Syllabus: 4th year BS (Hons) Program
GEB-401 Advanced Molecular Biology
GEB-402 Recombinant DNA Technology and Cell Signaling
GEB-403 Plant Cell and Tissue Culture and Genetic Engineeing
GEB-404 Biotechnology of Microbial System
GEB-405 Human Molecular Genetics and Diagnostics
GEB-406 Proteomics, Genomics and Bioinformatics
GEB-407 GMOs, Biosafety Regulation and Environmental Management
GEB-411 Viva voce
GEB 401: Advanced Molecular Biology
1. Chromosome structure: Basic chemical aspects – DNA, histones and non-histones; Basic structural aspects – the nucleosomes, euchromatin and heterochromatin
2. Organization of the genome in Eukaryotes: Gene and gene number; C-value paradox; Organization of replication; Gene amplification, Chromosomal redundency, Repetitive DNA and its relevance to plants and animals, inverted and tandem repeats
3. Regulation of gene expression: Transcription – multiple RNA polymerases, sigma like factors in eukaryotes; Heterogeneous nuclear RNA; Messenger RNA -- structure and complexity; Interrupted genes and RNA splicing; Expression of specific genes; Genes for ribosomal RNA; Histone genes; Globin genes; Heat-shock genes; Leghaemoglobin genes; genes for storage proteins of legumes and cereals; possible role of middle middle repetitive DNA in control of gene expression; Britten –Davidson model.
4. The dynamic genome: Mobile genetic elements in eukaryotes (jumping genes) – relevance to plants; studies in maize; Generation of antibody diversity.
5. Regulation of gene expression in prokaryotes; Lac and Trp operon, inducible and repressible systems; positive and negative control; Brief introduction to the complexity of eukaryotic genetics
6. Mutation and repair of DNA: Type of mutaion; Spontaneous and Induced mutation; Physical and chemical mutagens; Molecular basis of mutaion; in vitro mutagenesis, site-directed mutagenesis; transposons and insertional elements; Repair mechanism in mutation, mutation rate and its measurement.
7. Gene expression in somatic cell hybrids
8. Molecular biology of organelles: Genomes of mitochondria and plastid -- interaction with nucleus; Rubisco -- a case study of duel control of its synthesis by nucleus as well as plastome.
1. Lewin B, Genes VII, Oxford University Press, Sixth Edition
2. Darn ell, J., Lodesh, H. and Baltimore, D. 1986. Molecular Cell Biology., W.H. Freeman and Company, New York.
3. Alberts, B. Bray, D. Lewis, J., 1989. Molecular Biology of the Cell. Garland Publishing, Inc. New York.
4. Wolfe, S.L., Molecular and Cellular Biology, Wardsworth, Belmont, CA.
GEB 402: Recombinant DNA technology and Cell Signaling
1. Restriction modification enzymes used in recombinant DNA technology
2. Cloning vectors: Plasmid cloning vector PBR322, other plasmid vectors
3. Gene library: Construction cDNA library and genomic library, Screening of gene libraries – screening by DNA hybridization, immunological assay and protein activity
4. Cloning of foreign genes: Vectors for cloning large piece of DNA --- Bacteriophage l vectors and other phage vectors; Cosmids, Phagemids; YAC and BAC vectors
5. DNA delivery methods -- physical methods and biological methods
6. Genetic transformation of prokaryotes: Transferring DNA into E.coli – Chemical induction and Electroporation.
7. Marker genes: Selectable markers and Screenable markers, nonantibiotic markers
8. Gene expression in prokaryotes: Tissue specific promoter, wound inducible promoters, Strong and regulatable promoters; increasing protein production; Fusion proteins; Translation expression vectors; DNA integration into bacterial genome; Increasing secretions; Metabolic load
9. Recombinant protein production in yeast: Saccharomyces cerevisiae expression systems; S. cerevisiae vectors
10. Mammalian cell expression vectors: Selectable markers; Two-vector expression system; two-gene expression vector.
11. Directed mutagenesis; transposon mutagenesis
12. Gene targeting
13. Site specific recombination
B. Cell Signalings
1. General principles of cell signaling: Extracellular signal molecule and their receptors, Operation of signaling molecules over various distances, Sharing of signal information, Cellular response to specific combinations of extracellular signal molecules; Different response by different cells to same extracellular signal molecule, NO signaling by binding to an enzyme inside target cell, Nuclear receptor; Ion channel linked, G-protein- linked and enzyme-linked receptors, Relay of signal by activated cell surface receptors via intracellular signaling proteins, Intracellular signaling proteins as molecular switches, Interaction between modular binding domain and signaling proteins, Remembering the effect of some signal by cells.
2. Signaling through G-protein-linked cell surface receptors: Disassembly of G proteins to relay signals from G-protein linked receptors, cAMP and G protein signaling, role of cAMP-dependant protein kinase (PKA) in mediating effects of cAMP, Inositol phospholipids signaling pathway, Ca2+ as a intracellular messenger, role of Ca2+/calmodulin-dependantprotein kinases in mediating actions of Ca2+, Regulation of ion channels by G-proteins, Amplification and extracellular signals by intracellular mediators and enzymatic cascade, desensitization of G-protein-linked receptors.
3. Signaling through enzyme-linked cell surface receptors: Receptor tyrosine kinases, docking sits for proteins, Activation of Ras, Ras cycles between active and inactive states, signals from activated Ras to a cascade of protein kinases including MAP-kinases, PI 3-kinase/ protein kinase B signaling pathway, Insulin receptor acts through PI 3-kinase pathway, Cytokine receptors and the JAK-STAT pathway, Two component signaling pathway of bacterial chemotaxis.
4. Signaling pathways that depends on regulated proteolysis: Activation of Notch receptor by cleavage, binding of Wnt proteins to Frizzled receptors, stressful and proinflammatory stimuli act through NF-kB dependant signaling pathway.
5. TGFß signaling receptors: Activated type I TGFß receptors phosphorylate Smad transcription factors, Smad signaling via negative feedback loop, TGFß signaling and abnormal cell proliferation.
6. Environmental approaches of signal-induced responses: Evolutionary conservation and proliferation of genes encoding signals and regulators, detection of transcription changes by in situ hybridization, Protein microarrays for monitoring cell responses, Regulation of glycogenolysis by multiple second messengers, Cellular response by oxygen deprivation.
1. Molecular Biotechnology. Glick, B.R. and Pasternak, J.J. 2003. ASM Press, USA.
2. DNA cloning 1 and 2. Glover, D.M. and Hames, B.D. 1995. IRL Press (Oxford University Press, USA).
3. Molecular Cloning, A laboratory Manual. Sambrook, J., Fritsch, E.F., Mariatis.3rd edition. 2001. Cold Spring Harbor Laboratory, USA.
4. Recombinant DNA. Watson, 1992.
5. Molecular Biology of the Cell (4th edition). Alberts, Johnson, Lewis, Raff, Roberts and Walter.
6. Molecular Cell Biology (5th edition). Lodish, Berk, Matsudaira, Kaiser, Krieger, Scott, Zipersky and Darnell.
7. Lehninger Principles of Biochemistry (4th edition). Nelson and Cox.
8. Molecular Biology of the Gene. Watson, Baker, Bell.
GEB 403: Plant cell and Tissue culture and Genetic Engineering
1. Introductory history: Laboratory organization; Sterile techniques; Nutrition of plant cells; Media composition – solid and liquid; Tissue and organ culture; Establishment and maintenance of callus and suspension cultures; Cellular differentiation and regulation of morphogenesis; Somatic embryogenesis; Control of organogenesis and embryogenesis; Single cell methods; Cytology of callus, Tissue culture & genetic engineering.
2. Tissue culture techniques: Haploid production - Androgenesis; Anther and microspore culture; Gynogenesis; Embryo culture and rescue in agricultural and horticultural corps; In vitro pollination and fertilization; Protoplast isolation; Culture – regeneration; Somatic hybrid-cybrids; Somatic embryogenesis and artificial seeds; In vitro selection of mutants –mutants for salts, disease, cold, drought, herbicide and other stress conditions; Plant micropropagation: Application of micropropagation in forestry and historical crops, Micrografting – in vitro clonal multiplication – Meristem culture and virus elimination; Shoot tip culture. Cryopreservation and germplasm conservation, In vitro conservation.
3. Tissue culture applications: Improved crop varieties through somaclonal variation in in vitro cultures -- Causes- stability and utilization – genetic and epigenetic basis; Establishment of cell lines and evaluation; Secondary metabolite in cell culture; Application of tissue culture for crop improvement in agriculture, horticulture and forestry.
Plant Genetic Engineering:
1. Introduction to Plant genetic Engineering: Genetic engineering of plants: Methodology; Plant transformation with Ti plasmid of Agrobacterium tumifacians; Ti plasmid derived vector systems; Physical methods of transferring genes to plants - Microprojectile bombardment, Electroporation; Use of reporter genes in transformed plant cells; Manipulation of gene expression in plants; Production of marker free transgenic plants.
2. Application of plant genetic engineering: Developing insect-resistance, disease-resistance and herbicide resistance in plants. Developing stress and senescence-tolerance in plants - oxidative, salt and submergance stress, fruit ripening. Genetic manipulation of flower pigmentation. Developing quality of seed storage. Provitamin A, iron proteins in rice. Modification of food plant taste and appearance, yield increase inplants, Wild plant relatives as a source of novel genes, Plants as bioreactor - antibodies, polymers, foreign proteins in seeds.
3. Genome mapping efforts in rice & maize, Potential applications
1. Principles and Practices in Plant Science. Walton, P.D. Prentice Hall 1988.
2. Plant Tissue Culture: Application and Limitations. Bhowjwani, S.S. 1990.
3. Plant Cell Culture: A practical approach. Dixon. 1994.
4. Plant Biotechnology and Developoment, SRC Series of Current Topics in Plant molecular Biology. Gresshoff, P.M.
5. Plant Cell Culture, Advances in Biochemical Engineering and Biotechnology. Anderson, L.A.,
6. Recombinant DNA. Watson, 1992.
7. Gene transfer to Plants. Portykns, 1995.
8. Plant Biotechnology. Mantell and Smith, 1984.
9. Genetic Engineering of Plants. Kosuge, 1983.
10. Biochemistry & Molecular Biology of Plants. Kosuge. 1983
GEB 404: Biotechnology of Microbial Systems
1. Microbial production of therpeutic agents: Pharmaceuticals – Isolation of interferon cDNAs; Engineering human interferone and human growth hormone; optimizing gene expression. Enzymes – DNAase I and Alginate lyase against cystic fibrosis. Monoclonal antibody as therapeutic agents – Production of antibodies in E. coli , HIV therapeutic agents.
2. Vaccines: Subunit vaccines – Herpes simplex virus, Foot and mouth disease, Tuberculosis, Peptide vaccines, Genetic immunization, Atteneuated vaccines – Vector vaccines.
3. Synthesis of commercial products by recombinant microorganisms: Restriction endonucleases, Small biomolecules - L-Ascorbic acid, Indigo, amino acids, Antibiotics, Biopolymers.
4. Biorecombination and biomass utilization: Microbial degradation of xenobiotics; Commercial production of fructose and alcohol; Silage fermentation, Utilization of cellulose.
5. Economically important primary and secondary metabolites. Production o fsingle cell protein from carbohydrates, n-alkanes, methane and methanol for use in food and feed. Liquid and gaseous fuel.
6. Production of beer wine, vinegar and distilled beverages, Microbial food products.
7. Use of immobilized cell systems for the production of industrially important chemicals.
8. Biomass utilization of food, fuels and chemicals.
9. Role of microbes in Dairy products, Flavours
10. Microbial ore leaching.
1. Primrose, Modern Biotechnology.
2. Fogerty, 1983. Microbial Enzymes and Biotechnology.
3. Bu’lock, 1987. Basic Biotechnology.
4. Gibson, 1994. Microbial degradation of organic compounds.
5. Lizuka, 1981. Microbial conversion of steroid and alkaloids.
6. Laskin, 1985. Enzymes and immobilized cells in biotechnology.
7. Davis, 1976. Single Cell protein.
GEB 405: Human Molecular Genetics & Diagnostics
1. Genetic linkage and gene mapping of
2. Detection and estimation of genetic linkage in humans
3. Genetic mapping of human chromosome
4. Physical mapping of human genome
5. The human genome project(HGP): What is HGP ? Goals of HGP, Sequence strategy, Ethical issues.
6. Cloning of human disease genes – Detection of mutations in human genes; Functional gene cloning; Candidate gene cloning; positional gene cloning.
7. Human gene therapy -- Ex vivo and in vivo gene therapy; Viral gene delivery systems; pro-drug activation therapy; Nucleic acid therapeutic agents; Oligonucleotide correction of genetic conditions.
8. Pharmacogenetics: Gene tests to guide drug therapy; who stands to benefit from a certain drug or be harmed by it.
2. Basic genetic principle
3. Variable Number of Tandem Repeats (VNTRs)/ Minisattellite sequences
4. Short Tandem Repeats (STRs)/ Microsattellite sequences
5. Hybridization based DNA fingerprinting (RFLP)
a) Radioactive method
b) Fluorescent method
c) Chemiluminescent method
6. PCR-based DNA fingerprinting.
7. Single locus and multi-locus DNA fingerprinting.
8. Isolation of DNA from whole blood, soft tissues, semen stains and swabs, bones, plant material.
9. Polymorphism: Polymorphism of some genetic locus in relation to disease (HLA, Apo and ACE gene).
10. Applications of DNA fingerprinting:
a) Criminal investigation (personal identification)
c) Paternity dispute
d) Identification of missing children, bodies found in plane crash, road accidents etc.
e) Varietal identification of plants
1. Diagnosis of Cystic fibrosis by multiplex PCR, Clinical implications: Abnormal mucus clearance from the respiratory tract with frequent infections, pancreatic insufficiency, abnormal salt transport, infertility in males.
2. Detection of -Thalassemia mutation using ARMS-PCR, Clinical implications: Anemia (red cell deficiency).
3. Detection of Fragile X syndrome by FMR-1 gene trinucleotide repeat analysis, Clinical implications: Mental retardation, long faces, large ear, prominent jaws, post-pubertal macroorchidism.
4. Detection of Philadelphia chromosome [BCL-ABL t(9:22) translocation] by genomic southern hybridization .Clinical implications: Acute leukemia (ALL) and Chronic myelogenous leukemia(CML).
5. Bone marrow engraftment: DNA analysis. Aim: To distinguish patient and donor cells as different using hypervariable tandem repeat polymorphic DNA markers.
6. Identification of bacterial species based on the sequences of their 16S ribosomal RNA genes.
1. Principles of Genetics. Snustad, D.P., Simmons, K.J., John Wiley & Sons, Inc.
2. Genes VIII. Lewin B. Oxfor University Press, U.K.
3. Recombinant DNA. Watson. 1992.
4. Human Genetics. Hart. 1998.
5. Human Genome Project. Lee, T.F. 1992. Plenum Press, New York.
6. Human Genome News, http:\\www.ornl.gov/hgmis/publicat/hgn/v10n1/06snps.html
7. DNA Science. Micklos, Davod A. and Freyer , Greg A. 2003. Cold Spring Harbor Laboratory Press and Carolina Biological Supply company.
8. Human Genetics - A Problem Based Approach. 2000. Bruce R. Korf.
9. Genetics From Genes to Genomics. Hartwell, Hood, Goldberg.
10. Human Molecular Genetics. Strachan & Read. 3rd Edition.
GEB 406: Proteomics, Genomics and Bioinformatics
1. Introduction to Bioinformatics: the fundamentals of protein and nucleic acid Sequence analysis, Database searching, pairwise alignments, database searching including BLAST, Sequence analysis with PERL, Multiple sequence alignments, phylogenetic analysis, Profile searches of databases, revealing protein motifs, 3D structural comparisons, predictions and modeling.
2. Genomics: What is genomics, Genetics to genomics, Whole genomes sequencing. Genome Sequence Acquisition and Analysis, Evolution and Genomes, Biomedical Genome Research: genomic sequences to make new vaccines, new types of antibiotics, new types of medications.
3. Genomic Variations: Variation in the human genome, known examples of SNPs that cause diseases, Pharmacogenomics, Ethical Consequences of Genomic Variations.
4. Expression Data Analysis: DNA/RNA Microarrays, The oligo microarray/chip technology, Affymetrix protocol and data generation, The spotted microarray technology, cDNA and oligo spotted arrays, Biomedical applications; Cancer and genomic microarrays. Nanotechnology, Gene therapy.
5. Proteomics: Introduction, Protein 3D Structures, Protein identifications (2-hybrid system, 2-D gel electrophoresis, mass spectrometry/MALDI-TOF, other arrays). Statistical models and stochastic processes in Proteomics, Signal Processing for Proteomics, Protein Interaction Networks, measureing protein interactions, Large-scale databases of information for protein sequences, structures, functions and interactions; mining of protein databases, applications to human disease studies.
6. Networks in Bioinformatics/Proteomics: Communication Networks, Biological networks (Protein Interaction Networks, Gene regulation networks, Metabolism, Biochemical reactions), Databases and search tools for biological network analysis. Genomic Circuits: in Single Genes, Complex integrated Genomic Circuits, Modeling Whole-Genome Circuits: Genomics vs. Proteomics Case study Yeast Protein Interaction Network (random network, Scale free network, Hierarchical network)
7. Structural and Functional Genomics Studies:
Plant genome: Arabidopsis genome covering identification and characterization of genes controlling flowering, vernalization, photoperiod, circadian clock.
1. Discovering Genomics, Proteomics, & Bioinformatics. Campbell & Heyer (2003) Pearson Education, ISBN: 0-8053-4722-4
2. Bioinformatics, Methods of Biochemical Analysis Series Vol. 43, Baxevanis & Ouellette (2001) John Wiley & Sons, ISBN 0-471-38391-0
3. Computational Molecular Biology. Pevzner, P.A. (2000) MIT Press, ISBN: 0262161974
4. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Andreas D. Baxevanis & B. F. Francis Ouellette (2004). 3rd Edition. Wiley & Sons, ISBN: 0-471-47878-4
GEB 407: GMOs, Biosafety Regulations and Environmental Management
GMOs and Biosafety regulations:
1. Transgenesis: Animal cell culture. Homologous recombination in mammalian cells. Classic transgenic mice: history, production and use. The cre/lox recombination system as a tool in transgenic engineering. Transgenic mice in immunology, neurobiology and oncogenesis. Transgenic animals. Methods for production of animals a) in production of proteins of pharmaceutical use, b) in understanding the basic organ and tissue specific gene expression in the living body, c) for production of animal models for human or animal disease, d) for improving desired characteristics and productivity of domestic animals. Transgenic animals in agriculture and nutritional science: a) Transgenic mice for biomedical research.
2. Risk for animal or human health - toxicity and food quality/safety, allergies, pathogen drug resistance (antibiotic resistance).
3. Risk for agriculture - weeds or superweeds, alteration of nutritional value (attractiveness of the organism to the pests), reduction of cultivars (increase of susceptibility) and loss of biodiversity.
4. Risk for the environment - Persistancy of gene or transgene or transgene products, resistance/tolerance of target organism or susceptibility of non-target organisms, increased use of chemicals in agriculture, unpredictable gene expression or transgene instability.
5. General concerns - loss of familiarity, higher cost of agriculture, field trials not planned for risk assessment, ethical issues (labelling).
6. Biosafety regulations to protect nature, growers and consumers interest and national interest.
1. Environmental Pollution: Metal pollution: source of metals, metal bioavailability in the environment, metal toxicity, mechanism of microbial metal resistance & detoxification, innovative microbial approaches to the remediation of metal contaminated aquatic system with special reference to Arsenic, Chromium, Lead & Mercury. Nitrate & Phosphorus pollution & their bioremediation
2. Recalcitrant molecules in the environment; Characterization of microbial activity & the biodegradation of recalcitrant substances including pesticides in soil. Persistence and biomagnification of xenobiotic molecules. Bioremidiation of contaminated soil and water bodies.
3. Isolation and enrichment of microorganisms capable of detoxifying environmental pollutants: Environmental and genetic approach.
4. Biosensors: Application of biosensors for the detection of environmental pollutants
5. Bio-deterioration of materials and their control: Leather, Wool, Fur, Feather, Stone, Plastics & Rubber.
6. Biological control of insects & pests: Biopesticide/insecticide.
7. Biotechnological aspects of waste management: Industrial wastewater/toxic effluents and their physical, chemical & biological treatment.
8. Water treatment system and measurement of treatment efficiency.
9. Viable But Non Culturable (VBNC) microorganism: Concept of VBNC, Recent advances in molecular genetic methods for the detection of VBNC in potable water. Implication & significance of VBNC in the environment & health.
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1. Modern Food Biotechnology, Human Health & Development: An Evidence Based Study. Food Safety Department, World Health Organization. 2005
2. Genetic Engineering in Agriculture and the Environemnt: Assessing risk and benefits. Maurizio G. Paoletti and David Pimentel. http:\\www.ag.auburn.edu/biotech/genetic.html.
3. The Ecological Risks of Engineered Crops. Rissler, J. and Mellon, M., 1996. Cambridge, USA: The MIT Press.
4. Molecular Biotechnology, Principles and applications of recombinant DNA. BR Glick; Jack J Peterson.2003.
5. Genes and genomes. Singer and Paul berg.1991. University Science books.
6. Gene therapy for infectious diseases. Bunnel BA and Morgan RA. 1998.
7. Human Molecular Genetics 2. 2nd ed. Strachan, Tom and Read, Andrew P.
Oxford, UK: BIOS Scientific Publishers, Ltd; 1999.
8. Modern Genetic Analysis. Griffiths, Anthony J.F.; Gelbart, William M.; Miller, Jeffrey H.; Lewontin, Richard C. New York: W. H. Freeman & Co. 2002.
9. Microbial Ecology. Atlas and Bartha. 4th edition.
10. Current Perspective in Microbial Ecology. Klung and Reddy
11. Ecological Systems and the Environment - I. Foin
12. Biotreatment Systems. D.L. Wise. Volume II.
13. Advances in Biotechnological Process. Mizrahi & Wezel
14. Biotechnology for Solving Agricultural Problems. Danforth & Bakst.
15. Introduction to Environmental Microbiology. R. Mitchell.
GEB 408: Immunology
1. Immunity to infection: bacterial, viral & parasitic infection
2. Immunological tolerance:
Experimental induction of tolerance, thymic tolerance of self antigens, B-cell tolerance, artificially induced tolerance, therapeutic application of tolerance.
Passive immunization, antigens used as vaccine, effectiveness of vaccines, vaccine safety, current vaccines and future vaccines, vaccination against cancer.
4. Antibody engineering:
Antibody gene cloning, recombinant antibody gene expression, application of engineered antibodies.
5. Hypersensitivity: Different types of hypersensitivity reactions:
a) Type I (Immediate hypersensitivity): IgE levels in disease, atopy, control of IgE production, role of T-cell in immune response to inhalant allergens, genetics of allergic diseases, mast cell triggering, factors influencing the symptoms of allergic disease, asthma and bronchial reactions to inhalant antigens.
b) Type II (antibody dependant cytotoxicity): Mechanism of damage, reaction against blood cells and platelets, reaction against tissue antigens, hemolytic diseases of newborn.
c) Type III (immune complex mediated hypersensitivity): Types of immune complex mediated diseases, mechanism, experimental models of immune-complex disease, persistence of complexes, deposition and detection of immune-complexes.
d) Type IV (delayed hypersensitivity): Contact hypersensitivity, tuberculin-type hypersensitivity, granulomatous hypersensitivity, cellular reaction in type IV hypersensitivity, diseases manifesting delayed hypersensitivity.
5. Transplantation and rejection: Barriers of transplantation, laws of transplantation, role of T-cell in rejection, genetic predisposition to graft rejection and prevention of rejection.
6. Tumor immunology: Immune surveillance, tumor antigens and their detection, immune response to tumor cells, immunodiagnosis and immunotherapy.
7. Autoimmunity and autoimmune diseases: Association of autoimmunity with disease, genetic factors, pathogenesis, etiology, diagnosis and treatment.
8. Immunodeficiency: Primary immunodeficiency, B and T cell deficiency, combine immunodeficiency, secondary immunodeficiency, immunodeficiency caused by drugs, mutation, and immune response, AIDS, human immunodeficiency virus and its life cycle, antiviral treatment.
1) Immunology (6th edition) by Roitt, Brostoff and Male
2) Roitt's Essential Immunology by Ivan M Roitt and peter J. Delves. 10th edition.
3) Cellular and Molecular Immunology by Abul K. Abbas, Andrew H. Lichtman.
4) Basic Immunology: Functions and Disorders of the Immune System by Abul K. Abbas, Andrew H. Lichtman.
GEB 409: Practicals
Practicals based on the courses