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Welcome to the level II course ‘Microbes, Infection and Immunity’ BI25M5. The course aims to introduce students to the diversity and countless activities of microbes (bacteria, fungi, algae, protozoa and viruses) and the techniques used to study them. The course also describes the role of microbes in disease, including a comprehensive review of immunology and how the immune system functions in combating infection. The course is delivered through a combination of lectures, homework assignments and practical classes. Additionally, throughout the course you will be able to test your knowledge and understanding of material covered during lectures, by completing online multiple-choice questions.
This manual contains all the information relevant for the course. It is an essential source of reference and you are expected to familiarise yourself thoroughly with its content. Remember – what you do not know you can find out by asking a lecturer, consulting books in the library or by ‘surfing’ the World Wide Web.
Completing this course will equip you with the necessary knowledge and skills to study advanced level courses in biology and related disciplines. The teaching team hope that you enjoy the course and are happy to answer student queries at any stage in the course.
Good Luck
Dr Frank Ward, BI25M5 Course Co-ordinator, School of Medicine, Institute of Medical Sciences, Foresterhill, Aberdeen. E-mail: f.j.ward@abdn.ac.uk or telephone: 01224 555862.
The aims of the course are to enable students:
(a) To introduce students to the full range of microbial life and the techniques used to study microorganisms.
(b) To introduce the diversity of microbial life (including metabolic diversity, morphological diversity and ecological diversity).
(c) To illustrate the important role of microbes in the environment and in industry.
(d) To explore pathogenic microbes, their interaction with the body and their immune system responses.
(e) To develop student’s basic microbiology laboratory skills.
The knowledge subject-specific learning outcomes are such that, at the end of the course, students should be able to:
• Appreciate the activities for good or ill of microbes in the living world.
• Explain the concept of prokaryotic and eukaryotic cells, using bacteria and yeast cells for examples.
• Understand the physiological requirements for microbial growth and cultivation.
• Describe the different nutritional classes of microorganisms to illustrate microbial diversity.
• Describe the basic biology of selected eukaryotic microbes.
• Understand the essential role of microbes in the environment and food industry.
• Describe the structure and replication of viruses.
• Explain the immune system, focusing on the body's response to invading microorganisms.
The ability subject-specific learning outcomes are such that, at the end of the course, students should be able to:
• Perform a variety of basic microbiological techniques.
• Record, analyse and interpret experimental data.
• Demonstrate an awareness of safety issues pertinent to working in a biology laboratory.
During the course you will also develop skills in data interpretation, communication as well as interpersonal and team-working skills. These represent ‘transferable skills’ that will benefit students across a range of disciplines. Graduate employers welcome ‘transferable skills’ acquired during a degree programme, skills such as communication, numeracy, use of IT, group work and time management. It is important that you keep a record of experiences that contribute to your skills and knowledge.
The aims of the course will be achieved through a combination of lectures, homework assignments laboratory classes and formative online multiple-choice question exercises.
Subject: Introduction to Microbiology & Immunology
No. of lectures: 1
Lecturer: Dr Frank Ward
The introductory lecture will answer the following questions: What does BI25M5 cover? How is the course taught? Which textbook does the course use? How many practical classes are associated with course? What are the formative and summative assessments for the course? What are the essential requirements to pass the course?
Subject: Biology of Bacteria
No. of lectures: 4
Lecturer: Dr Gail Ferguson
These lectures will describe the basic biology of bacterial cells and will in particular concentrate on those structural elements that are specific to pathogenic bacteria. The topics covered will include: Cell walls: peptidoglycan, teichoic acid, Gram stain action of penicillin; cell membranes: structure, roles in transport and energy transduction; Gram-negative outer membrane; Special bacterial structures: spores, and heterocysts; Motility: flagella and chemotaxis; Bacterial growth and environmental diversity.
Subject : Microbial Growth
No. of lectures: 2
Lecturer: Dr Ian Stansfield
These lectures will explore the way bacteria and other microorganisms grow and divide in response to different environmental conditions, as well as solutions to the problem of how to reliably estimate bacterial numbers. The importance of these issues to medical microbiology, and more broadly to microbiology will be considered.
Subjects to be covered; exponential growth and binary fission; the batch growth cycle; the specific growth rate measurement; the effect of environment on growth; growth of microbial pathogens in the human body.
Subject: Biology of Eukaryotic Microorganisms
No. of lectures: 4
Lecturer: Dr Pieter van West
Comparison of prokayotic and eukaryotic microorganisms. Classification of and evolutionary relationship between eukaryotic microorganisms. Organelles that are specific for Eukaryotic microbes. General overview of the different groups (algae, protists, fungi, and Stramenopila). Some species that are medically or economically important will be discussed in detail.
Subject: Microbial Diversity
No. of lectures: 3
Lecturer: Dr Gail Ferguson
These lectures aim to give a general overview of microbial diversity and phylogeny.
Lecture 1: The diversity of different proteobacteria will be covered including bioluminescent, human pathogens, predators, stalked and “multi-cellular” bacterial species. Lecture 2: The diversity of other bacterial phyla will be explored including wall-less, human pathogens and highly ionizing radiation resistant bacterial species. The diversity of the different archael phyla will then be covered including hyperthermophiles, halophiles and methanogens. Lecture 3: This lecture will focus on enrichment culture techniques to isolate microorganisms from the environment and will then give an overview of how we can investigate unculturable microorganisms using FISH and metagenomic approaches.
Subject: Gene Expression & Pathogenesis
No. of lectures: 3
Lecturer: Professor Maggie Smith
These lectures will provide an overview of the molecular biology of medically important organisms and their role in pathogenesis. Microbial molecular control mechanisms, including gene expression & regulation and biochemical signalling pathways will be explored.
Subject: Microbiology of Food-borne Pathogens
No. of lectures: 3
Lecturer: Dr Iain Ogden
Introduction outlining key pathogens (e.g. Salmonella, Campylobacter, VTEC, listeria and others) discussing their reservoirs, routes of infection, symptoms and treatment of disease. Phenotypic and genotypic methods of detection and ways to reduce incidences of human infection.
Subject: Environmental Microbiology
No. of lectures: 4
Lecturer: Dr Debbie McLaggan
These lectures will examine standard methods of wastewater treatment and purification and a variety of waterborne microbial diseases. Procedures to monitor and assess water to ensure clean water for public health will be examined. The role of microbes in the biogeochemical cycling of nitrogen and sulphur will also be covered.
Subject: Medical Microbiology
No. of lectures: 3
Lecturer: Dr Phil Cash
Basic concepts of infection: epidemiology, hygiene, sterilization and disinfection. Principles of diagnosis of infectious disease. The spectrum of tissue damage from commensalism to obligate parasitism. Microbial virulence factors exemplified for specific infectious diseases.
Subject: Introduction to the Immune System
No. of lectures: 1
Lecturer: Professor Janet Liversidge
This lecture will revise the cells of the immune system and the primary and secondary immune organs, and develop the concepts of immune surveillance, leukocyte recirculation, and leukocyte recruitment during inflammation. Introduce innate versus adaptive immune responses.
Subject: The Innate Immune System
No. of lectures: 2
Lecturer: Dr Simon Wong
These lectures will describe the “first line of defence” against infection. I) Phagocytes that ingest and kill microbes, induction of inflammation via cytokines, complement and acute phase proteins. Role of Mast cells and eosinophils in combating parasites and natural killer cells in detecting virally infected cells. 2) Macrophage expression of receptors involved in non-self recognition: pattern recognition receptors, mannose receptor, Toll-like receptors, CD14 and scavenger receptors. Concept of how these receptors trigger different intracellular signalling pathways to “tailor” inflammation to the pathogen. Introduce dendritic cells as the interface between innate and adaptive immune responses.
Subject: The Adaptive Immune System
No. of lectures: 2
Lecturer: Dr Simon Wong
These lectures will describe the “second line of defence” against infection. 1) How T and B lymphocyte genes generate receptor diversity to recognise specific antigen and introduce the concept of central and peripheral tolerance mechanisms to discriminate self from non-self. Introduce clonal expansion, T cell effector function and B cell antibody production and function. 2) Describe T cell and B cell activation and effector function: Activation of CD4 T helper lymphocytes by exogenous (bacterial) antigens processed and presented via MHC Class II pathway, activation of CD8 cytotoxic T cells by endogenous (viral) antigens. Introduce T and B cell co-operation to eliminate infection and the concept of “immunological memory”.
Subject: Evasion of the Immune System
No. of lectures: 2
Lecturer: Professor Janet Liversidge
These lectures will describe how man and microbes can co-exist, how microbes evade detection by the immune system and how epidemics occur. 1) Mechanisms of immune subversion by stealth, sabotage or exploitation and how individual pathogens deploy these strategies. Effects on antigen processing and presentation pathways, disruption of chemokine receptors and leukocyte trafficking, secretion of decoy molecules, invasions and superantigens. 2) Specific examples: HIV, measles, TB, Chlamydia and parasitic protozoa. Information on Third year course.
Subject: Regulation of the Immune System
No. of lectures: 2
Lecturer: Professor Robert Barker
These lectures will describe how the immune system is controlled to “switch off” unnecessary or damaging inflammation and maintain homeostasis, and how disease can occur when things go wrong. 1) Interaction between cellular and humoral components of the immune response, complement and antibodies, co-stimulation, activation induced cell death, immunological memory, T cell suppression, Th1/Th2 balance and T regulatory cells. 2) Control of the immune system, immunologic tolerance and autoimmunity, MHC and disease susceptibility, hypersensitivity diseases, vaccines.
As part of the course all students will complete the following lab. classes and homework assignments:
1. Identification & Growth of Pathogens
2. Molecular Microbiology
3. Environmental Microbiology
4. Haematology & Medical Microbiology
Course work for Microbes, Infection and Immunity will consist of the marks from the four written practical reports AND the four homework assignments. Each assignments must be submitted by the date shown in the manual and will be marked by the demonstrators. You must hand in your practical report and homework assignment at the next practical class (e.g. students taking practicals on Tuesday will hand in reports on Tuesday at the next practical class). Do NOT hand in your whole lab book; instead hand in only the papers relevant to the practical and homework assignment. Please note that some practical exercises run over two weeks. In these cases, hand in the report after the end of the second week of the practical, respectively. A timetable for the practical submissions is provided in the ‘Practical Work’ section.
At the start of the practical exercise all students will be instructed on the correct behaviour and level of safety expected in the laboratories. All students are expected to possess and wear a laboratory coat during practical classes. Additional forms of personal protection including safety glasses and disposable gloves will be provided. Students will also be instructed on the correct handling of chemicals and biological materials used as part of the practical.
You are strongly encouraged to purchase a copy of the following textbook:
M.T.Madigan, J.M.Martinko, P.V.Dunlap, D.P.Clark, T.Brock
BROCK BIOLOGY OF MICROORGANISMS
Pearson Education 12th Ed (2008)
ISBN 0321536150
[576 Bro] (£49.99)
The Website for Brock Biology of Microorganisms (12th Edition) is:
http://www.prenhall.com/brock/
Other Useful Web Sites:
These Web sites are not a substitute for the course textbook but they do contain a lot of valuable information relevant to your course.
http://www.accessexcellence.com/AB/GG/
http://gened.emc.maricopa.edu/Bio/BIO181/BIOBK/BioBookTOC.html
http://textbookofbacteriology.net/themicrobialworld/homepage.html
http://www.bact.wisc.edu/microtextbook/index.html
http://pathmicro.med.sc.edu/book/welcome.htm
Plagiarism is a form of cheating and is treated as a serious disciplinary offence by the University. It is defined as 'the use, without adequate acknowledgement, of the intellectual work of another person in work submitted for assessment. A student cannot be found to have committed plagiarism where it can be shown that the student has taken all reasonable care to avoid representing the work of others as his or her own.'
There is detailed advice on how to recognise and avoid plagiarism on the University's web-site at www.abdn.ac.uk/writing/plag/page1.htm, including a self-test on how to recognise plagiarism, and the University's Academic Quality Handbook sets out procedures for dealing with plagiarism offences at;
www.abdn.ac.uk/registry/quality/appendix5x15.pdf.
The course is assessed by two means, which are course work and the end of course examination. The course work represents 30% of the total mark and is made up of marks from the laboratory reports and homework exercises. The end of course two hour examination contributes 70% of the total mark. The time, date and location of the final course exam will be given to you in plenty of time.
Extended matching questions (EMQs) will be used for the format of the end of course exam. EMQs will be used to test your knowledge and understanding of material covered in both practicals and lectures. A mock EMQ examination paper is scheduled as part of the practical classes on the 26th and 28th April. Start your revision early, to avoid last-minute panic!
To achieve an overall pass for the course you MUST obtain a CAS score of 9 or better for the entire course AND you must pass the end-of-course examination with a score of 9 or better.
Dr Frank Ward, Course Organiser Prof Janet Liversidge Prof Maggie Smith Prof Rob Barker Dr Gail Ferguson Dr Debbie McLaggan Dr Pieter van West Dr Iain Ogden Dr Phil Cash Dr Simon Wong Dr Carol Munro
The University is keen to help you successfully complete your studies. If at any time you feel you need assistance, there is a range of support services available to help you. These include support to help with unexpected and/or exceptional financial difficulty, support for disabled students and academic learning support through the Student Learning Service. Further details about all these services are available at http://www.abdn.ac.uk/studenthelpguide/.
We value student’s opinions in regard to enhancing the quality of teaching and its delivery; therefore in conjunction with the Students Association we support the operation of a Class representative system.
The students within each course, year, or programme elect representatives by the end of the fourth week of teaching within each half-session. In this course we operate a system of course representatives. Any students registered within a course that wishes to represent a given group of students can stand for election as a class representative. You will be informed when the elections for class representative will take place.
What will it involve?
It will involve speaking to your fellow students about the course you represent. This can include any comments that they may have. You will attend a Staff Student Liaison Committee and you should represent the views and concerns of the students within this meeting. As a representative you will also be able to contribute to the agenda. You then feedback to the students after this meeting with any actions that are being taken.
Training
Training for class representatives will be run by the Students Association. Training will take place in the fourth or fifth week of teaching each semester. For more information about the Class representative system visit www.ausa.org.uk or email the VP Education & Employability vped@abdn.ac.uk.
If you would like to be a class representative please e-mail me (f.j.ward@abdn.ac.uk)
The University operates a system for monitoring students' progress to identify students who may be experiencing difficulties in a particular course and who may be at risk of losing their class certificate. If the Course Co-ordinator has concerns about your attendance and/or performance, the Registry will be informed. The Registry will then write to you (by e-mail in term-time) to ask you to contact their office in the first instance. Depending on your reason for absence, the Registry will either deal directly with your case or will refer you to your Adviser of Studies or a relevant Support Service. This system is operated to provide support for students who may be experiencing difficulties with their studies. Students are required to attend such meetings with their Adviser of Studies in accordance with General Regulation 8.
Set criteria are used to determine when a student should be reported in the monitoring system. You will be asked to meet your Adviser if any of the following criteria apply for this course:-
either (i) if you are absent for a continuous period of two weeks or 25% of the course (whichever is less) without good cause being reported;
or (ii) if you are absent from two small group teaching sessions (e.g. tutorial, laboratory class) without good cause;
or (iii) if you fail to submit a piece of summative or a substantial piece of formative in-course assessment by the stated deadline'
If you fail to respond within the prescribed timescale (as set out in the e-mail or letter), you will be deemed to have withdrawn from the course concerned and will accordingly be ineligible to take the end-of-course assessment or to enter for the resit. The Registry will write to you (by e-mail in term-time) to inform you of this decision. If you wish consideration to be given to reinstating you in the course you will require to meet with the Convener of the Students' Progress Committee.
Students who attend and complete the work required for a course are considered to have been awarded a ‘Class Certificate’. Being in possession of a valid Class Certificate for a course entitles a student to sit degree examinations for that course. From 2010/11 class certificates will be valid for two years and permit a total of three attempts at the required assessment within that two year period i.e. the first attempt plus up to two resits.
You will receive a University e-mail account when you register with the University Computing Centre. The University will normally use e-mail to communicate with you during term-time. These e-mails will be sent to your University e-mail account.
It is your responsibility to check your e-mail on a regular (at least weekly) basis and to tidy the contents of your e-mail inbox to ensure that it does not go over quota (see http://www.abdn.ac.uk/dit/student/email/index.php?S776475303438=d660bfec0a7efc03ac41e5838b6921c6 for guidance on managing your e-mail quota). It is recommended that you use your University e-mail account to read and respond to University communications. If you already have a non-University e-mail account that you use for personal correspondence, it is possible to set up automatic forwarding of messages from your University e-mail account to your personal e-mail address (see http://www.abdn.ac.uk/studentmail/) but, should you do so, it is your responsibility to ensure that this is done correctly. The University takes no responsibility for delivery of e-mails to non-University accounts.
You should note that failure to check your e-mail or failure to receive e-mail due to being over quota or due to non-delivery of an e-mail forwarded to a non-University e-mail account would not be accepted as a ground for appeal. For further information on appeals procedures, please refer to;
http://www.abdn.ac.uk/registry/quality/appendix5x18a.pdf)
