Research Methodology in Biotechnology
This course is dedicated to teaching students basic research methodologies, as applied to the biological sciences, based on a solid theoretical framework and an educationally sound learning procedure. Students will be provided with practical suggestions on various aspects of the research process to guide them from problem selection to writing a completed research report. Major topics covered in this course include recognizing good research, tools of research, selecting research problems, literature search, planning research design, design and execution of experiments, reporting research results and communicating information. Students will also learn the approaches for collecting and analyzing experimental data as well as the statistical techniques for analyzing quantitative data. Application of the principles learned in this course will be immediately applied to the students' own research projects, as each student will be required to write a research proposal for the project of their choice.
The goal of this course is to develop the students’ skills in communicating their ideas to other researchers and scientific peers. Students will be presented with effective strategies for improving their written and verbal communication skills. The course focuses on practicing scientific writing, giving oral presentations and evaluating research publications. Students will hone their expertise on the effective communication of research results in the form of written publications, oral presentations, PowerPoint presentations and scientific posters. At the end of the course, the students will give presentations of research topics that they select under the guidance of their instructor. The students must also write up their oral presentations in the form of a scientific paper.
Current Concepts and Techniques in Biotechnology
This Course Provides a general introduction to the field of biotechnology that will help the students develop a broad understanding of the scientific, political, ethical and legal issues that have driven the development of the biotechnology industry. Discussion Focuses primarily on the research trends and methodologies currently exploited within the field along with the impact of these endeavors in the areas of industry, agriculture, health and environment. Students will also be introduced to the ethical issues surrounding contemporary bio-techniques, such as genetic testing, cloning and stem cells research, which help shape policy regarding different applications of biotechnology.
This Course focuses on providing the student with a thorough theoretical and practical exposure to current biochemical techniques as applied to the isolation, purification, a characterization of major classes of biologically important compounds. Topics covered include, biochemical calculations, quantification of protein concentration, spectrophotometry of biomolecules, enzymatic methods of analysis, overview of protein overview of protein purification, separation and identification of biomolecules by chromatography, characterization of biomolecules by electrophoretic methods, radioisotopes in biochemistry and centrifugation. The practical part provides students with hands-on experience in the following techniques and instruments spectrophotometry, chromatography, electrophoresis, electrochemical techniques, centrifugation, filtration, protein blotting, TLC, HPLC, GC, flame emission and atomic absorption spectroscopy.
Cell Biology and Genetics
The course provides the fundamentals of structural and functional organization of prokaryotic and eukaryotic cells, the relationship between the different organelles and their function. The course covers cell cycle, replication, the genetic makeup of chromosomes, genes, and transferable genetic elements and their essential role in heredity. Students will gain knowledge on the causes of gene dysfunction due to mutations, chromosomal aberrations, chromosomal disjunction and DNA repair mechanisms. In addition, the course covers the basis of Mendelian and extranuclear inheritance, molecular and biochemical basis of heredity and population genetics.
Techniques in Molecular Biology
This course is designed to give students experience in recombinant DNA techniques and introduce them to principles and research methodologies of modem molecular biology. Techniques include: genomic DNA and plasmid isolation, restriction analysis, DNA fragments ligation, DNA labeling, and DNA electrophoresis; bacteria transformation, cloning, screening for clones and DNA sequencing; Southern and northern Blot hybridization; polymerase chain reactions (PCR), primer design, RT-PCR and microarray technology as well as DNA analysis in forensic science.
The course provides the latest techniques used in information technology to access huge databases from different organisms containing DNA, RNA and protein sequences. The students will learn how to retrieve these data from public and private data banks and identify key information regarding nucleic acids and proteins. The course provides students with hands on experience using special software to execute reverse genetics by looking for DNA open reading frames, conserved sequences, sequence homology analysis, pair-wise and multiple sequence alignment, construction of DNA- & protein-based phylogenic relationship, design primers for research and perform restriction analysis. The course emphasizes the integration of basic and applied knowledge on genome projects in particular, human gene mapping, molecular cloning, large-scale restriction mapping, DNA sequencing and computational analysis, and 3-dimensional structures of potential genes.
LSC EB 630
This course provides the students with fundamental understanding of the effect of microbial communities on the environment, particularly their role in soil, water and waste management. Students will be introduced to the important microbes involved in environmental microbiology and the nature of the different environments in which the microbes are situated and methodologies used to monitor the microbes and their activities. Students will also evaluate the effects of these microbes on the environment and on human activities including, the role of microorganisms in pollutant degradation, waste treatment and geochemical cycling.
Environmental Pollution and Ecotoxicology
LSC EB 631
The aim of this course is to provide background knowledge so that the short- and long term effects of chemical pollution can be evaluated and the risks understood. The course introduces the major classes of organic and inorganic pollutants, their entry into the environment and their movement, storage and transformation within the environment. The effects of pollutants at the level of population, community and whole ecosystems will also be studied. Topics covered in this course include, major classes of environmental pollutants, fate of pollutants in ecosystems, biomarkers and biomonitoring, measuring the impact of pollutants on ecological systems and environmental risk assessment.
Biotransformation of Pollutant Xenobiotics
LSC EB 632
Microorganisms inhabiting polluted environments have gained amazing catabolic potentialities to transform a wide range of xenobiotics. Therefore, this course addresses microbial-mediated biotransformations of xenobiotics and explores the diversity of metabolic pathways involved in their degradation. The main classes of xenobiotics such as halogenated compounds, mono- and polyaromatics, heterocyclic compounds, pesticides, surfactants, plastic polymers, and some petrochemical compounds, their nature, structure and physicochemical properties will be discussed. Peripheral metabolic pathways linking the transformation of xenobiotics to central metabolites and the key enzymes will be addressed. Energy gain under oxic-anoxic conditions coupled to the biodegradation of different xenobiotic classes will be studied. The fundamentals and principles regulating the biodegradation rates and the biodegradability of these compounds as well as the concepts of co-metabolism, co-oxidation, synergism, antagonism, substrate toxicity, threshold concentration, diauxic growth and carbon catabolite repression will be highlighted.
Molecular Basis of Xenobiotics Biodegradation
LSC EB 633
The process of natural selection of microorganisms inhabiting polluted ecosystems via adaptation, mutation, genetic recombination and acquisition of mobile genetic elements has resulted in a tremendous capacity to metabolize xenobiotics. Many genes encoding catabolic pathways for xenobiotics are plasmid-borne although other are encoded on chromosomes. This course aims to provide a comprehensive knowledge about the catabolic operons, gene organization, gene duplication, functional analysis, regulation and expression of these genes under different environmental conditions. The stability as well as the transfer of catabolic plasmids between different bacterial species will be addressed. The course will focus on the catabolic genes involved in the upper metabolic pathways converting xenobiotics to central metabolites as well as on the catabolic genes of aromatic ring cleavage. The catabolic operons encoding the biodegradation of haloaromatics, polyaromatics, PTEX, NOS-heterocyclic and benzoic acid as well as the catabolon encoding various catabolic pathways leading to phenyl-acetyl-CoA will be studied.
LSC EB 634
This course aims to provide survey knowledge of the theory and practices of different remediation technologies involved in treating polluted ecosystem. The various bioremediation technologies actively used in treating contaminated soils and water bodies in situ and ex situ, which represent the core of the course, will be treated in details. The applicability and the criteria determining the selection of the bioremediation technique as well as the factors enhancing or suppressing the process will be addressed. Methods involved in monitoring and evaluating the efficiency of the applied technique will be discussed. Cases of successful bioremediation techniques will be presented which will introduce the students to the feasibility of application and highlight the potentiality of bioremediation as a safe and cost efficient technique for eradication or detoxification of hazardous pollutants in the environment.
Biocatalysis and Biosensors
LSC EB 635
This course gives insight on the feasibility of using enzymes, biological products or a whole genetically engineered microorganisms in various biotechnological applications to develop biologically-based devices for quantitative, qualitative and diagnostic assays for many molecules that have industrial importance or that threat the health and the environment. The course will address the specificity and the efficiency of enzymes catalyzing a wide array of chemical reactions and introduces the different techniques used to produce a biocatalyst with elevated catalytic potentiality and broader specificity and detection limits. Emphasis will be given for protein immobilization technology. The course aim is also to introduce the students to the concept of biosensors. It will present the molecular biology approaches used to design a biosensor such as hybrid or fused proteins or bioluminescent reporter microorganisms used to monitor environmental pollution. The course will also cover the use of biological and physical processes of signal transduction in the manufacture of a bio-device of medical importance such as the one used for the detection of diabetes or cholesterol.
Recombinant DNA in Environmental Biotechnology
LSC EB 636
Recombinant DNA technologies have opened up new and promising possibilities in a wide range of applications and can be expected to bring considerable benefits to humankind and to restore healthy environment. This course will focus on important applications of recombinant DNA technology in the environmental sector to prepare genetically engineered organisms with improved traits. The course will introduce the students to various applications of recombinant DNA such as in treatment of environmental pollution, the construction of reporter organisms to trace hazardous toxic chemicals and for risk assessment, to expand substrate profile of early enzymes of catabolic pathways. The course will also cover the following:
1- The global cycling of bio elements
2- The bio mining and bioleaching of metals from metal ores as well
3- The study of soil community structure and microbial activity, for production of bio fertilizers, bio pesticides, biopolymers and biosurfactants
4- The improvement of air quality via desulfurization of fuels and treatment of waste water.
5- The dangers of creating genetically modified organisms and safety considerations and guidelines for environmental applications of organisms derived by recombinant DNA technology.
LSC EB 637
The course starts with an overview that covers topics like definition, origin, and composition of petroleum, the common practices in petroleum refining and processing, environmental impact of the extensive use of petroleum products and their hazardous effect on the human health. This is followed by discussing the various aspects of the petroleum industry in which biotechnology can be implemented. Then the various groups of microorganisms that can be found in oil reservoirs and their origin are described. The course focuses on sulfate reducing bacteria, the problems they cause in the petroleum industry, as well as their control strategies through biotechnology. Another important aspect of petroleum microbiology, microbial enhanced oil recovery, will be also discussed. The following parts of the course are dedicated to the emerging applications of biotechnology in the petroleum industry such as the use of biocatalysts in petroleum refining, up-grading, and biocatalysis on petroleum products. Eventually, the potential applications of bacterial biosensors in the petroleum industry, and the biodegradation of petroleum components are highlighted.
LSC EB 638
This course explores the exploitation of the enormous but uncharted functional diversity of marine organisms towards finding new genes organisms, biosensors, natural products and unusual biochemical processes of importance to industry, nutrition, medicine and the environment. Students will examine the recent progress in the discovery of novel products from marine organisms, the role of marine microbes in bioremediation, genomics of marine organisms, sustainable aquaculture, development of new methods for the production of marine organisms as well as the use of biosensors for the assessment of environmental quality and management of marine environments.
Selected Topics in Environmental Biotechnology
LSC EB 649
The course deals with topics of increasing concern in environmental biotechnology and that are related to ongoing research in the biotechnology program. The student will write a comprehensive literature review about one of those topics and make a presentation. Eventually, the student will define the important research questions that can be addressed with our current facilities and write a proposal including the plan for his/her MSc work during the second year. The knowledge to be acquired depends on the topic.