GEB 301: Physiology & Biochemistry of Living Organisms II (1.0 Unit)

A. Structure & Function of Plant Cells and Tissues and other General Aspects

1. The Plant Body and the typical Plant Cell --- An overview of general structure, diversity of organs, tissues meristems and cells in green plan, and physiology of plant cells

2. Plant – Water Relations and Mineral Nutrition --- Permeability; Osmosis and imbibition; Evaluation of water status of a cell; Mechanism of water absorption; Conduction and transportation; Stomatal opening; Essential elements and their functions; uptake of mineral and their transpor.

3. Transport phenomena in Plants --- Characteristics of transport in xylem and Phloem. Mechanism of phloem transport



B. Biochemistry and Metabolic processes of Plants

4. Photosynthesis --- History; Pigments in prokaryotes and eukaryotes; The organization of photosystem; Carbon dioxide reduction cycle in C3 and C4 plants; the CAM plants; Photorespiration.

5. Respiration and Carbohydrate metabolism --- aerobic and anaerobic respiration; Electron transport and oxidative phosphorylation; Storage of carbohydrates; Starch and its biosynthesis.

6. Lipid metabolism --- Chemical composition of lipids; Biosynthesis and degradation of lipids; Significance and mobilization of fat reserve for growth.

7. Nitrogen metabolism --- Uptake and assimilation of nitrate; assimilation of ammonia; Nitrogen fixation – Symbiotic and asymbiotic; The nif genes

C. Growth, Development and Reproduction in Plants

8. Vegetative growth --- Basic concepts of growth and development; Principles and problems of cell differentiation and morphogenesis in plants.

9. Plant growth regulators --- Biosynthesis, analysis, physiological effects of auxins, gibberellins, cytokines, abscisic acid, and ethylene. Current ideas of action of hormones.



10. Light and plant life --- Light sensing by plants; Photomorphogenesis; Phytochromoe and blue light photoreceptors; Effect of UV light on biological systems; Significance of biological clocks.
11. Reproductive growth --- Physiology and flowering; Seed germination; Dormancy and senesence.


Suggested readings:

1. Galstone, A.W. and Davies, P.J. 1970. Control Mechanism in Plant Development., Prentice Hall Inc, Englewood Cliffs, New Jersey.
2. Galstone, A.W. and Davies, P.J. 1980. A Life of a Green Plant., Prentice Hall Inc, Englewood Cliffs, New Jersey.
3. Noggle, G.R. and Fritz, G.J. 1983., Introductory Plant Physiology., Prentice Hall Inc, Englewood Cliffs, New Jersey.
4. Salisbury, F.B. and Ross, C.W. 1983., Plant Physiology., Wardsworth Pub. Co. USA.
5. Devlin, R.M. 1988., Plant Physiology., Reinhold Pub. Co. New York.



GEB 302: Basic concepts of Genetics and the Molecular Biology of the Gene (1.0 Unit)

A. Concepts in Genetics

1. Mendelian Principle: Mendel and his experiments and the laws of inheritance

2. Variation on Mendel’s Theme: Incomplete dominance; Gene interactions ( Epistasis; Duplicate, Complementary, Supplementary and lethal factors)

3. The chromosomal theory of inheritance: Clues from inheritance of sex; linkage and crossing over; gene mapping; Genetic recombination in Prokaryotes and Eukaryotes.

4. Sex determination: A closer look at the chromosomal and genetic level.

B. Rise of Molecular Genetics

1. Chemical basis of heredity: Evidence for DNA (and RNA ) as genetic material; Basic equivalence in DNA; The Watson and Crick model of DNA structure. Different physico-chemical properties of DNA (Tm value, Cot values, hybridization kinietics, different combinations of DNA).



2. Structural organization of Genetic material: A closer look in the genome organization in Viruses, bacteria and the organells of eukaryotes.

3. Replication of DNA: Mode of replication; Experimental findings of Meselson and Stahl and of Taylor and Carins; Mechanism of replication; control of DNA synthesis for prokaryotic and eukaryotic system
4. Transcription: Prokaryotic and eukaryotic RNA polymerases, Regulation of transcription; promoters, enhancers, terminators, mechanism of RNA splicing and RNA processing, mRNA structure and its relation to its stability.

5. Translation: The path from gene to proteins; Gene protein relationship, Genetic code, specificity, redundancy and wobble hypothesis, colinearity of gene and protein structure, post translational modifications.

6. Protein synthesis: Ribosome structure, protein synthesis: initiation, elongation and termination. Control of translation bothe in prokaryotes and eukaryotes.

Suggested readings:

1. Snustad, D.P. Simmons, M.J. and Jenkins, J.B. Principles of Genetics., Jacaranda/Wiely publishers, 1997.
2. Klung, W.S. and Cummings, M.R. 1980., Concepts of Genetics., Scott, Foresman and Company USA.
1. Watson, J.D. and Hopkins, A.M., Roberts, J.W., Steitz, J.A. amd Weiner, A.M. 1988. Molecular Biology of the Gene., Benjamin/Cummings Scientific Publishing, Menlo Park, California.
2. Lewin, B. Genes VI., Oxford University Press, sixth Edition.



GEB 303: Basic Immunology (½ Unit)

1. Molecular and cellular basis of immune system
2. Self verses non-self recognition; antigen recognition and the clonal selection theory of the immune response; 
3. The humoral immune response; antibodies- structure, diversity function and mechanism of action
4. The cell mediated immune response; recognition of antigen by T cells; antigen presentaiton; the major histocompatibility proteins; the role of cytokines and the regulation of immune responses
5. The immune system in health and disease – response to infection, development of vaccines; the development of allergies; auto-immune disease; and immunodeficiencies; transplantation immunology; manipulation of the immune system.
6. Complements: Activities of complement proteins, activation of complement, classical pathway, regulation of classical pathway activation, alternative pathway activation and amplification loop, their regulation, membrane attack complex, biological effects of complement.

7. The techniques of immunology and their application: Precepitation, agglutination, simple immunodiffusion, double immunodiffusion, immunoelectrophoresis; twodimensional and counterimmunoelectrophoresis, immunofluorescence, complement fixation, RIA, ELISA, Immunoblotting and immunoprecipitation.



Suggested readings:

1. Jains Kuby, Immunology., W.H. Freeman & Co. N.Y.
2. Alberts, B. Bray, D. Lewis, J., 1989. Molecular Biology of the Cell. Garland Publishing, Inc. New York.
3. Roitt, Brostoff, Nale, 1999. Immunology.
4. Roitt, 1998. Essential Immunology.


GEB 304: Microbial Genetics (½ Unit)

Introduction

The evolution of microbial genetics; Early concept of bacterial variation; Adaptation, mutation and selection, multinuclear conditions, dominance and recessiveness of characters; reproductive mechanism in bacteria & fungi and segregation of genetic characters.

Molecular aspects of genetics

Components of DNA and RNA, arrangement of nucleotides in DNA, Replication of DNA, RNA synthesis, In vitro denaturation and renaturation of DNA, RNA as source of information.



Mutaions

Back mutations, reversion and suppression and mutation rates, mutagenic agents and molecular basis of mutagenesis, biochemical mutations; mechanism of mutation, site directed mutagenesis, Tn mutagenesis.

Genetics of Bacteria

Genetic transfer of characters; Bacterial conjugation, conjugation mating type; Recognition of factors, chromosomal transfer, interrupted mating experiments, chromosome mapping, Types of plasmids, detection of plasmids, Transfer of plasmid DNA, plasmid replication, Partition of plasmids at cell division, Sexduction, Transformation – transformation of pneumococcal capsular types – cellular competence and environmental conditions required for transformation – linkages; Transduction – general, restricted and abortive transductions; Fine structure study through transduction.

Genetics of fungi

Alternation of generation, study of Aspergillus nidulans, Neurospora crassa and yeasts.



Genetics of Viruses

Genetics of bacteriophage (Lambda) and phage induced mutation, DNA and its gene organization.


Suggested readings:

1. Snustad, D.P. Simmons, M.J. and Jenkins, J.B. Principles of Genetics., Jacaranda/Wiely publishers, 1997.



GEB 305: Cell & Developmental Biology (½ Unit)

1. Cytoskelton and sub-cellular organization of eukaryotic cells.
2. Signal transduction
3. Plant developmental process and their control by hormone and environment
4. General principles and concepts of development. Basic types of animal development, Developmental potential, determination and differentiation; Cell interactions and induction; mesoderm induction in Xenopus
5. Introduction to the development in Dictoyostelium and Drosophila
6. Common developmental proteins from Drosophila to Man, use of these proteins for production of developmentally specific protein.
7. The eukaryotic cell cycle



Suggested readings:

1. Darn ell, J., Lodesh, H. and Baltimore, D. 1986. Molecular Cell Biology., W.H. Freeman and Company, New York.
2. Alberts, B. Bray, D. Lewis, J., 1989. Molecular Biology of the Cell. Garland Publishing, Inc. New York.


GEB 306: Environmental Biology, Society & Impact of Molecular Biology (1.0 Unit)

A. Basic Concepts in Ecology and Environmental Biology

(a) What is meant by Ecology or Environmental Biology
(b) Atmosphere, Oceans and & Biomes: The general circulation of atmosphere; the sun; the major circulation pattern, Precipation; Climate
(c) The Ocean and the Fresh Waters
(d) The World’s Biomes ( deserts, grasslands, foressts, tundra etc.)
(e) Dynamics of Ecosystems- Biogeological Cycles
(f) The flow of Energy and Tropical level
(g) Ecological Succession
(h) Communities; Predator-pray Interactions
(i) Population Ecology – Population Genetics



B. Environmental Biology and Man: The Future of Biosphere

(a) Global Climate Changes

Changes in atmosphere
Increase of CO2: The greenhouse effect; The rise of temperature; Ozone hole; Impact on living beings; Commenting on El Nino and oscillations in world’s climate; Desertification as affected by climate changes.

(b) Social Forestry and Agroforestry

Threatening issues in forest cover depletion; Desertification due to overgrazing; the tragedy of Chernobyl; Challenges and approaches; Role of biotechnology in research on forestry and recovering barren lands

(c) Environment and Organismal health

Pollution of air, water and soil and their mitigation; Acid rain; Transfer of harmful compounds through ecosystems; Microbial technologies for waste disposal; Biogas, human and livestock health

The nuclear winter: The biological consequences



Focus on human ecology – The last Winter, Population growth and the threatened biosphere. Resource Cycling: Scientific and political issues

C. Impact of Molecular Biology and Biotechnology in Human Survival

(a) Biotechnology, Environment and man

Ethical and environmental issues concerning use of cloned gene in medicinal, agricultural and industrial fields; GMs, effects of GMs on biodiversity conservation, Safety considerations; Inventory of World’s plants; Cryopreservation; ; Germplasm banks

(b) Biology and Future of Man

New application of biological sciences towards human welfare. Human gene therapy; Human population growth. When we began sidesteping ? Control of human fertility; Ethical considerations; Possible means of birth control, Invitro fertilization, Eugenics, Guarding the genetic quality of man. Future of Homo sapiens



Suggested readings:

1. Handler, P. 1970, Biology and the Future of Man., Oxford University Press. U.K.
2. Watson, J.D. and Tooze, J. 1981. DNA Story. W.H. Freeman and Comapany N.Y.
3. Ricklef, R.E. 1990. Ecology . W.H. Freeman and Comapany N.Y.


GEB 307: Biochemistry & Molecular Biology of Diseases (1.0 Unit)

1. 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); Insulin gene; Biosynthesis of insulin; mechanism of insulin action; Complications of DM; Diagnosis and treatment (brief treatment), Diabetes insipidus.

2. Cardiovascular disease: Brief anatomy of the heart

Atherosclerosis: Molecular mechanism of the formation atheromatus plaque – involvement of LDL & foam cells; Ishchemic heart disease; Myocardial infraction (MI); Biochemical markers for the diagnosis of MI; Heart failure; Disorders of lipoprotein metabolism.



3. Cancer

Type of cancer cells; Chemical carcinogens; Methods of testing chemical carcinogens; Oncogenic viruses; Oncogenes. Hematological malignancies: Leukemia, Lymphoma and Myeloma. Cancer chemotherapy: Antimetabolites, Alkylating agents. Plant alkaloids, Antibiotics and miscelleneious compounds.

4. Liver disease

Microarchitecture of the liver, Hyperbilirubinemia, Dubin-Jhonson symdrome, 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

The biology of HIV; Genomic organization; Origin – mode of transmission; HIV and the immune system; Pathogenesis of AIDS: Asymptomatic carriere – PGL – ARC – Full blown AIDS; Diagnostic test, Anti-AIDS drugs; Vaccin possibilities.



6. Diarrheal disease

Acute and chronic diarrhea; Causative agent of acute diarrhea: E. coli, Shigella, Vibrio cholera and Salmonella; Molecular mechanism of the action of cholera and shigella toxin; Treatment: Antibiotics and vaccine posibilities.

7. Some Brain diseases

Alzhimer’s disease, Parkinson’s Disease, Huntington’s Disease. 

8. Genetic basis of some metabolic disorders

Phenylketonuria, Alkaptonuria, Maple syrup urine disease, Nieman-pick disease, Gaucher’s disease, Glycogen storage disease, Gout.

9. Chromosomal abnormalities

Variations in the number and structure of chromosomes: Haploids; Missing or extra chromosomes ( Euploids, Aneuploids); Deletion; Duplication; Abberations; Translocation and other structural rearrangements. Chromosomal studies – Karyotyping; Amniocentesis – Chorionic villi sampling – alpha fetoprotein sampling; Chromosomal abnormalities in man: Fragile-X syndrome, Metafemales; Structural modification of a chromosome: Down’s syndrome, Cystic fibrosis etc. 



Suggested readings:

1. John Macloed., Davidson’s principles and Practice of Medicine., 24th Ed. Churchill Livingstone, 1988.
2. Gillham, B., Despo, K.P., Thomas, J.H., Will’s Biochemical Basis of Medicine., Reed Educational and Profesional Publishing Ltd. 1997.
3. Harper’s Review of Biochemistry, 24th Ed.
4. Devlin, 1997. Textbook of Biochemistry with clinical correlations.


GEB 308: Analytical Methods in Biotechnology (½ unit)

Gel filtration; Column chromatography: Ion-exchange, Affinity etc; 
Electrophoresis: Agarose, Polyacrylammide; Spectrophotometry; 
DNA isolation techniques from bacteria, plant and different biological samples. Southern Hybridization, Western blotting, Norther hybridization, Microarray technology, complementation techniques
Polymerase chain reaction (PCR); RFLP, AFLP, RAPD; 
DNA sequencing; Mutation analysis; 
Rcombination models: Rec system, conjugation, transduction transfection and transformation.
Molecular methods for structure determination: Ultraviolet (UV), Infra-red (IR), Nuclear magnetic Resonence (NMR), Electron Spin Resonence (ESR) and Mass spectroscopy 



Suggested readings:

1. Rob Reed, David Holmes, Jonthan., Practical Skills in Biomolecular Sciences., Weyers and Allan Jones. Addison Wesley Longman Ltd. 1998.
2. Williams and Fleming, 1980. Spectroscopic Methods in Organic Chemistry.
3. Walker, 1987. Techniques in Molecular Biology.
4. Hamilton and Sewell, 1982. Introduction to HPLC.
5. Ausubel, 1995. Short protocols in molecular biology.


GEB 309: Biostatistics (1.0 Unit)


I. Introduction

1. Research and experimentation
2. The role of statistics
3. The nature of statistics
4. Scoope of this presentation



II Sampling techniques

Basic statistical principles and terminology


1. Populations and parameters: Samples and statistics
2. Variables
3. Statistical characterization of samples
4. Distributions
5. Statistical concepts pertaining to interpretation and decision
6. 

III. Descriptive statistics: Estimation of uncertainty

1. Calculation of the mean, variance and standard deviation
2. Machine method of calculating the variance and standard deviation
3. Estimation of standard deviation from the range
4. Standard deviation of the mean
5. Confidence limit of the mean



IV. Test of significance: Measurement data

The t test

a) The t test in paired experiments
b) The t test in non-paired experiments
c) Selection of appropriate method of calculating t
d) Confidence limits of a difference between means

Analysis of variance: The F test

a) Analysis of variance: Single characterization data
b) Analysis of variance: Single classification data with subgroups
c) Analysis of variance: Multiple classification data
d) Ducan’s multiple range test: Least significance difference test
e) The relationship between t and F test
f) General remarks


V. Test of significance: Enumeration data

The chi-square (x2) test

1. The 1 x n table
2. The 2 x n table
3. The use of x2 with occurence-nonoccurence data
4. x2 analysis of a 2 x 2 or four fold table
5. Alternate methods of calculating x2
6. Tests of significance when cell frequencies are small
7. General remarks



Statistical methods based on binomial

1. Confidence limit of the mean
2. Significance of difference between rates


VI. The relationship between variables

1. Correlation
2. Linear regression

a) The ‘least squares’ regression line
b) Test of linearity of a regression
c) Confidence limit of the regression coefficient
d) Significance of a difference between regression coeficient

VII. Dosage-Response data

1. The estimation of 50 percent endpoints

a) Graphic approximation of ED50 value
b) The Reed-Muench method of estimation of 50 percent endpoints
c) The estimation of relative potency
d) General remarks



VIII. Nonparametric tests



GEB 310: Practical (1.0 Unit)

Practical based on course (1 – 8) 

GEB 311: Viva voce (½ Unit)