MS In Biotechnology Course Details Of Brac University

February 23, 2015 | Category: Course Details | Posted By - Md Jewel | 0 Comments

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Basic Info of:
BRAC University

The postgraduate program of MS in Biotechnology (36 credits) started in Fall 2007.  The course is so designed for creating highly competent biotechnologists to serve in the universities and other academic institutions, R&D organizations and biotech-related industries both in the public and private sectors of the country. With this academic background the graduates will be able to pursue higher studies leading to Ph.D. both at home and abroad.

For the fulfillment of the MS degree requirement a student needs to complete 36 credits out of which 6 credits are assigned to Research Project/Thesis.

So far, thirty six students have graduated with MS degree in Biotechnology and at present we have a total of seventy students pursuing the degree, who are at different stages (semesters) of their study.

MNS Department has active collaboration with the University of Dhaka, ICDDR,B, BRAC ARDC, BIRDEM with excellent research and training facilities for research and project work of our MS Biotech students. 

BTC 501 Plant Biotechnology 3 Credits

The plant biotechnology course covers principles and different aspects of plant biotechnology.

Topics include:

- Plant cell cultures; growing tissue-, axillary bud, root- and meristem cultures
- Protoplast culture, somatic hybridisation and importance, cybridization
- Application of mass propagation (micropropagation) for virus-free vegetatively propagated crops such as potatoes, ornamentals, forest trees and medicinal plants
- Plant growth regulators: auxin, cytokinin, gibberellin, zeatin, 2iP and their role and putative mode of action
- Regeneration pathways: organogenesis vs somatic embryogensis; concepts and applications
- Plant transformation- application of the technique in transferring useful genes such as genes for disease-, insect resistance, those that add nutritional values to the crops of interest across wide genetic barriers
- Production of genetically modified (transgenic) plants: indirect and direct methods, selectable markers, transient and stable expression, merits and demerits of the respective methods
- A critical assessment of GM crops containing genes for herbicide-, virus-, bacterial-, fungal-, nematode- and insect pests resistance. evaluation of GM crops for their adoption in developing countries
- Germplasm preservation-ex situ and in situ preservation; gene bank
- Plant secondary metabolites of medicinal importance
- Commercial exploitation of plant tissue culture and possibilities in Bangladesh

Recommended Books:

1. An Introduction to Plant Tissue Culture, M. K. Razdan, 1998
2. Plant Tissue Culture: Theory and Practice, S. S. Bhojwani and M. K. Razdan, 1996
3. Biochemistry & Molecular Biology of Plants, Bob B. Buchanan, 2000
4. Biotechnology: Theory and Techniques: Plant Biotechnology, Animal Cell Culture, Immunobiotechnology (Vol I), Jack G Chirikjian (Ed.), 1995
5. Plant Biotechnology: Perspectives and Prospects, P. C. Trivedi, 2006
6. Plant Tissue Culture & Biotechnology, P. C. Trivedi, 2007
7. Principles and Practices in Plant Science, P. D. Walton, 1988

BTC 502 Plant Biotechnology (Lab) 3 Credits

The Plant Biotechnology (Lab) course will cover the following experiments:
- Setting up tissue culture experiments for callusing
- Differentiation as well as different aspects of molecular biology beginning from DNA and RNA isolation, running them in gel for their characterization based on their kb length
- Use of restriction enzymes for DNA and RNA fragmentation at predetermined sites
- Ligation of different pieces of DNA in a suitable plasmid vector such as pBluescripts
- Plant cell cultures; media: sterilization techniques
- Initiation of primary cultures; morphogenesis and phytohormones
- DNA extraction from E. coli plasmids, total RNA isolation from model plants
- Construction of cDNA library and isolating cDNA clones; minipreparation of plasmid DNA
- Computer analysis of DNA and protein sequence
- Plant genomic DNA isolation
- Restriction digestion of DNA and Southern transfer; RNA gel electrophoresis and Northern transfer; non-radioactive hybridisation of Southern and Northern Blots.
- Agrobacterium-mediated gene transfer (vector construction, co-cultivation); RAPD and microsatellite analyses for confirmation of hybridity/ DNA fingerprinting, biolistics, analyses of transgenic plants (PCR and RT-PCR)
- Southern analyses, chromosome preparations and physiological analyses of transgenic plants

Recommended Books:

1. Plant Tissue Culture: Theory and Practice, Bhojwani, S. S. & Razdan, M. K., 1996
2. Biotechnology: Theory and Techniques: Plant Biotechnology, Animal Cell Culture, Immunobiotechnology (Vol I), Jack G Chirikjian (Ed.), 1995
3. Plant Tissue Culture & Biotechnology, Trivedi, P. C. (Ed.), 2007
4. Plant Tissue Culture: Application and Limitations, Bhowjwani, S.S. 1990
5. Plant Cell Culture: A Practical Approach, Dixon, 1994

BTC 503 Animal Tissue Culture Techniques and Applications 3 Credits

The course has been designed to impart basic knowledge in animal biotechnology so that students may take up a topic on animal biotechnology leading to cloning of useful genes from important animals such as cattle in Bangladesh.

Topics include:
- Definition, principle and significance of animal tissue culture, basic differences between plant and animal cell cultures
- Mycoplasm and viral contaminants of animal cell culture; maintenance of sterility and use of antibiotics
- Various systems of tissue culture: their distinguishing features, advantages and limitations
- Culture medium: logic of formulation (natural media, synthetic media and sera)
- Methodology- i) primary culture: behavior of cells, properties, utility ii) explant culture iii) suspension culture
- Nutrient media: obligatory and optional constituents
- Incubation systems: static agitated culture systems
- Hormone signaling and mechanisms of signal transduction, fertilization, early embryogenesis
- Applications of gamete and embryo manipulations for biomedical purposes, tissue-specific gene expression and tumorigenesis
- Development and preparation of vaccines against infecting organisms
- Artificial animal breeding; in vitro fertilization
- Cloning: techniques and technologies; Dolly, the cloned sheep
- Mutant cell lines: significance in biomedical research, identification and isolation of mutants
- Application of genetic manipulation, medicinally important compounds; screening of cell lines for novel variations: disease resistance, stress tolerance
- Gene transfer to animal cell, viral vector (development and use), gene therapy; transgenic animal
- Cytotoxicity and diagnostic tests; development and preparation of vaccines against infecting organisms

Recommended Books:
1. Biotechnology: Theory and Techniques: Plant Biotechnology, Animal Cell Culture, Immunobiotechnology (Vol I), Jack G Chirikjian (Ed.), 1995
2. Animal Biotechnology, M. M.Ranga, 2004
3. Molecular Biotechnology, B. R. Glick and J. J. Pasternak, 2003
4. Molecular Biology, Primrose, 2003
5. Animal Cell Biotechnology, R.E. Spier and J.B. Griffiths, 1988

BTC 504 Fermentation and Industrial Biotechnology 3 Credits

The course outlines the process of fermentation and industrial biotechnology from organism and environmental points of view.

Topics include:
- Industrially important microorganisms-bacteria, fungi, actinomycetes and yeasts
- Major classes of microbial products and processes
- Growth of microorganisms in batch, semibatch and continuous culture
- Microbial growth kinetics for primary and secondary metabolites in batch and continuous culture
- Industrial applications of continuous culture-potentials and limitations
- Upstream and downstream processing of microbial fermentations
- Twin faceted core of industrial biotechnology- genetic manipulation including application of genetic engineering techniques for microbial strain improvement
- Optimization of media and fermentation conditions for maximizing productivity
- Scale up of fermentation processes; criteria for scale up; physical, chemical and sterilization factors
- Bioreactor design-batch, semi-batch and continuous bioreactor operations
- Aeration and agitation; sterilization: batch and continuous
- Process monitoring- off line and on-line sensors; and process control
- Unit operations in product recovery and purification
- Principles and methods of cell immobilization and their industrial applications
- Biotechnological production of representative metabolites: organic acid, amino acids, alcohol, industrial enzymes, antibiotics, recombinant proteins; biopharmaceuticals and vaccines
- Anaerobic fermentations- industrial production of alcohol, acetone, butanol etc.
- Scope of industrial biotechnology in Bangladesh

Recommended Books:
1. Modern Industrial Microbiology and Biotechnology, Nduka Okafor, 2007
2. Principles of Fermentation Technology, Peter F. Stanbury, Stephen J. Hall, and Allan Whitaker, 1999
3. Prescott & Dunn's Industrial Microbiology, 4th Edition, G. Reed, (Ed.), 1999

4. Microbial Biotechnology-Fundamentals of Applied Microbiology, Alexander N. Glazer, Hiroshi Nikaido, 2007
5. Fermentation Microbiology and Biotechnology, 2nd Edition, E.M.T. El-Mansi, C.F.A. Bryce, A.L. Demain and A.R. Allman, (Eds), 2007
6. Microbial Biotechnology Principles and Applications, 2nd Edition, Lee Yuan Kun (Ed.), 2008

BTC 505 Environmental Biotechnology 3 Credits

This course details the dangers of pollution; how the environment is rapidly being polluted due to setting up of industries all over the world and in Bangladesh as well; how the effluents from factories along the shores of rivers and water bodies are killing the aquatic life in and around the cities and possible remedial measures.

Topics include:
- Microbes and metabolism; genetic blueprint for metabolic capability; metabolic pathways of particular relevance to environmental biotechnology
- Fundamentals of biological interventions: extremophiles with diverse degradative capabilities;
- Pollution and pollution control biotechnology: types of pollution and pollution control strategies and available technologies
- Contaminated land and in situ and ex situ techniques for remediation
- Aerobes and effluents-sewage treatment tank; activated sludge systems; oxidation ditch; membrane bioreactors
- Phytotechnology- metal phytoremediation, rhizofiltration; organic phytoremediation; algal treatment systems
- Biotechnology of wastes- composition of wastes; biological waste treatment; composting and application in waste treatment; anaerobic digestion; biogas and other technologies
- Bioremediation; suitability and factors affecting bioremediation; essential features of biological treatment systems
- Environmentally transmitted pathogens; risk assessment; microorganisms and metal pollutants
- Biosensors
- Concept of viable but non-culturable cells (VBNC); present status of VBNC; molecular genetic methods for detection and identification of VBNC; implication and significance of VBNC in environment and health
- Use of commercial blends of micro-organisms and enzymes in wastewater treatment; immobilized cells in the waste treatment; potential application of recombinant DNA technology in waste treatment
- Xenobiotic degrading bacteria and their catabolic genes in bioremediation: in situ analysis of microbial community and activity in bioremediation, DNA- and RNA-based methods; genetic finger printing techniques; recent powerful sensitive techniques for detection of specific compounds
- Integrated approaches in environmental biotechnology

Recommended Books:
1. Environmental Biotechnology: Theory and Applications, GM Evans and J.C Furlog, 2003
2. Environmental Biotechnology: Principles and Applications, B.E Rittman and P.L. McCarty, 2001
3. Environmental Biotechnology, Alan Scragg, 2002
4. An Introduction to Environmental Biotechnology, Milton Wainwright, 2004
5. Environmental Biotechnology, Hemant Rawat, 2008
6. Environmental Biotechnology: Concepts and Applications, Hans-Joachim Jördening,
Josef Winter (Ed.), 2005

BTC 506 Research Project Preparation 3 Credits

This course gives research orientation to students so that they can carry out research projects with efficiency and confidence.

Topics include:
- Project design, planning, implementation and evaluation: writing project proposals; essential components of a project- overall development objectives, specific objectives, output, verifiable indicators, means of verification, assumptions; logical framework matrix; project monitoring and evaluation methods
- Research project planning: literature review through search engines, such as Google, HINRARI, Altavista, PubMed, and other online literature survey to dig out information relevant to a research project
- Design of methodology and experiments supported by knowledge in biostatistics, record observations, interpret results
- Writing a scientific paper following the format of a particular journal including bibliography
- Use of search engines to be up to date in the line of research
- Selection of a suitable research topic, steps to be followed-idea and concept, objective analysis, theme development and chronological design of different plans of activities
- Selection of a suitable guide for research; communication skill for interacting with the guide at different stages of work
- Writing a thesis- different components to be included; relevance of objectives to literature review, methodology, overview of study design and results, comparative analysis with the existing information in the selected project; analysis of uniqueness of findings; discussion and interpretation
- Writing a research paper for journal publication, structure of a scientific paper- the IMRAD format- selection of suitable title, key words, abstract , introduction materials and methods, arrangements of tables and figures in a self-explanatory way, results and discussion and references all based on thematic approach
- Convenient order of reading or writing a paper; modern methods of communication- electronic submission, e- journals etc.
- Presentation of paper- oral presentation, poster presentation; logical organization of powerpoint presentation-structuring the presentation largely as a story

Recommended Books:

1. Thesis and Dissertation Accomplished: A Comprehensive CD-Rom, Carter W. Tada F. 2006, http://www.tadafinallyfinished.com/
2. Writing and Publishing Your Thesis, Dissertation, and Research: A Guide for Students in the Helping Professions, Heppner, P. P., & Heppner, M. J., 2004
3. The Elements of Style (4th ed.), William Strunk, Jr., E. B. White, 2000
4. . Dissertations and Theses from Start to Finish: Cone, J. D., Foster, S. L., 2006

BTC 507 Biostatistics and Experimental Design (Theory and Lab) 3 Credits

This course has been tailored to the need of molecular biologists who are often confronted with the problem of making a valid conclusion for want of properly organized experimental layout.

Topics include:
- Definition and scope of biostatistics, measures of central value; mean, median, mode, measures of dispersion, range, quartile deviation, mean deviation, variance, standard deviation, standard error, coefficient of variation
- Sampling distribution, confidence limit; correlation and regression: calculation of correlation coefficient and test for its significance, regression coefficient, regression line, multiple regressions
- Concept of probability, probability rules, conditional probability and independence
- Probability distributions: binomial, Poisson and normal distributions and their applications; hypothesis testing, null hypothesis; level of significance; comparison of two means, t-test, t-tests for small and large samples, paired t-test, chi-squared test, goodness of fit test, test of independence, contingency tables
- Analysis of variance; one-way and two-way classifications, comparison of three or more samples, F-test; concepts of experimental design, principles of experimental design, completely randomized design (CRD), randomized bock design (RBD), latin square design, factorial experiments, split-plot design
- Multiple comparisons, least significant difference test (LSD test), Duncun’s multiple range test

Recommended Books:
1. The Design of Experiments, R. A. Fisher, 1975
2. Statistical Table for Biology, Agriculture and Medical Research, R. A. Fisher and T. Yates, 1965

BTC 508 Seminar 3 Credits

The course aims at development of presentation skill of the students about topics chosen from literatures and their own findings

Topics include:
- Presentation of the contents of a complex article in a short, concise and comprehensive form
- General structure of a seminar talk: title, list of contents, conceptual background as to why the topic is interesting, hypothesis or research objectives, presentation of materials and methods to depict only what is needed to understand the results (short), presentation of results preferably with clearly understood more figures and less tables (little long), discussion to explain if the objectives of the study have been achieved, what are the alternative explanations or whether are more experiments are needed (little long), summary containing the most interesting part to attract the audience
- Seminar talk on the selected published paper keeping in mind the following pertinent points:
problem investigated; research question answered; primary motivation for investigating the problem; background information (context); relevance to understanding the problem; key points of the paper; method(s) or experimental design used; results reported in the paper; unexpected results, if any and if so whether such results are explained sufficiently
- The paper’s conclusions, implications of the investigation, how does the investigation influence future work?
- Weaknesses if any of the paper, personal evaluation
- Points to consider about the audience: why the audience should be interested in this particular topic; what they already know about it; what terms or definitions are new to them; which key points or concepts will be the most interesting and which ones will be difficult for them to grasp

Recommended Books:

1. Survival Skills for Scientists, Federico Rosei, T. W. Johnston, 2006
2. Speaking Your Mind: Oral Presentation and Seminar Skills‎, Rebecca Stott, Tory Young, Cordelia Bryan, 2001
3. The Craft of Scientific Presentations: Critical Steps to Succeed, Michael, 2003

BTC 509 Genomics (Bioinformatics) 3 Credits

The course outlines a number of software tools used for characterizing an unknown gene or a part of it on the basis of stored data of DNA base sequences of a similar gene.

Topics include:
- Web based methods in molecular genetics, computer aided analysis of genetic sequences
- Genome analysis, identification and characterization of important functional genes with the help of NCBI data base and suitable software
- Modern applications of genetic mapping and importance of genome synteny between species revealing their relationship on phylogenic trees
- Current research in molecular genetics and genome analysis, with particular emphasis on modern applications of genetic mapping and the importance of genomic synteny between species
- Gene tagging, plant transposons, gene banks and genome databases
- Gene cloning based on genome maps, sequencing programs and protein sequence motifs
- Principles of algorithms and software for sequence alignment, similarity search of biological databases and DNA sequence analysis
- Motif discovery, estimation of molecular phylogenetic trees
- Structural prediction and functional inference; predicting the structure and evolution of macromolecules

Recommended Books:

1. From Molecular to Modular Cell Biology, L H. Hartwell, J. J. Hopfield, S. Leibler and A. W. Murray, Nature, 402: 47-52, 1999
2. Genomics, Gene expression and DNA Arrays, Lockhart, D.J. and Winzeler, E.A. Nature 405: 827-836, 2000
3. Automated DNA Sequencing and Analysis, M.D. Adams, C. Fields, J. C. Venter (Eds.), 1994
4. Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins, A. Baxevanis and F. B. F. Ouellette (Eds.), 1998
5. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, D. Gusfield and A. M. Lesk (Ed.), 1997
6. The Internet and the New Biology: Tools for Genomic and Molecular Research, L. F. Peruski Jr., and A. Harwood Peruski, 1997
7. Molecular Bioinformatics: Algorithms and Applications, S. Schulze-Kremer, 1995
8. Introduction to Computational Molecular Biology, J. Setubal and J. Meidanis, 1996
9. Molecular Databases for Protein Sequences and Structure Studies: an Introduction, J. Sillince and M. Sillince, 1992
10. Biocomputing, Informatics and Genome Projects, D.W. Smith (Ed.), 1994

BTC 510 Fundamental and Applied Aspects of Plant Genetic Manipulation 3 Credits

The course aims at giving biotech students an in-depth knowledge in fundamental and applied aspects of plant genetic manipulation.

Topics include:
- Introduction to plant genetic manipulation
- Plant tissue culture, transgenic plant production (factors and elements)
- GM technologies and GMOs: recent development and future trends
- Agrobacterium-mediated transformation
- Chloroplast transformation method
- Biotic stress resistance transformation- resistant molecules
- Fungus resistant transgenic plant production
- Abiotic stress resistant transgenic plant production
- Innovative techniques for genetic manipulation of plants against a background of a continuing need for plant improvement in agriculture, horticulture and forestry
- Cell fusion technology for novel somatic hybrid production
- Development of plant transformation systems comprising Agrobacterium-mediated gene delivery, direct DNA uptake and biolistics; vector design; molecular methods in crop improvement alongside the value of gene mapping and genetic fingerprinting for germplasm evaluation
- Biopharming
- Biofuel

Recommended Books

1. Plants, Genes, and Crop Biotechnology, J. Chrispeels, Maarten and David E. Sadava, 2003
2. Plant Biotechnology: The Genetic Manipulation of Plants, Slater Adrian, 2006
3. Genes IX, B. Lewin, 2008
4. Transgenic Plants (Vol. 1 and 2), Kung and R. Wu, 1993
5. Plant Biotechnology in Agriculture, K. Lindsey and M.G.K. Jones, 1990

BTC 511 Commercial Production of Horticultural and Ornamental Plants 3 Credits

This course has been designed to train students to work in biotech farms dedicated to commercial production of horticultural, ornamental, timber and medicinal plants through tissue culture techniques.

Topics include:
- Cost saving devices in tissue culture: used glass jars from hotels, locally made unscrewed plastic caps to replace cotton plugs, preparation of distilled, deionized water, making of various kinds of culture media under sterile conditions
- Adoption of extra precautionary measures to eliminate bacterial and fungal contamination
- Different techniques used for preparing explants for callusing and differentiation, procedure for hardening plantlets after they are taken out of culture bottles
- Maintenance of plants inside the greenhouse in accordance with their requirements for light, temperature and moisture
- Lessons on construction of greenhouses creating microclimate for the growth of different types of horticultural plants, installation of misting and ventilation system including the cost involved
- Packing of tissue culture derived material for marketing, without damage during the transport of the material
- Status of commercial production of horticultural and ornamental plants in Bangladesh and other neighbouring countries
- Potentials of tissue culture technology

Recommended Books:

1. Commercial Production of Horticultural Crops, Kunal Mitra, 2008
2. Scientific Horticulture (Vol. 10), S.P. Singh (Ed.), 2007
3. Advances in Arid Horticulture (Vol. I) Present Status, P.L. Saroj, B.B. Vashishtha, D.G. Dhandar, 2004
4. Advances in Horticulture Science Research, R.C. Upadhyaya, 2008
5. Advances in Ornamental Horticulture (6 Vols), Supriya Kumar Bhattacharjee, 2006
6. Biotechnology of Horticultural Crops (3 vols), V.A. Parthasarathy (Ed.), T.K. Bose, P.C. Deka, P. Das, 2001
7. Clonal Tissue Culture of Important Fruit Crops, Atul Kumar, Vandana A. Kumar, 1998
8. Floriculture : From Greenhouse Production to Floral Design, Ronald J. Biondo, Dianne A. Noland, 2006
9. Ornamental Crop Production Technology, Supriya Kumar Bhattacharjee (Ed.), 2006
10. Ornamental Plant Propagation in the Tropics, Carmine Damiano, Giovanni Ferraiolo, W.O. Baudoin, 2005

BTC 512 Sex, Flowers and Biotechnology 3 Credits

The course will outline floral development, senescence and incompatibility status.

Topics include:
- Introduction to plant alternation of generation
- Reproduction and senescence
- Haploid production through tissue culture
- In vitro pollination and fertilization
- Embryo culture under in vitro condition
- Flower colour modification through genetic manipulation
- Terminator seed technology
- RNAi and PTGS
- Gene silencing for the crop improvement
- Hybrid seed technology
- Methods and achievements in the genetic engineering of crops by modifying floral development
- Reproduction in higher plants and the implications for horticulture and crop production
- Genetic control of floral development; applied aspects of flowering and reproduction
- Molecular basis of self incompatibility, floral senescence, seed storage proteins and the physiology
- Biochemistry and molecular biology of fruit ripening

Recommended Books:
1. The Plant: the Flower, Better Farming Series 3, Food and Agriculture Organization of the United Nations-Rome, 1997
2. Plant Propagation: Principles and Practices, Hudson T. Hartmann, Dale E Kester, Fred T Davies, Robert L Geneve, 2002
3. A Text book of Biotechnology, R.C.Dubey, 1995
4. Biotechnology: Theory and Techniques: Plant Biotechnology, Animal Cell Culture Immunobiotechnology (Volume I), Jack G Chirikjian (Ed.), 1995
5. Plant Tissue Culture & Biotechnology, P. C.Trivedi, (Ed.), 2007
6. Gene Transfer to Plants, Portykns, 1995

BTC 513 Gene Function and Its Regulation 3 Credits

This course will give the students an in depth knowledge about how a gene controls different steps in a biochemical pathway leading to the formation of an end product.

Topics include:

- Molecular structure of gene and chromosomes, mobile DNA
- Chromosomal DNA: functional rearrangements and organelle DNAs
- Regulation of gene expression: prokaryotic system
- Prokaryotic gene expression regulation-II and eukaryotic gene expression regulation
- Transcription control at termination and RNA processing step
- Gene expression fidelity and cancer
- Environmental effect and gene expression
- Mutation and repair of DNA, DNA damage and repair regulations
- Modern concept of homologous recombination
- Operon model; signal transduction, cyclic nucleotides and hormones in gene regulation
- Genetic recombination in vivo, homologous recombination by hybrid DNA formation
- Site-specific recombination
- Transposons and non-homologous recombination, retro-transposons
- Mutation: site-directed mutagenesis and ‘protein engineering’
- Mutations in human genetic diseases and clinical medicine
- DNA amplification in vitro: Polymerase chain reaction (PCR), applications of PCR in research, clinical medicine and forensic science
- DNA diagnostics: ribotyping; pulsed field gel electrophoresis
- DNA fingerprinting ; non-radioactive DNA probe technology
- Molecular biology in animal biotechnology: tissue-specific gene expression, gene transfer in animal cells: viral vectors, embryonic stem cells, gene knock-out organisms

Recommended Books

1. Molecular Biology of the Cell, Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, 5th Edition, 2007
2. Principles of Genetics, D. P. Snustad, M. J. Simmons and J. B. Jenkins, 1997
3. Genes IX, B. Lewin, 2008
4. Molecular Cell Biology, J. Darn ell, H. Lodesh and D. Baltimore, 1986
5. Molecular Biotechnology. B. R. Glick and J. J. Pasternak, 2003
6. DNA Cloning 1 and 2, D. M. Glover, and B. D. Hames, 1995
7. Molecular Cell Biology (5th Edition). Lodish, Berk, Matsudaira, Kaiser, Krieger, Scott, Zipersky and Darnell, 2003

BTC 514 Gene Organization and Regulation 3 Credits

The course will outline the recent developments in gene regulations, protein folding etc.

Topics include:
- Structures of genes and chromosomes in relation to regulation of gene expression
- Regulation by transcription factors and enhancers/repressors
- Co-transcription regulation and the effects of chromatin structure
- Details of mRNA processing including the splicesomes, auto-catalysis, polyA addition, differential splicing and RNA editing
- Adenosine deaminases acting on RNAs (ADARS)
- Transcriptional RNA silencing: small RNAs and insights into a new level of gene regulation
- Non-coding RNAs, processes affected by non-coding RNAs
- Post-transcriptional RNA silencing (PTGS) - components of PTGS e.g. dicer, RISC (RNA induced silencing complex), RdRP (RNA dependent RNA polymerase)
- Molecular steps in RNA silencing, RNA silencing as a tool for knocking out genes
- RNA viruses and RNA silencing
- Use of various expression systems for the production of recombinant proteins including strategies for protein isolation and refolding including the use of molecular chaperons
- Epigenetic control of gene regulation- environmental interplay with genetic elements
- Web-based methods in molecular genetics, computer-aided analysis of genetic sequences

Recommended Books:

1. An Introduction to Genetic Analysis. W. H. Freeman, 7th Edition
2. Gene Regulation and Metabolism: Post-Genomic Computational Approaches-Computational Molecular Biology, Ralf Hofestädt (Ed.), 2004
3. Anatomy of Gene Regulation, Panagiotis A. Tsonis, 2003
4. Gene Regulation. David Lachman, 2005
5. Epigenetics, C. David Allis, Thomas Jenuwein, Danny Reinberg, Marie-Laure Caparros, 2007
6. Epigenetic Mechanisms of Gene Regulation, Vincenzo E.A. Russo (Ed.), 1996

BTC 515 Structural and Functional Genomics Studies 3 Credits

The course is intended to give a clear concept about genome, its location and functions of the major genes in normal congenital disease-conditions in living systems.

Topics include:
- Structural genomics and functional genomics
- Genome elements: genes - their sites, location and function; mitochondrial genome
- Genome mapping: genetic mapping; physical mapping - low resolution and high resolution
- Structural genomics: molecular modeling: method for unraveling protein structure and function
- Human genome: the physical structure, variations, evolution, genetic disorder
- Human genome project: goal and achievements so far
- Genome sequencing, ESTs, SNPs, microarrays
- Plant genome: general features, chloroplast genome
- Comparative use of RAPD, RFLP, AFLP, ISSR and micro-satellite markers in plant gene mapping and selection
- Model plant genome: Arabidopsis thaliana and Oryza sativa
- Identification and characterization of important plant genes: salt-, insect, disease, submergence resistance genes
- Identification and characterization of genes controlling (a) flowering, (b) vernalization (c) photoperiod (d) circadian clock
- Use of different web sites in the identification of important genes and their functions
- DNA finger printing and its utilization as molecule markers in selection of important agronomic characters

Recommended Books:

1. From Structural Genomics to Functional genomics Methods and Applications, Ioannis Ragoussis, to be published 2010
2. Sequence - Evolution - FunctionComputational Approaches in Comparative Genomics, Koonin, Eugene V., Galperin, Michael Y. 2002
4. Genomes. Sussman, Hillary (Ed.), Smit, Maria (Ed.), 2006
5. Introduction to Genomics, A. Lesk, 2004
6. The Implicit Genome Caporale, Lynn (Ed.), 2006 ,
7. Quantitative Genetics, Genomics, and Plant Breeding. Manjit S. Kang, 2002
8. The Dictionary of Gene Technology : Genomics, Transcriptomics, Proteomics, Gunter Kahl, Volume 3rd, 2007

BTC 516 Special Study 3 Credits

The course has been designed to acquaint the students with a number of important websites containing valuable information about genomics and proteomics of important plants and organisms.

Websites include:

- Hinari: http://www.who.int/hinari/en/
- The National Center for Biotechnology Information (NCBI) runs the most useful website for bioinformatics
- Bioinformatics Web, offering links and information on bioinformatics and computational biology
- Bio-computing.org, covers recent literature, tutorials, a bioinformatics lab registry, links, bioinformatics database, jobs, and news - updated daily
- BioMedNet, biomedical and bioinformatics resources
- CAMDA: Critical Assessment of Techniques for Microarray Data Analysis, includes data and papers from CAMDA conferences
- Ensembl, up-to-date sequence data and the best possible automatic annotation for many genomes
- Ergito, high-quality books and information on molecular biology and related topics, some sections free
- GeneCards, a database of human genes, their functions, and related diseases
- Genome KnowledgeBase, a collection of mini-reviews in the field of basic molecular biology
- icademic.org, Bioinformatics, Genetics, and other Life Sciences Information Sources.
- ISCB, International Society for Computational Biology
- Lipi's Bioinformatics World, tutorials, tools, databases, and more
- PubMed (Free MEDLINE Search)
- UniGene from NCBI
- UCSC Genome Bioinformatics, contains the reference sequence for the human genome and the working drafts for the mouse and rat genomes
- Y. F. Leung genomics and bioinformatics site

The students will study these websites critically and thoroughly. Familiarity with these websites will enable the students to use similar sites to retrieve relevant information in their respective area of research. Students choosing this course will study all the sections of selected websites and prepare their summaries bringing out salient points of these sections. During the examination, students will be allowed to use these websites to find answers to the questions such as location of a gene in a particular chromosome, its length, sequence and promoter and other particulars.

BTC 517 Enzymology 3 Credits

The study of enzymatic properties will enable a biotechnologist to plan his experiments on biodegradation and bioremediation to be applicable on bioconversion; softening of basal jute stem cuttings or softening of hides of sacrificed animals, bioremediation etc.

Topics include:
- Three-dimensioal structure of enzyme, active site, cofactors, activators, prosthetic groups, coenzymes, enzyme-substrate complex, energy of activation
- Factors affecting rate of enzyme reaction, regulations of enzyme reaction
- Basic aspects of chemical kinetics, molecular interpretation of rate constants
- Activation free energies, enthalpies and entropies, kinetics of enzyme-catalyzed reaction; significance of Km and Vm values
- Allosteric sites, homotropic effects, cooperativity, heterotropic effects, allosteric effect
- Enzyme inhibition- kinetics of competitive non-competitive and uncompetitive inhibition; partially competitive inhibitors
- Enzyme immobilization: different methods of immobilization, advantages and disadvantages of immobilization; applications of immobilized enzymes in industry
- Enzyme technology in industries: biological detergent, baby food, brewery industry, baking industry, fruit juice, dairy industry, starch industry, rubber industry, paper industry, photographic industry; applications of enzymes in bio-conversion and biotransformation.
- Enzymes as biosensors, enzyme technology in biodegradation of industrial toxic pollution: role of lignocellulosic enzymes in removing industrial toxic pollution
- Purification and characterization of an enzyme: (1) gel-filtration - determination of molecular weight (size exclusion chromatography) (2) affinity chromatography (ion-exchange chromatography). (3) gel electrophoresis.
- Assaying different enzymes: laccase, cellulase, pectinase, xylanase, a-amylase, test for presence of enzymes in different plant materials, applications of enzymes in industries (visit to different industries to observe the applications), applications of enzymes in biodegradation

Recommended Books

1. Enzymes: Biochemistry, Biotechnology, Clinical Chemistry, Trevor Palmer and L. Philip, 2007
2. Handbook of Enzyme Biotechnology, A. Wiseman, 1995
3. Microbial Enzymes and Biotransformations (Methods in Biotechnology), Jose Luis Barredo, 2005
4. Industrial Enzymes: Structure, Function and Applications, Julio Polaina and Andrew P. MacCabe, 2007
5. Immobilization of Enzymes and Cells (Methods in Biotechnology), Gordon F. Bickerstaff, 1997
6. Biotechnology Processing Steps for Enzyme Manufacturing, R. C. Tripathi, 2007
7. Microbial Enzymes and Biotechnology, W.M. Fogarty and C.T. Kelly, 1990
8. Applications of Enzyme Biotechnology, Jeffery W. and Thomas O. Baldwin, 2004
9. Biocatalysts and Enzyme Technology, Klaus Buchholz, Volker Kasche and Uwe Theo Bornscheuer, 2005
10. White Biotechnology, R. Ulbeer, D. Sell and P. Baiakeds, 2007

BTC 518 Recombinant DNA Technology 3 Credits

This course outlines the basis of modern techniques in the applications of recombinant DNA technology, its recent progress and application in plant and animal development.

Topics include:
- Introduction to recombinant DNA technology, enzymes used in recombinant DNA technology
- Cloning vectors, gene cloning and transformation techniques
- Analysis of recombinant DNA techniques, gene targeting and site specific recombination
- Genetic transformation of prokaryotes, manipulation of gene expression of prokaryotes
- Principles, techniques and applications of recombinant DNA technology relevant to medical research, and the investigation and therapy of infectious and inherited diseases
- Site-directed mutagenesis, protein engineering; DNA sequencing
- Production of protein from cloned genes: production of recombinant protein in E. coli
- Production of recombinant protein by eukaryotic cells (yeast), mammalian cell expression vectors
- Special vectors for expression of foreign genes in E. coli, using animal cells for recombinant protein production; recombinant proteins from plants
- Molecular enzymology and protein engineering: the alteration of a protein structure by site directed mutagenesis of the DNA coding for that protein
- Molecular basis of binding specificity, catalysis, subunit interactions etc., examined by physico-chemical methods on proteins and enzymes mutated at key amino acid residues
- Construction of genomic library and cDNA library, isolation of gene

Recommended Books

1. Recombinant DNA: Genes and Genomes - a Short Course, James D. Watson, Richard M. Myers, Jan Witkowski, Amy A. Caudy, 2006
2. Recombinant DNA, Watson, 1992. An Introduction to Genetic Engineering, Desmond S. T. Nicholl, 2008
3. Principles of Genetics, D. P. Snustad, M. J. Simmons and J. B. Jenkins, 1997
4. Genes IX, B. Lewin, 2008
5. Molecular Biotechnology, B. R. Glick and J. J. Pasternak, 2003
6. DNA Cloning 1 and 2, D. M. Glover and B. D. Hames, 1995
7. Molecular Biology, Primrose, 2003

BTC 519 Medical Biotechnology 3 Credits

This course will focus on the recent biotechnological and molecular development in disease diagnosis and treatment emphasizing on the immunological aspects of human.

Topics include:
- Laboratory aspects of research in biotechnology related to health
- Important areas of biotechnology including biochemistry, pathology, microbiology, molecular biology, immunology and immunobiology
- Aspects of specimen handling, storage and biosafety issues
- Research in medical biotechnology with special reference to developing countries
- Routine diagnostics, modern diagnostic tools
- Immunological aspects of host defense- innate immunity: both humoral and cellular
- Immunological aspects of host defense- adaptive immunity: both humoural and cellular
- Molecular methods for diagnosis of infectious agents common in developing countries
- Immunological methods for diagnosis of infectious agents common in developing countries
- High throughput techniques for studies of genetics of host and pathogens in infectious diseases
- Genetic disorders- inborn error of metabolism, metabolic disorders
- Gene therapy- ethical, legal and social implications
- Vaccine development and production

Recommended Books:

1. Medical Biotechnology, S.N. Jogdand, 2000
2. Medical Biotechnology, Judit Pongracz and Mary Keen, 2009
3. Medical Biotechnology: Achievements, Prospects and Perceptions, Albert Sasson, 2006
4. Biotechnology and Biopharmaceuticals: Transforming Proteins and Genes into Drugs,‎
Rodney J. Y. Ho, Milo Gibaldi, 2003

BTC 520 Cell Dynamics, Cell Cycle and Cell Death; Gene Mapping in Phages, and Bacteria 3 Credits

The course is designed to impart in-depth knowledge about the cell-cell interaction and cell communication and factors that contribute to the death of cells known as apoptosis, physiological changes that occur in a transformed cell.

Topics include:
- Role of chromatin in gene expression and DNA damage detection at molecular level
- Cell dynamics, cytoskeleton and cell surface, extra-cellular matrix, cell-cell interaction and cell matrix interaction
- Cell differentiation
- Hormones and growth factors, apoptosis
- Cell cycle regulation and cancer: the Biology of oncology; role of p53, p21 and other oncogenes and suppressors; treatment approaches for cancer
- Transformed cell, gene mapping in phages, bacteria: conditional lethal and suppressor mutations
- Control of gene expression in bacteria, genetics of biosynthetic pathways
- Transposons in prokaryotes and eukaryotes, detection of DNA damage at molecular level

Recommended Books:

1. Molecular Biology of the Cell, Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, 5th Edition, 2007
2. Molecular Cell Biology. Harvey Lodish, Paul Matsudaira, Arnold Berk, Hidde Ploegh, 2004
2. Animal Cell Biotechnology: Methods and Protocols, R. Portner, (Ed.), 2nd Edition, Humana press, 2007
3. Animal Cell Culture and Technology, 2nd Edition. M. Butler, BIOS Scientific, 2004
5. Basic Cell Culture: A Practical Approach, Davis, (Ed.), 2nd edition, 2002
6. Cell Growth, Differentiation and Senescence: A Practical Approach. G.P. Studzinski, (Ed.), 1999
7. Cell-Cell Interactions: A Practical Approach, 2nd edition, T. Fleming, 2002
8. Culture of Animal Cells: A Manual of Basic Techniques, 5th Edition, R. Ian Freshney, 2005
9. Dynamics of Cell Division, S. Endow and D. Glover, (Ed.), 1998
10. Molecular Cell Biology for the 21st Century, 5th Edition, 2008
11. The Biological Basis of Cancer, Robert G. McKinnell, Ralph E. Parchment, Alan O. Perantoni, G. Barry Pierce, Ivan Damjanov, 2nd Edition, 2006
12. Recent Advances in Clinical Oncology, Frank Branicki, Abdu Adem (Ed.), Saad Ghazal-Aswad (Ed.), Fawaz Chikh Torab (Ed.), 2008

BTC 521: Genetically Modified (GM) Crops, Biosafety and Intellectual Property Rights 3 credits

The course gives emphasis on global differences in acceptance or lack of it of GM food crops in the backdrop of national culture and history, economic conditions, and government initiatives or responses related to the issue.

Topics include:
- Risk perception related to the precautionary approach, benefits of GMOs, public acceptance, case study: the Monarch Butterfly, StarLinkTM corn
- Introduction to biosafety concept and its risk, transgenesis in plants
- Risk for animal or human health - toxicity and food quality/safety, allergies, pathogen drug resistance (antibiotic resistance)
- 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
- Risk for the environment - persistence 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
- General concerns - loss of familiarity, higher cost of agriculture, field trials not planned for risk assessment, ethical issues (labelling)
- Critical assessment of biosafety rules operating in developing countries and the importance of its strict enforcement to protect the population of the third world countries from harmful effects of indiscriminate introduction of GM products
- Global status of acceptance or lack of it regarding GM food crops
- Critical evaluation of "Golden" rice and its Bangladesh version BRRI Dhan-29 evolved at IRRI by Bangladeshi scientists
- Case studies to examine in-depth the interplay of these factors particularly in the context of the developing world
- Convention on biological diversity (CBD), Cartagena Protocol
- Biosafety regulations to protect nature, growers and consumers interest and national interest, biosafety regulations in Europe, Canada, EU and different countries in the Asia and the Pacific region
- National biosafety guidelines of Bangladesh, biosafety framework, biosafety clearing house
- Public perception and biotechnology
- Intellectual property rights-categories of IP, patents, international legal framework, WTO
- TRIPS-the significance of horizontal provisions in the TRIPS agreement
- Existing TRIPS flexibilities and exceptions: checks and balances
- Indigenous community knowledge and TRIPS
- Importance of IPR for protecting biodiversity and biotech products

Recommended Books
1. Genetically Modified Organisms and Biosafety: A Background Paper for Decision-Makers and Others to Assist in Consideration of GMO Issues, Tomme R. Young, IUCN Policy and Global Change Group, 2004
2. Modern Food Biotechnology, Human Health & Development: An Evidence Based Study, Food Safety Department, World Health Organization, 2005
3. Genetic Engineering in Agriculture and the Environment: Assessing Risk and Benefits, Maurizio G. Paoletti and David Pimentel,
4. Molecular Biotechnology, Principles and Applications of Recombinant DNA, B. R. Glick and Jack J Peterson, 2003
5. Plants, Genes and Crop Biotechnology, Chrispeels, J. Maarten and E. David Sadava, 2003
6. National Biosafety Framework, GoB, 2008
7. Focus on Intellectual Property Rights, US Department of State, Bureau of International Information Programs, http/usinfo.state.gov/
8. Intellectual Property Rights: An Introduction for Scientists and Technologists, M.B.E Faez, 2005

BTC 550 Research Project (Thesis) 6 credits

All students will be required to do a research project of 6 credits during one full semester. The research project can be carried out either at BRACU or at any other university or research institutes under the joint supervision of a BRACU biotech faculty and a recognized professor/biotechnologist of the concerned institution. A student will have the option of choosing her/his potential guide and the problem she/he will undertake in consultation with the Coordinator, Biotechnology Programme of BRACU and the final decision about her/his choice of guide(s) and the topic will rest on the Chairperson of the Department.

 

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