M.Sc. Microbiology, Lecture notes of Microbiology

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M.Sc. Microbiology

NEP Syllabus- 2022- (CBCS system)

Raja Mahendra Pratap Singh State University,

Aligarh(UP)202001.

M.Sc. Microbiology

Scheme of Semester System Examination (NEP-2022-23) First Semester Paper Code

SUBJECTS Credits Internal Marks

External Marks

Total

Compulsory Course

RB080701T Mycology 4 25 75 100 RB080702T Virology^4 25 75 RB080703T Bacteriology^4 25 75 RB080704T (^) Microbial Biochemistry 4 25 75 100 Compulsory Course Practical

RB080705P Practical (based on course 701-704) 4 25 75 100

RB080706R Research work/ Tour/Review^ -^ -^ -^ - MINOR RB080707* ( Any One ) from other Faculty^4 25 75 Total 24 230 470 700

Second Semester Paper Code SUBJECTS Credits InternalMarks ExternalMarks Total Compulsory Course

RB0807801T Microbial Metabolism 4 25 75 100 RB080802T Microbial Genetics^4 25 RB080803T Bioanalytical Technology 4 25 75 100 Elective I

RB080804T (^) Medical Microbiology (^4 25 75 ) RB080805T Clinical Microbiology Compulsory Course Practical

RB080806P Practical (based on course 801-805) 4 25 75 100

GE-II RB080807R ( Any One ) Review / Tour 4 25 75 100 Total 24 230 470 700

Third Semester Paper Code SUBJECTS Credits InternalMarks ExternalMarks Total

Compulsory Course

RB080901T (^) Immunology 4 25 75 100 RB080902T Molecular Biology and RDT (^4 25 75 ) RB080903T Biostatistics & Comp. Application (^4 25 75 )

RB080701- MYCOLOGY

UNIT –I

Status of fungi in living world, general features of fungi and fungus like organisms, recent trends in the classification of fungi, physiology and growth of fungi, nutritional and environmental factors affecting growth, saprotrophs, parasites of Mutualistic symbionts, physiology of reproduction in fungi, Phylogeny of fungi. Fungi and Biotechnology Production of alcoholoic beverages, antibiotics, organic acids, ergot alkaloids, the cultivation of fungi for food- Mushrooms, mycofoods, Role of fungi in agriculture and forestry- Mycorrhizae and their application.

UNIT-II Fungal Diversity- major taxonomic groups, structure, reproduction, life cycle and significance of the following representative:

1. Gymnomycota- Cellular slime moulds (Dictyostelium), Plasmodial slime moulds (myxomycetes)
2. Mastigomycotina- Coelomomyces, Lagenidium, Achlya, Phytophthora, Peronospora, Plasmodiophora
3. Amastigomycotina- Zygomycotina, Mucor, Syncephalastrum, Blakeslea, Cunninghamella, Entomorphthora.

UNIT- III Fungal diversity contd,

1. Ascomycotina- Taphrina, Chaetomium, Morchella, Neurospora.
2. Basidiomycotina- Puccinia, Melampsora, Polyporus, Lycoperdon.
3. Deuteromycotina- Fusarium, Cercospora, Curvularia, Beauveria, Microsporum.

UNIT- IV

1. Life cycle and sexual process in fungi,
2. Genetic variation in fungi- Nonsexual variations- haploidy, heterokaryosis, parasexuality, sexual variations, homothallisum and heterothallium, Mutation, physiological specialization.
3. Mycopesticides Mycotoxins.

Suggested Books:

1. Introductory Mycology, CJ Alexopoulos, CW Mims, M Blackwel, JohnWiley & Sons.
2. The Fungi: An Advanced Treatise, GC Ainsworth, KF Sparrow, AS Sussman.
3. An Introduction to Fungi, HC Dube, VikasPubl, New Delhi.
4. The Fungi, PD Sharma, Rastogi Publications, Meerut.
5. Fungi: Experimental Methods in Biology, R Maheshwari, CRC Press, Boka Raton, Florida.
6. Introduction to Fungi, J Webster & WS Roland, Cambridge University Press.
7. A Text Book of Modern Plant Pathology, KS Bilgrami, HC Dube.
8. Plant Pathology, RS Mehrotra.
9. Fungi and Plant Disease, VK Gupta, TS Paul 10.Diseases of Crop Plants in India, Rangaswamy & Mahadevan.
10. Plant Pathology, GN Agrio Elsevier Academic Press.
11. Molecular Plant Pathology, Dickinson CM, Bios Scientific Publisher
12. Plant Pathology: Concepts and Laboratory Exercises, NT Robert, MT Windham, AS Windham, CRC Press.
13. Principles of Plant Pathology, RS Sing, Oxford and IBH Publishing Co. Pvt Ltd.

Mycology –Lab  Isolation and identification of fungi from different environmental samples,

 Study the nutritional requirement of fungi,

 Cultivation of fungi in submerged and solid state fermentation,

 Production of enzymes, organic acids and other metabolites by fungi,

 Collection and study of basidiomycetous fungi,

 Study and culturing of yeasts, study yeast dimorphism,

 Isolation and identification of algae from different habitats,

 Culturing of algae under lab conditions,

 Study hydrogen and bioethanol production by algae,

 Algae as a source of SCP,

 Study pollution control by algae.

Symptoms of plant virus diseases, transmission of plant viruses, viral and viroid diseases and their control: General discussion on symptoms caused by viruses and viroids in diseased economically important trees and agricultural crops, and their control including development of virus disease resistant transgenetics Microbial viruses: Diversity, classification, characteristics and applications of bacteriophages, and general account on algal, fungal and protozoan viruses.

Suggested Books

1. Medical Virology 10 Th Edition by Morag C and Tim bury M C. ChurchilLivingstone, London.
   2. Introduction to Modern Virology 4th Edition by Dimmock N J, Primrose S. B.. Blackwell Scientific Publications. Oxford.
2. Virology by Conrat H.F., Kimball P.C. and Levy J.A.Prentice Hall, Englewood Cliff, New Jersey.
3. Text Book on Principles of Bacteriology, Virology and Immunology Topley and Wilsons.
4. Molecular Biology, Pathogenesis and Control by S.J. Flint and others. ASM Press, Washington, D.C.
5. Applied Virology. 1984. Edited by Edonard Kurstak. Academic Press Inc.
6. Introduction to Modern Virology by Dimmock. MB.

PRACTICAL PAPER –VIROLOGY

1. One step growth curve for determination of virus titre.
2. Phage typing of E.coli bacteriophages.
3. Induction of lambda lysogen by UV radiations.
4. Studies on Specialized transduction.
5. Isolation of lambda DNA and their characterization.
6. Amplification of lambda DNA by PCR
7. Cultivation and assay of viruses using embryonated eggs and Tissue culture Technique.

RB080703- BACTERIOLOGY

UNIT –I

History, scope and development of bacteriology, Sterilization, isolation, enrichment, pure culture and staining techniques, systematic study of bacteria; morphological, physiological, biochemical and serological studies, genetic characterization. Habitat, structure, reproduction & classification of bacteria. UNIT- II

1. The photosynthetic bacteria; cyanobacteria, green bacteria, halobacteria and their economic importance 2. Methanogenic bacteria and their significance 3. Chemoautotrophs and Methylotrophs: Nitrifying bacteria, sulphur oxidizers, iron bacteria and their economic importance.

UNIT- III

1. Enterobacteriaceae and related organisms, their morphological & physiological characters, genetic interrelationship, taxonomic sub-division & their importance in human health. 2. Myxobacteria, cytophage group, filamentous & gliding chemoheterotrophs & filamentous sulphur oxidizing bacteria.

UNIT IV

1. Gram positive spore forming bacteria: Unicellular endospore former-bacillus Clostridia.
2. Miscellaneous bacteria: Lactic acid bacteria, Micrococci, Corynebacteria, Mycobacteria.
3. Actinomycetes, Mycoplasma, Rickettsiae, Chlamydiae and their significance.

Suggested reading:

1. General Microbiology: R Y Stanier, Adelberg E A and J L Ingraham, Mac Millan Press Inc
2. Introduction to microbiology: Ingraham J L and Ingraham C A Thomson Brooks/ Cole
3. Principles of microbiology R M Atlas Wm C brown Publishers
4. Brock’s biology of Microorganisms Madigan M T and Martinko J M Pearson Education Inc
5. Microbiology: An introduction: Tortora G J, Funke B R and Case C L Pearson Education Inc

BACTERIOLOGY -LAB

1. Cell Signaling: paracrine, endocrine, autocrine. Signaling molecules – hormones, neurotransmitter, proteins and environmental factors. Cell surface receptors - G protein coupled receptor, receptor protein tyrosine kinase, cytokine receptor and non-receptor protein tyrosine kinase, receptor linked to other enzymatic activities.
2. Signaling pathways : Cyclic AMP pathway (second messenger and protein phosphorylation), cyclic GMP pathway, phospholipids and Ca 2+ pathway, Ras-Raf and MAP kinase pathway, JAK/STAT pathway,

Unit IV

1. Enzymes – Classification and factors affecting enzyme activity
2. Allosteric Enzymes and their regulation
3. Enzyme kinetics – Equilibrium and steady state theory (MichalisMenten equation) and determination of kinetic parameters.
4. Enzyme inhibition – reversible and irreversible inhibition, competitive, non-competitive and un- competitive inhibition

Suggested Books:

1. Biochemistry, Voet Donald and Voet J.G ., John Wiley and sons INC
2. Biochemistry, Zubay .G. - Wm.C.brown Publishers
3. The Physiology and Biochemistry of prokaryotes White .D. -Oxford Univ.press
4. Principles of Biochemistry, Lehninger A.L.Cox and Nelson , CBS Publishers and Distribution Pvt.Ltd
5. Biochemistry, Stryer .L., W.H.Freeman and Co
6. Principle and Techniques –Practical Biochemistry Wilson. K. and Walker.J. -Cambridge University press
7. Biochemistry, Murray, Harpers Mc Graw Hill
8. Biochemistry, Satyanarayana and Chakrapani, Books and Allied Publishers
9. Fundamentals of Biochemistry, Voet Donald,J.W.Voet and Ch.W.Pratt, Jhon Willey & Sons Inc.
10. 10. Enzyme Kinetics by Paul Engel. John Wiley and Sons.

BIOCHEMISTRY -LAB

Biochemistry:

 Preparation of standard and buffer solutions;

 Use of simple techniques in laboratory (spectrophotometery-verification of Beer's law,

relation between O.D. and percentage transmission; Centrifugation)  Estimation of sugars,

 Estimation of Proteins by Lowry„s method;  Estimation of DNA and RNA by diphenylamine and orcinol methods;

 Determination of enzyme activity and study of enzyme kinetics;

 Separation of biomolecules by electrophoresis.

RB080801-MICROBIAL METABOLISM

Unit I

Nutritional Categories of microorganisms based on carbon and energy sources, Metabolite Transport- Passive and facilitated, Primary and secondary active transport, Group translocation (phosphotransferase system), symport, antiport and uniport, electrogenic and electro neutral transport, transport of Iron.

Unit II

Microbial Growth- Definition balanced and unbalanced growth, growth curve, the mathematics of growth, Generation time, specific growth rate, batch and continuous culture, synchronous growth, diauxic growth curve. Types of Culture media, Isolation of pure cultures.

Unit III Brief account of photosynthetic and accessory pigments - chlorophyll, bacteriochlorophyll, rhodopsin, carotenoids, phycobiliproteins; Carbohydrates- anabolism. Autotrophy, oxygenic,

 Effects of incubation temperature on the growth of microorganisms.

 To study the lethal effect of temperature.

 Effects of different pH on the growth of microorganisms.

 To study the bacterial growth under aerobic, microaerophilic and anaerobic conditions.

 Effect of salt concentration on the growth of microorganisms.

 Preparation of selective and differential media for the growth of microorganisms.

 Ferrmentation of different carbohydrates.Morphological, Physiological and Biochemicaltests of selected bacterial cultures.

RB080802-MICROBIAL GENETICS

Unit I Mendel‟s work on transmission of traits; Genetic Variation; Molecular basis of Genetic Information;Mitosis and Meiosis; Linkage and crossing over; Molecular mechanism of crossing over; Recombination and recombination frequency.

Unit II Mutations-Induced versus Spontaneous mutations, Suppressor mutations, Molecular basis of Mutations,mutant enrichment; Complementation tests; recombination tests and gene replacements; Cloning genes by complementation and marker rescue; DNA repair mechanisms, Mutation and Microbial evolution.

Unit III Molecular mechanism of gene transfer by conjugation. Regulation of gene transfer by conjugation. Mapping bacterial genomes using Hfr strains. Transfer systems in gram positive bacteria. Ti plasmid and application.

Unit IV Transformation and transduction:Natural transformation and competence. Molecular basis

of natural transformation; Regulation of competence in B.subtilis. Artificially induced competence. Generalized versus specialized transduction, Mapping bacterial genes by transduction;Tetrad analysis in fungi,Positive and negative gene regulation and attenuation, using the lac , gal , trp and ara operons, with emphasis on recent advances.

Unit V Lytic cycle of T4 and T7 bacteriphages, Regulation of expression of genes in phage T and T7. Replication and packaging of filamentous phages M13. Benzer‟s experiments with the rII genes of phage T4 to construct phage genetic linkage maps. Lambda phage – Lytic and lysogenic cycles. Other lysogenic phages – P1 and x174. Transposons and gene regulation.Yeast Ty-1 transposon. Phase variation in bacteria , Transplantation (Synthetic genome).

MICROBIAL GENETICS-LAB

Microbial Genetics:

 Inactivation of microorganisms by different mutagens.

 Production, isolation and characterization of mutants.

 Determination of mutation rate.

 Isolation, characterization and curing of plasmids.

 Preparation of competent cells,

 Transformationof E.coli. using plasmid DNA

 Transfer of plasmid by conjugation, electroporation. T

 etrad and random spore analysis

RB080803-BIOINSTRUMENTATION

Unit I

1. Photometry – Basic principles, Instrumentation and applications of UV-Visible spectrophotometry
2. Infrared (IR) spectroscopy and its applications
3. Fluorescence spectroscopy – principle, instrumentation and applications.

4. Spectroscopy. Volume 1. Edited by B.B. Straughan and S. Walker. Chapman and Hall Ltd.
5. Chromatography: Concepts and Contrasts- 1988 by James Miller. John Wiley and Sons. Inc., New York.
6. Analytical Biochemistry by Holme.
7. Introduction to High Performance Liquid Chromatography by R. J. Hamilton and P. A. Sewell.

BIOANALYTAL TECHNIQUES -LAB

 Determination of absorption maxima of some important chemicals from their

absorptionspectra,  Estimation of biomolecule using spectrophotometer,

 Separation of carbohydrates and amino acids by paper chromatography,

 Separation of lipids by thin layer and column chromatography,

 Separation of proteins by ion exchange and gel filtration chromatography,

 Electrophoretic techniques to separate proteins and nucleic acids,

 Preparation of stock solutions and buffers;

 Standard curves of BSA;

 Estimation of protein, RNA and DNA;

 SDS-PAGE of proteins;

 Polymerase chain reaction;

 RAPD analysis;

 DNA restriction analysis.

RB080804-MEDICAL MICROBIOLOGY

Unit I

Early discovery of pathogenic microorganisms, development of medical microbiology as adiscipline, normal microbial flora of the human body and their importance. Host parasite relationships:

Definitions: infection, invasion, pathogen, pathogenicity, toxigenicity, virulence, carrier, types of carriers, opportunistic infections. Role of aggressins, depolymerizing enzymes, organotrophism. Transmission and spread of infection. Hospital acquired infections and their management.

Unit II Principle of different diagnostic tests (ELISA, Immunofluorescence, agglutination based tests). Modern approaches for diagnosis of infectious diseases: Basic concepts of gene probes, dot hybridization and PCR assays. Mechanism of action of various chemotherapeutic agents (antibacterial, antifungal and antiviral). Principle of drug resistance. Various methods of drug susceptibility testing, passive and active prophylactic measures.

Unit III

Study of important bacterial diseases caused by the following generawith reference to causative agent, pathogenesis, symptoms, transmission, control measures, epidemiology and diagnosis. Bacillus anthracis, Staphylococcus, E.coli, Salmonella typhii, Shigella dysenteriae, Vibrio cholerae, Haemophilus influenzae, Mycobacterium tuberculosis , Corynebacterium diptheriae , Treponema palladium. Emerging and reemerging bacterial pathogens.

Unit IV Study of important viral diseases wih reference to causative agent, pathogenesis, symptoms, transmission, control measures, epidemiology and diagnosis. Hepatitis, influenza, rabies, polio, chicken pox, herpes, dengue fever, AIDS and viral cancers. An overview of emerging and reemerging viral diseases: Ebola, SARS, Hanta and Chikungunya.

Unit V

Introduction to protozoan, fungal and helminthes diseases:Malaria, Giardiasis, & leishmaniasis; Superficial, subcutaneous, systemic and opportunistic mycose.

RB080805T-CLINICAL MICROBIOLOGY

UNIT-I

Bacteriology of air, water, food, milk, soil

SUGGESTED BOOKS: 1.Tortora, G.J., Microbiology: An Benjamin/Cummings Funke, B.R., Introduction Publishing And Case, C.L Company, Inc. 2 Pelczar, M.T. Microbiology Tata Mcgraw Hill Publication, New Delhi.

3. Schegel, H.G General Microbiology Cambridge University Press
4. Stanier, R.Y. General Microbiology Macmillian Press London

CLINICAL MICROBIOLOGYLAB Simple staining of bacteria  To prepare bacterial smear and perform simple staining using methylene blue Gram staining  To perform Gram staining of different bacterial cultures Special stain  To perform endospore staining, acid-fast staining and Albert's staining of bacterial cultures Counting of bacterial cell  To perform viable count of bacteria using pour plating technique Effect of nutritional factors on growth  To study the effect of different carbon & nitrogen sources on the growth of microorganisms Effect of environmental factors on growth  To study the effect of pH on the growth of microorganisms  To study the effects of UV radiation on growth of microorganisms Bacteriological examination of water & milk  To perform the bacteriological examination of water and milk  To perform the bacteriological examination of milk by methylene reductase test Microbes in hospital environment  To isolate and identify the bacteria and fungi from hospital environment Qualitative analysis of biomolecules  Qualitative test for carbohydrates: Molisch Test, Benedict test  Qualitative test for amino acid and protein: Biuret test, Ninhydrin test  Qualitative test for lipid: Acrolein test Quantitative analysis of blood parameters  Quantitative estimation of blood cholesterol  Quantitative estimation of blood glucose

 Quantitative estimation of blood urea Quantitative analysis of blood parameters  Quantitative estimation of creatinine  Quantitative estimation of protein albumin  Quantitative estimation of uric acid Quantitative analysis of liver enzymatic markers  Quantitative estimation of SGPT  Quantitative estimation of ALP Quantitative analysis of heart enzymatic marker  Quantitative estimation of SGOT a cardiac marker Quantitative analysis of prostate gland enzymatic marker  Quantitative estimation of ACP

RB080901-IMMUNOLOGY

Unit I:

Introduction to the immune system: Innate immunity; anatomic, physiological, phagocytic & inflammatory barriers. Adaptive immunity; natural & artificial immunity. Cells involved in immune response: lymphoid lineage (producing B & T lymphocytes) & Myeloid lineage (phagocytes: macrophages, neutrophils & eosinophils and auxillary cells; basophils, mast cells &platelets). Organs involved in immune system: primary & secondary lymphoid organs.

Unit II: Antigens: preparation of antigens, types of antigens- haptens, superantigens & cluster of differentiation molecules (CDs), Processing and presentation of antigens.. Immunoglobulins: structure & types of immunoglobulins, genetic diversity of immunoglobulins, catalytic antibodies. B-cell biology & T-cell biology (major histocompatibility complex (MHC) molecules). HLA and H-2 systems.

Unit III: Vaccines immunizations: types of vaccines (DNA vaccines, recombinant DNA vaccines, synthetic peptide vaccines, multivalent subunit vaccines) & their characteristics. Immunization of test animals, hyperimmune antisera; Prophylactic immunization; Immune Disorders: hypersensitivities, autoimmune diseases, transplantation (tissue) rejection, immunodeficiency’s.