Goa University Courses

M.Sc. (Microbiology)

Course Structure

 Course Detail

Semester - I

MI101 – Microbial Biochemsitry

Proteins and Enzymology

• Proteins: structure, principles of separation and purification, molecular weight determination; sequencing and synthesis
• Enzymes: Activity, Inhibition, Mechanism of action; Regulatory – Allosteric and Covalently Modulated Enzymes and their significance in metabolism.
• Amino acid biosynthethic pathways and their regulation

Carbohydrates and Lipids

• Carbohydrate Metabolism
  • Carbohydrates: Central pathways of metabolism – regulatory mechanisms, bioenergetics and significance - EMP and alternate pathways: Entner-Doudoroff, HMP and oxidative pentose phosphate; TCA cycle (glucose aerobic and anaerobic, malate metabolism), Glyoxylate cycle Utilization of sugars such as lactose, galactose, maltose and of polysaccharides such as starch, glycogen, cellulose, pectin
• Carbohydrate Metabolism
  • Gluconeogenesis from TCA intermediates / amino acids / acetyl-CoA; biosynthesis of polysaccharides and interconversion of sugars
• Lipid Metabolism
  • Lipids: fatty acids - structure, properties; classification of lipids, structure, properties, lipid composition of microorganisms
  • Catabolism: Bioenergetics of _-oxidation of fatty acids, long chain fatty acids
  • Anabolism:
    • Biosynthesis of fatty acids: saturated, unsaturated
    • Biosynthesis of triglycerides, phospholipids, sterols
      

Other Metabolic Pathways and Bioenergetics of Metabolism

• Nucleotide biosynthesis
  • Biosynthesis and its regulation of purine and pyrimidine nucleotides,
  • deoxyribo nucleotides
  • Biosynthesis of nucleotide coenzymes
• Bioenergetics and ATP generation
  • Exergonic and endergonic reactions;
  • Redox enzymes, aerobic electron transport and oxidative phosphorylation;
  • Intermediary metabolism - flexibility economy.
• Photosynthetic Metabolism
  • Organisms and photosynthetic pigments, fundamental processes in photosynthesis
  • Photosynthetic electron transcript and photophosphorylation
• Chemolithotrophy
  • Organisms, substrates, bioenergetics of metabolism
• Antimicrobials
  • Bacteriocins and antibiotics - mode of action and resistance

Practical

• Study of standard protein sample.
  • Precipitation of protein from solution by salting out; dialysis
  • Gel filtration / molecular exclusion chromatography
  • Specific activity, fold purification, percentage yield of enzyme
• Extraction of microbial whole cell protein
  • Growth and harvesting of the culture
  • Cell lysis: homogenisation/ sonication
  • Protein estimation of lysate - quantification per unit biomass
• Protein Profile / Molecular weight determination by SDS-PAGE

MI102 - Microbial Genetics

• Classical Mendelian Genetics and Deviation from Mendelian Principles, Genomes in Mitochondria and Plastids, mitochondria and chloroplast have diverse genomes, Mitochondrial genes have been inherited by Non-Mendelian mechanism, why mitochondria and plastids (chloroplast) have their own genetic system?
• Special types of chromosomes-Polytene and Lampbrush chromosomes and their genetic significance Structural chromosomal Aberrations and their significance: Deletion, Duplication, Inversion, Translocation Bacterial genomes – organization, replication, segregation and regulation Structure of Prokaryotic and Eukaryotic Genes (interrupted Genes), Prokaryotic genes are colinear with their proteins, Prokaryotic & Eukaryotic genome Size, Gene numbers, types and families of genes, pseudogenes and their significance.
• Viral Genetics : Genomic organization and Replication of viruses- T4,Lambda , M13, SV40, Hepatitis B, Poliomyeletis, HIV, H-1 N-1 (Swine Flu). Lambda Phage and its strategies-Lytic and Lysogenic cycles. Retroviruses and Retroposons-introduction and genetic significance.
• Genomic (DNA) Rearrangements: Mechanism of General and programmed DNA rearrangements, Role of transposons in DNA rearrangements. Transposons: IS elements – Composite transpo sons (Tn3, Tn 5, Tn 7,  Tn 10), Copia and P type , Mechanism of transposition, transposons as research tools.
• Mutagenesis, mutation and mutants: spontaneous and induced mutations, different types of mutants, molecular basis of mutagenesis, site specific and random mutagenesis. Tn mutagenesis; transition & transversion, tautomeric shift Point mutations and consequences: silent mutation, missense mutation, nonsense mutation, Read through mutation Mutagenic chemicals and radiations and their mechanism of action: EMS, MMS, acridines, Acriflavins, NTG, Hydroxylamine; mutagenic radiations- UV and gamma rays Importance of mutations
• Fungal Genetics: Yeast (Saccharomyces cerevisiae, S.pombe) and Neurospora genomes as model genetic systems; Chromosome replication, yeast artificial chromosomes, Crosses, tetrad analysis, genetic compatibility and non-compatibility genes, heterokaryosis, Parasexuality, Parthenogenesis, Gene conversion, mutagenesis (Petite mutants of yeast); Bacterial plasmids: Types of plasmids, F plasmids and their use in genetic analysis, colicin and col plasmids, R plasmids and plasmids with genes encoding metal resistance and degradation of organic recalcitrants (PAH, PCB’s, etc)., Replication mechanism of plasmids, regulation of copy number and compatibility; Bacterial plasmids as research tools.

4 Practical

• Isolation of plasmid DNA from recombinant E.coli cells by Boil Prep method (Holmes and Quigley,1989).
• Isolation of Genomic DNA of Bacterial cells using Rapid genomic DNA extraction method.
• Isolation of plasmid DNA from bacterial cells by Alkaline Lysis method  (Birnboim and Doly,1979).
• Agarose gel electrophoresis, visualization and documentation of plasmid DNA using Gel Doc system.
• Agarose gel electrophoresis of genomic DNA, visualization of genomic DNA and recording of gel using Gel doc system.
• Spectrophotometric quantitation and purity of genomic DNA of bacterial cells.
• Recovery of genomic DNA embedded in agarose gels (Freeze Squeeze, column)
• UV mutagenesis and screening of pigment deficient mutants of Serratia sp.
• Determination of UV survival of Serratia sp.

MI103 - Microbial Taxonomy and systematics

•  Microbial taxonomy and systematics - Concepts of classification of microorganisms, three domain and sixkingdom systems.
• Methods for identification
• Phenotypic characters - Morphology, Biochemical tests (e.g. API, BIOLOG), Bacteriophage typing, Serotyping
• Methods for identification Chemotaxonomic markers – Cell wall components, lipid composition, isoprenoid, quinones, protein profiles, cytochrome composition.

• Methods for identification
• Nucleic acid based techniques - DNA-DNA hybridization, G+C content, PCR based fingerprinting - RAPD, ribotyping; DNA sequencing for phylogenetic analysis, 16S rRNA sequencing
• Tools for Systematics - Numerical taxonomy, Polyphasic taxonomy, Phylogenetic analysis
• Salient features of division, class and orders with representative examples under following kingdoms – Archaea, Mycota and viruses
• Salient features of division, class and orders with representative examples under following kingdoms - Eubacteria (bacteria, cyanobacteria, actinomycetes), Protista (algae, protozoan, diatoms, yeast)

Practical

• Identification of bacteria using Bergey’s Manual 6
• Chemotaxonomic analysis - cell wall, cell lipid, quinines, cytochromes 6
• Isolation, identification and characterization of actinomycetes (Streptomyces sp.)
• Isolation, identification and characterization of yeast (Saccharomyces cerevisiae, Schizosaccharomyces pombe)
• Anaerobic microorganisms 3
• solation and identification of Cyanobacteria 
  

MI104 – Techniques and Instrumentation in Microbiology

• Chromatographic techniques: GC, HPLC/FPLC, Ion-exchange, Affinity, Molecular exclusion
• Centrifugation: Principles, methodology, application; Density gradient centrifugation; Ultracentrifugation
• Spectrophotometry: Atomic Absorption Spectrophotometry (AAS), UV-VIS, fluorimetry, Fourier transformation infra red spectroscopy (FTIR), MALDI-TOF, IR, NMR, MS
• Microscopy: Epifluroscence filter technique (DEFT), SEM, TEM and AFM.
• Radio-isotope and tracer techniques : Isotope and types of isotopes, Radio-activity counters, Autoradiography, Radiorespirometry
• Cell and tissue culture techniques: Primary & secondary/established cell lines, Monolayer & suspension cultures, Fluorescence activated cell sorting (FACS)
• Electrophoretic technique: PAGE, IEF, Agarose gel electrophoresis, PFGE, DGGE, TGGE, Capillary electrophoresis, Single stranded conformation polymorphism (SSCP)
• Isolation of cell organelles: Different methods of cell lysis/ breakage and isolation and purification of various cell organelles - Cell surface structures, Cell envelopes, Plasma membranes, Peptidoglycan, Outer membrane, ribosomes, Protoplasts, Vesicles, Spheroplast, DNA, RNA
• Others: X-ray diffraction, Oxygen analyser, Biosensors
  
• Isolation of mitochondria
• Preparation of protoplast
• Density gradient (sucrose) centrifugation
• Native PAGE
• Phase Contrast microscopy
• Lyophilisation
• Cell disruption by sonicator
• UV-Vis
• Fluorimetry
• Demonstration: HPLC, GC, Atomic absorption spectrophotometer, NMR, IR, MS

MI105 - Biomathematics and Biostatistics

• Characteristics of biological data: Variables and constants, discrete and continuous variables, relationship and prediction, variable in biology (measurement, ranked, attributes), derived variables (ratio, index, rates), types of measurements of biological data (interval scale, ratio scale, ordinal scale, nominal scale, discrete and continuous data);
• Elementary theory of errors: exact and approximate numbers, source  and classification of errors, decimal notation and rounding off numbers, absolute and relative errors, valid significant digits,  relationship between number of valid digit and error, the error of sum, difference, product, quotient, power and root, rules of calculating digits,
• Differentiation and Integration – rules and analysis, limits, solving equation;
• linear and exponential function - DNSA conversion by reducing sugar, survival/growth of bacteria
• Matrix and vector: principal operations involving matrices and vectors, transpose, determinant, inverse matrix, solving equations and matrix, concept of vector and analysis, solving systems of linear equations and non-linear equations, iterative method, concept of Eigenvalues and Eigenvectors, matrix and vector in solving differential equations and problems in integration; Effect of factor and relation to growth response
• Population and samples, random samples, parameter and statistics, accuracy and precision, accuracy in observations Tabulation and  frequency distribution, relative frequency distribution, cumulative frequency distribution, Graphical representation: types of graphs, preparation and their applications
• Measures of central tendency: characteristics of ideal measure, Arithmetic mean – simple, weighted, combined, and corrected mean, limitations of arithmetic mean; Median – calculation for raw data, for grouped data, for continuous series, limitations of median; Mode – computation of mode for individual series, by grouping method, in a continuous frequency distribution, limitations of modes; Relationship  between mean, median and mode; mid-range, geometric mean, harmonic mean, partition value, quartiles, deciles, percentiles Measure of dispersion: variability, Range, mean deviation, coefficient of mean deviation, , standard deviation (individual observations, grouped data, continuous series),  variance, coefficient of variance, limitation
• Skewness – definition, positive, negative, purpose, measure, relative measure, Karl pearson’s Coefficient, Bowley’s Coefficient, Kelly’s Measure, Moments Correlation analysis – Correlation, covariance, correlation coefficient for ungrouped data, Spearson’s Rank Correlation coefficient, scatter and dot diagram (graphical method) Regression analysis – regression coefficients, properties, standard error of estimates, prediction, regression analysis for linear equation
• Probability: Probability, Combinatorial Techniques, Elementary Genetics, Conditional Probability, Bayes' Rule, Statistical Independence, Binomial, Poisson, Normal Distributions
• Hypothesis Testing – parameter and statistics, sampling theory, sampling and non-sampling error, estimation theory, confidence limits testing of hypothesis, test of significance; Students’ T-test, tdistribution, computation, paired t-test
• Chi-square test, F-test

4 Practical

• Excel spreadsheet and data analysis
• Linear equation analysis
• Exponential equation analysis (Survival curve)
• Chi square test
• Normal distribution
• Hypothesis testing

Semester - II

MI201 - Industrial Microbiology

• History of Industrial Microbiology, fermentation processes, descriptive layout and components of fermentation process for extracellular and intracellular microbial products
• Microbial growth kinetics: Batch kinetics – Monod’s model (single substrate), deviations from Monod’s model, dual substrates – sequential utilization, multiple substrates – simultaneous utilization, substrate inhibition, product  synthesis (primary and secondary metabolite), toxic inhibition, death constant
• Microbial growth kinetics: Fed-batch kinetics – fixed volume, variable volume and cyclic fed-batch, applications and examples of fed-batch systems, Continuous cultivation system – relationship between μ and dilution rate, multistage systems, feedback systems (internal and external feedback), applications and examples of continuous cultivation system; comparison between various cultivation systems
• Optimization and modeling of fermentation process – single variable  design, multivariate screening designs, critical factor analysis, optimization designs for two or more factor, singlet method; Metabolic and flux control analysis
• Bioreactor design and operation: classification of reactors; Ideal mixed v/s plug flow reactor; designing parameters for reactors (stirred tank reactor, airlift reactor, plug flow reactor), rheology of fermentation broth
• Bioreactor design and operation: gas-liquid mass transfer, heat transfer, analysis of dimension less parameters and their application (aeration number, power number and Reynold’s number; Scale-up of bioprocesses: parameters used in scale-up and problems associated with scale-up
• Solid substrate fermentation (SSF): Principles and application; Surface fermentation Comparison between SSF, Surface fermentation and SmF. Problems in fermentation process and handling (foam, contamination, strain degeneration, etc), Immobilized enzymes and cell systems
• Fermentation monitor and control: Common measurement and control systems (speed, temperature, gas, pH, Dissolved oxygen, foam, redox, air flow, weight, pressure, biomass), On-line and off-line analysis, Digital controllers, control algorithm, flow charting, incubation control, advanced fermentation control and computer-based automation of process.
• Industrial scale Down-stream processing and product recovery: principle and general description of instrumentation, Recovery of particulates (cells and solid particles), recovery of intracellular products,   primary isolation (extraction, sorption), precipitation, industrial processes for chromatography and fixed bed adsorption, membrane separations; Type Processes - Antibiotic (Penicillin including semi-synthetic)

Practical

• Fermentation kinetics – growth of E.coli/S.cerevisiae and determination of μ max, Ks, Yx/s, m
• Rheology of substrate solutions, culture broth and harvested cell suspension
• Designing of fermentor – stirred tank reactor
• Aeration efficiency using dissolved oxygen analysis
• Immobilization using alginate
• Baker’s yeast – ISI quality assurance

MI202 - Archaea - Ecology, Physiology, Biochemistry and Genetics

• Emergence of Archaeobacteria and the domain Archaea: Three major lineages of life – Archaea, Eubacteria, Eukarya  Similarities and dissimilarities - Archaea, eubacteria and eukaryotes Uniqueness of archaebacteria v/s other Extremophilic microorganisms
• Significance of Archaea: Biotechnology, Biogeochemical cycling, Evolutionary developments
• Ecology, physiology and diversity of Archaea: Global econiches; Culture – Retrieval- methods, novel samplers, Nonculture- methods. Preservation Nutrition, Growth and growth kinetics and physiological versatility, Stress Response, Methanogens (Methanobacterium thermoautotrophicum); Halophiles (Halobacterim halobium); Thermophiles (Thermoplasma) and Thermoacidophiles (Sulfolobus).
• Cell structure and architecture of Archaea: Cellular organization - cell morphotypes, cell envelopes, Purple membrane, cell organelles - ribosomes, appendages; molecular organization Novel bio-molecules: GDEMs and macrocyclic lipid, enzymes, Coenzymes Methanopterin, formaldehyde activation factor, Component B, Coenzyme M, F420, F430, corrinoids. DNA Binding and Repair proteins
• Metabolism and energetics of Archaea: Modified anabolic pathways. (carbohydrates, lipids), Methanogenesis and acetoclastic reactions
• Modified Central metabolic pathways including C1, C3 compounds. Incomplete TCA; Carbon dioxide reduction pathways
• Bioenergetics:
  
  • respiration driven
  • light driven
  • chloride driven
  • cation driven ATP synthesis. Anaerobiosis.
• Bacterioruberin pathway.
• Lipid synthesis
• Genome of Archaea
• Size of genome, G + C content, associate proteins
• FI-DNA, FII-DNA, Plasmids, IS elements, AT-rich-islands. Modifications in tRNA and rRNA structure. Novel 7S rRNA. Signature sequences. DNA Replication, Recombination and DNA Repair in archaea
• Gene organization in Archaea:
• fdh operon
• his operon
• bob
• operon
• mcr operon.
• Archaeal viruses like particles and phages.

Practical

• Isolation and Culturing of Archaea
• Identification of isolate:
  • Analysis of morphological features by SEM.
  • Cellular lipids - Extraction and chromatographic resolution of lipids
• Bioprospecting for hydrolytic enzymes/ for Archaeocin

MI203 - Molecular Biology

Nucleic Acids- structure of DNA and RNA, Bondings and different types of DNA (B-DNA & Z-DNA); DNA packaging in bacteria, viruses and eukaryotes, Hybrid genome of Eucaryotes: Regulatory sequences, yeast as a minimal model eukaryote, Arabidopsis as a model of higher eukaryote; Diversity of genomes and the tree of life.

DNA, chromosomes and Genomes: structure and function of DNA, chromosomal DNA and its packaging in the chromatin fibre, chromatin structure, structural features (Telomere, Centromere and Repetitive sequences) of chromosomes and their functions. Packaging of Viral genomes; bacterial genome - nucleoid, Evolution of Genomes; Gene duplication and mutations.

DNA Damage and repair, recombination

DNA damage elements/factors, Types of DNA damage(spontaneous and induced DNA damage), mechanisms/pathways to remove damaged DNA: Excision repair, mismatch repair, recombination repair in E.coli, SOS Repair, role of Rec A in DNA damage repair, Photoreactivation repair in E.coli involving photolyase.

Mechanisms of Genetic Recombination: General and site specific recombination, Heteroduplex DNA formation (Homologous recombination), Synaptonemal Complex, Bacterial Rec BCD system and its stimulation of chi sequences; role of Rec A protein, homologous recombination, Holliday junctions.

How cells read the Genome: From DNA to Proteins -

• From DNA to RNA
• From RNA to Protein
• The RNA world and origin of life

Gene structure & Control of Gene expression in Prokaryotes and eukaryotes:

An overview of Gene control, DNA binding motifs in Gene regulatory proteins, Genetic switches and their role in control of gene expressions; molecular Genetic mechanisms that create specialized cell types, Post-transcriptional controls-transcription attenuation, Riboswitches, Alternate splicing, RNA editing, RNA Interference, Translation of mRNA in Prokaryotes and Eukaryotes and role of Regulatory Switches, leader sequences and protein localization.

Practical

• Demonstration of working principle of Gel Documentation system.
• Demonstration of working principle of Thermal Cycler.
• PCR amplification of a specific gene (target DNA sequence) from genomic DNA. Agarose Gel analysis of PCR product to check it’s size and purity.
• Curing of plasmid DNA by acridine orange/SDS and determination of plasmid loss by loss of resistance to antibiotic and agarose gel electrophoresis.
• Fluctuation test
• NTG –Mutagenesis and Screening of NTG - induced heavy metal resistant Mutants

MI204 - Marine Microbiology I

• Microbes in the marine environment
• What is marine microbiology, Biological organization and the evolution of life, The world’s oceans and seas, Chemical and physical factors in the marine environment, Properties of seawater, Marine microbial habitats - water column, Sediments, coastal ecosystems, mangroves salt marshes. Biofilms and Microbial mats, Microbial life at surfaces of living and non-living systems
• Methods in marine microbiology
• Sampling and experimental approaches, specific staining procedures for Microscopy, study of cellular and sub-cellular organisation using Confocal laser scanning microscopy (CLSM), particulate and cellular composition using Flow cytometry (FCM)
• Methods in marine microbiology
• Laboratory culture: The importance of cultural conditions, viable but non-culturable (VBNC) organisms, Enrichment culture, Isolation, Biochemical methods for identification and taxonomy
• Molecular tools
• Molecular tools in study of marine microbial diversity, Phylogenetic analysis, Metagenomics; Community fingerprinting, Limitations of analysis of nucleic acids directly from marine environment, Genomic fingerprinting and molecular markers; RAPD; Fluorescence in situ hybridization (FISH)
• Physiology of marine prokaryotes
• Metabolic diversity and the importance of microbial communities Energy-yielding processes: Phototrophy and primary productivity
• Physiology of marine prokaryotes
• Energy-yielding processes: Fermentation Respiration, Methanogenesis. Carbon dioxide fixation in autotrophs, Nitrification and denitrification Specific nutrients needed for growth: Macronutrients, micronutrients and trace elements
• The role of microbes in ocean processes
• Carbon cycling in the oceans, Photosynthesis and primary productivity, Microbes in nitrogen cycling, importance of iron, microbial loop in ocean food webs, Microbial processes in eutrophication of coastal waters, Microbial processes and climate change
• Practical

MI205 - Mycology

Fungal diversity and distribution

• Origin and phylogeny;
• Terrestrial fungi
• Fresh water fungi
• Marine fungi - (a) Coastal Habitats (saltmarsh, mangrove), (b) Estuarine
• water marine, (c) Hypersaline waters (salterns, Salt Lakes, Dead Sea)
• Extremophilic Fungi - Alkaliphiles, acidophiles, barophiles,
• thermophiles, halophiles
• Identification: cultural, morphological and molecular finger printing
• Physiology, Genetics, Pathogenesis of fungi, Antifungal Therapy
  • Physiology of fungi
    • Growth and development.
    • Fungal hormones - autotactic attraction, morphogenetic or mating differentiation.
    • Adaptation to extreme environments
    • Microbial interactions
    • Secondary metabolites: antimicrobials, mycotoxins, pigments
  • Fungal genetics
    • Life-cycle - Neurospora crassa, Cross over and tetrad analysis, gene conversion; parasexuality, cytoplasmic inheritance; Karyotyping.
  • Fungal Pathogenesis
    • Mycoses - Systemic, sub-cutaneous, cutaneous and superficial,
    • opportunistic.
    • Plant pathogens
  • Antifungals
    • Drugs acting on cell membrane, protein synthesis inhibitors.
• Applications of Fungi
  • Industrially important enzymes and secondary metabolites
    • Biodegradation
    • Bioremediation
    • Biocontrol
• Practical
•  Study and Identification of fungi
  • Study of standard cultures: (a) Colony and (b) Morphological characteristics
  • Identification:
    • Observation of colonial and morphological characteristics
    • Reference to identification keys

• Fungal Genetics - Isolation of fungal DNA
• Application of fungi for bioremediation - Metal biosorption and removal from solution