B. Sc. Honours Microbiology Syllabus under CBCS

Structure of B. Sc. Honours Microbiology under CBCS

Core Course

C-1: Introduction to Microbiology and Microbial Diversity
C-2: Bacteriology
C-3: Biochemistry
C-4: Virology
C-5: Microbial Physiology and Metabolism
C-6: Cell Biology
C-7: Molecular Biology
C-8: Microbial Genetics and Genomics
C-9: Environmental Microbiology
C-10: Food and Dairy Microbiology
C-11: Industrial Microbiology
C-12: Immunology
C-13: Medical Microbiology
C-14: Recombinant DNA Technology

Discipline Centric Elective (Any Four)

DSE-1: Bioinformatics
DSE-2: Microbial Biotechnology
DSE-3: Advances in Microbiology
DSE-4: Plant Pathology
DSE-5: Biomathematics and Biostatistics
DSE-6: Inheritance Biology
DSE-7: Microbes and Sustainable Development
DSE-8: IPR and Biosafety
DSE-9: Project Work

Generic Electives (Any Four)

GE-1: Introduction and Scope of Microbiology
GE-2: Bacteriology and Virology
GE-3: Microbial Metabolism
GE-4: Industrial and Food Microbiology
GE-5: Microbes in Environment
GE-6: Medical Microbiology and Immunology
GE-7: Genetic Engineering and Biotechnology
GE-8: Microbial Genetics and Molecular Biology

Ability Enhancement Compulsory Courses

AE-1: Environmental Sciences
AE-2: English/MIL Communication

Skill Enhancement Elective Courses (Any Two)

SE-1: Microbial Quality Control in Food and Pharmaceutical Industries
SE-2: Microbial Diagnosis in Health Clinics
SE-3: Biofertilizers and Biopesticides
SE-4: Food Fermentation Techniques
SE-5: Management of Human Microbial Diseases
SE-6: Microbiological analysis of air and water

Core Course

C-1: Introduction to Microbiology and Microbial Diversity

Topic	Subtopics
History of Development of Microbiology	Development of microbiology as a discipline, Spontaneous generation vs. biogenesis, Contributions of Anton von Leeuwenhoek, Louis Pasteur, Robert Koch, Joseph Lister, Alexander Fleming, Role of microorganisms in fermentation, Germ theory of disease, Development of microbiological techniques and the golden era of microbiology, Development of soil microbiology (Contributions of Martinus W. Beijerinck, Sergei N. Winogradsky, Selman A. Waksman), Establishment of medical microbiology and immunology (Paul Ehrlich, Elie Metchnikoff, Edward Jenner)
Diversity of Microbial World	A. Systems of Classification: Binomial Nomenclature, Whittaker’s five kingdom classification, Carl Woese’s three kingdom classification, Difference between prokaryotic and eukaryotic microorganisms B. General Characteristics of Different Groups: Acellular Microorganisms (Viruses, viroids, prions), Structure of TMV, poliovirus, T4 and λ phage, lytic and lysogenic cycles, one-step multiplication curve; Bacteria (eubacteria, chlamydiae, rickettsiae, mycoplasma, archaebacteria); Algae (History of phycology, occurrence, thallus organization, cell structure, reproduction, life cycles, applications in agriculture, industry, environment, food); Fungi (Historical developments, general characteristics, cell structure, reproduction, economic importance in agriculture, industry, medicine, food); Protozoa (General characteristics of Amoeba, Paramecium, Giardia)
An Overview of Scope of Microbiology

C-2: Bacteriology

Topic	Subtopics
Cell Organization	Cell size, shape and arrangement, glycocalyx, capsule, flagella, endoflagella, fimbriae and pili. Composition and detailed structure of gram-positive and gram-negative cell walls, Archaebacterial cell wall, Gram and acid fast staining mechanisms, lipopolysaccharide (LPS), sphaeroplasts, protoplasts, and L-forms. Effect of antibiotics and enzymes on the cell wall. Structure, function, and chemical composition of bacterial and archaeal cell membranes. Cytoplasm: Ribosomes, mesosomes, inclusion bodies, nucleoid, chromosome and plasmids. Endospore: Structure, formation, stages of sporulation.
Bacteriological Techniques	Pure culture isolation: Streaking, serial dilution, and plating methods; cultivation, maintenance, and preservation/stocking of pure cultures; cultivation of anaerobic bacteria, and accessing non-culturable bacteria.
Microscopy	Bright Field Microscope, Dark Field Microscope, Phase Contrast Microscope, Fluorescence Microscope, Transmission Electron Microscope, Scanning Electron Microscope.
Growth and Nutrition	Nutritional requirements in bacteria and nutritional categories; Culture media: components of media, natural and synthetic media, chemically defined media, complex media, selective, differential, indicator, enriched, and enrichment media. Physical methods of microbial control: heat, low temperature, high pressure, filtration, desiccation, osmotic pressure, radiation. Chemical methods of microbial control: disinfectants, types, and mode of action.
Reproduction in Bacteria	Asexual methods of reproduction, logarithmic representation of bacterial populations, phases of growth, calculation of generation time and specific growth rate.
Bacterial Systematics	Aim and principles of classification, systematics, and taxonomy, concept of species, taxa, strain; conventional, molecular, and recent approaches to polyphasic bacterial taxonomy, evolutionary chronometers, rRNA oligonucleotide sequencing, signature sequences, and protein sequences. Differences between eubacteria and archaebacteria.
Important Archaeal and Eubacterial Groups	Archaebacteria: General characteristics, phylogenetic overview, genera of Nanoarchaeota (Nanoarchaeum), Crenarchaeota (Sulfolobus, Thermoproteus), Euryarchaeota [Methanogens (Methanobacterium, Methanocaldococcus), thermophiles (Thermococcus, Pyrococcus, Thermoplasma), Halophiles (Halobacterium, Halococcus)]. Eubacteria: Morphology, metabolism, ecological significance, and economic importance of groups: Gram Negative: Non proteobacteria, Alpha proteobacteria, Beta proteobacteria, Gamma proteobacteria, Delta proteobacteria, Epsilon proteobacteria (General characteristics with examples). Gram Positive: Low G+C (Firmicutes), High G+C (Actinobacteria), Cyanobacteria (Introduction).

C-3: Biochemistry

Topic	Subtopics
Bioenergetics	First and second laws of Thermodynamics, Definitions of Gibb’s Free Energy, enthalpy, and entropy, mathematical relationship among them, Standard free energy change and equilibrium constant, Coupled reactions and additive nature of standard free energy change, Energy-rich compounds: Phosphoenolpyruvate, 1,3-Bisphosphoglycerate, Thioesters, ATP.
Carbohydrates	Families of monosaccharides: aldoses and ketoses, trioses, tetroses, pentoses, and hexoses. Stereo isomerism of monosaccharides, epimers, mutarotation and anomers of glucose. Furanose and pyranose forms of glucose and fructose, Haworth projection formulae for glucose, chair and boat forms of glucose. Sugar derivatives: glucosamine, galactosamine, muramic acid, N-acetyl neuraminic acid. Disaccharides: concept of reducing and non-reducing sugars, occurrence and Haworth projections of maltose, lactose, and sucrose. Polysaccharides: storage polysaccharides (starch, glycogen) and structural polysaccharides (cellulose, peptidoglycan, chitin).
Lipids	Definition and major classes of storage and structural lipids. Storage lipids: Fatty acids structure and functions, essential fatty acids, triacylglycerols structure, functions and properties, saponification. Structural lipids: Phosphoglycerides (building blocks, structure, functions), phosphatidylethanolamine and phosphatidylcholine. Sphingolipids: building blocks, structure of sphingosine and ceramide, sphingomyelins, cerebrosides, gangliosides. Lipid functions: cell signals, cofactors, prostaglandins, lipid micelles, monolayers, bilayers.
Proteins	Functions of proteins. Primary structure: Amino acids as building blocks, general formula, zwitterion concept, titration curve and its significance, classification, biochemical structure and notation of standard protein amino acids. Ninhydrin reaction. Natural modifications of amino acids: hydrolysine, cystine, hydroxyproline. Non-protein amino acids: Gramicidin, beta-alanine, D-alanine, D-glutamic acid. Oligopeptides: Structure and functions of naturally occurring glutathione and insulin, synthetic aspartame. Secondary structure: Peptide unit, alpha helix, beta pleated sheet. Tertiary and quaternary structures: forces holding the polypeptide together. Human hemoglobin structure and quaternary structures.
Enzymes	Structure of enzymes: apoenzyme and cofactors, prosthetic group (TPP), coenzyme (NAD), metal cofactors. Enzyme classification, Mechanism of action: active site, transition state complex, activation energy, Lock and Key hypothesis, Induced Fit hypothesis. Enzyme kinetics: hyperbolic and double reciprocal plots, Km, allosteric mechanisms. Definitions: enzyme unit, specific activity, turnover number. Multienzyme complex (pyruvate dehydrogenase), isozymes (lactate dehydrogenase). Effect of pH and temperature on enzyme activity. Enzyme inhibition: competitive (sulfa drugs), non-competitive (heavy metal salts).

C-4: Virology

Topic	Subtopics
Nature and Properties of Viruses	Introduction: Discovery of viruses, nature and definition of viruses, general properties, concept of viroids, virusoids, satellite viruses, and prions. Theories of viral origin. Structure of viruses: Capsid symmetry, enveloped and non-enveloped viruses. Isolation, purification, and cultivation of viruses. Viral taxonomy: Classification and nomenclature of different groups of viruses.
Bacteriophages	Diversity, classification, one-step multiplication curve, lytic and lysogenic phages (lambda phage), concept of early and late proteins, regulation of transcription in lambda phage.
Viral Transmission, Salient Features of Viral Nucleic Acids and Replication	Modes of viral transmission: Persistent, non-persistent, vertical, and horizontal. Salient features of viral nucleic acids: Unusual bases (TMV, T4 phage), overlapping genes (ɸX174, Hepatitis B virus), alternate splicing (HIV), terminal redundancy (T4 phage), terminal cohesive ends (lambda phage), partial double-stranded genomes (Hepatitis B), long terminal repeats (retrovirus), segmented (Influenza virus) and non-segmented genomes (picornavirus), capping and tailing (TMV). Viral multiplication and replication strategies: Interaction of viruses with cellular receptors and entry of viruses. Replication strategies of viruses as per Baltimore classification (phi X174, Retroviridae, Vaccinia, Picorna), assembly, maturation, and release of virions.
Viruses and Cancer	Introduction to oncogenic viruses. Types of oncogenic DNA and RNA viruses: Concepts of oncogenes and proto-oncogenes.
Prevention & Control of Viral Diseases	Antiviral compounds and their mode of action. Interferon and their mode of action. General principles of viral vaccination.
Applications of Virology	Use of viral vectors in cloning and expression, gene therapy, and phage display.

C-5: Microbial Physiology and Metabolism

Topic	Subtopics
Microbial Growth and Effect of Environment on Microbial Growth	Definitions of growth, batch culture, continuous culture, generation time, specific growth rate. Temperature and temperature ranges of growth. pH and pH ranges of growth. Effect of solute and water activity on growth. Effect of oxygen concentration on growth. Nutritional categories of microorganisms.
Nutrient Uptake and Transport	Passive and facilitated diffusion. Primary and secondary active transport, concept of uniport, symport, and antiport. Group translocation. Iron uptake.
Chemoheterotrophic Metabolism – Aerobic Respiration	Concept of aerobic respiration, anaerobic respiration, and fermentation. Sugar degradation pathways: EMP, ED, Pentose phosphate pathway. TCA cycle. Electron transport chain: Components of respiratory chain, comparison of mitochondrial and bacterial ETC, electron transport phosphorylation, uncouplers, and inhibitors.
Chemoheterotrophic Metabolism – Anaerobic Respiration and Fermentation	Anaerobic respiration with special reference to dissimilatory nitrate reduction (Denitrification; nitrate/nitrite and nitrate/ammonia respiration; fermentative nitrate reduction). Fermentation: Alcohol fermentation and Pasteur effect; Lactate fermentation (homofermentative and heterofermentative pathways), concept of linear and branched fermentation pathways.
Chemolithotrophic and Phototrophic Metabolism	Introduction to aerobic and anaerobic chemolithotrophy with an example each. Hydrogen oxidation (definition and reaction) and methanogenesis (definition and reaction). Introduction to phototrophic metabolism: Groups of phototrophic microorganisms, anoxygenic vs. oxygenic photosynthesis with reference to photosynthesis in green bacteria and cyanobacteria.
Nitrogen Metabolism – An Overview	Introduction to biological nitrogen fixation. Ammonia assimilation. Assimilatory nitrate reduction.

C-6: Cell Biology

Topic	Subtopics
Structure of Cell	Plasma membrane: Structure and transport of small molecules. Cell Wall: Eukaryotic cell wall, extracellular matrix, and cell-matrix interactions. Cell-Cell Interactions: Adhesion junctions, tight junctions, gap junctions, and plasmodesmata (structural aspects). Mitochondria, chloroplasts, and peroxisomes. Cytoskeleton: Structure and organization of actin filaments, association of actin filaments with plasma membrane, cell surface protrusions, intermediate filaments, and microtubules.
Nucleus	Nuclear envelope, nuclear pore complex, and nuclear lamina. Chromatin: Molecular organization. Nucleolus.
Protein Sorting and Transport	Endoplasmic Reticulum: Structure, targeting and insertion of proteins in the ER, protein folding, processing and quality control in ER, smooth ER, and lipid synthesis, export of proteins and lipids. Golgi Apparatus: Organization, protein glycosylation, protein sorting, and export from Golgi Apparatus. Lysosomes.
Cell Signalling	Signalling molecules and their receptors. Function of cell surface receptors. Pathways of intra-cellular receptors: Cyclic AMP pathway, cyclic GMP, and MAP kinase pathway.
Cell Cycle, Cell Death, and Cell Renewal	Eukaryotic cell cycle and its regulation. Mitosis and Meiosis. Development of cancer, causes, and types. Programmed cell death. Stem cells: Embryonic stem cells, induced pluripotent stem cells.

C-7: Molecular Biology

Topic	Subtopics
Structures of DNA and RNA / Genetic Material	DNA Structure: Miescher to Watson and Crick – historic perspective, DNA structure, salient features of the double helix. Types of DNA, types of genetic material, denaturation and renaturation, cot curves. DNA topology: Linking number, topoisomerases. Organization of DNA in prokaryotes, viruses, and eukaryotes. RNA Structure. Organelle DNA: Mitochondrial and chloroplast DNA.
Replication of DNA (Prokaryotes and Eukaryotes)	Bidirectional and unidirectional replication, semi-conservative and semi-discontinuous replication. Mechanism of DNA replication: Enzymes and proteins involved in DNA replication – DNA polymerases, DNA ligase, primase, telomerase (replication of linear ends). Various models of DNA replication: Rolling circle, D-loop (mitochondrial), Ө (theta) mode of replication. Mismatch and excision repair.
Transcription in Prokaryotes and Eukaryotes	Transcription: Definition, difference from replication. Promoter: Concept and strength of promoter. RNA polymerase and the transcription unit. Transcription in eukaryotes: RNA polymerases and general transcription factors.
Post-Transcriptional Processing	Split genes, concept of introns and exons. RNA splicing, spliceosome machinery, concept of alternative splicing. Polyadenylation and capping. Processing of rRNA. RNA interference: siRNA, miRNA, and its significance.
Translation (Prokaryotes and Eukaryotes)	Translational machinery, charging of tRNA, aminoacyl tRNA synthetases. Mechanisms of initiation, elongation, and termination of polypeptides in prokaryotes and eukaryotes. Fidelity of translation. Inhibitors of protein synthesis in prokaryotes and eukaryotes.
Regulation of Gene Expression in Prokaryotes and Eukaryotes	Principles of transcriptional regulation. Regulation at initiation with examples from lac and trp operons. Sporulation in Bacillus, yeast mating type switching. Changes in chromatin structure: DNA methylation and histone acetylation mechanisms.

C-8: Microbial Genetics and Genomics

Topic	Subtopics
Genome Organization and Mutations	Genome organization: E. coli, Saccharomyces, Tetrahymena. Mutations and mutagenesis: Definition and types of mutations; Physical and chemical mutagens; Molecular basis of mutations; Functional mutants (loss and gain of function mutants); Uses of mutations. Reversion and suppression: True revertants; Intra- and inter-genic suppression; Ames test; Mutator genes.
Plasmids	Types of plasmids – F plasmid, R plasmids, colicinogenic plasmids, Ti plasmids, linear plasmids, yeast 2 μ plasmid. Plasmid replication and partitioning, host range, plasmid-incompatibility, plasmid amplification, regulation of copy number, curing of plasmids.
Mechanisms of Genetic Exchange	Transformation: Discovery, mechanism of natural competence. Conjugation: Discovery, mechanism, Hfr and F’ strains, interrupted mating technique, and time of entry mapping. Transduction: Generalized and specialized transduction, LFT & HFT lysates, mapping by recombination and co-transduction of markers.
Phage Genetics	Features of T4 genetics. Genetic basis of lytic versus lysogenic switch of phage lambda.
Transposable Elements	Prokaryotic transposable elements: Insertion sequences, composite and non-composite transposons, replicative and non-replicative transposition, Mu transposon. Eukaryotic transposable elements: Yeast (Ty retrotransposon), Drosophila (P elements), Maize (Ac/Ds). Uses of transposons and transposition.

C-9: Environmental Microbiology

Topic	Subtopics
Microorganisms and their Habitats	Structure and function of ecosystems. Terrestrial Environment: Soil profile and soil microflora. Aquatic Environment: Microflora of freshwater and marine habitats. Atmosphere: Aeromicroflora and dispersal of microbes. Animal Environment: Microbes in/on human body (Microbiomics) & animal (ruminants) body. Extreme Habitats: Extremophiles – microbes thriving at high & low temperatures, pH, high hydrostatic & osmotic pressures, salinity, & low nutrient levels. Microbial succession in decomposition of plant organic matter.
Microbial Interactions	Microbe interactions: Mutualism, synergism, commensalism, competition, amensalism, parasitism, predation. Microbe-Plant interaction: Symbiotic and non-symbiotic interactions. Microbe-animal interaction: Microbes in ruminants, nematophagus fungi, and symbiotic luminescent bacteria.
Biogeochemical Cycling	Carbon cycle: Microbial degradation of cellulose, hemicelluloses, lignin, and chitin. Nitrogen cycle: Nitrogen fixation, ammonification, nitrification, denitrification, and nitrate reduction. Phosphorus cycle: Phosphate immobilization and solubilization. Sulphur cycle: Microbes involved in the sulfur cycle. Other elemental cycles: Iron and manganese.
Waste Management	Solid Waste Management: Sources and types of solid waste, Methods of solid waste disposal (composting and sanitary landfill). Liquid Waste Management: Composition and strength of sewage (BOD and COD), Primary, secondary (oxidation ponds, trickling filter, activated sludge process, and septic tank), and tertiary sewage treatment.
Microbial Bioremediation	Principles and degradation of common pesticides, organic (hydrocarbons, oil spills), and inorganic (metals) matter, biosurfactants.
Water Potability	Treatment and safety of drinking (potable) water, Methods to detect potability of water samples: (a) Standard qualitative procedure: presumptive test/MPN test, confirmed and completed tests for fecal coliforms. (b) Membrane filter technique. (c) Presence/absence tests.

C-10: Food and Dairy Microbiology

Unit	Subtopics
Unit 1: Foods as a substrate for microorganisms (8 hours)	Intrinsic and extrinsic factors that affect growth and survival of microbes in foods, natural flora and source of contamination of foods in general.
Unit 2: Microbial spoilage of various foods (10 hours)	Principles of spoilage, spoilage of vegetables, fruits, meat, eggs, milk and butter, bread, canned foods.
Unit 3: Principles and methods of food preservation (12 hours)	Principles and physical methods of food preservation: temperature (low, high, canning, drying), irradiation, hydrostatic pressure, high voltage pulse, microwave processing, and aseptic packaging. Chemical methods: salt, sugar, organic acids, SO2, nitrites and nitrates, ethylene oxide, antibiotics, and bacteriocins.
Unit 4: Fermented foods (10 hours)	Dairy starter cultures, fermented dairy products (yogurt, acidophilus milk, kumiss, kefir, dahi, cheese). Other fermented foods: dosa, sauerkraut, soy sauce, tampeh. Probiotics: health benefits, types of microorganisms used, probiotic foods available in the market.
Unit 5: Food borne diseases (10 hours)	Food intoxications: Staphylococcus aureus, Clostridium botulinum, mycotoxins. Food infections: Bacillus cereus, Vibrio parahaemolyticus, Escherichia coli, Salmonellosis, Shigellosis, Yersinia enterocolitica, Listeria monocytogenes, Campylobacter jejuni.
Unit 6: Food sanitation and control (5 hours)	HACCP, indices of food sanitary quality, and sanitizers.
Unit 7: Cultural and rapid detection methods of food borne pathogens in foods and introduction to predictive microbiology	(No specific duration provided for this unit)

C-11: Industrial Microbiology

Unit	Subtopics
Unit 1: Introduction to industrial microbiology and fermentation processes (10 hours)	Brief history and developments in industrial microbiology. Types of fermentation processes: Solid-state and liquid-state (stationary and submerged) fermentations. Batch, fed-batch (e.g., baker’s yeast), and continuous fermentations.
Unit 2: Types of bio-reactors and measurement of fermentation parameters (12 hours)	Components of a typical bio-reactor. Types of bioreactors: Laboratory, pilot-scale, and production fermenters. Constantly stirred tank and air-lift fermenters. Measurement and control of fermentation parameters: pH, temperature, dissolved oxygen, foaming, and aeration.
Unit 3: Isolation of industrially important microbial strains and fermentation media (10 hours)	Sources of industrially important microbes and methods for their isolation, preservation, and maintenance of industrial strains. Strain improvement. Crude and synthetic media: Molasses, cornsteep liquor, sulphite waste liquor, whey, yeast extract, and protein hydrolysates.
Unit 4: Down-stream processing (6 hours)	Cell disruption, filtration, centrifugation, solvent extraction, precipitation, lyophilization, and spray drying.
Unit 5: Microbial production of industrial products (18 hours)	Micro-organisms involved, media, fermentation conditions, downstream processing, and uses for: Citric acid, ethanol, penicillin, glutamic acid, Vitamin B12. Enzymes (amylase, protease, lipase), wine, and beer.
Unit 6: Enzyme immobilization (4 hours)	Methods of immobilization, advantages and applications of immobilization. Large scale applications of immobilized enzymes: Glucose isomerase and penicillin acylase.

C-12: Immunology

Unit	Subtopics
Unit 1: Introduction (4 hours)	Concept of Innate and Adaptive immunity. Contributions of key immunologists: Edward Jenner, Karl Landsteiner, Robert Koch, Paul Ehrlich, Elie Metchnikoff, Peter Medawar, MacFarlane Burnet, Niels K Jerne, Rodney Porter, and Susumu Tonegawa.
Unit 2: Immune Cells and Organs (7 hours)	Structure, functions, and properties of immune cells: Stem cell, T cell, B cell, NK cell, Macrophage, Neutrophil, Eosinophil, Basophil, Mast cell, Dendritic cell. Immune organs: Bone marrow, Thymus, Lymph node, Spleen, GALT, MALT, CALT.
Unit 3: Antigens (4 hours)	Characteristics of antigens: Foreignness, molecular size, and heterogeneity. Haptens, epitopes (T & B cell epitopes). T-dependent and T-independent antigens. Adjuvants.
Unit 4: Antibodies (6 hours)	Structure, types, functions, and properties of antibodies. Antigenic determinants on antibodies: Isotypic, allotypic, idiotypic. VDJ rearrangements. Monoclonal and chimeric antibodies.
Unit 5: Major Histocompatibility Complex (MHC) (5 hours)	Organization of MHC locus (Mice & Human). Structure and functions of MHC I & II molecules. Antigen processing and presentation: Cytosolic and endocytic pathways.
Unit 6: Complement System (4 hours)	Components of the complement system. Activation pathways: Classical, Alternative, and Lectin pathways. Biological consequences of complement activation.
Unit 7: Generation of Immune Response (10 hours)	Primary and secondary immune response. Humoral immune response (Plasma and memory cells). Cell-mediated immune response: Self-MHC restriction, T cell activation, co-stimulatory signals. Killing mechanisms by CTL and NK cells. Introduction to tolerance.
Unit 8: Immunological Disorders and Tumor Immunity (10 hours)	Types of autoimmunity and hypersensitivity with examples. Immunodeficiencies: Animal models (Nude and SCID mice), SCID, DiGeorge syndrome, Chediak-Higashi syndrome, Leukocyte adhesion deficiency, CGD. Tumor immunity: Types of tumors, tumor antigens, causes, and therapy for cancers.
Unit 9: Immunological Techniques (10 hours)	Principles of immunological techniques: Precipitation, agglutination, immunodiffusion, immunoelectrophoresis, ELISA, ELISPOT, western blotting, immunofluorescence, flow cytometry, immunoelectron microscopy.

C-13: Medical Microbiology

Unit	Subtopics
Unit 1: Normal Microflora of the Human Body and Host-Pathogen Interaction	Normal microflora of the human body: Importance of normal microflora, microflora of skin, throat, gastrointestinal tract, urogenital tract. Host-pathogen interaction: Definitions of infection, invasion, pathogen, pathogenicity, virulence, toxigenicity, carriers and types, opportunistic infections, nosocomial infections. Transmission of infection, pathophysiologic effects of LPS.
Unit 2: Sample Collection, Transport, and Diagnosis	Collection, transport, and culturing of clinical samples. Principles of diagnostic tests: ELISA, Immunofluorescence, agglutination-based tests, complement fixation, PCR, DNA probes.
Unit 3: Bacterial Diseases	List of diseases affecting various organ systems. Detailed study of diseases: Respiratory: Streptococcus pyogenes, Haemophilus influenzae, Mycobacterium tuberculosis. Gastrointestinal: Escherichia coli, Salmonella typhi, Vibrio cholerae, Helicobacter pylori. Others: Staphylococcus aureus, Bacillus anthracis, Clostridium tetani, Treponema pallidum, Clostridium difficile.
Unit 4: Viral Diseases	List of viral diseases affecting various organ systems. Detailed study of viral diseases: Polio, Herpes, Hepatitis, Rabies, Dengue, AIDS, Influenza (including swine flu), Ebola, Chikungunya, Japanese Encephalitis.
Unit 5: Protozoan Diseases	List of protozoan diseases affecting various organ systems. Detailed study of diseases: Malaria, Kala-azar.
Unit 6: Fungal Diseases	Overview of types of mycoses and diseases: Cutaneous mycoses: Tinea pedis (Athlete’s foot), Systemic mycoses: Histoplasmosis, Opportunistic mycoses: Candidiasis. Transmission, symptoms, and prevention.
Unit 7: Antimicrobial Agents – General Characteristics and Mode of Action	Antibacterial agents: Modes of action (nucleic acid synthesis, cell wall synthesis, membrane function, protein synthesis, metabolism) with examples. Antifungal agents: Mechanisms (Amphotericin B, Griseofulvin). Antiviral agents: Mechanisms (Amantadine, Acyclovir, Azidothymidine). Antibiotic resistance: MDR, XDR, MRSA, NDM-1.

C-14: Recombinant DNA Technology

Unit	Subtopics
Unit 1: Introduction to Genetic Engineering	Milestones in genetic engineering and biotechnology.
Unit 2: Molecular Cloning – Tools and Strategies	Cloning Tools: Restriction modification systems (Types I, II, III): Mode of action, nomenclature, and applications of Type II restriction enzymes. DNA modifying enzymes: DNA polymerases, Terminal deoxynucleotidyl transferase, kinases, phosphatases, and DNA ligases. Cloning Vectors: Definition and properties, Plasmid vectors (pBR and pUC series), Bacteriophage lambda and M13 based vectors, Cosmids, BACs, YACs, Use of linkers and adaptors. Expression vectors: E.coli lac and T7 promoter-based vectors, yeast YIp, YEp, and YCp vectors, Baculovirus-based vectors, mammalian SV40-based expression vectors.
Unit 3: Methods in Molecular Cloning	Transformation of DNA: Chemical method, Electroporation. Gene Delivery: Microinjection, electroporation, biolistic method (gene gun), liposome and viral-mediated delivery, Agrobacterium-mediated delivery. DNA, RNA, and Protein Analysis: Agarose gel electrophoresis, Southern- and Northern-blotting techniques, dot blot, DNA microarray analysis, SDS-PAGE, and Western blotting.
Unit 4: DNA Amplification and DNA Sequencing	PCR: Basics of PCR, RT-PCR, Real-Time PCR. Sanger’s Method of DNA Sequencing: Traditional and automated sequencing, Primer walking, and shotgun sequencing.
Unit 5: Construction and Screening of Genomic and cDNA Libraries	Genomic and cDNA Libraries: Preparation and uses. Screening of Libraries: Colony hybridization, colony PCR, Chromosome walking, and chromosome jumping.
Unit 6: Applications of DNA Technology	Products of Recombinant DNA Technology: Insulin, hGH, antisense molecules. Transgenic crops: Bt cotton, Bt brinjal. Gene Therapy, Recombinant Vaccines, Protein Engineering, and Site-Directed Mutagenesis.

Discipline Centric Elective (Any Four)

DSE-1: Bioinformatics

Unit	Subtopics
Unit 1: Introduction to Computer Fundamentals	RDBMS: Definition of relational database. Mode of Data Transfer: FTP, SFTP, SCP; Advantages of encrypted data transfer.
Unit 2: Introduction to Bioinformatics and Biological Databases	Biological Databases: Nucleic acid, genome, protein sequence and structure, gene expression databases, metabolic pathway databases. Mode of Data Storage: File formats like FASTA, GenBank, Uniprot. Data Submission & Retrieval: From NCBI, EMBL, DDBJ, Uniprot, PDB.
Unit 3: Sequence Alignments, Phylogeny, and Phylogenetic Trees	Sequence Alignment: Local and global sequence alignment, pairwise and multiple sequence alignment. Scoring Alignments: Scoring matrices, PAM & BLOSUM series. Phylogenetic Trees: Types of trees, and tree construction methods: UPGMA, Neighbour joining, Maximum Parsimony, Maximum Likelihood.
Unit 4: Genome Organization and Analysis	Diversity of Genomes: Viral, prokaryotic, and eukaryotic genomes. Omics Analysis: Genome, transcriptome, proteome, 2-D gel electrophoresis, Maldi-ToF spectroscopy. Completed Genomes: Features of genomes of E. coli, S. cerevisiae, Arabidopsis, and humans.
Unit 5: Protein Structure Predictions	Protein Structure: Hierarchy – primary, secondary, and tertiary structures. Modeling: Structural classes, motifs, folds, and domains. Structure Prediction: In presence and absence of a template. Evaluation: Energy minimizations and Ramachandran plot. Applications: Protein structure and rational drug design.

DSE-2: Microbial Biotechnology

Unit	Subtopics
Unit 1: Microbial Biotechnology and its Applications	Microbial Biotechnology: Scope and applications in human therapeutics, agriculture (biofertilizers, PGPR, mycorrhizae), environmental and food technology. Microbial Roles: Use of prokaryotic and eukaryotic microorganisms in biotechnological applications. Genetically Engineered Microbes: Applications in industry (bacteria and yeast).
Unit 2: Therapeutic and Industrial Biotechnology	Recombinant Microbial Production: Pharmaceutical industry products like streptokinase, recombinant vaccines (e.g., Hepatitis B vaccine). Microbial Polysaccharides and Polyesters: Production of bio-pesticides and bioplastics. Microbial Biosensors: Applications in industry.
Unit 3: Applications of Microbes in Biotransformations	Steroid and Sterol Biotransformations: Microbial transformation processes. Bio-catalytic Processes: Industrial applications like high fructose syrup and cocoa butter substitute production.
Unit 4: Microbial Products and their Recovery	Purification Techniques: Filtration, ion exchange, and affinity chromatography. Immobilization Methods: Whole cell immobilization and its industrial applications.
Unit 5: Microbes for Bio-energy and Environment	Bio-Ethanol and Bio-Diesel Production: Commercial production from lignocellulosic waste and algal biomass. Biogas Production: Methane and hydrogen production via microbial cultures. Bioremediation: Degradation of xenobiotics, mineral recovery, and heavy metal removal from aqueous effluents.
Unit 6: RNAi	RNA Interference (RNAi): Mechanism and applications in gene silencing, drug resistance, therapeutics, and host-pathogen interactions.
Unit 7: Intellectual Property Rights (IPR)	IPR Concepts: Patents, copyrights, and trademarks.

DSE-3: Advances in Microbiology

Unit	Subtopics
Unit 1: Evolution of Microbial Genomes	Microbial Genome Features: Salient features of sequenced microbial genomes, core genome pool, flexible genome pool, and the concept of pangenome. Horizontal Gene Transfer (HGT): Mechanisms and impact on microbial evolution. Evolution of Bacterial Virulence: Genomic islands, pathogenicity islands (PAI), and their characteristics.
Unit 2: Metagenomics	Development of Metagenomics: History and advancements in the field. Bacterial Diversity: Exploring microbial diversity using metagenomic approaches. Biotechnological Gene Prospecting: Identifying genes of interest. Viral Metagenomics: Basic knowledge of viral metagenomes, metatranscriptomics, metaproteomics, and metabolomics.
Unit 3: Molecular Basis of Host-Microbe Interactions	Plant Pathogens: Epiphytic fitness and its mechanisms in plant pathogens. Hypersensitive Response (HR): Plant defense mechanisms against pathogens. Type Three Secretion Systems (TTSS): Their role in plant and animal pathogens. Biofilms: Types of microorganisms in biofilms, their molecular aspects, and significance in the environment, healthcare, virulence, and antimicrobial resistance.
Unit 4: Systems and Synthetic Biology	Networking in Biological Systems: Overview of biological networks and interactions. Quorum Sensing in Bacteria: Mechanisms of bacterial communication. Regulation of Bacterial Virulence: Co-ordinated control of bacterial virulence factors. Synthesis of Poliovirus: Basics of synthetic biology in the laboratory. Future Implications of Synthetic Biology: Applications to bacteria and viruses.

DSE-4: Plant Pathology

Unit	Subtopics
Unit 1: Introduction and History of Plant Pathology	Plant Disease Concept: Definitions, disease cycle, pathogenicity, symptoms associated with microbial plant diseases. Types of Plant Pathogens: Economic losses and social impact. Historical Milestones: Contributions of Anton DeBary, Millardet, Burrill, E. Smith, Adolph Mayer, Ivanowski, Diener, Stakman, H.H. Flor, Van Der Plank, molecular Koch’s postulates. Indian Contributions: Contributions of eminent Indian plant pathologists.
Unit 2: Stages in Development of a Disease	Disease Progression: Infection, invasion, colonization, dissemination of pathogens, and perennation.
Unit 3: Plant Disease Epidemiology	Disease Dynamics: Monocyclic, polycyclic, and polyetic diseases. Disease Triangle and Pyramid: Importance in disease prediction. Forecasting of Plant Diseases: Relevance in the Indian context.
Unit 4: Host-Pathogen Interaction	A. Microbial Pathogenicity: Virulence factors (enzymes, toxins, growth regulators, viral factors), pathogen effects on host physiology (photosynthesis, respiration, translocation). B. Genetics of Plant Diseases: R gene and avr gene; gene-for-gene hypothesis; resistance types (horizontal, vertical, apparent). C. Defense Mechanisms in Plants: Constitutive and inducible defenses (histological and biochemical responses like HR, SAR, phytoalexins, oxidative bursts).
Unit 5: Control of Plant Diseases	Disease Management: Regulatory (quarantine, pathogen-free propagative material), cultural (crop rotation, sanitation), chemical (protectants, fungicides, antibiotics), biological (suppressive soils, antagonistic microbes, trap plants). Genetic Engineering: Disease-resistant plants using plant-derived and pathogen-derived genes.
Unit 6: Specific Plant Diseases	Fungal Diseases: White rust of crucifers (Albugo candida), Downy mildew of onion (Peronospora destructor), Late blight of potato (Phytophthora infestans), Powdery mildew of wheat (Erysiphe graminis), Ergot of rye (Claviceps purpurea), Black stem rust of wheat (Puccinia graminis), Loose smut of wheat (Ustilago nuda), Wilt of tomato (Fusarium oxysporum), Red rot of sugarcane (Colletotrichum falcatum), Early blight of potato (Alternaria solani). Bacterial Diseases: Angular leaf spot of cotton, bacterial leaf blight of rice, crown galls, bacterial cankers of citrus. Phytoplasma Diseases: Aster yellow, citrus stubborn. Viral Diseases: Papaya ring spot, tomato yellow leaf curl, banana bunchy top, rice tungro. Viroid Diseases: Potato spindle tuber, coconut cadang cadang.

DSE-5: Biomathematics and Biostatistics

Unit	Subtopics
Unit 1: Biomathematics	Sets, Functions, and Their Graphs: Polynomial, sine, cosine, exponential, and logarithmic functions. Motivation through examples like projectile motion, simple pendulum, biological rhythms, cell division, and muscular fibers. Observations on Functions: Increasing, decreasing, and periodic behavior. Sequences and Recursion: Finite sequences, recursion, and difference equations (e.g., Fibonacci sequence in trees and rabbits). Infinite Geometric Series and Series Formulas: Series formulas for exe^xex, log⁡(1+x)\log(1+x)log(1+x), sin⁡(x)\sin(x)sin(x), and cos⁡(x)\cos(x)cos(x). Discontinuity and Continuity: Step function, limits. Differentiation: Motivation through biological and physical science examples. Differentiation methods: Chain rule, product rule, quotient rule. Second-order derivatives. Integration: Reverse process of differentiation, integrals of introduced functions. Differential Equations: First-order linear differential equations. Matrices in Biological Sciences: Points in plane and space, matrices in biological networks, sum and product of matrices up to order 3.
Unit 2: Statistical Methods in Biological Sciences	Measures of Central Tendency and Dispersion: Mean, variance, skewness, and kurtosis. Probability and Random Variables: Elementary probability, discrete and continuous random variables, mathematical expectation. Curve Fitting, Correlation, and Regression: Examples from biological sciences. Probability Distributions: Mean and variance of binomial, Poisson, geometric, Weibull, logistic, and normal distributions. Fitting of distributions. Statistical Analysis: Utility and misuse of statistics, sampling parameters, sample vs population, sampling errors, censoring, parametric vs non-parametric statistics. Sampling Distributions and Testing of Hypotheses: Standard error, level of significance, degrees of freedom. Large and Small Sample Tests: Tests based on normal distribution, t-test, Z-test, F-test. Confidence Intervals and Non-Parametric Tests: Chi-square test. Multivariate Statistics: Basic introduction to multivariate statistical methods.

DSE-6: Inheritance Biology

Unit	Subtopics
Unit 1: Introduction to Genetics	Historical developments in genetics. Model Organisms: Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, and their roles in genetic analyses and experimentation.
Unit 2: Mendelian Principles	Mendel’s Laws: Dominance, segregation, independent assortment. Deviation from Mendelian inheritance. Rediscovery of Mendel’s principles and the chromosome theory of inheritance. Alleles and Inheritance: Alleles, multiple alleles, pseudoalleles, and complementation tests. Extensions of Mendelian Genetics: Allelic interactions, dominance, recessiveness, incomplete dominance, co-dominance, multiple alleles, epistasis, penetrance, and expressivity.
Unit 3: Linkage and Crossing Over	Gene Linkage and Recombination: Cytological and molecular basis of crossing over. Mechanism of Crossing Over: Crossing over at the four-strand stage, molecular mechanism, and gene mapping.
Unit 4: Extra-Chromosomal Inheritance	Extra-Nuclear Inheritance: Organelle heredity, chloroplast mutations in Chlamydomonas, mitochondrial mutations in Saccharomyces. Maternal Effects: Shell coiling in Limnaea peregra. Infectious Heredity: Kappa particles in Paramecium.
Unit 5: Characteristics of Chromosomes	Chromosome Structure and Organization: Centromeres, telomeres, repetitive DNA, euchromatin, and heterochromatin. Chromosome Packaging: Normal and abnormal karyotypes in humans. Chromosome Banding: Polytene and lampbrush chromosomes. Chromosome Abnormalities: Structural variations such as deletions, duplications, inversions, translocations, and abnormalities in chromosome number, including Klinefelter syndrome, Turner syndrome, and Down syndrome.
Unit 6: Recombination	Types of Recombination: Homologous and non-homologous recombination, transposition, and site-specific recombination.
Unit 7: Human Genetics	Pedigree Analysis: Lod score for linkage testing, karyotypes, and genetic disorders.
Unit 8: Quantitative Genetics	Polygenic Inheritance: Heritability and its measurement. QTL Mapping: Quantitative trait locus (QTL) mapping.

DSE-7: Microbes and Sustainable Development

Unit	Subtopics
Unit 1: Soil Microbiology	Soil as a microbial habitat. Soil Profile and Properties: Soil formation, diversity, and distribution of microorganisms in soil.
Unit 2: Soil Organic Matter	Mineralization Processes: Decomposition of cellulose, hemicelluloses, lignocelluloses, lignin, and humus.
Unit 3: Microbial Activity in Soil and Greenhouse Gases	Production and control of greenhouse gases: Carbon dioxide, methane, nitrous oxide, and nitric oxide.
Unit 4: Microbial Control of Soil-Borne Plant Pathogens	Biocontrol Mechanisms: Methods and microorganisms used as biocontrol agents against microbial plant pathogens, insects, and weeds.
Unit 5: Biofertilization, Phytostimulation, Bioinsecticides	Plant growth-limiting compounds. Biofertilizers: Symbiotic (Bradyrhizobium, Rhizobium, Frankia) and non-symbiotic (Azospirillum, Azotobacter, Mycorrhizae, MHBs, Phosphate solubilizers, algae). Novel Microbial Combinations: PGPRs (Plant Growth Promoting Rhizobacteria).
Unit 6: Secondary Agriculture Biotechnology	Biotechnology in Agriculture: Biotech feed, silage, biomanure, biogas, biofuels—advantages, and processing parameters.
Unit 7: GM Crops	Genetically Modified Crops: Advantages, social and environmental aspects, Bt crops, golden rice, transgenic animals.

DSE-8: IPR and Biosafety

Unit	Subtopics
Unit 1: Biosafety	Introduction to Biosafety: Biosafety issues in biotechnology, Biological Safety Cabinets & their types, Primary containment for biohazards, Biosafety levels of specific microorganisms.
Unit 2: Biosafety Guidelines	Biosafety guidelines and regulations (national and international). GMOs/LMOs: Concerns and challenges, Role of Institutional Biosafety Committees, RCGM, GEAC for GMO applications in food and agriculture. Risk Analysis: Risk assessment, management, and communication. International Agreements: Overview of Cartagena Protocol.
Unit 3: Radioisotope Safety	AERB/RSD/RES guidelines for using radioisotopes in laboratories and safety precautions.
Unit 4: Introduction to Intellectual Property	Types of Intellectual Property: Patents, trademarks, copyrights, industrial design, and rights. Traditional Knowledge: Geographical Indications, patentable and non-patentable inventions, patenting life forms, legal protection of biotechnological inventions. WIPO: World Intellectual Property Rights Organization.
Unit 5: Grant of Patent and Patenting Authorities	Types of Patent Applications: Ordinary, PCT, Conventional, Divisional, and Patent of Addition. Patent Filing Procedures: Patent licensing, agreements, and patent infringement. Patent Litigation: Scope, case studies, and rights and duties of patent owners.
Unit 6: Agreements and Treaties	International Agreements: GATT, TRIPS, Madrid Agreement, Hague Agreement, WIPO Treaties, Budapest Treaty on international recognition of microorganism deposits. UPOV & Brene Conventions: Patent Cooperation Treaty (PCT), Indian Patent Act 1970 & recent amendments.

Generic Electives (Any Four)

GE-1: Introduction and Scope of Microbiology

Unit	Subtopics
Unit 1: History of Development of Microbiology	Development as a Discipline: Spontaneous generation vs. biogenesis. Contributions: Anton von Leeuwenhoek, Louis Pasteur, Robert Koch, Joseph Lister, Alexander Fleming. Microbiological Techniques: Role of microorganisms in fermentation, Germ theory of disease, Golden era of microbiology. Soil Microbiology: Contributions of Martinus W. Beijerinck, Sergei N. Winogradsky, Selman A. Waksman. Medical Microbiology and Immunology: Contributions of Paul Ehrlich, Elie Metchnikoff, Edward Jenner.
Unit 2: Diversity of Microorganisms	Classification Systems: Binomial nomenclature, Whittaker’s five kingdom, Carl Woese’s three kingdom systems. Microbial Groups: Acellular microorganisms (Viruses, Viroids, Prions) and Cellular microorganisms (Prokarya: Archaea and Bacteria, Eukarya: Algae, Fungi, Protozoa). Protozoa: Methods of nutrition, locomotion, and reproduction (Amoeba, Paramecium, Plasmodium).
Unit 3: Microscopy	Types of Microscopes: Bright Field, Dark Field, Phase Contrast, Fluorescence, Transmission Electron Microscope, Scanning Electron Microscope.
Unit 4: Sterilization	Sterilization Techniques: Moist Heat, Autoclave, Dry Heat, Hot Air Oven, Tyndallization, Filtration.
Unit 5: Microbes in Human Health & Environment	Medical Microbiology & Immunology: List of important human diseases and their causative agents in various human systems. Definitions of immunity (active/passive), primary and secondary immune response, antigen, antibody and their types. Environmental Microbiology: Important microbial interactions (mutualism, commensalism, parasitism), microorganisms used as biopesticides, biofertilizers, and in biodegradation, biodeterioration, and bioremediation (e.g. hydrocarbons in oil spills).
Unit 6: Industrial Microbiology	Fermentation: Definition, primary and secondary metabolites, types of fermentations, fermenters, and microbes producing industrial products through fermentation.
Unit 7: Food and Dairy Microbiology	Microorganisms in Food: Microorganisms as food (SCP), microorganisms in food fermentations (dairy and non-dairy based products), probiotics. Food Spoilage and Infections: Microorganisms in food spoilage and foodborne infections.

GE-2: Bacteriology and Virology

Unit	Subtopics
Unit 1: Cell Organization	Cell Structure: Cell size, shape, and arrangements. External Structures: Capsule, flagella, and pili. Cell Wall: Structure and composition of Gram-positive, Gram-negative, and archaeal cell walls. Membranes: Structure, chemical composition, and functions of bacterial and archaeal cell membranes. Cell Components: Ribosomes, inclusions, nucleoid, plasmids. Sporulation: Structure, formation, and stages of sporulation.
Unit 2: Bacterial Growth and Control	Culture Media: Components of media (synthetic/defined, complex, enriched, selective, differential, enrichment culture media). Pure Culture Isolation: Streaking, serial dilution, plating methods, cultivation, maintenance, and stocking of pure cultures, anaerobic bacteria cultivation. Bacterial Growth: Binary fission, phases of bacterial growth.
Unit 3: Bacterial Systematics and Taxonomy	Taxonomy and Nomenclature: Concepts, types of classification. Morphology & Classification: Ecological significance and economic importance of the following groups: Archaea: Methanogens, thermophiles, halophiles. Eubacteria: Gram-negative and Gram-positive bacteria. Gram-negative bacteria: Non-proteobacteria (Deinococcus, Chlamydiae, Spirochetes), Alpha-proteobacteria (Rickettsia, Rhizobium, Agrobacterium), Gamma-proteobacteria (Escherichia, Shigella, Pseudomonas). Gram-positive bacteria: Low G+C (Mycoplasma, Bacillus, Clostridium, Staphylococcus), High G+C (Streptomyces, Frankia).
Unit 4: Introduction to Viruses	Virus Properties: General nature and important features. Subviral Particles: Viroids, prions, and their importance. Virus Isolation and Cultivation: Techniques for isolating and cultivating viruses.
Unit 5: Structure and Multiplication of Viruses	Virus Morphology: Capsid symmetry and different shapes (examples: bacteriophages, plant viruses, human viruses). Viral Multiplication: Lytic and lysogenic cycles. Virus Examples: Features of viruses infecting different hosts, such as Bacteriophages (T4 & Lambda), Plant viruses (TMV & Cauliflower Mosaic Virus), Human viruses (HIV & Hepatitis viruses).
Unit 6: Role of Viruses in Disease and its Prevention	Viruses as Pathogens: Role of viruses in causing diseases. Prevention and Control: Viral vaccines, interferons, and antiviral compounds.

GE-3: Microbial Metabolism

Unit	Subtopics
Unit 1: Microbial Growth and Effect of Environment on Microbial Growth	Growth Definitions: Definitions of growth, batch culture, continuous culture. Growth Rates: Generation time and specific growth rate. Temperature Effects: Temperature and temperature ranges for microbial growth. pH Effects: pH and pH ranges for microbial growth. Osmotic Effects: Effect of solute and water activity on growth. Oxygen Effects: Effect of oxygen concentration on growth. Nutritional Categories: Nutritional categories of microorganisms.
Unit 2: Nutrient Uptake and Transport	Transport Mechanisms: Passive and facilitated diffusion. Active Transport: Primary and secondary active transport, including uniport, symport, and antiport. Group Translocation: Concept of group translocation. Iron Uptake: Mechanisms for iron uptake.
Unit 3: Chemoheterotrophic Metabolism – Aerobic Respiration	Metabolism Concepts: Concept of aerobic respiration, anaerobic respiration, and fermentation. Sugar Degradation Pathways: EMP pathway, ED pathway, Pentose phosphate pathway. TCA Cycle: Overview of the TCA cycle. Electron Transport Chain: Components of the respiratory chain, comparison of mitochondrial and bacterial ETC, electron transport phosphorylation, uncouplers, and inhibitors.
Unit 4: Chemoheterotrophic Metabolism – Anaerobic Respiration and Fermentation	Anaerobic Respiration: Dissimilatory nitrate reduction (denitrification; nitrate/nitrite and nitrate/ammonia respiration; fermentative nitrate reduction). Fermentation Pathways: Alcohol fermentation and Pasteur effect; lactate fermentation (homofermentative and heterofermentative pathways), concept of linear and branched fermentation pathways.
Unit 5: Chemolithotrophic and Phototrophic Metabolism	Chemolithotrophy: Introduction to aerobic and anaerobic chemolithotrophy with examples. Hydrogen Oxidation: Definition and reaction of hydrogen oxidation and methanogenesis. Phototrophic Metabolism: Groups of phototrophic microorganisms, anoxygenic vs. oxygenic photosynthesis (e.g., photosynthesis in green bacteria and cyanobacteria).
Unit 6: Nitrogen Metabolism – An Overview	Nitrogen Fixation: Introduction to biological nitrogen fixation. Ammonia Assimilation: Overview of ammonia assimilation. Nitrate Reduction: Assimilatory nitrate reduction.

GE-4: Industrial and Food Microbiology

Unit	Subtopics
Unit 1: Introduction to Industrial Microbiology	History and Developments: Brief history and developments in industrial microbiology. Fermentation Processes: Types of fermentation processes (solid state, liquid state, batch, fed-batch, continuous). Types of Fermenters: Laboratory, pilot-scale, and production fermenters. Bioreactor Components: Components of a continuously stirred tank bioreactor.
Unit 2: Isolation of Industrial Strains and Fermentation Medium	Strain Screening: Primary and secondary screening. Strain Maintenance: Preservation and maintenance of industrial strains. Fermentation Medium Ingredients: Use of molasses, corn steep liquor, whey, yeast extract.
Unit 3: Microbial Fermentation Processes	Downstream Processing: Filtration, centrifugation, cell disruption, solvent extraction. Industrial Products: Microbial production of citric acid, ethanol, and penicillin. Enzyme Production: Industrial production and uses of enzymes (amylases, proteases, lipases, cellulases).
Unit 4: Food as a Substrate for Microbial Growth	Growth Parameters: Intrinsic and extrinsic parameters affecting microbial growth in food. Food Spoilage: Microbial spoilage of milk, egg, bread, and canned foods.
Unit 5: Principles and Methods of Food Preservation and Food Sanitation	Physical Methods: High temperature, low temperature, irradiation, aseptic packaging. Chemical Methods: Salt, sugar, benzoates, citric acid, ethylene oxide, nitrate, and nitrite. Food Sanitation: Food sanitation and control methods (HACCP).
Unit 6: Dairy Products, Probiotics, and Food-borne Diseases	Fermented Dairy Products: Yogurt, acidophilus milk, kefir, dahi, and cheese. Probiotics: Definition, examples, and benefits. Food-borne Diseases: Food intoxication by Clostridium botulinum and Staphylococcus aureus. Food infection by Salmonella and E. coli.

GE-5: Microbes in Environment

Unit	Subtopics
Unit 1: Microorganisms and their Habitats	Ecosystem Structure and Function: Overview of ecosystems. Terrestrial Environment: Soil profile and soil microflora. Aquatic Environment: Microflora of freshwater and marine habitats. Atmospheric Environment: Aeromicroflora and microbial dispersal. Animal Environment: Microbes in/on human body (Microbiomics) & ruminants. Extreme Habitats: Extremophiles (microbes thriving in extreme temperatures, pH, pressures, salinity, and nutrient limitations).
Unit 2: Microbial Interactions	Types of Interactions: Mutualism, synergism, commensalism, competition, amensalism, parasitism, predation. Microbe-Plant Interactions: Symbiotic and non-symbiotic interactions. Microbe-Animal Interactions: Microbes in ruminants, nematophagus fungi, and symbiotic luminescent bacteria.
Unit 3: Biogeochemical Cycling	Carbon Cycle: Microbial degradation of cellulose, hemicelluloses, lignin, and chitin. Nitrogen Cycle: Nitrogen fixation, ammonification, nitrification, denitrification, and nitrate reduction. Phosphorus Cycle: Phosphate immobilization and solubilization. Sulfur Cycle: Microbes involved in sulfur cycling. Other Elemental Cycles: Iron and manganese cycling.
Unit 4: Waste Management	Solid Waste Management: Sources, types, and disposal methods (composting, sanitary landfills). Liquid Waste Management: Composition and strength of sewage (BOD, COD), Primary, secondary (oxidation ponds, trickling filters, activated sludge process, septic tanks), and tertiary sewage treatment.
Unit 5: Microbial Bioremediation	Principles of Bioremediation: Microbial degradation of pesticides and hydrocarbons (e.g., oil spills).
Unit 6: Water Potability	Water Treatment and Safety: Methods for ensuring drinking water safety. Water Testing Methods: Qualitative procedures (Presumptive test/MPN test, confirmed and completed tests for fecal coliforms), Membrane filter technique, Presence/absence tests.

GE-6: Medical Microbiology and Immunology

Unit	Subtopics
Unit 1: Normal Microflora of the Human Body and Host-Pathogen Interaction	Normal Microflora: Importance of normal microflora; microflora of skin, throat, gastrointestinal tract, and urogenital tract. Host-Pathogen Interaction: Definitions – Infection, Invasion, Pathogen, Pathogenicity, Virulence, Toxigenicity, Carriers (types), Opportunistic infections, Nosocomial infections, Transmission of infection.
Unit 2: Sample Collection, Transport, and Diagnosis	Collection, transport, culturing of clinical samples, and their identification characteristics.
Unit 3: Bacterial Diseases	List of diseases affecting various organ systems and their causative agents.
Unit 4: Viral Diseases	List of diseases affecting various organ systems and their causative agents.
Unit 5: Protozoan Diseases	List of diseases affecting various organ systems and their causative agents.
Unit 6: Fungal Diseases	Brief description of various types of mycoses.
Unit 7: Antimicrobial Agents: General Characteristics and Mode of Action	Antibacterial Agents: Five modes of action with examples – Inhibitors of nucleic acid synthesis, cell wall synthesis, cell membrane function, protein synthesis, and metabolism. Antifungal Agents: Mechanism of action of Amphotericin B and Griseofulvin. Antiviral Agents: Mechanism of action of Amantadine, Acyclovir, and Azidothymidine.
Unit 8: Immune Cells and Organs	Structure, functions, and properties of immune cells: Stem cells, T cells, B cells, NK cells, Macrophages, Neutrophils, Eosinophils, Basophils, Mast cells, Dendritic cells. Immune Organs: Bone Marrow, Thymus, Lymph Nodes, Spleen.
Unit 9: Antigens and Antibodies	Antigens: Characteristics (Foreignness, Molecular size, Heterogeneity); Haptens, Epitopes (T & B cell epitopes), Adjuvants. Antibodies: Structure, Types, and Functions.
Unit 10: Generation of Immune Response	Primary and Secondary Immune Response: Humoral and Cell Mediated immune responses. Humoral Immune Response: Generation of plasma and memory cells. Cell Mediated Immune Response: T-cell and macrophage involvement.
Unit 11: Immunological Disorders and Tumor Immunity	Autoimmunity and Hypersensitivity: Types and examples. Immunodeficiencies: Animal models (e.g., Nude mice, SCID mice).
Unit 12: Immunological Techniques	Principles and applications of techniques: Precipitation, Agglutination, Immunodiffusion, Immunoelectrophoresis, ELISA, ELISPOT.

GE-7: Genetic Engineering and Biotechnology

Unit	Subtopics
Unit 1: Introduction to Genetic Engineering	Milestones: Key developments in genetic engineering and biotechnology. Restriction Modification Systems: Mode of action, applications of Type II restriction enzymes in genetic engineering. DNA Modifying Enzymes: DNA polymerases, terminal deoxynucleotidyl transferase, kinases, phosphatases, and DNA ligases. Cloning: Use of linkers and adaptors. Transformation of DNA: Chemical method, electroporation. Methods of DNA, RNA, and Protein Analysis: Agarose gel electrophoresis, Southern and Northern blotting techniques, dot blot, DNA microarray analysis, SDS-PAGE, and Western blotting.
Unit 2: Vectors	Cloning Vectors: Definition and properties. Plasmid Vectors: pBR and pUC series. Bacteriophage Vectors: Lambda and M13-based vectors. Cosmids, BACs, YACs: Specialized vectors for large DNA fragments. Expression Vectors: E. coli lac and T7 promoter-based vectors, yeast YIp, YEp, YCp vectors, Baculovirus-based vectors, mammalian SV40-based expression vectors.
Unit 3: DNA Amplification and DNA Sequencing	PCR (Polymerase Chain Reaction): Basics, RT-PCR, Real-Time PCR. Genomic and cDNA Libraries: Preparation and uses, genome sequencing. Sanger’s Method of DNA Sequencing: Traditional and automated sequencing techniques.
Unit 4: Application of Genetic Engineering and Biotechnology	Gene Delivery Methods: Microinjection, electroporation, biolistic method (gene gun), liposome and viral-mediated delivery, Agrobacterium-mediated delivery. Products of Recombinant DNA Technology: Human therapeutic products (insulin, hGH, antisense molecules), Bt transgenic crops (cotton, brinjal, flavosavo tomato), gene therapy, recombinant vaccines, protein engineering.
Unit 5: Intellectual Property Rights	Patents, Copyrights, and Trademarks: Overview of IP rights in biotechnology.

GE-8: Microbial Genetics and Molecular Biology

Unit	Subtopics
Unit 1: Structures of DNA and RNA / Genetic Material	DNA Structure: Salient features of the double helix, types of DNA, denaturation, and renaturation. Topoisomerases: Role in DNA replication and structure. Organization of DNA: Differences in DNA organization in prokaryotes, viruses, and eukaryotes. RNA Structure: Overview of RNA molecules and their characteristics.
Unit 2: Replication of DNA	Bidirectional and Unidirectional Replication: Mechanisms of replication. Semi-conservative and Semi-discontinuous Replication: DNA replication models. Mechanism of DNA Replication: Enzymes and proteins involved: DNA polymerases, ligase, primase, and telomerase (for replication of linear ends).
Unit 3: Transcription	Transcription Overview: Definition and key components. Promoter Concept: Strength of promoter and its role in transcription initiation. Transcriptional Machinery: Mechanism and key enzymes involved in transcription.
Unit 5: Translation	Genetic Code: Characteristics and properties of the genetic code. Translational Machinery: Role of ribosomes, mRNA, tRNA, and aminoacyl-tRNA synthetases. Mechanisms of Translation: Initiation, elongation, and termination of polypeptide synthesis.
Unit 6: Regulation of Gene Expression	Transcriptional Regulation: Principles of gene regulation, with examples from lac and trp operons.
Unit 7: Mutations	Mutations and Mutagenesis: Types of mutations and their causes. Physical and Chemical Mutagens: Examples and their roles in mutation induction. DNA Repair Mechanisms: How cells repair mutations.
Unit 8: Mechanisms of Genetic Exchange	Transformation: Discovery and mechanism of natural competence. Conjugation: Discovery, mechanism, Hfr and F’ strains. Transduction: Generalized and specialized transduction mechanisms.
Unit 9: Plasmids and Transposable Elements	Plasmids: Properties, types, and function. Prokaryotic Transposable Elements: Insertion Sequences, composite and non-composite transposons, replicative and non-replicative transposition. Uses of Transposons and Transposition: Role in genetic variation and applications.

Skill Enhancement Elective Courses (Any Two)

SE-1: Microbial Quality Control in Food and Pharmaceutical Industries

Topic	Subtopics
Microbiological Laboratory and Safe Practices	Good Laboratory Practices (GLP): Overview and best practices for microbiological work. Biosafety Cabinets: Function, operation, and specifications (BSL-1, BSL-2, BSL-3). Biohazardous Waste Disposal: Disinfection methods, autoclaving, and incineration.
Determining Microbes in Food / Pharmaceutical Samples	Culture and Microscopic Methods: Standard plate count, MPN, direct microscopic counts. Biochemical and Immunological Methods: Limulus lysate test, gel diffusion, sterility testing. Molecular Methods: Nucleic acid probes, PCR-based detection, biosensors.
Pathogenic Microorganisms of Importance in Food & Water	Enrichment Culture Technique: Methods for selective growth of pathogens. Detection of Specific Microorganisms: XLD agar, Salmonella-Shigella agar, Mannitol salt agar, EMB agar, MacConkey agar, Sabouraud agar. Microbial Quality of Milk: MBRT test, rapid detection methods (COB, 10-min Resazurin assay).
HACCP for Food Safety and Microbial Standards	HACCP Principles: Hazard analysis and critical control points, flow diagrams, limitations. Microbial Standards: BIS standards for food and drinking water quality.

SE-2: Microbial Diagnosis in Health Clinics

Topic	Subtopics
Importance of Diagnosis of Diseases	Bacterial, Viral, Fungal, and Protozoan Diseases of Various Human Body Systems. Disease-Associated Clinical Samples for Diagnosis.
Collection of Clinical Samples	How to Collect Clinical Samples (oral cavity, throat, skin, blood, CSF, urine, and feces) and Precautions Required. Method of Transport of Clinical Samples to Laboratory and Storage.
Direct Microscopic Examination and Culture	Examination of Sample by Staining: Gram stain, Ziehl-Neelsen staining for tuberculosis, Giemsa-stained thin blood film for malaria. Preparation and Use of Culture Media: Blood agar, Chocolate agar, Lowenstein-Jensen medium, MacConkey agar. Distinct Colony Properties of Various Bacterial Pathogens.
Serological and Molecular Methods	Serological Methods: Agglutination, ELISA, immunofluorescence. Nucleic Acid-Based Methods: PCR, Nucleic acid probes.
Kits for Rapid Detection of Pathogens	Typhoid, Dengue, HIV, Swine Flu.
Testing for Antibiotic Sensitivity in Bacteria	Importance of Antibiotic Sensitivity Testing. Determination of Resistance/Sensitivity of Bacteria Using Disc Diffusion Method. Determination of Minimal Inhibitory Concentration (MIC) of an Antibiotic by Serial Double Dilution Method.

SE-3: Biofertilizers and Biopesticides

Topic	Subtopics
Biofertilizers	General account of the microbes used as biofertilizers for various crop plants and their advantages over chemical fertilizers. Symbiotic N2 fixers: Rhizobium – Isolation, characteristics, types, inoculum production and field application, legume/pulses plants. Frankia – Isolation, characteristics, Alder, Casurina plants, non-leguminous crop symbiosis. Cyanobacteria, Azolla – Isolation, characterization, mass multiplication, role in rice cultivation, crop response, field application.
Non-Symbiotic N2 Fixers	Free living Azospirillum, Azotobacter – Free isolation, characteristics, mass inoculum production and field application.
Phosphate Solubilizers	Phosphate solubilizing microbes – Isolation, characterization, mass inoculum production, field application.
Mycorrhizal Biofertilizers	Importance of mycorrhizal inoculum, types of mycorrhizae and associated plants, mass inoculum production of VAM, field applications of ectomycorrhizae and VAM.
Bioinsecticides	General account of microbes used as bioinsecticides and their advantages over synthetic pesticides, Bacillus thuringiensis – Production, field applications. Viruses – Cultivation and field applications.

SE-4: Food Fermentation Techniques

Topic	Subtopics
Fermented Foods	Definition, types, advantages and health benefits.
Milk Based Fermented Foods	Dahi, Yogurt, Buttermilk (Chach) and cheese: Preparation of inoculums, types of microorganisms and production process.
Grain Based Fermented Foods	Soy sauce, Bread, Idli and Dosa: Microorganisms and production process.
Vegetable Based Fermented Foods	Pickles, Sauerkraut: Microorganisms and production process.
Fermented Meat and Fish	Types, microorganisms involved, fermentation process.
Probiotic Foods	Definition, types, microorganisms and health benefits.

SE-5: Management of Human Microbial Diseases

Topic	Subtopics
Human Diseases	Infectious and non-infectious diseases, microbial and non-microbial diseases, deficiency diseases, occupational diseases, incubation period, mortality rate, nosocomial infections.
Microbial Diseases	Respiratory microbial diseases, gastrointestinal microbial diseases, nervous system diseases, skin diseases, eye diseases, urinary tract diseases, sexually transmitted diseases: Types, route of infection, clinical symptoms and general prevention methods, study of recent outbreaks of human diseases (SARS/Swine flu/Ebola) – causes, spread and control, mosquito-borne diseases – Types and prevention.
Microbial Diseases and Societal Issues	Importance of personal hygiene (Typhoid Mary), judicious use of antibiotics, importance of completing antibiotic regimen, emergence of antibiotic resistance, current issues of MDR/XDR microbial strains.
Vaccines	Importance, types of vaccines, vaccines available against microbial diseases, vaccination schedule (compulsory and preventive) in the Indian context.
Cancers	Types, causes, prevention, detection and treatment.

SE-6: Microbiological analysis of air and water

Topic	Subtopics
Aeromicrobiology	Bioaerosols, Airborne microorganisms (bacteria, viruses, fungi) and their impact on human health and environment, significance in food and pharma industries and operation theatres, allergens.
Air Sample Collection and Analysis	Bioaerosol sampling, air samplers, methods of analysis, CFU, culture media for bacteria and fungi, identification characteristics.
Control Measures	Fate of bioaerosols, inactivation mechanisms – UV light, HEPA filters, desiccation, incineration.
Water Microbiology	Waterborne pathogens, waterborne diseases.
Microbiological Analysis of Water	Sample collection, treatment and safety of drinking (potable) water, methods to detect potability of water samples: (a) standard qualitative procedure: presumptive test/MPN test, confirmed and completed tests for faecal coliforms (b) membrane filter technique and (c) presence/absence tests.
Control Measures	Precipitation, chemical disinfection, filtration, high temperature, UV light.