Understand the specimen collection techniques and identification of pathogens by conventional and recent molecular methods.



Page 3 of 3

3. Students will understand the significance of vaccination, antiviral compound and their mode of action.


Sr. No. References

1. Textbook of Microbiology by Surinder Kumar

2. Medical Parasitology by R. Karyakarte.

3. Text Books of Medical Laboratory Technology by P. B. Godkar.

4. A Text Book of Medical Microbiology by Anathanarayana&Panikar

5. A Text Book of Microbiology by P. Chakraborthy

6. Parasitology by Chatterjee, KD

7. Textbook of medical mycology by JagdishChander,

8. An Introduction to Viruses by Biswas SB and Biswas


https://www.cdc.gov/

https://www.icmr.gov.in/


*****




Page 1 of 3


Course Code PS02EBIT54 Title of the Course Microtechniques


Week 04

Course Objectives:

1. To teach various light and electron microscopes.

2. To teach material processing for permanent slide preparation light and electron microscopes.

3. To teach various microtomes for wax embedded and resin embedded material.

4. To teach the techniques for enzyme localization

Course Content


1. Light microscopy Properties of lenses, Optical corrections, Properties and types of objectives, Oculars and Illumination. Light microscopes: Bright field, dark field, fluorescence, phase contrast, polarizing, differential interference contrast. Micrometry and photomicrography.

2. Basic components of electron microscopes. Thermionic and field emission guns. Types of electron microscopes: TEM, SEM, STEM, ESEM and HVEM

3. Maceration, squash and clearing techniques. Sample preparation for light microscopy. Classification of fixatives, formulas', (Plant and animal samples). Sample preparation for light microscopy: Fixation, dehydration and infiltration procedures. Embedding media for light microscopy. Stains and staining procedures- negative and positive staining procedures. Microtomes: Rotary, sliding, cryostat. Histochemical localization of metabolites for light microscopy: Starch, proteins, lipids, total carbohydrates, lignins, polyphenols, nucleic acid, histones, cutin, suberin and waxes. Localization of enzymes: Peroxidase, acid phosphatase and succinic dehydrogenase.

4. Freeze etching and freeze fracturing. Sample preparation for Electron microscope: Fixatives, double fixation, dehydration and infiltration procedures, embedding media for electron microscopy. Fixation and embedding of particulate samples like bacteria, virus etc. ultra-microtome and freezing ultramicrotomesemi thin sectioning, ultrathin sectioning, grids, formavar coating, Staining for electron microscopy. Ultrastructural cytochemistry: Tannin, protein, cell wall



Page 2 of 3

polysaccharide, lignin and membrane. Enzymes: Peroxidase and phosphatase. Immunocytochemistry.

...


Evaluation Pattern

Sr. No.




15%



1. Students will have thorough understanding of modern development in light and electron microscopy.

2. Students will be able to process plant/ animal samples for permanent slide preparation.

3. Students will gain knowledge regarding various biological stains.

4. Students will be able to localize various enzymes in plant/animal tissue.


Sr. No.

References

1. Microscopy and Microtechnique: R Marimuthu MJP Publisher, Chennai



Page 3 of 3

2. • The study of plant structure: Principles and selected methods- T. P. O’ Brien and M E McCully

3. Plant Microtechnique- Johansen, DA, McGraw Hill Book Co., New York.

4. Botanical Microtechnique and Cytochemistry;Graeme P. Berlyn and Jerome P Micksche.


On-line Resources

*****



Page 1 of 3

Master of Science (Biotechnology) M.Sc. (Biotechnology) Semester (III)

Course Code PS03CBIT51 Title of the Course Fermentation technology


Week 04

Course Objectives:

1. To understanding of upstream and downstream processing 2. To understand Isolation, preservation, improvement, handling of organisms and optimization of media 3. To understand various types of small and large scale equipment, controls and concept of scale up 4. To understand basic concepts of growth, cultivation and product recovery 5. To understand biochemistry for overproduction of various industrially important microbial metabolites. 6. To learn about fermentation processes for various primary metabolites, secondary metabolites, microbial biomass and biotransformations.

Course Content


1. Introduction to bioprocess technology, Isolation, preservation and improvement of industrially important organisms. Substrates for fermentation processes. Medium optimization Bioreactor design: Laboratory, pilot and large scale reactors. Plug flow reactors, enzyme reactors. Inoculum development and aseptic inoculation Sterilization of media and air

25

2. Kinetics of growth and substrate utilization in batch, fed batch and continuous systems. Mass transfer of oxygen: Agitation and aeration, Determination of KLa, factors affecting KLa, fluid rheology. Control of process parameters: Instrumentation for monitoring bioreactor and fermentation processes, Sensors, Controllers, fermentation control systems and architecture, Incubation and sequence control, advanced control. Downstream processing: Methods of Cell separation, Disruption and product purification. Fermentation economics

25

3. Fermentative production and applications of primary metabolites: Citric acid, L Glutamic acid, L Lysine ,Vitamins B12 and Vitamin B2 Industrially important microbial enzymes: Types, mode of action and

25



Page 2 of 3

applications of microbial amylases and proteases Microbial production of therapeutically important secondary metabolites:. Penicillin , Ergot alkaloids

4. Biotransformations of steroids: Hydroxylations and dehydrogenations, Sterol biotransformations. Production and applications of microbial exopolysaccharides: Classification, biological functions, Structure and Biosynthesis of Xanthan and Alginate, Factors affecting fermentative production of exopolysaccharides and recovery. Technology of Beer brewing: Single cell proteins: Production and applications. Production of bioplastics

25

...



Evaluation Pattern

Sr. No.




15%



1. Appreciate the concept and scope of Bioprocess upstream and downstream processing and the economics of industrial processes

2. Handle and work with Microbial cultures, especially its screening, maintenance,



Page 3 of 3

preservation and cultivation

3. Get trained and work with industrial processes for large scale sterilization, inoculation, production and product recovery

4. Develop ability to understand various strategies for enhanced fermentative production of various primary and secondary metabolites of microorganisms.


Sr. No.

References

1. Principles of Fermentation Technology : Whitekar & Stanbury

2. Comprehensive Biotechnology : Murray Moo Young

3 Methods in Industrial Microbiology : Sikyta

4 Fermentation Microbiology and Biotechnology, El Mansi and Bryc

5 Microbial technology by Peppler

6 Biotechnology by Rehm and Reid

On-line resources will be provided by teacher from time to time

*****



Page 1 of 3


Course Code PS03CBIT52 Title of the Course Genetic Engineering


Week 04

Course Objectives:

1 To understand the basic tools and techniques used for manipulation of DNA 2. To become familiar with the strategies for production of transgenic organisms 2. To learn applications of genetic engineering in agriculture, industry and medicine

Course Content


1. Concept and importance of Genetic Engineering; General strategies and Steps involved in gene cloning: Extraction and purification of DNA and RNA from bacteria, virus, plant and animal cells; physical and enzymatic methods for cutting DNA; Introduction of DNA into host cells; screening and selection methods for recombinant clones.

25%

2. Basic properties and cloning strategies for vectors derived from Plasmids, bacteriophages and their chimeric vectors, YAC, BAC, HAC/MAC and viral vectors for Plant and animal cells. Salient features of expression vectors for heterologous expression in E. coli, Yeast, insect and mammalian system. Shuttle vectors and gene trapping vectors. Vector design and modification strategies; chemical synthesis of oligonucleotides.

25%

3. DNA sequencing and sequence assembly: Maxam-Gilbert’s and Sanger’s methods, Shot gun sequencing, Next generation sequencing strategies for large genomes. DNA mapping and DNA fingerprinting: Physical and molecular mapping, Hybridization and PCR based methods of fingerprinting. Site directed mutagenesis: Methods and applications. Polymerase Chain Reaction: Principle and basic types of PCR; Reverse Transcription and Real Time PCRs. Construction genomic and cDNA libraries;

25%

4. Applications of Genetic engineering in improvement of plants, animals and microbes; Gene editing and its applications; Metagenomics and Metabolic engineering; Gene therapy; Restriction and regulations for

25%



Page 2 of 3

the release of GMOs; Biosafety and levels of Physical and Biological containment; The Indian Guidelines for release and use of GM organisms.



Evaluation Pattern

Sr. No.




15%



1. Explain different steps involved in gene cloning, different enzymes available and how to choose an enzyme for a particular application in genetic engineering.

2. Describe salient features of different vectors available, their design and strategies to be applied for cloning and selection of recombinants.

3. Explain details of preparation of genomic and cDNA libraries as well as discuss various strategies for screening of recombinant clones.

4 Explain the PCR and its variants in detail along with their applications. Students will be able to design PCR primers and reaction parameters.

5 Describe different types of molecular markers and their applications in detail.

6 Explain various DNA sequencing techniques and their applications in detail.

7. Describe genetic engineering guidelines and regulatory procedures to be followed while



Page 3 of 3

conducting genetic engineering experiments


Sr. No.

References

1. Principles of Gene Manipulation and Genomics” by Sandy B Primrose and Richard Twyman

2. Genetic Engineering by Smita Rastogi and Neelam Pathak

3. Gene cloning: An introduction. T. A. Brown


On-line Resources

*****



Page 1 of 3


Course Code PS03CBIT53 Title of the Course Plant Biotechnology


Week 04

Course Objectives:

1.To make the students understand the concepts of modern techniques in plant propagation 2.To facilitate the students with knowledge on recent developments in crop improvement 3. To address the pros and cons of GM crops. 4. To facilitate technical and theoretical know how for the application of molecular tools in crop improvement and crop production.

Course Content


1. Cell & tissue culture in plants; in-vitro morphogenesis, organogenesis and embryogenesis; Artificial Seeds, Micro propagation (Clonal propagation); Haploidy; anther and ovule cultures, Embryo cultures; Protoplast isolation, culture and protoplast fusion and somatic hybridization, Cybrids, Somaclonal Variation;; Virus elimination, pathogen indexing; Cryopreservation

25%

2. Production of secondary metabolites; Sources of plant secondary metabolites;criteria for cell selection, factors affecting the culture of cells; different bioreactorsand their use in secondary metabolite production; biochemical pathways for theproduction of different secondary metabolites; and biotransformation.

25%

3. Methods for genetic transformation and transgenic plants production throughAgrobacterim tumefaciens and A. rhizogenes; Gene transfer methods in plants; PEG mediated, particle bombardment, Molecular markers and their importance in plant breeding, Marker Assisted Selection (MAS).

25%

4. Commercially grown Transgenic plants: BT crops, Golden rice, transgenic crops for herbicide tolerance, disease and abiotic stress resistance. Indian laws and regularions for the release and cultivation of transgenic plants. Biotechnology and intellectual property rights (IPR); Plant geneticresources GATT & TRIPS; Patent for higher plant genes and DNA sequence

25%

Teaching-Learning

Topics will be taught and discussed in interactive sessions using



Page 2 of 3

Methodology conventional black board and chalk as well as ICT tools such as power point presentations and videos. Practical sessions will be conducted in a suitably equipped laboratory either individually or in groups depending on the nature of exercise as well as availability of infrastructure. Course materials will be provided from primary and secondary sources of information.

Evaluation Pattern

Sr. No.




15%



1. Understand the significance of plant biotechnology for improving crop productivity

2. They can apply this knowledge to establish clonal propagation methods for important as well as endangered plants

3. Students will also understand the pros and cons of transgenic plants as well as intellectual property management and handling of GMOs.

…


Sr. No.

References

1. Plant Biotechnology: The genetic manipulation of plants – Adrial Slater, Nigel W. Scott and Mark R. Fowler

2. An Introduction to Plant Biotechnology: H.S. Chawla

…



Page 3 of 3


On-line Resources

*****



Page 1 of 2

Course Objectives:

1. To learn to isolate bacterial cells and carry out fermentation experiments. 2. To learn Molecular Biology techniques like isolation of Plasmids,

Restriction digestion, agarose gel electrophoresis etc. 3. To learn RAPD analysis.

PS03CBIT54 (Lab 1)

1. Cellulase production by Solid State Fermentation (SSF)

a. Endoglucanase assay b. Filter paper activity c. Protein estimation by Folin’s and Lowry’s method 2. Saccharification of agro-waste by cellulose 3. Yoghurt making 4. Isolation of lactic acid bacteria 5. Antimicrobial activity of Lactobacillus strains 6. Screening and isolation of proteolytic bacteria 7. Screening and isolation of Amylase producing bacteria 8. Isolation of plasmid DNA by alkali lysis method and agarose gel electrophoresis 9. Restriction digestion of plasmid DNA 10. Transformation of E.coli by a suitable plasmid 11. Elution of DNA from agarose gel 12. RAPD

Evaluation Pattern

Sr. No.




15%



LAB-I


Week 04



Page 2 of 2


1. Work in industrial microbiology laboratory.

2. Carry out Molecular Biology experiments.

3 Isolate plasmids and modify it.

References:

1 Thimmaiah S. K.(2012). Standad Methods of Biochemical Analysis. Kalyani Publishes, New Delhi, India.



Page 1 of 2

Course Objectives:

1. To learn selection of explants, induction of callus and plant tissue culture technique.

2. To learn organogenesis and embryogenesis. 3. To learn embryo isolation and culture.

PS03CBIT55 (Lab 2 A) 1. Preparation of MS medium and Hormone stocks 2. Callus induction from Tobacco leaf/carrot explants (Medium preparation, surface

sterilization, inoculation, observation and interpretation of results) 3. Micropropagation of banana 4. Shoot induction through organogenesis from tobacco callus 5. Somatic embryogenesis induction from carrot cell suspension 6. Tobacco anther culture for haploid plant production 7. Culture of zygotic embryos (embryo isolation and culture) 8. Synthetic seed preparation.

PS03CBIT55 (Lab 2 B) Practicals related to elective papers

Evaluation Pattern

Sr. No.




15%




LAB-I


Week 04



Page 2 of 2

1. Carry out fundamental plant tissue culture experiments.

2. Do organogenesis and embryogenesis from suitable materials.

3 Culture zygotic embryos.

References:

1 J. Reinert and M. M. Yeoma. Plant cell and tissue culture: A laboratory manual. Springer



Page 1 of 3


Course Code PS03EBIT51 Title of the Course

Biomanufacturing principles and practices


Week 03

Course Objectives:

1. To make the students understand the concept, development and use of SOPs in Biomanufacturing 2. To impart knowledge on essential quality parameters and their measurement in Biomanufacturing. 3. Familiarize the students to the basic needs of a Biotechnology industry

Course Content


1. Overview and design of biomanufacturing, quality by design approach, technical considerations, phases and scale up: life cycle of manufacturing, raw material considerations, compliance and quality in biomanufacturing, lean biomanufacturing; Standard manufacturing operating procedures of biotechnology, quality control of protein production, and final fill and finish of product; Case studies to be included at least: therapeutic proteins, monoclonal antibodies, human vaccines.

25%

2. Introduction to quality system, main elements of a quality system; Essential of quality system; Practical implementation of a quality system; Structure of quality manual, correlation between GMP requirements (WHO) and ISO 9001:2000.

20%

3. Personnel: Principles of human resource management, duties of senior management, organizational structures, qualification and profiles requirement.

Premises: Official requirements, material & personnel flow and layout, air cleanliness classes and grades, construction elements, barrier systems, isolators and safety cabinets, building services, heating ventilation air conditioning (HVAC), process gases, qualification of premises and HVAC systems, pharma monitoring of HVAC systems, particle monitoring.;

Process Validation: Official requirements, Validation - a key element of quality management, validation planning and procedure, validation documentation, process validation and product lifecycle; Cleaning

30%



Page 2 of 3

Validation: Official requirements, how to validate cleaning procedures.

4. Production: Sanitation, GMP in production process, sterilisation processes, aseptic processing, freeze-drying, testing for sterility, testing for endotoxins, testing for leakage and for particles, microbiological monitoring, packaging materials, packaging process.

Information: National bodies and pharmaceutical associations; Pharmacopeia; EU directives and guidelines, USA: CFR and FDA guidelines, ICH-guidelines, PIC/S guidelines, GMP of other regions, WHO guidelines.

25%



Evaluation Pattern

Sr. No.




15%



1. Understand fundamental operations, procedures and rules of Industrial manufacturing with special reference to Biological products.

2. Learn the basic components of an industry, GMP and SOP along with industry standards of testing, sterilization and packing



Page 3 of 3

3. Become familiar with industry certification process, it’s significance and relevance

4. Learn various guidelines and regulations for biomanufacturing in detail


Sr. No.

References

1. Introduction to Biomanufacturing, by Northeast Biomanufacturing Center and collaboration, 2012.

2. Introduction to Biomanufacturing, by Mark Witcher. In Encyclopedia of Industrial Biotechnology.

3. Good Manufacturing Practices for Pharmaceuticals (e-resource): A Plan for Total Quality Control. Sidney Willig and James Stoker

4. Biotechnology Operations: Principles and Practices, by John M. Centanni, Michael J. Roy; CRC press

5. GMP Manual; Publisher Maas & Peither America, Inc. GMP Publishing.


On-line Resources

*****



Page 1 of 3


Course Code PS03EBIT52 Title of the Course Toxicology


Week 03

Course Objectives:

i. To learn about the dose-response relationships and understand the toxicity of various substances

ii. To comprehend the knowledge of absorption, distribution, metabolism and elimination of xenobiotics

iii. To provide an overview on legislative measures in the field of food, drugs and environmental toxicants

Course Content


1. Definition and scope of toxicology: Eco-toxicology and its environmental significance, Biochemical Aspects of Toxicology Toxic effects: Basic for general classification & nature. Measurement of Dose-Response Relationships, Synergism and Antagonism Acute and Chronic exposures, Factors influencing Toxicity. Pharmacodynamics & Chemodynamics, dose conversion between animals and human Diagnosis of toxic changes in liver and kidneys: Metabolism of drugs: paracetamol and aspirin with their toxic effects on tissues.

25

2. Xenobiotics Metabolism: Absorption & distribution. Phase I reactions. Oxidation, Reduction, Hydrolysis and Hydration. Phase II reaction/Conjugation: Methylation, Glutathione and amino acid conjugation. Detoxification. Biochemical basis of toxicity: Metabolism of Toxicity: Disturbances of Excitable membrane function. Altered calcium Homeostasis. Covalent binding of cellular macromolecules & Genotoxicity. Tissue specificity of Toxicity. Toxicity testing: Models for toxicity testing; Acute and Chronic toxicology testing, Experimental design; Genetic toxicity testing & Mutagenesis assays In vitro Test systems – Bacterial Mutation Test, Ames test, In vivo Mammalian Mutation tests –DNA repair assays, Chromosome damage test, Evaluation of Apoptosis and necrosis

25

3. Pesticides: Insecticides: Organochlorines, Anti cholinesterases- Organophosphates and Carbamates, Fungicides: Captan, Di-thiocarbamates, Herbicides:2,4 D, Atrazine; Food additives:

25



Page 2 of 3

Preservatives, Processing aids, Flavor and taste modifiers, Nutritional additives; Role of diet in cardio-vascular disease and cancer. Toxicology of food additives; Metal Toxicity: Toxicology of Arsenic, mercury, lead and cadmium.

4. Regulatory Toxicology: Rules and regulations of Nuclear Regulatory Commission (NRC); Environmental Protection Agency (EPA); Food and Drug Administration (FDA); Drug Enforcement Administration (DEA); Occupational Safety and Health Assessment (OSHA); Committee for Purpose of Control and supervision of experimental on animals (CPCSEA)

25



Evaluation Pattern

Sr. No.




15%



1. Learn the toxicity testing methods and designing of animal experimentations in pharmaceutical and drug industries or research organizations

2. Correlate concentrations of doses, duration of exposure and animal responses




Page 3 of 3

Sr. No.

References

1. Klaassen, C., D.,(Ed) (2013). Casarett and Doull'stoxicology : the basic science of poisons. McGraw-Hill Education,New York.

2. Timbrell, J. A., (2008). Principles of biochemical toxicology. Taylor and Francis Ltd., London.

3. Smart, R. C., Hodgson, E., (Ed.) (2013). Molecular and biochemical toxicology. John Wiley and Sons, Inc.


On-line Resources

*****



Page 1 of 6


Course Code PS03EBIT22 Title of the Course Bioinformatics


Week 04

Course Objectives:

1. To get knowledge and awareness of the basic principles and concepts of biology, computer science and mathematics

2. To explore existing software effectively to extract information from large databases and to use this information in computer modelling

3. To get problem-solving skills, including the ability to develop new algorithms and analysis methods.

4. To train student for understanding of the intersection of life and information sciences, the core of shared concepts, language and skills the ability to speak the language of structure-function relationships, information theory, gene expression, and database queries.

Course Content


1. Introduction to Bioinformatics: Introduction and Bioinformatics Resources: Knowledge of various databases and bioinformatics tools

available at these resources, the major content of the databases, Literature databases:

Describe about various approaches in genome sequencing and NGS

Overview of Sequence trace files (or chomatograms) raw data output from sequencer machines, Assembling and storing of the sequencer data files.

Nucleic acid sequence databases: GenBank, EMBL, DDBJ Protein sequence databases: SWISS-PROT, TrEMBL, PIR,

PDB, SCOP, CATH Genome Databases at NCBI, EBI, TIGR, SANGER Other Databases of Patterns/Motifs/System Biology (Gene and

protein network database and resources) Sequence analysis: Various file formats for bio-molecular sequences: GENBANK,

FASTA, GCG, MSF, NBRF-PIR etc. Basic concepts of sequence similarity, identity and homology,

Definitions of homologues, orthologues, paralogues, xenologus. Scoring matrices: basic concept of a scoring matrix, PAM and

BLOSUM series. Database Searches: what are sequence-based database searches,

25%



Page 2 of 6

BLAST and FASTA algorithms, various versions of basic BLAST and FASTA.

Pairwise and Multiple sequence alignments: basic concepts of sequence alignment, Needleman & Wuncsh, Smith & Waterman algorithms for pairwise alignments, Progressive and hierarchical algorithms for MSA.

Use of pairwise alignments and Multiple sequence alignment for analysis of Nucleic acid and protein sequences and interpretation of results.

2. Gene prediction: Gene structure in Prokaryotes and Eukaryotes, Gene prediction

methods: Neural Networks, Pattern Discrimination methods, Signal sites Predictions, Evaluation of Gene Prediction methods.

Computational RNA Structure analysis: Secondary and tertiary structure of RNA. Various algorithms of

RNA folding and their analysis. Energy minimization in RNA folding. RNA sequence alignment based on secondary structure and its applications in functional genomics and phylogeny.

Transcriptomics: Complete transcript cataloguing and gene discovery sequencing Microarray based technologies and computation based

technologies

25%

3. Genomics: Concepts and tools for genomics and comparative Genomics Ancient conserved regions Horizontal gene transfer Functional classification of genes Gene order (synteny) is conserved on chromosomes of related

organisms. Prediction of gene function based on a composite analysis. Functional genomics. Putting together all of the information into a genome database.

Phylogenetic analysis: Definition and description of phylogenetic trees and various

types of trees, Molecular basis of evolution, Method of construction of Phylogenetic trees: Distance based method (UPGMA, NJ), Character Based Method (Maximum Parsimony and Maximum Likelihood method).

25%

4. Proteomics and Protein Computational Biology: Tools for proteomics: Acquisition of protein structure

information, databases and applications. Structural classification of proteins, Protein structure analysis

structure alignment and comparison, Secondary structure and evaluation: algorithms of Chou

Fasman, GOR methods.

25%



Page 3 of 6

Tertiary Structure: Basic principles and protocols, Methods to study 3D structure; Prediction of specialized structures. Protein folding, Protein modelling, Method of protein structure evaluation; Active site prediction.

Protein-protein and protein-ligand interaction/Docking; Drug Designing, QSAR studies.

Protein structure comparison and classification: Classes, Folds, Motif, Domain; Purpose of structure comparison Algorithms such as FSSP, VAST and DALI. Principles of protein folding and methods to study protein

folding.



Evaluation Pattern

Sr. No.




15%



1. To get introduced to the basic concepts of Bioinformatics and its significance in Biological data analysis.

2. To get introduced to the basics and advance of sequence alignment and analysis.

3. To get overview about biological macromolecular structures and structure prediction methods.

4. To understand the structural organisation, structural properties and various techniques employed in the structure determination of Biological macromolecules – DNA & Protein.

5. To get exposed to computational methods, tools and algorithms employed for Biological Data Interpretation.

6. To have hands on training on various computational tools and techniques employed in



Page 4 of 6

Biological sequence analysis.

7. To get exposed to various tools and methodologies used in multiple sequence alignment, phylogenetic analysis and genetic diversity analysis observed in biological sequences.

8. To impart knowledge on chemical databases, various advanced techniques and tools like docking, QSAR studies etc employed in computational drug discovery.

9. To get knowledge about various approaches in genome sequencing and NGS.


Sr. No.

References

1. Bioinformatics: A Beginners Guide, Clavarie and Notredame

2. Bioinformatics: David Mount

3. Bioinformatics: Rastogi

4. Introduction to Bioinformatics: Arthur M. Lesk

5. Bioinformatics: Principles and applications, Ghosh and Mallick

6. Bioinformatics: Genes, Proteins and Computer, C A Orengo

7. Protein Structure Prediction: Methods and Protocols, Webster, David (Southern Cross Molecular Ltd., Bath, UK)


On-line Resources

Nucleotide Sequence Databases (the principal ones) • NCBI - National Center for Biotechnology Information • EBI - European Bioinformatics Institute • DDBJ - DNA Data Bank of Japan

Protein Sequence Databases • SWISS-PROT & TrEMBL - Protein sequence database and computer annotated

supplement • UniProt - UniProt (Universal Protein Resource) is the world's most comprehensive

catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.

• PIR - Protein Information Resource • MIPS - Munich Information centre for Protein Sequences • HUPO - HUman Proteome Organization

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

http://www.ebi.ac.uk/

http://www.ddbj.nig.ac.jp/

http://www.expasy.ch/sprot/sprot-top.html

http://www.ebi.uniprot.org/

http://pir.georgetown.edu/pirwww/

http://www.mips.biochem.mpg.de/mips/

http://www.hupo.org/



Page 5 of 6

Database Searching by Sequence Similarity • BLAST @ NCBI • PSI-BLAST @ NCBI • FASTA @ EBI • BLAT Jim Kent's Blat is just superb in terms of speed and the integrated view you get

for viewing the results

Sequence Alignment • USC Sequence Alignment Server - align 2 sequences with all possible varieties of

dynamic programming • T-COFFEE - multiple sequence alignment • ClustalW @ EBI - multiple sequence alignment • MSA 2.1 - optimal multiple sequence alignment using the Carrillo-Lipman method • BOXSHADE - pretty printing and shading of multiple alignments • Splign - Splign is a utility for computing cDNA-to-Genomic, or spliced sequence

alignments. At the heart of the program is a global alignment algorithm that specifically accounts for introns and splice signals.

• Spidey - an mRNA-to-genomic alignment program

Protein Domains: Databases and Search Tools • InterPro - integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL • PROSITE - database of protein families and domains • Pfam - alignments and hidden Markov models covering many common protein

domains • SMART - analysis of domains in proteins • ProDom - protein domain database • PRINTS Database - groups of conserved motifs used to characterise protein families • Blocks - multiply aligned ungapped segments corresponding to the most highly

conserved regions of proteins

Protein 3D Structure • PDB - protein 3D structure database • RasMol / Protein Explorer - molecule 3D structure viewers • SCOP - Structural Classification Of Proteins • UCL BSM CATH classification • The DALI Domain Database • FSSP - fold classification based on structure-structure alignment of proteins • SWISS-MODEL - homology modeling server • Structure Prediction Meta-server • K2 - protein structure alignment • DALI - 3D structure alignment server • DSSP - defines secondary structure and solvent exposure from 3D coordinates • HSSP Database - Homology-derived Secondary Structure of Proteins • PredictProtein & PHD - predict secondary structure, solvent accessibility,

transmembrane helices, and other stuff • Jpred2 - protein secondary structure prediction • PSIpred (& MEMSAT & GenTHREADER) - protein secondary structure prediction

(& transmembrane helix prediction & tertiary structure prediction by threading)

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

http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?ALIGNMENTS=250&ALIGNMENT_VIEW=Pairwise&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&CDD_SEARCH=on&DESCRIPTIONS=500&ENTREZ_QUERY=%28none%29&EXPECT=10&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&HITLIST_SIZE=500&I_THRESH=0.002&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on&SERVICE=plain&SET_DEFAULTS.x=36&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&AUTO_FORMAT=yes&END_OF_HTTPGET=Yes

http://www.ebi.ac.uk/fasta3/

http://genome.ucsc.edu/

http://www-hto.usc.edu/software/seqaln/seqaln-query.html

http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html

http://www.ebi.ac.uk/clustalw/

http://www.ibc.wustl.edu/ibc/msa.html

http://bioweb.pasteur.fr/seqanal/interfaces/boxshade.html

http://www.ncbi.nlm.nih.gov/sutils/splign/

http://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/Spidey/index.html

http://www.ebi.ac.uk/interpro/

http://www.expasy.ch/prosite/

http://genome.wustl.edu/Pfam/

http://smart.embl-heidelberg.de/

http://www.toulouse.inra.fr/prodom.html

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/PRINTS/PRINTS.html

http://www.blocks.fhcrc.org/

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

http://www.umass.edu/microbio/rasmol/

http://scop.mrc-lmb.cam.ac.uk/scop/

http://www.biochem.ucl.ac.uk/bsm/cath/

http://www2.ebi.ac.uk/dali/domain/2.0/

http://www2.ebi.ac.uk/dali/fssp/fssp.html

http://www.expasy.ch/swissmod/SWISS-MODEL.html

http://www.bioinfo.pl/meta/

http://zlab.bu.edu/k2

http://www2.ebi.ac.uk/dali/

http://bioweb.pasteur.fr/seqanal/interfaces/dssp-simple.html

http://swift.embl-heidelberg.de/hssp/

http://cubic.bioc.columbia.edu/predictprotein/

http://jura.ebi.ac.uk:8888/

http://insulin.brunel.ac.uk/psipred/



Page 6 of 6

Phylogeny & Taxonomy • The Tree of Life • Species 2000 - index of the world's known species • TreeBASE - a database of phylogenetic knowledge • PHYLIP - package of programs for inferring phylogenies • TreeView - user friendly tree displaying for Macs & Windows

Gene Prediction • Genscan - eukaryotes • GeneMark • Genie - eukaryotes • GLIMMER - prokaryotes • tRNAscan - SE 1.1 - search for tRNA genes in genomic sequence • GFF (General Feature Format) Specification - a standard format for genomic

sequence annotation

Metabolic, Gene Regulatory & Signal Transduction Network Databases • KEGG - Kyoto Encyclopedia of Genes and Genomes • BioCarta • DAVID - Database for Annotation, Visualization and Integrated Discovery - A useful

server to for annotating microarray and other genetic data. • stke - Signal Transduction Knowledge Environment • BIND - Biomolecular Interaction Network Database • EcoCyc • WIT • PathGuide A very useful collection of resources dealing primarily with pathways • SPAD - Signaling Pathway Database • CSNDB - Cell Signalling Networks Database • PathDB • Transpath • DIP - Database of Interacting Proteins • PFBP - Protein Function and Biochemical Networks

*****

http://phylogeny.arizona.edu/tree/phylogeny.html

http://www.sp2000.org/

http://www.herbaria.harvard.edu/treebase/

http://evolution.genetics.washington.edu/phylip.html

http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

http://genes.mit.edu/GENSCAN.html

http://opal.biology.gatech.edu/GeneMark/

http://www.cse.ucsc.edu/~dkulp/cgi-bin/genie

http://www.tigr.org/softlab/glimmer/glimmer.html

http://www.genetics.wustl.edu/eddy/tRNAscan-SE/

http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml

http://www.genome.ad.jp/kegg/

http://www.biocarta.com/

http://apps1.niaid.nih.gov/david/upload.asp

http://www.stke.org/

http://binddb.org/

http://ecocyc.pangeasystems.com/ecocyc/ecocyc.html

http://wit.mcs.anl.gov/

http://www.pathguide.org/

http://www.grt.kyushu-u.ac.jp/spad/

http://geo.nihs.go.jp/csndb/

http://www.ncgr.org/software/pathdb/

http://193.175.244.148/

http://dip.doe-mbi.ucla.edu/

http://www.ebi.ac.uk/research/pfmp/



Page 1 of 3

Master of Science (Biotechnology) M.Sc. (Biotechnology) Semester (IV)

Course Code PS04CBIT51 Title of the Course Downstream processing


Week 04

Course Objectives:

Students should be able to :

- Device a strategy and separate bioactive molecules.

Course Content


1. Introduction to downstream processing principles, characteristics of biomolecules and bioprocesses. Cell disruption for product release – mechanical, enzymatic and chemical methods. Pretreatment and stabilization of bio products.

25

2. Physical methods of separation: centrifugation and filtration. Adsorption, liquid-liquid extraction, aqueous two-phase extraction, membrane separation – ultrafiltration and reverse osmosis, dialysis, precipitation of proteins by different methods.

25

3. Purification methods: Chromatography – principles, instruments and practice, adsorption, Reverse phase, ion-exchange, size exclusion, hydrophobic interaction, bio affinity and pseudo affinity chromatographic techniques.

25

4. Purification strategies: Case studies of animal based products -Tissue Plasminogen Activator, Erythropoietin; plant based products- shikonin and seed proteins; bacterial products- lipases, amylase, subtilisin, ethanol and citric acid.

25


Topics will be taught and discussed in interactive sessions using conventional black board and chalk as well as ICT tools such as power point presentations and videos. Practical sessions will be conducted in a



Page 2 of 3

suitably equipped laboratory either individually or in groups depending on the nature of exercise as well as availability of infrastructure. Course materials will be provided from primary and secondary sources of information.

Evaluation Pattern

Sr. No.




15%



1. Students should be able to handle downstream processing laboratory.


Sr. No.

References

1. Gary Walsh Proteins: Biochemistry and Biotechnology. 2nd edition, Wiley Blackwell. 2002

2. J.C. Janson and L. Ryden, (Ed.) – Protein Purification – Principles, High ResolutionMethods and Applications, VCH Pub. 1989.

3. R.K. Scopes – Protein Purification – Principles and Practice, Narosa Pub., 1994.

4. B. Sivasanker –Bioseperations –Principles and Techniques, Prentice –Hall of India, 2005.

5. Roger G.Harrison, Paul Todd- Bioseparations Science and Engineering, Oxford University Press, 2006.

6. D. G. Rao, Introduction to Biochemical Engineering, Tata McGraw-Hill Education, 2005



Page 3 of 3


On-line Resources


*****



Page 1 of 3


Course Code PS04CBIT52 Title of the Course Environmental Biotechnology


Week 04

Course Objectives:

1. To address environment issues using biotechnology. 2. To understand characterization and treatment of waste waters. 3. To understand fundamentals of waste water treatment processes and

biochemistry for removal of pollutants from water and technologies developed for that..

4. To understand basic concepts of biodegradation and bioremediation strategies for conservation of environment.

5. To understand some of the major pollution problems and their biotechnological solutions

6. To learn about eco-friendly biotechnological processes for recovery of various resources.

7. To learn about need and applications of various biofertilizers and biocontrol agents.

Course Content


1. Waste water treatment- Waste water characterization and its significance: COD, BOD, TOC, TOD, Inorganic constituents, solids, biological components. Principles and aims of biological wastewater treatment processes: Primary, secondary and tertiary treatment of waste water. Biochemistry and microbiology of inorganic phosphorus and nitrogen removal from waste water. Suspended growth processes: Activated sludge process: Biology of activated sludge, flocculation, sludge settling, oxidation ditches, waste stabilization ponds. Fixed film processes: Biofilm formation and slaughing, Trickling filters, rotating biological contactors, fluidized bed and submerged aerated filters.

25

2. Anaerobic digestion: microbiological and biochemical fundamentals, factors influencing anaerobic digestion. Anaerobic waste water treatment systems: Upflow anaerobic sludge blanket , rotating biological contactors, anaerobic filters. Merits and demerits of anaerobic treatment of waste. Composting: Objectives, fundamentals, microbiology, factors influencing composting and composting systems. Compost quality and

25



Page 2 of 3

uses. Vermicomposting. Toxicity testing in waste water treatment plants using microorganisms: Monitoring environmental processes with biosensors: BOD biosensor, Pesticide biosensor

3. Biodegradation of organic pollutants: Xenobiotic and recalcitrant organic compounds, mechanisms of biodegradation, factors affecting biodegradation, Acclimation phase in biodegradation. Biodegradation of simple aliphatic, aromatic, polycyclic aromatic hydrocarbons, halogenated hydrocarbons, azo dyes and lignin. Bioremediation approaches: Intrinsic bioremediation, Biostimulation, Bioaugmentation: Use of genetically modified organisms.. In situ and ex situ bioremediation technologies with examples. Bioremediation of heavy metal pollution, Phytoremediation. Biological treatment of waste gas (polluted air): biofilters, bioscrubbers, membrane bioreactors, biotrickling filters.

25

4. Bioleaching of metals: Characteristics of commercially important microbes, mechanisms of bioleaching, factors affecting bioleaching and current biomining processes. Biobeneficiation of gold ores. Biodesulfurization of coal: Removal of organic and inorganic sulfur from coal. Microbially enhanced oil recovery. Microbial Insecticides: Bacterial, fungal and viral insecticides in pest management. Biofertilizers: applications of nitrogen fixing and phosphate solubilising/ mobilizing biofertilizers.

25



Evaluation Pattern

Sr. No.




15%




Page 3 of 3


1. Get trained with analysis of waste waters to judge pollution potential and biological waste water treatment.

2. Develop ability to understand various biotechnological strategies to overcome pollution problems caused by various pollutants in air, water and soil.

3. Understand and apply solid waste management technologies and significance of generating valuable products from waste.

4. Gain technical knowledge about environment friendly biotechnological processes for recovery of valuable resources .

5. Understand the need and production of biofertilizers and biopesticides for enhanced crop production in agriculture.

Suggested References: • Comprehensive Biotechnology Vol-4, Murray Moo Young. • Biotechnology-Rehm and Reid. • Waste water microbiology by G. Bitton • Biodegradation and bioremediation by M.Alexander • Waste water treatment for pollution control, 2nd edition. Arceivala • Environmental Biotechnology by H. Jordening and Josef Winter • Handbook of water and waste water Microbiology by Horan • Topic related review articles


On-line Resources

*****



Page 1 of 2

Course Objectives:

1. To learn to do water analysis. 2. To learn analysis of environmental samples.

PS04CBIT54 (Lab 1) 1) Qualitative analysis of amino acids by TLC

2) Elution and quantitative estimation of amino acids

3) HPTLC separation of secondary metabolites

4) Waste water characterization.

a) BOD

b) COD

c) Nitrate estimation

d) Sulfate estimation

5) Study of phosphate solubilizing activity

6) Isolation of 2,4 dichlorophenoxyacetic acid degrading bacteria

7) Isolation of naphthalene degrading bacteria

8) Dehydrogenase activity of soil

9) Bioremoval of chromium from polluted water

10) Decolourization of Azo dyes by microorganisms.

Evaluation Pattern

Sr. No.




15%



LAB-I


Week 04



Page 2 of 2


1. Contribute to the field of environmental Biotechnology.

References:

1 Thimmaiah S. K. (2012). Standad Methods of Biochemical Analysis. Kalyani Publishes, New Delhi, India.



Page 1 of 4


Course Code PS04EBIT531 Title of the Course IPR and Biosafety


Week 04

Course Objectives:

1. To introduce basic concepts of ethics and safety that are essential for different disciplines of science and procedures involved and protection of intellectual property and related rights. 2. To understand balanced integration of scientific and social knowledge in sustainable development.

Course Content


1. Biotechnology and society: Biotechnology and social responsibility, public acceptance issues in biotechnology, issues of access, ownership, monopoly, traditional knowledge, biodiversity, benefit sharing, environmental sustainability, public vs private funding. Bioethics: Social and ethical issues in biotechnology. Principles of bioethics. Ethical conflicts in biotechnology- interference with nature, unequal distribution of risk and benefits of biotechnology, bioethics vs business ethics. Introduction and need of bioethics, its relation with other branches, types of risk associated with genetically modified microorganisms, Ethical Issues involving GMOs; ethics related to human cloning, human genome project, prenatal diagnosis, agriculture and animal rights, data privacy of citizens health; ethical issues in India and abroad through case studies; Socio-economic impact of biotechnology.

25%

2. Bio- safety: Definition of bio-safety; History, evolution and concept of biosafety; need and application of biosafety in laboratories and industries; biosafety guidelines and regulations, international and national norms of biosafety; Implementation of biosafety guidelines; Classification and Description of Biosafety levels; Design of clean rooms and biosafety cabinets; Risk assessment and containment levels; biohazard, bio-medical and hazardous wastes, handling and disposal; transportation of biological materials; bio-terrorism; biosafety protocol (Cartagena biosafety protocol) regulations to protect nature, growers and consumers interest and nation interest; Good laboratory practice (GLP) and Good manufacturing practice (GMP), Use of GMO’s and their release, GM products, issues in use of GMO’s, risk for animal/human/agriculture and environment owing to GMOs., Biotechnology and bio-safety concerns at the level of individuals,

25%



Page 2 of 4

institutions, society, region, country and world. Bio safety regulation: handling of recombinant DNA products and process in industry and in institutions.

3. IPR I: The Concept/History of Intellectual Property; Intellectual Property System in India; Kinds of Intellectual Property Rights; Advantages and Disadvantages of IPR. International Instruments concerning Intellectual Property Rights: the Berne Convention, Universal Copyright Convention, The Paris Convention, Patent Co-operation Treaty, Trade Related Intellectual Property Rights (TRIPS), The World Intellectual Property Organization (WIPO) and the United Nations Educational, Scientific and Cultural Organization (UNESCO) World Intellectual Property Organisation (WIPO); World Trade Organization (WTO) European Patent Office (EPO). Patents Act, 1970 ; Trade Mark Act, 1999; The Designs Act, 2000; The Geographical Indications of Goods (Registration and Protection) Act, 1999; Copyright Act, 1957 ; The Protection of Plant Varieties and Farmers’ Rights Act, 2001; The Semi Conductor Integrated Circuits Layout Design Act, 2000; Trade Secrets; Utility Models; IPR & Biodiversity; The Convention on Biological Diversity (CBD) 1992; Application forms of IPR and Intellectual property protection. Concept of property with respect to intellectual creativity, Tangible and Intangible property.

25%

4. IPR II: Classification of patents in India, Classification of patents by WIPO, Categories of Patent, Special Patents, Patenting Biological products, Patent document, Granting of patent, Rights of a patent, Patent Searching, Patent Drafting, filing of a patent, different layers of the International patent system, Utility models, Concept related to patents novelty, non-obviousness, utility, anticipation, prior art etc. Type of patents. Indian patent act and foreign patents. Patentability, Patent application, Revocation of patent, Infringement and Litigation with case studies on patent, Commercialization and Licensing. Patent Cooperation Treaty (PCT); Copyright Overview of Copyright, Importance of Copyrights, Process for copyright, case studies. Overview of Trademarks & Trade Secret, Importance of Trademarks & Trade secret, Rights of Trademark & Trade Secret, Types of Trademarks, Registration process for Trademark & Trade Secret, Duration of Trademark and trade secret, Case Studies Geographical Indications Overview of Geographical Indications, Importance of Geographical Indication Protection, Case studies

25%



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Infringement: Direct, Contributory, and Induced Infringement; How Infringement is Determined; Who Is an Infringer; Official Machinery, Controller, Powers and Functions Defences to Infringement; Case studies



Evaluation Pattern

Sr. No.




15%



1. Interpret basics of biosafety and bioethics and its impact on all the biological sciences and the quality of human life.

2. Recognize importance of biosafety practices and guidelines in research.

3. Comprehend benefits of GM technology and related issues.

4. Recognize importance of protection of new knowledge and innovations and its role in business.


Sr. No.

References

1. Fleming, D.A., Hunt, D.L., (2000). Biotechnology and Safety Assessment (3rd Ed) Academic press.ISBN-1555811804,9781555811808.

2. Thomas, J.A., Fuch, R.L. (1999). Biotechnology and safety assessment (3rd Ed). CRC press, Washington. ISBN: 1560327219, 9781560327219



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3. Law and Strategy of biotechnological patents by Sibley. Butterworth publication.(2007) ISBN: 075069440, 9780750694445.

4. Intellectual property rights- Ganguli-Tat McGrawhill. (2001) ISBN-10: 0074638602,

5. Intellectual Property Right- Wattal- Oxford Publicatiopn House.(1997) ISBN:0195905024.

6. Biotechnology - A comprehensive treatise (Vol. 12). Legal economic and ethical dimensions VCH. (2nd ed) ISBN-10 3527304320.

7. Encyclopedia of Bioethics 5 vol set, (2003) ISBN-10: 0028657748.

8. Thomas, J.A., Fuch, R.L. (2002). Biotechnology and safety Assessment (3rd Ed) Academic press.

9. B.D. Singh. Biotechnology expanding horizons.

10. H.K.Das. Text book of biotechnology 3rd edition.

11. Sateesh, M.K., Bioethics and Biosafety, IK International Publishers (2008)

12. Singh I. and Kaur, B., Patent law and Entrepreneurship, Kalyani Publishers (2006).

13. Srinivasan, K. and Awasthi, H.K., Law of Patents, Jain Book Agency (1997)

14. Deepa Goel, ShominiParashar, (2013), IPR, Biosafety and Bioethics, Pearson.


On-line Resources

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Course Code PS04EBIT52 Title of the Course Research Ethics and Scientific Writing


Week 04

Course Objectives:

1. To inculcate professional ethics in students of Science, especially in Biology 2.To familiarize types of plagiarism and tools for their detection 3. To teach various modes of data collection and its processing 4. To impart professional, scientific writing skills …

Course Content


1. Definition and significance of ethics; Professional ethics in Scientific research and development: Common ethical breaches; data fabrication; data falsification. Plagiarism: redundant publication; duplicate publication.

25%

2. Types of plagiarism; tools and techniques for detection of plagiarism. Conflict of interest; salami slicing and authorship issues. Good Laboratory Practices (GLP): Instrument validation, reagents and materials certification, documentation and its record, Quality assurance and certification of laboratory facilities.

25%

3. Data collection methods: Primary data and secondary data. Internet, online data collection, journals and books. References: Basic types of referencing; Quoting, paraphrasing and citing. APA, MLA and the Chicago/ Turabian styles of listing references.

25%

4. Scientific writing: Basic differences between popular and scientific writing; fundamental rules of scientific writing; structure and content of research papers, thesis and dissertations. Do’s and don’t for scientific writing. Tools and techniques for correction and editing of manuscripts. Selection and publication in journals.

25%

Teaching-Learning

Topics will be taught and discussed in interactive sessions using conventional black board and chalk as well as ICT tools such as power



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Methodology point presentations and videos. Practical sessions will be conducted in a suitably equipped laboratory either individually or in groups depending on the nature of exercise as well as availability of infrastructure. Course materials will be provided from primary and secondary sources of information.

Evaluation Pattern

Sr. No.




15%



1. Understand the significance of professional ethics in Scientific research

2. Appreciate the types and pitfalls of plagiarism

3. Learn how to collect data from primary and secondary sources

4. Understand the differences between, common, popular and scientific writing and learn the basics of scientific writing


Sr. No.

References

1. Professional ethics and human values: M. Govindarajan, S. Natarajan and V.S. Senthilkumar

2. The craft of Scientific writing: Michael Alley

3. Science and Technology ethics: Raymond Spier

4. Scientific writing and research quality: Prasanna Kumar and Pawan Kumar Bharti




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On-line Resources

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Course Code PS04EBIT52 Title of the Course Systems Biology


Week 04

Course Objectives:

1. To introduce the concept of systems and synthetic Biology to the students 2. To provide insight into quantitative modelling of biological systems at the molecular and cellular level, as well as how they are used, analysed and developed

Course Content


1. Concepts and working principles of System Biology - Practical applications of System Biology in Life Sciences - Introduction to System Biology platforms, Proprietary system Biology platform. Microarray data analysis - Microarray analysis platforms - Introduction to Concepts and principles of Microarray technology

25%

2. Models and Modeling: purpose, adequateness, advantage of computational modeling, basic notion for computational models, model scope, statements, system state, variables parameters constants, behavior, classification, steady states.

25%

3. Analysis of complex biological systems: Sequencing (DNA & amino acid), Protein structure analysis. Metabolic networks and flux balance analysis: Mathematical modeling of metabolic networks; formulation and optimization of Flux Balance Analysis; computational tools for FBA.

25%

4. Introduction to synthetic biology. Modeling synthetic Biology; Applications of synthetic Biology. Human and Pathogens--Cancer genomics (Tumor complexity)--Gene regulatory network Codon optimization Algorithmic Drug designs. Current and emerging areas in the field of computational and systems biology.

25%




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Evaluation Pattern

Sr. No.




15%



1. Model macromolecular complexes on different time and length scales model macromolecular structures with the help of experimental information

2. Explain cellular processes by describing the interactions between macromolecules in a kinetic network

3. Appreciate the significance of synthetic Biology and its potential in future


Sr. No.

References

1. System Biology: Computational Systems Biology (Hardcover) by Andres Kriete (Editor), Roland Eils (Editor)

2. Microarray Data Analysis: Gene Expression Data Analysis. A Beginner's Guide By: Helen Causton (Imperial College), J Quackenbush and AlvisBrazma (The European Bioinformatics Institute)

3 Klipp E (2009) Systems biology: a textbook. Wiley-VCH, 1/e.


On-line Resources

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Course Code PS04EBIT54 Title of the Course Biomaterials and Tissue Engineering


Week 04

Course Objectives:

1. To impart knowledge on the types and properties Biomaterials used in medicine. 2. Understand the composition of implants and their pros and cons. 3. Learn tissue engineering and its applications 4. Gain an understanding of stem cells and their emerging role in treatment of genetic and somatic disorders.

Course Content


1. Biomaterials: Introduction-definition of biomaterials, applications of biomaterials, classification of biomaterials, Comparison of properties of some common biomaterials. Effects of physiological fluid on the properties of biomaterials. Biological responses (extra and intra-vascular system). Surface properties, physical properties and mechanical propertie of materials.Types of implant materials: Metallic, polymeric, ceramic an composite materials.

25%

2. Properties of commonly used implant materials: Stainless steel and alloy importance of stress- corrosion cracking; role of passive films in tissue adhesion. Polymeric implant materials: general classification; Polyolefin polyamides, acrylic polymers, fluorocarbon polymers, silicon rubbers, acetals. Biodegradable polymers and synthetic polymers and their applications. Ceramic implant materials: Bioceramics; Common types of bioceramics. Bio -reabsorbable and bioactive ceramicsHost tissue reactions: importance of interfacial tissue reaction (e.g. ceramic/bone tissue reaction).Composite implant materials: different reinforcement materials, Composite theory of fiber reinforcement.

25%

3. Tissue engineering: Introduction, stem cells, morphogenesis, generatio of tissue in the embryo, Tissue homeostasis, Cellular signalin Extracellular matrix as a biologic scaffold for tissue engineerin Scaffold fabrication, bioactive scaffold, Natural polymers in tissu engineering applications, Degradable polymers for tissue engineering.

25%

4. Basic Biology Of Stem Cells: Stem Cells : Introduction, hematopoietic differentiation pathway; Potency and plasticity of stem cells, sources,

25%



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embryonic stem cells, hematopoietic and mesenchymal stem cells, Stem Cell markers, FACS analysis and differentiation. Stem cell systems- Liver, neuronal stem cells, Types and sources of stem cell with characteristics: embryonic, adult, haematopoetic, fetal, cord blood, placenta, bone marrow, primordial germ cells, cancer stem cells induced pleuripotent stem cells.



Evaluation Pattern

Sr. No.




15%



1. Understand about various types of biomaterials for a wide range of biomedical applications.

2. Basic functions and performance of implant materials as well as corrosion and degradation mechanisms of biomaterials.

3. Choice of biomaterials based on function, biological environments, toxicity. bioadhesion and implant surface interaction with tissues. Scaffolds for tissue-engineering, growth factor, stem cell signaling.


Sr. No.

References



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1. Tissue Engineering: Bernhard O Palsson, Sangeeta N. Bhatia.

2. Fundamentals of Tissue Engineering and Regenerative Medicine: Meyer, U,: Meyer, Th.; Handschel, J.; Wiesmann,H.P .

3 Biomaterials: Science and Engineering: J B Park

4 Biomaterials: Sujata V. Bhat


On-line Resources

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Course Code PS04EBIT55 Title of the

Course Biodiversity and Conservation

Total Credits of the Course

04 Hours per Week

04

Course Objectives:

1. To impart knowledge of fundamental concepts of biodiversity, the range of its extant and the need for conservation.

2. To provide information of the main threats to biological diversity and the ability to evaluate the effects of human influences on biodiversity.

3. To demonstrate the differences between the different categories of red listed species.

4. To understand different modes of biodiversity conservation, their merits and limitations.

5. To integrate the information generated from scientific investigations and use findings to address conservation and biodiversity issues.

Course Content


1. Biodiversity: Concepts, levels and types, changes in tune and space, evolution, species concept; significance of biodiversity for life security.Biogeography. Terristrial, Marine, Aquatic and Agricultural biodiversity: Changing patterns and practices. Influence of modern lifestyle on biodiversity. Pros and cons of genetically modified species

25

2. Global conservation measures, institutions and conventions; IUCNconcept of threatened and endangered species. The Red Data Books of Indian plants and animals. Causes and consequences of loss of biodiversity. Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES): aims, major ratifications and amendments. Exotic andinvasive species: A few case studies of intentional and non-intentional introduction of exotic species and their influence on local biodiversity.

25

3. Principles and strategiesof biological diversity conservation: in-situ conservationand ex-situ conservation. Biosphere reserves, major protected areas (sanctuaries, national parks, biosphere reserves) of India and Gujarat.Wetlands, mangroves and coral reefs for conservation of wild biodiversity. Concept of Sacred groves and their role in biodiversity conservation.

25



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Role of botanical gardens, field gene banks, seed banks, in vitro repositories, cryobanks in conservation of plants and animal sperms. Role of Zoos, breeding centers in conservation of animals.

4. Biodiversity hot spots in India and world; IndianBiodiversity Act 2002;Major objectives of biodiversity authority board; Biodiversity and economics with special reference to India;People's Biodiversity register: Objectives, importance and modality of preparation. General account of the activities of Botanical Surveyof India (BSI) and Zoological Survey of India (ZSI), National Bureau of Plant Genetic Resources (NBPGR), Indian Council of Agricultural Research (ICAR), Council of Scientific & Industrial Research (CSIR), Department of Biotechnology (DBT) and Department of Environment and Forest, Wild life Protection Society of India, Wildlife Instititute of India (WII), Animal Welfare Board of India and Bombay Natural History Society (BNHS) in the context of Indianbiodiversity conservation.

25



Evaluation Pattern

Sr. No.




15%



1. Understand the concept of biodiversity, its role for our survival, different direct and indirect threats on biodiversity.

2. Appreciate the global and national initiatives and local traditions for biodiversity



Page 3 of 3

conservation.

3. Become familiar with different modes of conservation, institutes involved in biodiversity conservation.

4. Learn various guidelines and regulations for utilizing the biodiversity judiciously.


Sr. No.

References

1. Wilson, E., O., (1988). Biodiversity. The National Academies Press. Harvard. Washington, DC.

2. Hunter, M., L., Gibbs, J.P.,(2007).Fundamentals of Conservation Biology. 3rdEdn. Blackwell Publishing, Malden.

3. Myers, N., Mittermeier, R., A., Mittermeier, C. G., Fonseca, G., A., da, Kent, J., (2000). Biodiversity Hotspots for Conservation Priorities. Nature, 403, 853-858.

4. Rodgers, N. A., Panwar, H. S. Planning a Wildlife Protected Area Network inIndia. Vol. 1. The Report Wildlife Institute of India, Dehradun.


On-line Resources

Biodiversity: Author: John Spicer

Brian W. van Wilgen: Biological Invasions in South Africa

Recent review articles and research papers

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https://www.lovereading.co.uk/book/9780861540174/isbn/Biodiversity-by-John-Spicer.html

https://www.lovereading.co.uk/author/John-Spicer/gd/John-Spicer.html

https://www.lovereading.co.uk/author/Brian-W-van-Wilgen/gd/Brian-W-van-Wilgen.html

https://www.lovereading.co.uk/book/9783030323967/isbn/Biological-Invasions-in-South-Africa-by-Brian-W-van-Wilgen.html



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Master of Science (Biotechnology) M.Sc. (Biotechnology) Semester IV

Course Code PS04EBIT56 Title of the Course Food and Dairy Microbiology


Week 04

Course Objectives:

1. To understand about types of food spoilage and factors influencing food spoilage as well as microorganisms associated with spoilage of food.

2. To learn about food borne pathogens and types of infections or poisoning caused upon consumption of pathogen contaminated food products..

3. Togain insights into methods of food preservation and production of fermented foods.

4. Togain information about detection of pathogens in food as well as analysis of food quality.

5. To learn about regulations governing and certifications for food quality and recommended sanitation practices for food processing plants.

Course Content


1. Scope of food microbiology Food as a substrate a) Microorganisms important in food microbiology – Bacteria, yeasts and moulds. b) Factors influencing microbial growth in food. Food Spoilage a) General principles underlying food spoilage and contamination. b) Spoilage of canned food, sugar products, vegetables, fruits, meat and meat products, milk and milk products fish, seafood and poultry

25

2. Food poisoning a) Indicator food borne pathogens b) Bacterial food borne infections and intoxications-Brucella, Campylobacter,Clostridium, Escherichia (ETEC/EHEC/EPEC/EAEC), Salmonella, Shigella, Listeria, Vibrio, and Yersinia. c) Non- bacterial food borne infections and intoxications- Nematodes, protozoa, algae,fungi, and viruses. d) Culture and non-culture based detection of food pathogens and viruses e) General methods for diagnosis of infections, intoxications and preventive measures.

25

3. Food preservation Principles of food preservation – Physical and chemical preservation

25



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methods,Bio preservatives Food fermentations Starter cultures for fermented foods: Biochemical activities in fermentation of foods. Oriental fermented foods: Shoyu, Temph, Kimchi etc Fermented milk products: Yogurt, Kefir, Koumiss etc. Fermented vegetables – Sauerkraut Application of microbial enzymes in food industry

4. Genetically modified foods. Biosensors in food Food research organizations/institutes in India Recent foodborne outbreaks Food sanitation – Microbiology of food plant sanitation, water and milk testing Food laws and quality control – HACCP, Codex alimentarius, PFA, FPO, MFPO, BIS, FSSAI AGMARK.

25

...



Evaluation Pattern

Sr. No.




15%





Page 3 of 3

1. describe the types of food spoilage and factors influencing food spoilage.

2 associate a type of food spoilage with the causative microorganisms

3. describedifferent types of food poisoning or infection and design a study to determine the cause of food poisoning or food borne infection.

4. recommend a method of preservation for a particular type of food and expected extension in the shelf life of foods preserved thereby.

5. understand science and technology in production of a fermented food of high quality.

6 decide a method of sanitation for a food processing plant

7 describe the applicable laws for food processing and/packaging as well as associated quality certifications.

Suggested References: • Food Microbiology, Frazier and Westhoff • Food microbiology, Adam and Moss • Dairy Microbiology by Robinson. Volume II and I. • Fundamental Food Microbiology, Bibek Ray and ArunBhuniya


On-line Resources

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sardar patel university vallabh vidyanagar, gujarat ......lipid biosynthesis: biosynthesis of...

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