Master of Science (Microbiology) - Sardar Patel University

SARDAR PATEL UNIVERSITY VallabhVidyanagar, Gujarat

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

of 3

Master of Science (Microbiology) M.ScMicrobiology Semester I

Course Code PS01CMIC51 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.

25

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.

25

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

25



of 3

(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.

25

...

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.



of 3

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

1 Watson, J. D., Tania, A. B., Stephen, P., B., Alexander, G., Michael, L., Richard, L., (2017). Molecular Biology of the Gene. 7thEdn. Pearson Education, United Kingdom

2 Henkin, T. M., Peters, J., E., (2020). Snyder and Champness Molecular Genetics of Bacteria. 5thEdn. ASM Press, Washington, DC.

3 Tropp, B. E., (2012). Molecular Biology: Genes to Proteins. 4thEdn. Laxmi Publications, New Delhi

4 Snustad, P. D., Simmons, M., J., (2011). Principles of Genetics. 6thEdn. Wiley Publications, New Jersey

5 Sinden, R. R. (1994). DNA structure and function. Gulf Professional Publishing.

6 Krebs, J. E., Goldstein, E. S., & Kilpatrick, S. T. (2017). Lewin's genes XII. Jones & Bartlett Learning.

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

On-line Resources

*****



Page 1 of 3

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


Course Biochemistry


Week 04

Course Objectives:

To expose the students to various techniques used for biochemical 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. Basic principle and application of Differential, density and ultracentrifugation Principle and applications of Native-PAGE, SDS-PAGE, Agarose and 2D gel electrophoresis. Capillary electrophoresis and its applications. Principle, methodology and applications of gel – filtration, ion –exchange and affinity chromatography; Thin layer and High Performance Thin Layer Chromatography. Gas chromatography, High performance liquid chromatography.

25%

2. Principles of Thermodynamics; Bioenergetics and energy metabolism in cells. Carbohydrate metabolism: Glycolysis and alternate pathways of glucose utilization, TCA cycle, glyoxylate cycle, Gluconeogenesis, Glycogen synthesis and utilization..

Oxidative phosphorylation and Electron transport chain: Electron carriers, iron sulphur proteins, cytochromes, PMF, ATP synthetase complex. Uncouplers and inhibitors of energy transfer.

25%

3. Lipids: Structure and properties of lipids, fatty acids, phospholipids, and other derived lipids; functions of lipoproteins, cholesterol, steroids and prostaglandins, membrane lipids.

Lipid metabolism: synthesis and oxidation of fatty acids (α, β and ω oxidation of fatty acids). Ketone bodies: Formation and degradation.

Vitamins: structure and function.

25%

4. Protein structure: primary, secondary, tertiary and quaternary structure 25%



Page 2 of 3

of proteins. Determination of protein structure and its analysis, Ramachandran plot, Hydropathy plot.

Structure, properties and classification of amino acids, amino acid metabolism, urea cycle and nitrogen balance. Disorders associated with amino acid metabolism.

Nucleotides: Structure and functions, Nucleotide metabolism.



Evaluation Pattern

Sr. No.




15%


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

1. Understand various techniques for biochemical studies and their role in understanding and elucidating structures and pathways.

2. Explain various metabolic activities leading to synthesis or breakdown of different macromolecules and their building blocks.

3. Understand and explain the process of energy generation in the cell.

Suggested References:

Sr. No.

References



Page 3 of 3

1. Lehninger’s Principles of Biochemistry: D L Nelson and M M Cox, Macmillan, Worth Pub. Inc., NY.

2. Biochemistry : LubertStryer 3. Harper’s Biochemistry: R. K. Murray and others, Appleton and Lange,

Stanford. 4. Microbial Physiology: Moat, Foster and Spector.


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



Page 1 of 3

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


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 tunneling 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

25%



Page 2 of 3

filaments; Actin, myosin and cell movement; Intermediate filaments; Microtubules and microtubule motors and movements); cilia and 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.



Page 3 of 3

2. Explain various cell organelles with their function and importance for the cell in its 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 Krebs, J. E., (2009). Lewin’s Genes X. 10thEdn. Jones & Bartlett Learning Publications, United States

2 Cooper, G., M., Hausman, R. E., (2015). The Cell: A Molecular Approach. 7thEdn. Sinauer Associates Inc, United States

3 Carp, G., (2013). Cell Biology. 7thEdn. Wiley, United States

4 Albert, B., Johnson, A., Lewis, J., Raff, M., Robert, K., Walter, P., (2014). Molecular Biology of the Cell. 6thEdn. Garland Science, United States

5 Lodish, H., Berk, A., Kaiser, C., A., (2007). Molecular Cell Biology. 6thEdn. W.H.Freeman & Co Ltd, South Asia



PS01CMIC54: Laboratory I

List of Practical Exercises:

1. Orientation to the Microbiology laboratory, general laboratory safety and good laboratory practices.

2. An orientation to common laboratory equipments used in Microbiology laboratory. 3. Biochemical calculations 4. Isolation of Pure culture 5. Isolation of genomic DNA from E. coli. 6. Quantification of DNA by UV absorption. 7. Estimationof DNA by DPA method 8. RNA estimation by orcinol method 9. Induction of beta-galactosidase and its assay 10. Separation of amino acids by thin layer chromatography. 11. Determination of λmax and validation of Beer-Lamberts law.

PS01CMIC55: Laboratory II


Part A: Practicals corresponding to PS01CMIC53

1. Microscopy 2. Localization of lipids present in plant cells. 3. Study of mitosis in plant cells. 4. Isolation of Chloroplast and Chlorophyll estimation. 5. To titrate amino acid and calculate pKa value. 6. Estimation of protein by Folins Lowry Method

Part B: Practicals related to corresponding elective paper

SARDAR PATEL UNIVERSITY Vallabh Vidyanagar, Gujarat


Page 1 of 3

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

Course Code PS01EMIC51 Title of the

Course Phytoresources

Total Credits of the Course

04 Hours per 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.

25

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.

25

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

25



Page 2 of 3

habitations, industrial zones, and highways. 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.

25



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. 2nd Edn. 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



Page 1 of 3

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

Course Code PS01EMIC52

Title of the Course

Human physiology


Week 04

Course Objectives:

Students should be able to :

- Understand structure function relationship of various body systems

Course Content


1. Homeostasis and the organization of body fluids Control of Homeostasis, Positive and negative feedback systems, Homeostatic Imbalances. An overview of human circulatory system. Anatomy of heart, cardiac cycle, cardiac output, blood pressure and regulation, ECG. The arterial system, venous system, the microcirculation and mechanics of capillary fluid exchange. Control of blood flow to the tissues. Portal circulations. Arterial pressure and its regulation. Blood-components and functional significance. Blood buffer systems, Blood coagulation and factors involved in coagulation. Laboratory tests to measure coagulation and thrombolysis. Hemopoiesis and blood groups, Disorders of circulatory system: coagulation disorders, hypertension, thalassaemias and anemias.

25

2. Digestive system – Composition, function of saliva, gastric, pancreatic intestinal and bile secretions – digestion and absorption of carbohydrates, lipids, proteins nucleic acids, minerals and vitamins. The Muscular System – Types of muscles and their functions. Physiology of m contraction in striated and non-striated muscle

25

3. Excretory system – structure of nephron formulation of urine, glomerular filtration, GFR, tubular reabsorption of glucose. renal and pulmonary control of blood pH, renal clearance. An overview of Respiratory System. Pulmonary ventilation, External and internal respiration, Structure and functions of the nose, pharynx,

25



Page 2 of 3

larynx, trachea, bronchi, bronchioles,and lungs. Mechanics of Breathing. Partial pressures of oxygen and carbon dioxide, Transport of oxygen and carbon dioxide in blood.

4. Nervous System- Structure of neuron, function and organization of nervous system, Blood brain barrier, Neurotransmitters, Nerve impulse transmission. Reproductive physiology – secretion and function of reproductive hormones, lactation. Hormonal disturbances.

25



Evaluation Pattern

Sr. No.




15%



1. Students should be able to read and understand diagnostic reports.

2. Student should be able to understand, how to maintain health



Page 3 of 3


Sr. No.

References

1. Guyton AC, Hall JE: Cerebral blood flow, the cerebrospinal fluid, and brain metabolism, Textbook of Medical Physiology, 10th edition. Edited by Guyton AC, Hall JE. Orlando, Florida, Harcourt, 2000, pp 709–17. 3

2. Ganong's Review of Medical Physiology, Twenty sixth Edition. 26th Edition. 1260122409 · 9781260122404.

3. Bryan H. Derrickson; Gerard J. Tortora. Principles of anatomy and physiology, Published : 2008; ISBN : 0470084715


On-line Resources

Related review articles and research papers



Page 1 of 3

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


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 interactionsand 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%



Page 2 of 3

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

*****




Page 1 of 3

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


Course BIOPROCESS AND BIOCHEMICAL

ENGINEERING Total Credits of the Course 04 Hours per

Week 04

Course Objectives:

1. Understanding of upstream and downstream processing 2. To understand Isolation, preservation, improvement, handling of organisms and optimization of media 3. Understand various types of small and large scale equipment, controls and concept of scale up 4. Understand basic concepts of growth, cultivation and product recovery

Course Content


1. Introduction to bioprocess technology & Upstream processes Industrially important microorganisms, Isolation, primary and secondary screening Preservation method and Microbial culture collections. Improvement of industrially important organisms Inoculum development and large scale inoculation and sampling Substrates for fermentation processes Medium optimization strategies

25

2. Bioreactor design: Laboratory, pilot and large scale reactors. Plug flow reactors, enzyme reactors, single use bioreactors. Approaches and bioreactor designs for cultivation of algal, plant and animal cells, suspension cultures, methods for microalgal cultivation, stem cell cultivation, high cell density cultivations, mixed cultures Sterilization of media and air. Scale up and Scale down

25

3. Mass transfer of oxygen: Agitation and aeration, Determination of KLa, factors affecting KLa, fluid rheology. Bioprocess kinetics: Kinetics of growth and substrate utilization in batch, fed batch and continuous systems. Control of process parameters: Instrumentation for monitoring bioreactor and fermentation processes, Sensors, Controllers, fermentation control systems and architecture, Incubation and sequence control, advanced control.

25

4. Introduction to Downstream processing: Bio-separation: Sedimentation, Filtration, Centrifugation, Cell Disruption: Mechanical and Non-mechanical

25



Page 2 of 3

Product Extraction and Concentration by Precipitation, Liquid-Liquid Extraction, Super critical fluid extraction, Aqueous two phase and three phase partitioning Product purification by various chromatographic techniques, Membrane processes (Dialysis, Reverse Osmosis and Ultrafiltration) Product drying and crystallization Fermentation Economics

...



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, preservation and cultivation

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



Page 3 of 3

Suggested References: •

Sr. No.

References

1. Principles of Fermentation Technology : Whitekar&Stanbury

2. Comprehensive Biotechnology : Murray Moo Young

3 Methods in Industrial Microbiology : Sikyta • Fermentation Microbiology and Biotechnology, El Mansi and Bryc

4 Bioprocess Engineering Basic Concepts: Shular and Kargi


https://onlinecourses.nptel.ac.in


*****

https://onlinecourses.nptel.ac.in/




Page 1 of 4

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


Course Microbial Genetics


Week 04

Course Objectives:

• To gain insights molecular basis of mutation and the pathways that safeguard DNA from damage.

• To learn about naturally occurring plasmids, plasmid copy number regulation and mechanism of segregation in daughter cells

• To learn about the classical methods of studying genetics in bacteriophages as well as fungi.

• To learn about molecular mechanisms of recombination in bacteria and eukaryotes

• To gain in depth knowledge about methods of horizontal gene transfer in bacteria and their application in genetics

• To learn biology of Agrobacterium, restriction modification systems and transposons.

Course Content


1. Mutation, DNA damage and Repair Spontaneous mutations (Random v/s Adaptive nature of mutation; Mutation rate and its determination,

Types of DNA damage and their consequences (spontaneous and chemical induced deamination, radiation induced DNA damage, loss of nitrogen bases, alkylation, intra and inter strand cross linking).

DNA repair pathways (Mis-match repair in prokaryotes and eukaryotes, Nucleotide excision repair in prokaryotes and in eukaryotes, base excision repair, recombinational repair, SOS pathway, specific repair of oxidative DNA damage, repair of pyrimidine dimers, repair of alkylation induced damage and adaptive response and other specific repair mechanisms).

25%

2. Plasmid Biology (Types of plasmids, compatibility, regulation of plasmid copy number and plasmid segregation)

Phage genetics (T-series, complementation and Fine structure analysis, biology of lambda phages)

25%



Page 2 of 4

Recombination (Types, Models of homologous recombination, Molecular mechanism of homologous, Homologous recombination in eukaryotes, mating type switching, Site specific recombination and its biological significance)

Fungal Genetics (Tetrad analysis and Mitotic recombination)

3. Transformation (Natural transformation in Bacillus subtilis, Streptococcus pneumonia and Haemophilus influenza). Transformation by inducing artificial competence, Gene linkage and mapping by transformation.

Transduction (Generalized transduction in P22, P1, T4 and Mu bacteriophages, homologous recombination with recipient’s chromosome, measuring transduction (co-transduction of markers, marker effects, abortive transduction, transduction of plasmids). Applications of generalized transduction, Specialized transduction and its applications.

Conjugation (F-factor mediated Conjugation in E. coli, Hfr conjugation and chromosomal transfer, F-prime conjugation and merodiploids, Conjugation of fertility inhibited F-like plasmids, Non conjugative mobilizable plasmids, chromosomal mobilization of non-F plasmids, Plasmid based conjugation in other bacteria (Salmonella, Pseudomonas, Streptomyces and streptococcus, Interrupted mating and conjugational mapping)

25%

4. Agrobacterium genetics: Ti plasmid, Interkingdom gene transfer (Key early experiments, vir regulon, protein secretion apparatus, conjugation model of T-DNA transfer, Integration products)

Restriction modification systems: Types of RM systems, Role of RM systems, salient features and insights into evolution of diverse types of Restriction endonucleases and Methyl transferases, Regulation of RM systems.

Transposable elements: Types of bacterial transposable elements; Structure, genetic organization and mechanism of transposition of Tn5, Tn3, phage Mu, Tn7, IS911, Integrons, Retrotransposons, conjugative and mobilizable transposons, Assays of transposition.

25%





Page 3 of 4

Evaluation Pattern

Sr. No.




15%



1. describe the types of mutations, mode of action of different mutagens, molecular basis of spontaneous mutations and the pathways existing in cells to safe guard its DNA against such damages.

2. explain how copy number of naturally occurring plasmids is regulated and the molecular basis of their stability in cell.

3. explain the models proposed to explain the molecular mechanism of recombination in bacteria and eukaryotes.

4 analyse tetrads and perform gene mapping in fungi.

5 describe the different modes of gene exchange in bacteria and perform mapping using these methods.

6 explain the biology of Agrobacterium tumefaciens and describe the interkingdom gene transfer in detail.

7 explain the biology of Restriction Modification systems in detail.

8 discuss different types of bacterial transposons, their genetic organization and mode of transposition.

Suggested References

Sr. No.

References

1 Watson, J. D., Tania, A. B., Stephen, P., B., Alexander, G., Michael, L., Richard, L., (2017). Molecular Biology of the Gene. 7thEdn. Pearson Education, United Kingdom

2 Henkin, T. M., Peters, J., E., (2020). Snyder and Champness Molecular Genetics of Bacteria. 5thEdn. ASM Press, Washington, DC.

3 Tropp, B. E., (2012). Molecular Biology: Genes to Proteins. 4thEdn. LaxmiPublications,



Page 4 of 4

New Delhi

4 Snustad, P. D., Simmons, M., J., (2011). Principles of Genetics. 6thEdn. Wiley Publications, New Jersey

5 Streips, U. N., &Yasbin, R. E. (Eds.). (2002). Modern microbial genetics (Vol. 344). New York: Wiley-Liss.

6 Krebs, J. E., Goldstein, E. S., & Kilpatrick, S. T. (2017). Lewin's genes XII. Jones & Bartlett Learning.

7 Maloy, S. R., Cronan, J. E., &Freifelder, D. (1994). Microbial genetics. Jones & Bartlett Learning.

8 Stent, G. S., & Calendar, R. Molecular Genetics. 1978.





Page 1 of 3

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


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%





Page 3 of 3

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

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 (7th Edn). New York: WH Freeman.

2. Murphy, K., & Weaver, C. (2016). Janeway's Immunobiology (9th Edn) Garland Science.

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

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

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





1. Bacterial Conjugation. 2. Transformation 3. Transduction. 4. Phage titration. 5. Isolation of plasmid from bacterial cell 6. spore counting 7. Determination of Del factor 8. Determination of KLa 9. Yeast growth curve 10. Reducing sugar estimation by Coles method 11. Cell Immobilization in Ca Alginate 12. Vital staining 13. Alcohol fermentation by free and immobilized S. cerevisiae




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. Estimation of Hemoglobin with the help of Sahli'sHemoglobinometer




Page 1 of 3

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


Course Principles of Ecology


04 Hours per 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. 5th Edn. 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

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

Course Code PS02EMIC52 Title of the Course Biostatistics


Week 4

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

Master of Science (Microbiology) M Sc (Microbiology) Semester II


Course Medical Microbiology


Week 04

Course Objectives:

1.To train students in the field of Medical Microbiology. Theoretical, as well as practical training is imparted to the candidates in the sub-specialities, namely, Bacteriology, Virology, Parasitology, and Mycology.

2.To impart and explain the students with the advanced molecular diagnostic techniques for the detection of medically important human microbial pathogens.

3. To train 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.Vaccine: Types and their mode of action. Recent advances in diagnostic microbiology: Automation, Nucleic acid based detection methods.

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 [chemical, plant metabolites and Ayurvedic

25%



Page 2 of 3

formulations] and their mode of action.

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, Wuchereria bancrofti, Schistosomes Mycology: Morphology, diseases caused, epidemiology and lab diagnosis of:- Opportunistic fungi - Cryptococcus, Candida, Aspergillus Mucormycosis Fungi causing Cutaneous mycoses- Dermatophytes Subcutaneous mycoses - Mycetoma, Systemic mycoses-Histoplasma

25%

...



Evaluation Pattern

Sr. No.




15%



1. Get acquainted with the basis ofpathogenesis and virulence of different bacterial, parasitological, viral and mycological pathogens, laboratory diagnosis techniques, and would also be sensitized to thesocial impact of most dreadful and emerging infections likeHIV,MARS, SARS-CoV-2,Mucormycosis etc.

2. Understand the specimen collection techniques and identification of pathogens by



Page 3 of 3

conventional and recent molecular methods.

3. Appreciate the significance of Vaccine, 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 Jagdish Chander,

8. An Introduction to Viruses by Biswas SB and Biswas


https://www.cdc.gov/

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


*****




Page 1 of 3

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


Course Microtechniques Total Credits of the Course 04 Hours per

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.

25

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

25

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.

25

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

25



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. Marimuthu, R. (2019). Microscopy and Microtechnique. MJP Publisher.



Page 3 of 3

2. O'Brien, T. P., &McCully, M. E. (1981). The study of plant structure principles and selected methods (No. 581.4 O2).

3. Johansen, D. A. (1940). Plant microtechnique. McGraw-Hill Book Company, Inc: London; 530p.

4. Berlyn, G. P. (1976). Botanical microtechnique and cytochemistry


On-line Resources



Page 1 of 3

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


Course Microbial biotechnology


Week 04

Course Objectives:

This course focuses on industrial applications of bioprocesses (Industrial Biotechnology) for the commercial manufacture of value-added biotechnological products like organic acids, vitamins, aminoacids, antibiotics, enzymes, biopharmaceuticals, fermented foods, microbial biomass etc. Major objectives are….. 1. To understand and critically evaluate the role of micro-organisms in

specific biotechnological processes. 2. To understand biochemistry for overproduction of various industrially

important microbial metabolites. 3. To learn about industrial fermentation processes(upstream and

downstream) for various primary metabolites, secondary metabolites, microbial biomass, biotransformations, and fermented foods.

Course Content


1. • Scope of Microbial biotechnology . • Microbial production and applications of primary metabolites:

Citric acid, Ethanol, L Glutamic acid, L Lysine ,Vitamins B12 and vitamin B2

• Industrially important microbial enzymes: Types, mode of action and applications of microbial amylases and proteases

25

2. • Microbial production of therapeutically important products:. o Antibiotics: Penicillin, Streptomycin o Ergot alkaloids : Production by Saprophytic cultivation

• Biotransformations of steroids: Hydroxylations and dehydrogenations, Sterol biotransformations.

• Probiotics and prebiotics: Fundamental aspects and health benefits

25

3. • Production of single cell protein from bacteria, fungi and algae: Characteristics, Nutritional value and safety. Substrates used, process examples, applications.

• Cultivation of edible and medicinal mushrooms: Nutritional and

25



Page 2 of 3

medicinal properties. • Production and applications of microbial exopolysaccharides:

Classification, biological functions, Structure and Biosynthesis of Xanthan and Alginate, Factors affecting fermentative production of exopolysaccharides and recovery.

• Production of bioplastics

4. • Physiological characteristics, functions and production oflactic starter cultures.

• Microbiology and technology of Fermented foods and dairy products:

o Cheese making: Cheese varieties, manufacture of cheddar cheese, Sources and properties of rennets.

o Yoghurt making: • Technology of Beer brewing:

25



Evaluation Pattern

Sr. No.




15%


Course Outcomes: Having completed this course, the learnerwill…….

1. Get acquainted with the industrial aspect of the field of Microbiology and also learn about growth pattern of microbes in different industrial systems.



Page 3 of 3

2. Develop understanding of the variety of fermentations and subsequent processing approaches available for the manufacture of biological products.

3. Acquire experimental knowhow of some of the industrial products produced by microorganisms such as enzymes, fermented foods etc.

4. Be able to demonstrate a clear understanding of how biochemical pathways relate to biotechnological applications.

Suggested References: • Comprehensive Biotechnology Vol-4, Murray Moo Young. • Biotechnology-Rehm and Reid. • Microbial Technology: Pepler • Microbiology and technology of fermented foods: R. W. Hutkins. Blackwell

publishing. • Topic related review papers


On-line Resources

*****



Page 1 of 3

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


Course Environmental Microbiology


Week 04

Course Objectives:

1. To understandmajor environmental pollution issues and possible solutions through knowledge of microbiolology.

2. To understandbiogeochemical cycling of essential elements and its implications.

3. To understand physiological and molecular adaptations in extremophiles and their possible biotechnological applications,

4. To understand various beneficial plant- microbes interactions and their importance in agriculture.

5. To learn various experimental approaches for detection and quantification of microbes in environment.

6. To understand fundamental aspects of microbial ecology.

Course Content


1. Global environmental problems: Global warming, Ozone depletion, Acid rain Water pollution: Sources and types, Physical, chemical and biological pollution of water.Eutrophication and its control. Microbial Indicators of water pollution Biodeterioration of wood and metals: Role of micro-organisms, mechanisms and control.

25

2. Biogeochemical cycles: Cabron, Nitrogen , Sulphur , Iron and Phosphorous cycles. Detrimental effects of diverted biogeochemical cycles: acid mine drainage, nitrous oxide emission, nitrate pollution of ground water Biological Nitrogen Fixation in detail:

Asymbiotic, symbiotic and associative nitrogen fixation. Structure, function and genetic regulation of nitrogenases.

25

3. Microorganisms in extreme environments: Characteristics of extreme environments ,Microbial diversity, habitat and adaptive strategies of thermophiles and hyperthermophiles, psychrophiles and psychrotrophs, halophiles, acidophiles and alkalophiles.Biotechnological applications of extremophiles Methods to study microorganisms in environment: Detection of microbial populations: Phenotypic detection, Lipid profileanalysis, molecular detection

25



Page 2 of 3

Determination of microbial biomass: Biochemical assays, physiologicalapproaches. Physiological methods to study microbial activity

4. Microbial communities and ecosystems:Microbial community dynamics, Structure of microbial communities, Ecosystems,Structure and function of some microbial communities in nature. Beneficial Interactions between microorganisms and plant:Mycorrhyzae,Symbiotic nitrogen fixing associations between rhizobia and legumes , Anabaena and Azolla, Plant growth promoting rhizobacteria: Transport / Mobility of microorganisms in soil and subsurface:Factors affecting transport, Novel approaches to facilitate microbial transport

25

...



Evaluation Pattern

Sr. No.




15%



1. Gain awareness about different Types of Environmental Pollution and Related Issues

2 Understand and appreciate crucial role of microbes invarious biogeochemical cycles .



Page 3 of 3

3. Appreciate the diversity of microorganism and microbial communities inhabiting a multitude ofextreme habitats and will be able to understand unique features of extremophiles which can be exploited for various industrially important activities/products and environmental conservation.

4. Learn different methods for detection of microbes from various environments and their characterization.

5. Understandfundamental aspects of microbial ecology and become familiar with current research in environmental microbiology.

6 Understand various plant microbes interactions especially rhizosphere, phyllosphere and mycorrhizae and their applications especially the biofertilizers

Suggested References: • .Environmental Microbiology. R. M. Maier, I. L. Pepper & G. P. Gerba. • Comprehensive Biotechnology Vol-4, Murray Moo Young. • Biotechnology- Rehm and Reid. • Microbial Ecology: Fundamentals and Applications- Atlas & Bartha, fourth edition,

Pearson Education. • Environmental science, B. J. Nebel and R. T. Wright. • The prokaryotes- 3 rd edition, volume 2 • Brock Biology of micro organisms by Madigan,Martinko, Dunlap, and Clark


On-line Resources

*****



Page 1 of 4

Master of Science (Microbiology) M Sc Microbiology Semester III


Course ENZYMOLOGY


Week 04

Course Objectives:

1.Understanding of basics properties of enzymes 2.Understand reaction kinetics of enzyme reactions, their mechanisms and experimental methods to study them 3. Understand the applications of enzymes and their engineering

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. 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 catalytic mechanisms and control of enzyme activity Enzyme catalytic mechanisms: Factors affecting catalytic efficiency, Mechanism of Lysozyme, Chymotrypsin, Carboxypeptidase,. Aspartate transcarbomylase

25



Page 2 of 4

Oligomeric enzymes: Sigmoidal kinetics and regulation, Protein ligand binding, Co-operativity, MWC & KNF models Experimental approaches to understand enzyme mechanisms Control of single enzyme activities by changes in covalent structure, ligand induced conformational changes and feedback inhibition.

4. Enzymes Technology and Applications Enzyme engineering: Structure function relationship, Methods of enzyme alterations, examples of engineered proteins Enzyme Immoblization, enzyme sensors, analytical and industrial applications of enzymes Enzymes in non conventional media, Isoenzymes and its physiological significance, Ribozymes and Abzymes

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 and work with the applications of enzymes in industries, therapeutics and other sectors and also the role of engineered enzymes

4 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: AnushaBhaskar 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: LubertStryer.

Biochemistry: D Voet and J Voet, Fourth edition, John Wiley Publishers



Page 4 of 4

Enzymology, T Devsena, Oxford Publication


On-line Resources:

https://www.expasy.org/

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

https://onlinecourses.nptel.ac.in


*****

https://onlinecourses.nptel.ac.in/


PS03CMIC54: Laboratory I List of Practical Exercises:

1. Cellulase production by Solid State Fermentation (SSF) (Endoglucanase assay, Filter paper activity, Protein estimation by Folin’s and Lowry’s method).

2. Saccharification of agro-waste by cellulase 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. Microbiological analysis of drinking water (Detection and enumeration of coliforms, Fecal

coliform MPN test, Detection of E. coli, Differentiation of coliforms) 9. Detection and enumeration of fecal Streptococcus and Enterococcus groups from

recreational water 10. Oxidation of sulphur in soil 11. Demonstration of Nitrification in soil and its inhibition 12. Isolation of sulphur oxidizing bacteria from soil 13. Isolation of phosphate solubilizing microorganisms from soil




1. Invertase Assay 2. Progress curve 3. Enzyme curve 4. Substrate saturation curve 5. Optimization of pH for invertase activity 6. Analysis of Substrate saturation data by various plots 7. Inhibition kinetics 8. Optimization of Temperature for invertase activity 9. Effect of temperature on Rate of reaction and determination of activation energy 10. Effect of temperature on enzyme stability 11. Enzymology workshop: kinetics, plots and numericals




Page 1 of 3

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


Course Biomanufacturing Principles and

Practices Total Credits of the Course 04 Hours per

Week 04

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

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


Course Toxicology


Week 03

Course Objectives:

i. To learn about the dose-response relationships and understand the tocixity 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 toxciants

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 conversionbetween animals and human Diagnosis of toxic changes in liver and kidneys: Metabolism of drugs: paracetamol andaspirin 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 Testsystems – Bacterial Mutation Test, Ames test, In vivo MammalianMutation tests –DNA repair assays, Chromosome damage test, Evaluation of Apoptosis andnecrosis

25

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

25



Page 2 of 3

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

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

Course Code PS03EMIC53 Title of the Course Bioinformatics


Week 4

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.

25%



Page 2 of 6

Database Searches: what are sequence-based database searches, 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 25%



Page 3 of 6

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. 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 &



Page 4 of 6

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 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

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

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

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



Page 5 of 6

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

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

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/

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/



Page 6 of 6

• 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)

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://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/

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) (Microbiology) (M. Sc.) (Microbiology) Semester (IV)


Course R-DNA Technology


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; Salient features of different enzymes used in R-DNA technology, 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

25%



Page 2 of 3

Metabolic engineering; Gene therapy; Restriction and regulations for 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.



Page 3 of 3

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

Master of Science (Microbiology) M.ScMicrobiology Semester IV


Course Environmental biotechnology


Week 04

Course Objectives:

1. To understand and address environment issues using knowledge of microbiology

2. To understand fundamentals of waste water treatment processes and biochemistry for removal of pollutants from water and technologies developed for that..

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

4. To understand some of the major pollution problems caused by organic and inorganic pollutants and bioremediation technologies.

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

6. To learn about need and applications of variousbiofertilizers 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 uses. Vermicomposting.

25



Page 2 of 3

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 bioremediation 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

*****



1. Restriction Digestion 2. Restriction Mapping 3. Ligation 4. Cloning of a gene in plasmid vector 5. Amplification of a desired fragment by PCR 6. RFLP 7. RAPD 8. Expression of a Recombinant Protein 9. Waste water characterization.

a. BOD b. COD c. Nitrate estimation d. Sulfate estimation

10. Study of phosphate solubilizing activity 11. Isolation of 2,4 dichlorophenoxyacetic acid degrading bacteria 12. Isolation of naphthalene degrading bacteria 13. Dehydrogenase activity of soil 14. Bioremoval of chromium from polluted water 15. Decolourization of Azo dyes by microorganisms.



Page 1 of 4

Master of Science (Microbioogy)) M.Sc. (Microbiology) Semester IV

Course Code PS04EMIC51 Title of the Course IPR and Biosafety


Week 4

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%



Page 3 of 4

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



Page 4 of 4

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

*****



Page 1 of 3

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


Course RESEARCH ETHICS AND

SCIENTIFIC WRITING Total Credits of the Course 04 Hours per

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



Page 2 of 3

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



Page 3 of 3


On-line Resources

*****



Page 1 of 3

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


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%

...

Teaching-



Page 2 of 3

Learning Methodology

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)



Page 3 of 3

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


On-line Resources

*****



Page 1 of 3

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


Course BIOMATERIALS AND TISSUE

ENGINEERING Total Credits of the Course 04 Hours per

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 properties of materials.Types of implant materials: Metallic, polymeric, ceramic and 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; Polyolefins 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, hematopoiet differentiation pathway; Potency and plasticity of stem cells, source

25%



Page 2 of 3

embryonic stem cells, hematopoietic and mesenchymal stem cells, Stem Cell markers, FACS analysis and differentiation. Stem cell system Liver, neuronal stem cells, Types and sources of stem cell wit characteristics: embryonic, adult, haematopoetic, fetal, cord bloo placenta, bone marrow, primordial germ cells, cancer stem cells induce 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.

…



Page 3 of 3


Sr. No.

References

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

*****



Page 1 of 3

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


Course Biodiversity and Conservation


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



Page 2 of 3

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. 3rd Edn. 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

*****

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



Page 1 of 3

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


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



Page 2 of 3

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

*****



Page 1 of 3

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


Course Mycology and Plant Pathology


Week 04

Course Objectives:

To understandthe fungal classification.

2. To studythestructure and reproduction fungi.

3. To understand modern techniques in mushroom cultivation

4. To understand structure and reproduction of lichens.

5. To understand various diseases caused by bacteria fungi and virus.

Course Content


1. Introduction to Fungi: History and classification of Fungi (Alexopoulas, 1962, Ainsworth 1973, Kirk et.al. 2008). Fungi: General characteristics. Economic importance of fungi. Life cycle, morphology, structure and reproduction in Kingdom: Fungi, Kingdom: Chromista and kingdom:Protozoa.

25%

2. Lichens: Morphology, reproduction and economic importance. Techniques of mushroom cultivation: Schedule and systems of cultivation; composting; peak heating; spawn preparation and mushroom stains spawning and mycelia growth; supplementation; cultivation technique from casing to ruffling and recovery growth to harvesting; pests and diseases and its protection.

25%

3. The disease triangle: Role of environment, host and pathogen in disease formation. Symptoms, life cycle and control of fungal diseases: Rusts, smuts, blast, red-rot, powdery mildew and tikka diseases. Symptoms, life cycle and control of bacterial and viral diseases: Leaf blight, canker, leaf spot, Mosaic, panama and leaf curl diseases.

25%

4. Control measures for plant diseases. Chemical control, biological control and integrated disease and pest management. Host- pathogen interactions, plant defense mechanisms. HR and SAR in plant defense. Molecular mechanisms and signaling pathways in plant defenses.

25%



Page 2 of 3

...



Evaluation Pattern

Sr. No.




15%



1. Students will have clear understanding of fundamentals of various classifications.

Students will have clear understanding of various diseases and their control.

2. Students will have clear understanding reproduction of various classes of fungi.

3. Students will have understanding techniques involved in cultivation of various mushrooms and their economic importance

4 Students will have clear understanding of biology and economic importance of lichens.

5 Students will have clear understanding of various diseases and their control.



Page 3 of 3


Sr. No.

References

1. Dube, H. C. (2013). An introduction to fungi. Scientific Publishers.

2. Alexopoulos, C. J., Mims, C. W., & Blackwell, M. (1996). Introductory mycology (No. Ed. 4). John Wiley and Sons.

3 Singh, R. S. (1980). Principles of Plant pathology.

4. Singh, R. S. (2018). Plant diseases. Oxford and IBH Publishing


On-line Resources

Master of Science (Microbiology) - Sardar Patel University

Documents

Transcript of Master of Science (Microbiology) - Sardar Patel University