MB3001 Medical Microbiology (5 credits; Teaching Period 2A) MB3006 Genetic Engineering and Molecular Biotechnology

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1 MICROBIOLOGY Spring Semester 2013/2014 academic year Timetables can be accessed at Click on Microbiology For information on building codes click on: Spring Semester/Teaching Period 2 Modules MB3001 Medical Microbiology MB3006 Genetic Engineering and Molecular Biotechnology MB3008 Immunology: Host Response to Pathogens MB3017 Environmental Systems Microbiology: Themes in microbe-host interactions MB4007 Advanced Medical Microbiology MB4008 Advanced Virology MB4013 Food Biotechnology MB4020 Environmental Microbial Genomics II: understanding and exploiting microbial communities MB4022 Microbial Diversity and Ecology MOLECULAR BIOLOGY Spring Semester/Teaching Period 2 Modules ML2001 Introductory Molecular Biology (5 credits; Teaching Period 2) MICROBIOLOGY University College Cork has built an international reputation in the excellence of its teaching and research programmes in Microbiology, and this is reflected in the caliber of its graduates and the success of the department in obtaining competitive research funding from National and International sources. 1

2 The Department of Microbiology is located in the Food Science and Technology Building and the BioSciences Institute. Please note that: Each Teaching Period is divided into two six-week teaching blocks. Teaching Period 2 Period 2A runs from Monday, January 6 th to Friday, February 14 th. Period 2B runs from Monday, February 17 th to Friday, March 28 th. Spring Semester/ Teaching Period 2 Modules Period 2A (Monday, 6 th January Friday, 14 th February) MB3001 Medical Microbiology (5 credits, Teaching Period 2A) This module introduces the concept of virulence and virulence factors using case studies. The content relates to body defences, virulence factors (adhesions, toxins, evasion strategies). Infection and disease; characteristics of pathogens; mechanisms of pathogenicity/toxigenicity, case studies. (Dr David Clarke). Describe the principal host defenses against infection Explain virulence strategies associated with pathogenic bacteria Describe the mechanism of action of bacterial exotoxins List and describe the principal pathogens associated with human bacterial infections Assessment: Total Marks 100: End of Year Written Examination 90 marks; Continuous Assessment 10 marks (Laboratory Work; Notebooks). MB3006 Genetic Engineering and Molecular Biotechnology This module aims to provide detailed information on genetic engineering and its impact on modern molecular biotechnology, microbial enzymes of industrial significance and provide an overview of the use of molecular biotechnology to engineering cell factories for production of biomolecules. The content includes: physiology and genetics of bacterial and fungal enzymes with industrial application such as proteases, lipases, amylases and cellulases. Modification of enzyme properties using protein engineering. Novel applications 2

3 including biopulping/biobleaching, bioremediation and biocatalysis. Manipulation of gene expression and heterologous production of proteins in: prokaryotes, yeasts, insect cells, mammalian cells and plants. Comparison of different expression systems [Expression vectors, fusion proteins, markers, selection, purification, rationale for one system over another]. Diagnostic biotechnology, production of recombinant vaccines and monoclonal antibodies, production of transgenic animals. (Dr John Morgan; Dr Max Dow). Write an account of molecular diagnostics, vaccine and monoclonal antibody production, transgenic and stem cell technologies Describe and explain in detail the molecular technology used to express proteins in prokaryotic and eukaryotic systems Compare and contrast different expression systems for the heterologous expression of therapeutic proteins Compare and contrast key molecular approaches to protein engineering Describe and discuss the construction and use of genetically engineered microorganisms in a number of environmental biotechnology applications MB4008 Advanced Virology This module aims to provide a comprehensive account of current knowledge and research in virology. The content includes: Systems virology molecular cross-talk between viruses and cells in the context of cellular transformation, apoptosis and innate immunity; consequences in terms of virus pathogenesis, persistent virus infections, and cancer. Advances in viral vaccines and antiviral drug development. Reverse genetics and virus manipulation; viruses as vectors for gene delivery/gene therapy. Emerging virus infections. (Dr Martina Scallan). Detail the molecular mechanisms underlying virus-induced cellular transformation and apoptosis, using specific virus examples Summarise innate antiviral immune responses Describe viral strategies to counteract /evade innate antiviral responses Compose an account of the epidemiology and underlying molecular mechanisms of virus associated human cancers Give an account of emerging/re-emerging virus infections currently of particular clinical 3

4 and/or veterinary concern worldwide Discuss the application of reverse genetics to the engineering of viruses for gene delivery/gene therapy Overview the current availability and development of antiviral drugs and vaccines worldwide Recount and reference current research in virology pertinent to each of the preceding learning outcomes (techniques and scientific papers) MB4013 Food Biotechnology This module aims to examine the role of molecular biotechnology in the food industry. The content includes: Molecular biology methodology; genetically modified foods; molecular methods of identifying foodborne micro-organisms; case studies in food biotechnology e.g. recombinant chymosin, control of bacteriophage, bacteriocins, metabolic engineering. (Professor Colin Hill). Describe the legislation governing GM foods in Europe Explain the molecular technologies underpinning GM foods Discuss the benefits and risks associated with GM technology MB4020 Environmental Microbial Genomics II: understanding and exploiting microbial communities This module aims to provide an understanding of the metagenomic technologies that are used to study and exploit microbial diversity; to learn how microbial communities can be exploited for drug and product discovery and to explain how genomic technologies can be used to determine the functioning complex dynamic microbial communities. The content includes: Technologies to study entire microbial communities ( meta-omics ) Metagenomics - construction and screening of metagenomics libraries, applications in discovery of drugs and novel microbial products. Metagenomic approaches to study community function - sequencing and genomic reconstruction, study of microbial function in 4

5 simple and complex, dynamic communities. Metaproteomic and metabonomic approaches to study community function. Applying genomics to study the role of microbes in geochemical cycles and processes. (Dr Max Dow). On successful completion of this module students should be able to: Explain the importance of meta-analysis of microbial communities Describe the methods that are used to study and exploit microbial diversity Integrate methodology and application to describe how metagenomics can yield new drugs and products Describe how total community analysis enables the understanding of integrated functioning of complex microbial systems Students departing from UCC at the end of Teaching Period 1 should check with the International Education Office regarding an assessment for this module. Spring Semester/ Teaching Period 2 Modules Period 2B (Monday, 17 th February Friday, 28 th March) MB3008 Immunology: Host Response to Pathogens This module aims to provide detailed information on the building blocks of the immune system, to present relevant new discoveries that help us better understand the complex working of our immune system. The content includes: an overview of the immune system. Cells (Th-cells, Tc-cells, NK-cells, B- cells, monocyes, neutrophils, granulocytes). Lymphoid organs (bone marrow, thymus, lymph nodes, spleen, Peyer's patches). Cell migration and chemotaxis. Innate immunity, Toll-like Receptors. Antibody structure, function, diversity and mode of action. T-Cell Receptor, MHC and antigen recognition, processing and presentation. Immunological tolerance. Immunity to viruses. Immunity to bacteria and fungi. Tumour immunology. Hypersensitivity Type I, II, III, IV, Immunodeficiencies. Transplantation and rejection. (Dr John Morgan). Outline in detail the innate and adaptive immune system and give examples of different aspects of the systems Identify ongoing developments and challenges in the study of the immune system 5

6 Discuss the importance of host surveillance/pathogen recognition and recall memory in a functioning immune system MB3017 Environmental Systems Microbiology: Themes in microbe-host interactions This module aims to provide a comprehensive overview of the types and importance of interspecies and inter-kingdom interactions involving microbes and to explore common molecule principles and mechanisms that underpin microbe host interactions. The content includes: Pathogenic and beneficial interactions between microbes (bacteria and fungi) and plants, microbes and animal hosts and within microbial communities. Role of endosymbiotic bacteria of fungi, plants and insects. Mechanisms of interaction between microbes and hosts: signals and nutrients. Important role of secretion systems, host recognition systems and signal transduction pathways. Case studies. (Dr David Clarke). describe in detail specific examples of different types of microbe-host interaction discuss, in detail, the mechanisms employed by microbes to monitor their environments identify and explain common molecular themes that underpin microbial interactions with diverse hosts MB4007 Advanced Medical Microbiology This module aims to provide comprehensive information on microbial disease in the context of specific body tracts and systems and to provide an overview of the molecular mechanisms of microbial pathogenesis. Microbial infection of the gastrointestinal tract; infections of the respiratory tract; infections of the central nervous system; emerging diseases; disease in the immunocompromised host; mechanisms of microbial pathogenesis; methodologies for the analysis of microbial pathogenesis. (Professor Michael Prentice; Dr Cormac Gahan). Illustrate with examples how molecular analysis informs us about pathways of disease 6

7 causation by microorganisms List the major infectious diseases and infecting agents causing mortality and morbidity in modern society Describe in detail the molecular mechanisms of infection for exemplar individual pathogens MB4022 Microbial Diversity and Ecology This module aims to develop students' knowledge of microbial diversity and evolutionary relationships between functionally similar microbes to use this information and relate it to the ecology of microbes and how we investigate their role in ecosystem function and maintenance. The content includes: Methodology of studying evolution of living organisms, present concepts of the evolution of major groups of bacteria and their current taxonomic characterization. Role of micro-organisms in the biosphere; significance of ecology; advantages and limitation of nucleic acid biomarkers to study microbial diversity; in situ study of function in microbial communities; community level physiology profiling; use of molecular biology techniques to study interactions of micro-organisms with each other and with their environment. (Dr David Clarke). Explain and appreciate the large microbial diversity on earth and the evolutionary relationships between microbes Describe the methods used by microbiologists to classify microbes into their respective phylogenetic groups Describe how microbiologists can determine the microbial diversity in an ecosystem and the ecological relevance of this diversity Explain how microbiologist can link function with identity 7

8 MOLECULAR BIOLOGY Spring Semester/Teaching Period 2 Modules ML2001 Introductory Molecular Biology (5 credits; Teaching Period 2) Genes and Genomes. DNA replication, DNA repair, RNA transcription and processing. Genetic code, and protein synthesis. Gene regulation, lac operon. Gene cloning, the tools and strategies. Polymerase chain reaction (PCR) and its applications. (Professor Douwe Van Sinderen). Compare and contrast the structure of the nucleic acids, DNA and RNA and prokaryotic and eukaryotic genes Describe the molecular mechanisms of replication, transcription, translation Describe the different types of post-transcriptional and post-translational modifications Describe the causes and nature of DNA mutations, the pathways used to repair DNA damage, and the consequences of failing to repair DNA damage Describe the structure of an operon and how its expression can be regulated Identify gene regulation and understand a number of different mechanisms of regulation Identify and understand some Molecular Biological technologies, e.g. PCR, cloning, Southern blotting Demonstrate competence in performing basic Molecular Biology and Microbiology techniques and understanding their basis and application Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Laboratory Work 10 marks; MCQ 30 marks). 8

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