Staff

Course directors
Dr. Noel Murphy, Room 3.19, Biosciences and Electronic Engineering Building, NUI
Maynooth, noel.mu...
Structure of the MSc programme
The programme consists of 12 taught modules, 6 in each semester and a research project,
whi...
Modules
BI 601: Fundamental Immunology
This module will give you a good grounding in the scientific theory underlying mode...
AN 610: Global Health and Development
Module Content: These factors include general levels of wealth within a society, but...
and will follow some prescribed introductory reading. Initial lectures will introduce the basic
tools and concepts of medi...
HM 601: Systems Biology
Module Content: Lectures 1-4 a broad introduces mathematical modelling of biological
systems, espe...
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Course Outline.doc.doc

  1. 1. Staff Course directors Dr. Noel Murphy, Room 3.19, Biosciences and Electronic Engineering Building, NUI Maynooth, noel.murphy@nuim.ie Dr. Derek G. Doherty, Room 2.19, Biosciences and Electronic Engineering Building, NUI Maynooth derek.g.doherty@nuim.ie Lecturers Dr. Wilhelm Huisinga, Hamilton Institute, NUI Maynooth Dr. Catherine Comiskey, Department of Mathematics, NUI Maynooth Dr. Richard Costello, Consultant Physician, Department of Respiratory Medicine, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin Dr. Derek G. Doherty, Institute of Immunology and Department of Biology, NUI Maynooth Dr. Mary Keogan, Consultant Immunologist, Department of Clinical Immunology, Beaumont Hospital, Dublin. Dr. Bernard P. Mahon, Institute of Immunology and Department of Biology, NUI Maynooth Dr. Sinead Miggin, Institute of Immunology and Department of Biology, NUI Maynooth Prof. Paul Moynagh, Institute of Immunology and Department of Biology, NUI Maynooth Dr. Noel Murphy, Institute of Immunology and Department of Biology, NUI Maynooth Mr. Conor O’Dea, GeneMedix plc, Business and Technology Park, Tullamore, Co. Offaly Dr. Shirley O’Dea, Institute of Immunology and Department of Biology, NUI Maynooth Dr. Dennis Pringle, Department of Geography, NUI Maynooth Dr. Jamie Saris, Department of Anthropology, NUI Maynooth Dr. Simon Travers, Molecular Evolution and Bioinformatics Laboratory, Department of Zoology, NUI Galway Administrators Ms. Loretta Jennings, Institute of Immunology administrator Ms. Terry Roche, Biology Department administrator Ms. Jean Burbridge and Ms. Alison Norton, Biology Departmental secretary
  2. 2. Structure of the MSc programme The programme consists of 12 taught modules, 6 in each semester and a research project, which is carried out during the summer months. Examinations for semester 1 modules will take place in January and examinations for semester 2 modules will take place in May. Semester 1 BI 601: Fundamental Immunology MT 601: Epidemiology and the modelling of human disease BI 602: Advanced Immunology BI 603: Molecular Parasitology and Diseases of Poverty BI 604: Bioethics, biopharmaceuticals and clinical trials HM 601: Systems Biology Semester 2 AN 610: Global Health and Development BI 605: Clinical Immunology BI 606: Applied and Molecular Immunology GY626: Medical Geography BI 607: Introduction to Bioinformatics BI 608: Vaccines and adjuvants Summer project BI 609: Immunology Masters Research Project
  3. 3. Modules BI 601: Fundamental Immunology This module will give you a good grounding in the scientific theory underlying modern immunology. Topics studied will include a 3-lecture survey/overview of the topic before 13 lectures covering innate immunology, B cell biology, the structure and function of antibody and how diversity is generated. Cell mediated immunology will be examined, contrasting T cell recognition with B cell recognition of antigen. T cell effector and regulatory functions and cytokine production will be discussed in detail, following an in depth examination of the major histocompatibility complex structure, organisation and function. Lecture material will be supported by tutorials and an essay assignment. Students will undertake 9 hours of practical work to introduce basic techniques in immunology. Course structure: 16 lecture hours, 9 hours practicals and 4 hours of workshops/tutorials with an essay assignment. MT 601: Epidemiology and the modelling of human disease Topics covered include: History of epidemic modelling, components of the modelling process, study design including case control, cross sectional, cohort and experimental studies. Analysing, solving and interpreting simple Susceptible, Infectious and Recovered (SIR) models using differential equations, applications to childhood diseases. The latent period and SLIR models. Models for diseases with no immunity, SIS models. Host-vector models with applications to malaria and models of sexually transmitted diseases including HIV/AIDS. Estimating epidemiological parameters and vaccination rates using serological and survey data. Throughout the course emphasis will be placed on the implications of the models and their results for policy and planning in the health services. Teaching Methods: 20 lecture hours and 4 hours of workshops/tutorials with class assignments. BI 602: Advanced Immunology This module will provide you with a detailed understanding of mechanisms of the immune system. It will include advance treatment of the structure, function and genetics of the molecules involved in immune recognition, including immunoglobulins, the T cell antigen receptor, major histocompatibility complex molecules, and the natural killer cell receptors. The molecules and pathways that mediate immune effector functions, including signalling pathways, messenger and effector molecules will also be covered. This information will then be applied to cover the mechanisms by which the body maintains immunity against infection and tumours, focusing on general inflammation and specific adaptive immunity against viruses, bacteria, fungi, parasites and tumours. Specialised immune mechanisms at mucosal surfaces and the mechanisms by which the immune system is regulated to avoid tissue damage will also be covered. Finally a survey of comparative immune responses in vertebrates will be undertaken. Course structure: 16 lecture hours, literature review, 4 problem-based tutorials, prescribed reading
  4. 4. AN 610: Global Health and Development Module Content: These factors include general levels of wealth within a society, but also inequalities within and between societies, the surprisingly variegated tapestry of international aid, as well as the decisions of specific individuals. The concatenation of these factors is not trivial. They determine, for example, whether infection with HIV will be similar to living with diabetes (as it is in much of the so-called First World) or be effectively a death sentence (as it is nearly everywhere else). They produce both diseases of scarcity and of excesses, increasingly within the same polity. As part of this assessment for this course, the student will develop a case study of a specific disease with the aim of tracing the connections between individual responses to infectious exposure and the social, cultural and political contexts in which this occurs. Main Text: Farmer, Paul (2003) Infections and Inequalities. Berkeley: University of California. A selection of articles and book chapters will also be read as supplements to this text. Course structure: 16 lectures, 6 Tutorials BI 603: Molecular Parasitology and Diseases of Poverty The taught component of the module will begin with an introduction to protozoan parasites, namely Plasmodium species that cause malaria, African trypanosomes, South American trypanosomes and Leishmania species. The parasite-host interface will be covered in detail focusing on the mechanisms by which protozoan parasites establish and maintain infection and cause disease. Topics will include molecular mechanisms of antigenic variation and immune modulation by protozoan parasite, host responses and host resistance mechanisms both innate and acquired. The application of parasite and host genomics to develop vaccines and other control options for these diseases will be covered. The course will also examine emerging and re-emerging infectious diseases of poverty, climate change and global travel to include HIV, TB, Dengue and West Nile Virus. Finally the interaction between nutritional status and disease susceptibility will be explored. Lecture material will be supplemented by dedicated tutorials that will be in the form of a journal club and a presentation assignment where students research and present on an assigned topic. Students will undertake a 3 hour practical to expose them to methods for parasite identification and disease diagnosis. Course structure: 18 lecture hours, 3 hours practical and 4 hours workshops/tutorials with a presentation assignment BI 604: Bioethics, biopharmaceuticals and clinical trials Lecture topics will include: bioethics in relation to scientific research and drug development; a survey of the biopharmaceutical development processes; the production of generic biopharmaceuticals; the regulatory issues facing the introduction of pharmaceuticals; the design and management of clinical trials. The module will also involve a site visit to a biopharmaceutical company, based in Ireland and an associated report on the processes observed. Workshops on clinical trials and regulatory affairs will support the lecture material and involve written assignments. Course structure: 16 lectures, 5 workshops, 1 site visit GY626: Medical Geography This module will have considerable overlap with medical Geography (GY326) but MSc students will take an alternative 4-lecture introduction to basic concepts in medical geography
  5. 5. and will follow some prescribed introductory reading. Initial lectures will introduce the basic tools and concepts of medical geography, before examining the topic in detail. The module will explore: The impact of social and ecological change upon the evolution of human disease. The role of disease as an influence upon societal change. The demographic and epidemiological transitions. Debates regarding the causes of the epidemiological transition. The evolution of modern medicine. Medical advances and improvements in life expectancy in the twentieth century. Re-emerging infectious diseases. Health in the Developing World. New infectious diseases and their potential implications for the developed world. Course structure: 24 lectures, 1 Tutorial BI 605: Clinical Immunology Module Content: Introduction to immunopathology and mechanisms of tissue injury. Diagnostic techniques. Normal defences against infection. Primary and secondary immunodeficiency with emphasis on how understanding of primary immunodeficiencies contributes to our understanding of the human immune system. Allergy. Mechanisms of autoimmunity. Organ-specific autoimmune disease. Non-organ specific autoimmune disease. Leukaemias and lymphomas. Abnormal immunoglobulins. Paraneoplastic syndromes. Infection related immunopathology. Haemopoietic stem cell transplantation. Solid organ transplantation. Active and passive immunisation. Therapeutic use of immunoglobulins and monoclonal antibodies. Immunosuppression. Evolving areas in clinical practice. Continuous assessment will based on two literature based case studies. Course structure: 16 lectures, 1 site visit, 2 case studies (literature based) BI 606: Applied and Molecular Immunology Module Content: The course will focus on the high-end immunology technologies, beginning with an introduction to modern molecular techniques. Through a series of lectures students will learn about the creation of transgenic animals, the Cre-lox system, knock-out mice, knock-in mice and tissue specific expression. Students will also discover modern imaging tools such as confocal, & epi-fluorescent microscopy, as well as the power of flow cytometry. Finally a series of lectures will introduce practical aspects of probing cell signal transduction pathways. The course will be supported by practical demonstrations for MSc students of time-lapse microscopy, confocal microscopy, and other technologies. In addition students will undertake a 4-hour problem based workshop on flow cytometry covering topics such as compensation, controls and data interpretation. Course structure: 16 lecture hours, 8 demonstration hours, 4 hours practical workshop on Flow cytometry BI 607: Introduction to Bioinformatics Module Content: The course will provide a practical approach to familiarise students with a number of bioinformatic approaches through lectures and workshops. In addition students will be given an introduction to the principals behind database queries, structure, tree construction etc. Lectures will be supported by tutorials with specific assignments designed to reinforce lecture material. Course structure: 12 lectures and 3 (x 3 hour) workshops
  6. 6. HM 601: Systems Biology Module Content: Lectures 1-4 a broad introduces mathematical modelling of biological systems, especially of biochemical reactions. Lectures 5-8 discuss models of gene regulatory systems. Lectures 9-14 present modelling approaches of signal transduction networks. Finally, lectures 15 & 16 discuss whole cell and higher-level models. Each topic is supplemented by computer laboratory exercises. Course structure: 16 lectures, 8 h computer based laboratory exercise BI 608: Vaccines and adjuvants This course will examine adjuvant use (3 lectures), building on concepts delivered in modules covering innate immunology. One lecture will survey the use of vaccines in a historical context (Jenner and prior to 1890) and in traditional folk medicines from around the work. The bulk of the course will survey the rational design of vaccines. This will begin with the history of poliovaccines (2 lectures) comparing the Salk v Sabin vaccines, the lesser known failed vaccines of the 1930s and the Cutter incident. The course will then survey all vaccines in common use and examine the particular challenges of protecting the neonate in the developing world. Finally the course (4 lectures) will examine the prospects for novel vaccines against the three major infectious diseases of poverty (TB, HIV malaria). Students will be expected to perform considerable reading of current literature in vaccinology and prepare a dissertation on a vaccination challenge specific to a resource poor region. Course structure: 16 lectures, 4 tutorials, 1 dissertation, prescribed extra reading BI 609: Immunology Masters Research Project Students undertake a 16-week research project under the guidance of a supervisor. Students may be provided with a reading list but are expected to perform a literature search to familiarise themselves with the topic assigned. Over the period of the project students must become competent in the techniques and equipment relevant to the project. Students will also contribute to the academic programme of their laboratory by attending regular seminars and laboratory meetings. All students provide a poster and 15-minute oral presentation of their research findings, as part of a day long showcase of the Masters students work. On completion of the project students must submit a minor thesis outlining their research. Course structure: 16-week full time research project (supervised) between June and September. A Masters research showcase day. Students may be based in NUIM or in the laboratory of an associated institute.

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