Third Year

Course for 3rd Year B.S. (Honors) in Genetic Engineering & Biotechnology

  1. Features of plant cell:Structural organization of a typical plant cell; functions of different components.
  2. Plant growth:Concept of growth and development; cell differentiation and morphogenesis in plants; transition to flowering from vegetative to reproductive stages; structure and development of flowers; seed dormancy and germination; cotyledon, endosperm and seed coat development; genetic regulation of vernalization; lateral and adventitious root development; root hair development; hormonal regulation in root development.
  3. Photosynthesis: Photosynthetic apparatus and light harvesting complexes; light absorption, emission and energy transfer; electron transfer; photophos-phorylation; CO2fixation; C3, C4, CAM plants; leaf morphology for different dark phase reactions; environment and its impact on photosynthesis.
  4. Respiration:Aerobic and anaerobic respiration; oxidative phosphorylation and electron transport; complex I, II, III and IV (in plant system).
  5. Plant water relations:Types of water movements in plant cells; properties of solutions; inhibition; permeability; water potential to plant cell; mechanisms of water absorption.
  6. Transport phenomena:Active and passive transport system; transport of nutrients across the primary root, genetic regulation of transport systems in response to nutrient availability and growth conditions.
  7. Nitrogen fixation and nutrient assimilation:Plant mycorrhiza association; mechanisms of nitrogen fixation; symbiotic and non-symbiotic nitrogen fixing bacteria and their fixation activity; uptake and assimilation of nitrate; assimilation of ammonia; thenif gene; nitrogen, iron, potassium, sulfur, phosphate and calcium metabolisms.
  8. Lipid metabolism:Fatty acid biosynthesis; membrane lipid biosynthesis; lipid desaturation; triacylglycerols; cell wall lipid; ceramides.
  9. Plant hormone:Types of hormones;auxins: the master growth hormone; distribution in plants; roles; auxin binding proteins; signal transduction; auxin-responsive genes/promoters; model of gene regulation; commercial uses; gibberellins: foolish seedling disease; functions of GAs, location, signal transduction of GAs; commercial uses; cytokinins: mechanisms of action; application; ethylene: location and functions, mechanisms of action; application; abscisic acid: a stress hormone; location and functions, mechanisms of action; application.
  10. Acclimation to environmental stress and adaptation to environment/ Programmed cell death:Hypersensitive response; relevance with diseases; induction and role of various apoptotic genes involved in cell death.
  11. Plant secondary metabolites and their importance

Suggested Reading:

Plant Physiology (5th edition) by Lincoln Taiz and Eduardo Zeiger. 2010. Publisher-Sinauer Associates Inc.

Introductory to Plant Physiology (4th edition) by William G. Hopkins, Norman P. A. Huner. 2008. Publisher-John Wiley & Sons Ltd. UK.

Plant Biochemistry & Molecular Biology (1st edition) by Hans-Walter Heldt. 1997. Publisher-Oxford University Press, USA.

Introduction to Plant Biochemistry (2nd edition)by Goodwin and Mercer. 1990. Publisher-Pergamon Press, Australia.

Plant Biochemistry and Molecular Biology by peter J. Lea & Richard C. Leegood. 1993. Pulisher-John Wiley & Sons Ltd.UK.

Plant Physiology by Mohr and Schopfer. 1995. Publisher-Springer.

Molecular Biology of the Cell (5th edition) by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roderts & Peter Walter.2007. Publisher-Garland Science.

 

Additional reading materials and internet learning resources will be suggested by the course instructors.

  1. Introduction:Physical and chemical properties of nucleosides and nucleotides; DNA structure; RNA structure; Tm value; cot value; central dogma; heredity.
  2. Organization of the genome:The complexity of eukaryotic genome; chromosome and chromatin; organization of histone octamer; genes and gene number; evolution of genes, chromosomal redundancy; repetitive DNA, SNPs and their relevance.
  3. DNA replication:Modes of replication; DNA polymerases; regulation of DNA replication.
  4. Transcription:Prokaryotic and eukaryotic RNA polymerases; transcriptional factors; mechanisms of transcription; reverse transcriptase; RNA processing; RNA editing; RNAi; miRNA.
  5. Translation:Structure of ribosome; functional site of ribosome; genetic code, amino acid-tRNA interaction; Wobble hypothesis; protein synthesis: initiation, elongation and termination; protein folding and processing; protein degradation; protein sorting and transportation.
  6. DNA repair and recombination:Variation and evolution; types and mechanism of mutation; DNA repair; homologous and non-homologous recombination; site-specific recombination and transposition rearrangement.
  7. Organelle genome:Genomes of mitochondria and plastid- their interaction with nucleus; replication; repair; inheritance; diseases associated with organelle genome.

Suggested Reading:

Molecular Biology of the Gene (7th edition) by James D. Watson, Tania A. Baker, Stephen p. Bell, Alexander Gann, Michael Levine & Richard Losick. 2013. Publisher-Benjamin Cummings.

Molecular Biology of the Cell (5th edition) by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roderts & Peter Walter.2007. Publisher-Garland Science.

Molecular Cell Biology (6th edition) by Harvey Lodish, Arnold Berk, Chris A. Kaiser & Monty Kreger. 2007. Publisher- W. H. Freeman.

Additional reading materials and internet learning resources will be suggested by the course instructors.

 

  1. Introduction: Properties and overview of the immune system; historical perspective.
  2. Innate and adaptive immunity:Innate immunity; external barriers against infection; features of innate and adaptive immunity; components of innate/adaptive immune system; humoral and cell-mediated immunity; clonal selection of B lymphocytes.
  3. Cells and organs of the immune system:Hematopoiesis; cells of innate immunity—structure and functions of monocytes/ macrophages, neutrophils, basophils, eosinophils, NK cells, mast cells, platelets and dendritic cells; cells of adaptive immunity—structure and functions of T and B lymphocytes; organs of immune system: primary lymphoid organs—thymus, bone marrow, lymphatic system; secondary lymphoid organs—lymph nodes, spleen, mucosa-associated lymphoid tissue.
  4. Antigens and antibodies:Immugenicity vs antigenicity; properties of antigen/immunogen; conformation of antigen-antibody binding; antibody affinity and avidity; structure and function of antibodies; antibody diversity generation.
  5. 5. T cell receptors and MHC molecules: Structural features of TCR; comparison between TCR and Immunoglobulin; structural features of class I and class II MHC molecules; genomic organization of MHC; MHC polymorphism.
  6. Antigen presentation: Processing and presentation of antigen by class I and class II MHC.
  7. The complement system:Functions, components, activation and regulation of complement system.

Suggested Reading:

Immunology  (8th edition) by Male, Brostoff, Rith & Roitt, 2012. Publisher- Elsevier.

Basic Immunology (3rd edition) by Abul K. Abbas & Andrew H. Lichtman. 2010. Publisher-Saunders.

Roitt Essential Immunology (12th edition)by Peter J. Delves, Seamus J. Martin, dennis R. Burton & Ivan M. Roitt. 2011. Publisher- Wiley & Blackwell.

Additional reading materials and internet learning resources will be suggested by the course instructors.

  1. Introduction: Differences between eukaryotic and prokaryotic Genetics; physical organization of bacterial genomes; genotype and phenotype; dominance and recessive characters, molecular biology of bacterial cell division and plasmid replication.
  2. Gene transfer:Molecular mechanism of transformation, conjugation and transduction; consequences of recombination; gene mapping; mosaic genes and chromosome plasticity.
  3. Movable genetic elements:Plasmids: structure, properties, functions and stability; transposons; mechanism of transposition; phase variation; CRISPR.
  4. Regulation of gene expression:Induction and repression; operon model of gene expression; transcriptional control; promoter, terminator, attenuator and anti-terminator; two component regulatory pathway; global regulatory systems; translational control.
  5. Genetics of bacteriophage:Bacteriophage structure; ssDNA bacteriophage; RNA containing phages; dsDNA phages; genetics and molecular biology of λ (lambda) phage; lytic and lysogenic cycle; restriction and modification; and bacterial resistance to phage attack.
  6. Genetics of yeast:Yeast as a model organism; advantages, life cycle, mating type switching in yeast; transformation and recombination; yeast artificial chromosome; yeast two-hybrid systems.

Suggested Reading:

Principles of Genetics by Snustes, D, P. Simmons, M. J.  and Jenkins & J. B.  Jacaranda. 1997. Publisher-Wiley

Molecular Genetics of Bacteria (4th edition) by Larry . Snyder, Joseph E. Peters, Tina M. Henkin & Wendy Champness. 2013. Publisher-ASM Press.

Molecular Genetics of Bacteria (5th edition) by Jeremy W. Dale, Simon F. Park. 2010. Publisher-Wiley.

Additional reading materials and internet learning resources will be suggested by the course instructors.

  1. Development of multi-cellular organisms:Universalmechanisms of animal development; basic anatomical features of animal; genes controlling developmental processes; cell fate and determination, positional values, inductive interaction and morphogenic effects.
  2. Cytoskeleton:Assembly and dynamic structure of actin filaments, microtubules and intermediate filaments; effects of drugs on filament polymerization; regulation of cytoskeletal filaments; molecular motor proteins- structural features and function of myosins, kinesins and dyenins.
  3. Caenorhabditis elegans:Cell fates; asymmetric division of egg; pattern formation; developmental signal and changes in cell; apoptotic cell death.
  4. Drosophila melanogaster:Synopsis of Drosophila development; syncytium development; genes involved in early patterning- role of egg-polarity genes, dorsoventral signaling genes, mutations and segmentation genes, homeotic selector genes and patterning of anteroposterior axis, organogenesis and patterning of appendages.
  5. Xenopus laevis: Synopsis of Xenopus development; asymmetries of Xenopus egg, blastula formation and gastrulation; convergent extension; neural tube formation.
  6. Neural development in higher animals:Neurulation in chick and human embryos.

Suggested Reading:

Development Biology (10th edition) by Scott F. Gilbert. 2013. Publisher-Sinauer Associates Inc.

Principles of Development (4th edition) by Lewis Wolpert, Cheryll Tickle. 2010. Publisher-Oxford University Press, USA.

Additional reading materials and internet learning resources will be suggested by the course instructors.

  1. Overview of virus structure and classification
  2. Cultivation, purification and enumeration of viruses:Cultivation of plant, animal and bacterial virus; one step growth curve; estimation of yields; methods for purification of viruses; quantitative measure of infectious centers: plaque assay; generation of transformed cell foci.
  3. Replication cycle:Entry of enveloped and non-enveloped animal virus; plant virus and bacteriophage; replication and expression of viral genome- dsDNA, ssDNA, dsRNA, +ssRNA; -ssRNA; bacteriophages- lytic and lysogennic cycle and its regulation; late events of viral infection- capsid assemble and virion release; non-specific method of introducing viral genomes into the cells.
  4. Pathogenesis of viral infection:Typical modes of virus spread; initial stages of infection; incubation period and spread; multiplication and occurrence of disease; the immune response; virus spread to the next individual; fate of the host; pathogenesis of hepatitis, HIV, EBV and influenza virus.
  5. Prevention and treatment of viral infection:Vaccination strategy; chemotherapy of viral diseases; interferon-its induction and action.
  6. Prions and viroids:General properties; hypothesis about prion generation; disease caused by prions and viroids.
  7. Viruses-promise and problems:Cloud of horizon-emerging disease; source and caused of emergent virus diseases; silver linings-virus as therapeutic agent; viruses for gene delivery.

Suggested Reading:

Basic Virology (2nd edition) by Edward K. Wagner and Martinez. J. Hewlett. 2004 .Publisher-Blackwell Science Ltd.USA.

Virology-Principles and Applications by John B. Carter and Venetia A. Saunders. 2009. Publisher-John Wiley & Sons Ltd. UK.

Fundamentals of Molecular Virology by Nicholas H. Acheson. 2007. Publisher -John Wiley & Sons Ltd.UK.

Principles of Molecular Virology (4th edition)by Alan J. Cann. 2005. Publisher-
Elsevier Academic Press. UK.

Introduction to Modern Virology (6th edition) by Nigel Dimmock, Andrew Easton and Keith Leppared. 2007. Publisher-John Wiley & Blackwell.

Additional reading materials and internet learning resources will be suggested by the course instructors.

 

  1. Cancer:Characteristics of tumor cells; genetic and epigenetic changes in tumor cells; oncogene and tumor suppressor genes; mechanisms of activation of proto-oncogene into oncogenes; chemical carcinogens; methods of testing chemical carcinogens; oncogenic viruses; mechanisms of oncogenic viruses in tumor formation; hematological malignancies- leukemia, lymphoma and myeloma; cancer chemotherapy- antimetabolites, alkylating agents, plant alkaloids, antibiotics and miscellencious compounds.
  2. Cardiovascular disease:Atherosclerosis- molecular mechanism of atheromatus plaque formation- involvement of LDL and foam cells; ishchemic heart disease; myocardial infarction (MI) and biochemical markers for the diagnosis of MI; heart failure; disorders of lipoprotein metabolism.
  3. Diabetes mellitus:Type I, type II and other major clinical classes; genetic basis of type I DM; HLA-DQ, HLA-DR and MHC pattern of inheritance in type II DM; MODY (maturity onset diabetes mellitus in young); Diabetes insipidus; insulin gene; biosynthesis of insulin; mechanism of insulin action; complications of DM; diagnosis and treatment.
  4. Liver disease:Microarchitecture of the liver; Hyperbilirubinemia; Dubin-Jhonson syndrome; Criglar-Najaar syndrome; viral hepatitis- types of hepatitis virus and their genomic organization; acute hepatocellular carcinoma; chronic hepato cellular carcinoma; cirrhosis of the liver; liver function tests. 
  5. AIDS:Definition; biology of HIV; genomic organization; origin – mode of transmission; HIV and the immune system; pathogenesis of AIDS: asymptomatic carrier, PGL, ARC, full blown AIDS; diagnostic test, anti-AIDS drugs; vaccine possibilities.
  6. Gastrointestinal diseases: Diarrheal disease caused byVibrio cholera-acute and chronic diarrhea; pathogenesis and epidemiology; virulence factors; regulation of virulence genes; mode of action of cholera toxin; treatment-antibiotics and vaccine possibilities; prevention; Dysentery caused by Shigella- virulence factors; adhesion, invasion, intracellular release and killing of mucosal cells; shiga toxin; Reiter’s syndrome-an autoimmune response; organization and regulation of virulence genes; treatment and prevention; E. coli gastrointestinal infection: serotypes and verotypes; virulence factors of ETEC, EaggEC, EPEC, EHEC and EIEC; Salmonella infection: diseases caused by species and serotypes of Salmonella; virulence factors and their regulation; treatment and prevention; Rota-virus.
  7. Brain diseases:Molecular basis of Alzheimer’s, Parkinson’s and Huntington’s disease.
  8. Metabolic disorders:Molecular basis of Phenylketonuria, Alkaptonuria, Maple syrup urine disease, Nieman-pick disease, Glycogen storage diseases and Gout.
  9. Chromosomal abnormalities:Variations in the number and structure of chromosomes- euploids, aneuploids and polyploids; deletion; duplication; aberrations; translocation and other structural rearrangements; chromosomal studies- karyotyping; amniocentesis (chorionic villi sampling, alpha fetoprotein sampling); chromosomal abnormalities- Down’s syndrome, Cystic fibrosis, Fragile-X syndrome, Meta females; etc. 

Suggested Reading:

Human Molecular Biology: An Introduction to the Molecular Basic of Health and Disease (1st edition) by RJ Epstein. 2002. Publisher-Cambridge University Press.

Textbook of Biochemistry with Clinical Correlations (7th edition) by Thomas M. Develin. 2010. Publisher- John Wiley & Sons Ltd. UK.

Herper’s Review of Biochemistry (24th edition) by Harold Anthony Harper, David W. Martin, peter A. Mayes, Victor W. Rodwell. Publisher-Lange Medical Publications.

Molecular Biology of Health and Disease (1st edition) by Undurti N. Das.  2011. Publisher-Springer.

Molecular Basis of Human Disease (1st edition) by William J. Tsongalis. 2009. Publisher-Academic Press.

Additional reading materials and internet learning resources will be suggested by the course instructors.

Isolation, detection and quantification of DNA, RNA and protein from bacteria, virus, plant and animal cells.

  1. Stand polymerase chain reaction (PCR) and real-time PCR; RFLP; AFLP; RAPD.
  2. Basic principles and uses of agarose and polyacrylamide gel electrophoresis.
  3. Hybridization; Southern, Western and Northern blotting; micro-array.
  4. Restriction digestion of DNA/plasmid, ligation and transformation; recombinant protein expression; protein extraction; protein purification.
  5. DNA sequencing; next generation DNA sequencing (whole genome, ChIP-seq, RNA-seq, methyl-seq; Exome-seq); RNA interference (RNAi).
  6. DNA-protein and RNA-protein interaction studies (EMSA, REMSA, ChIP, ChIP on chip, DNAase foot-printing, DNase protection, in vitro transcription); Y2H and B2H systems.
  7. Chromatography techniques: Hydrophobic column chromatography; ion-exchange chromatography; affinity chromatography; HPLC; GLC.
  8. Flow cytometry.
  9. Mutation analysis; recombination models; Rec system; conjugation, transduction, transfection and transformation.

Suggested Reading:

Analytical Techniques in Biochemistry and Molecular Biology (1st edition) by Rajan Katoch. 2011 Publisher-Springer.

 

Protein Purification (1st edition) by Phillip L. R. Bonner. 2007. Publisher-Taylor and Press.

 

Spectroscopic Methods and Analysis: NMR, Mass Spectrometry and Metalloprotein Techniques (1st edition) by Christopher Jones, Barbara Mulloy and Adrian H.Thomas. 1993. Publisher-Springer.

 

Short Protocols in Molecular Biology, (5th edition, 2 Volume) by Frederick M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J. G. Seidman, John A. Smithand Kevin Struhl. 2002. Publisher- Wiley.

 

Additional reading materials and internet learning resources will be suggested by the course instructors.

  1. Introduction to fermentation Processes:History, general concept of fermentation processes.
  2. Sterilization of fermenters and media:Design of batch continuous sterilization processes; sterilization of the media, fermenter; feed and air.
  3. Inoculum preparation and development:Development of inoculum for bacterial, yeast and fungal processes; scale-up principles; methods of scale-up and their analysis.  
  4. Fermentor/bioreactor:Types, configuration, mixing and aeration; power requirements; impeller designs baffle; oxygen demand and supply. 
  5. Batch and plug flow culture:Open and close systems; batch, fed-batch, continuous culture and their control variations in actual practice; plug flow culture with and without feedback.
  6. Fermentation modeling:Rate equations for cell growth, substrate utilization and product formation; transfer across phase boundaries.
  7. Instrumentation and process control:Control systems- manual, automatic, and combinations of methods of control; methods of control of process variables as temperature, pH, flow measurement, pressure measurement, pressure control, safety valves, agitation-shaft power, rate of stirring foam sensing and control weight, measurement and control of dissolved oxygen; exit-gas analysis; redox and carbonidoxide electrodes.
  8. Introduction to bioprocess technology:Importance and development of bioprocess technology; upstream and downstream processing.
  9. Applications of bioprocess technology to various industries:Biopharmaceuticals; food, feed and fuel; biochemicals; biocomposts; mammalian cell culture; stem-cell bio-processing and tissue engineering.

Suggested Reading:

Principles of Fermentation Technology (2nd edition) by P.F. Stanbury, A. Whitaker & S.J. Hall. 2003 publisher Elsevier Science.

 

The Art of Fermentation: An in-Depth Exploration of Essential Concepts and Processes form Around the World by Sandor Ellix Datz. 2012. Publisher-Chelsea Green Publishing.

 

Wild Fermentation: The Flavor, Nutrition, and Craft of Live-Culture foods by Snador Katz. 2003 Publisher-Chelsea Green Publishing Co.

 

 

Additional reading materials and internet learning resources will be suggested by the course instructors.

  1. Introduction to biostatistics:Definition, application and scope of statistics and biostatistics; basic statistical principles and terminologies- population, sample, parameter, statistic, variable, etc.
  2. Frequency distribution:Frequency distribution; necessity of frequency      distribution, principles of classification, numerical examples.
  3. Graphical representation of data:Histogram; bar-diagram; pie chart;         line-graph; Ogive.
  4. Descriptive statistics: Central tendency-Concept, objectives of measure of central tendency and different measures as arithmetic mean, geometric mean, harmonic mean, median, quartiles, percentiles, deciles, mode; properties of different measures and their uses; dispersion- concept, objectives of measures of dispersion, different; measures- absolute measures, relative measures, range, quartiles deviation, standard deviation, variance, co-efficient of variation, properties of different measures of dispersion and their uses.
  5. Sample regression and correlation: regression analysis-concept, definition and properties of regression co-efficient, least square method to estimate the parameters of simple linear regression model, uses of regression analysis;correlation analysis-concept, definition and properties of correlation co-efficient, different methods of studying correlation co-efficient, uses of correlation co-efficient.
  6. Sampling techniques:Concept; sampling frame; sampling design; simple random sampling; stratified random sampling.
  7. Probability and probability distribution:Definition of probability; different approaches of probability; conditional probability; definition of random variable; probability distribution, binomial distribution, Poisson distribution and normal distribution; concept and different measures of skewness and kurtosis.
  8. Hypothesis testing:Concept; tests of hypotheses; statistical hypothesis; null hypothesis; alternative hypothesis; level of significance; type 1 error; type 2 error; mean test- test of hypothesis about single mean, test of hypothesis about quality of two means; proportion; confidence interval; paired t-test; general test of independent in one rxe contingency level; p-value; Z-score; non-parametric test; analysis of variance (ANOVA) test- one-way and two-way classifications.
  9. Use of software in biostatistics:Hands on training on SPSS/SAS.
  10. Epidemiology:Definition and scope of epidemiology; types of   epidemiologic research- experimental (laboratory, clinical trial, community intervention), quasi experimental (clinical/laboratory, program/policy), observational studies; design options in observational studies methods; typology of observational study designs (cohort, case-control, cross-sectional studies).
  11. Quantification of disease events:Basic measures of disease frequency, incidence and prevalence; mortality measures- age, period and cohort effects; measures of association- ratio measures and different measures (relative risk odds ratio; risk difference, etc.

Suggested Reading:

Basic Biostatistics for Geneticists and Epidemiologists: A Practical Approach by Robert C. Elston, William D. Johnson. 2008. Publisher-John Wiley & Sons, Ltd.

 

Statistics for Biologist (3rd editin) by R.C. Campbell. 1989, publisher-Cambridge University press.

Epidemiology and Biostatistics by Kestenbaum & Bryan 2009. Publisher-Springer.

 

Fundamentals of Biostatistics (7th edition) by Bernard Rosner. 2010, publisher-Cengage Learning.

 

Basic Biostatistics for Geneticists and Epidemiologists: A Practical Approach by Robert C. Elston, Willam D. Johnson. 2008. Publisher-wiley.

 

Tex Book of Biostatistics by A.K. Sharma. 2005 Publisher-Discovery Publishing House

 

Additional reading materials and internet learning resources will be suggested by the course instructors.