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The course is concerned with modern aspects of molecular microbiology including examination of the regulation of the growth of viruses, bacteria and fungi and the molecular determination of virulence in pathogenic microorganisms. The role of the immune system and the use of antimicrobial drugs in combating infection is also considered in detail. New insights into the phylogenetic relationships between microorganisms based on molecular systematics are also discussed. Medical aspects of Molecular Microbiology are supplemented with studies on microbial interactions in the environment. Together this information provides an in-depth description of how the growth and interaction between microorganisms and the environment as well as the human host is regulated at the molecular level.
The aims of the course are to enable students:
(a) To establish a broad coverage of modern aspects of microbiology reflecting areas of high profile and research activity;
(b) To establish an understanding of in the principles underlying modern molecular mechanisms related to medical microbiology and environmental microbiology; and
(c) To obtain direct experience of practical work that reflects research topics of special interest to the research staff in the School of Medical Sciences and the general disciplines of Microbiology.
The subject-specific learning outcomes are such that, at the end of the course, students should be able to:
(a) To describe and understand the major features of fungal pathogens of plants and animals;
(b) To understand the basic features of virus replication of animal viruses at the molecular level with specific reference to the molecular pathogenesis of reovirus, poliovirus and herpes virus;
(c) To describe how micro-organisms interact with their environment to both grow and survive external stress;
(d) To describe at the molecular level how pathogenic bacteria interact with their host cells. To understand how these bacteria adhere to the host cell and survive within the host cell. To understand the mechanisms by which chronic bacterial infections can develop.
(e) To understand the mechanisms by which bacteria can survive extreme environmental conditions.
(f) To describe how micro-organisms interact with each other when growing in mixed populations and to describe positive and negative signaling between micro-organisms in the environment;
(g) To understand how bacteria grow and develop including the process of cell division and spore formation.
(h) To understand the process of DNA replication and how the process is regulated in complex intracellular environments.
(i) To describe the general principals of antimicrobial drug action and how these can target specific aspects of bacterial and fungal growth and metabolism as a means of treatment.
Students will also develop practical 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.
The aims of the course will be achieved through a combination of lectures, tutorial and practical classes.
Subject: Fungal pathogens of plants and animals
Lecturer: Prof N A R Gow
Lecture 1-2: The first two lectures will cover the life cycles and virulence traits of plant pathogens as well as the resistance mechanisms that are employed by plants such as the hypersensitive response and the gene-for-gene hypothesis of pathogen recognition.
Lecture 3-4: These two lectures of human fungal pathogens will mention the main agents of superficial and systemic fungal disease, their virulence traits and the ways in which antifungal drugs inhibit their growth. Similarities and differences between plant and animal pathogenic fungi will be underlined.
Subject: Molecular virology
Lecturer: Dr P Cash
The aim of these lectures is to look at the principle mechanisms employed by DNA and RNA viruses to infect human cells and subvert the host metabolism for viral replication.
Lectures 1-2: Viral replication strategies. The general mechanism of replication for animal viruses will be described. The replication strategies of viruses possessing DNA and RNA genomes is described since, although viruses with DNA genomes replicate using mechanisms similar to those found in eukaryotic cells, the RNA viruses show diverse replication strategies dependent upon the nature of the virus genome.
Lectures 3-4: Molecular pathogenesis of human viruses. The pattern of pathogenesis of reovirus and poliovirus, two RNA viruses with distinct modes of replication will be discussed. The strategies used to investigate virus pathogenesis at the molecular level will be considered. The development of latent infections by herpes simplex virus, a DNA virus, will be reviewed.
Subject: Bacterial Molecular Pathogenesis
Lecturer: Dr K J Forbes
The aim of these lectures is to look at a number of bacterial pathogens and compare and contrast the mechanisms they have evolved to adhere to, invade and survive within, human, host cells.
Lectures 1-4: This series of four lectures will deal with molecular aspects of the interactions between bacterial pathogens and the human host, including: The conflicts between the pathogens and their host and how these affect the ability of the pathogens to survive. Model systems to study pathogenesis. Colonization, adherence and pili. Intracellular lifestyles: benefits, gaining access and staying alive. The bacterium’s manipulation of its environment: toxins. Getting complex proteins out of bacterial cells: secretion systems.
Subject: Bacterial Cell Stress and Survival
Lecturer: Dr S Miller
The aim of these lectures is to examine the mechanisms that bacterial cells such as E. coli have evolved to enable survival of a diversity of stresses.
Lectures 1-4: Bacterial cells are able to survive a diversity of stresses such as changes in external pH, osmolarity and exposure to toxic compounds. The series of four lectures will summarise the mechanisms that bacteria, for example E.coli, have evolved to enable cell growth despite diverse environmental challenges. We will study the nature of environmental signals that are sensed by cells that allow them to respond to stressful environments, the mechanisms cells use to combat such stresses and the integration of signals.
Subject: Bacterial growth and development
Lecturer: Prof M Smith
Escherichia coli undergoes a simple cell cycle of growth and division. Other bacteria have a more complex cell cycle leading to differentiated cell types. The objective of these lectures is to review bacterial developmental processes in particular the signals that lead to the choice of a developmental pathway. To illustrate how developmental choices are made we will study a range of processes including cell divisioin, the lysis versus lysogenic decision in bacteriophage and spore formation in Bacillus.
Lecture 1: Cell division
Lecture 2: The option of dormancy, sporulation in B. sutillis.
Lecture 3: The simplest developmental choice of all. How does bateriophoage lambda decide whether to go lytic or lysogenic?
Lecture 4: Stochastic switches. Unprogrammed developmental choices; phase variation in Neisseria. Opa proteins, cell tropisms, adherence and escaping the immune response.
Subject: Chronic bacterial-host Interactions
Lecturer: Dr G P Ferguson
These lectures will lead to better understanding of the molecular mechanisms used by bacterial cells to form chronic intracellular infections within their host cells. The first lecture will focus on the molecular basis of the Sinorhizobium-legume symbiosis and then the second lecture will demonstrate the parallels between the Sinorhizobium symbiosis and chronic mammalian pathogenesis. In particular, the second lecture will focus on Brucella species, which are potential bioterrorism/biowarefare agents.
Subject: Growth under extreme conditions
Lecturer: Dr G P Ferguson
These lectures aim to provide a better understanding of the molecular mechanisms used by bacterial cells to grow optimally in extreme environments. The two lectures will focus primarily on pressure-loving bacterium known as piezophiles. In particular, they will show how Photobacterium profundum SS9 has been used as a model system to understand more about pressure-adapted growth.
Subject: Genome duplication in the real world
Lecturer: Dr P McGlynn
The aim of these lectures is investigate the problems associated with DNA replication in the complex environments found within cells and to examine the mechanisms that organisms employ to try and overcome barriers to genome duplication.
Lectures 1-3: All organisms have evolved elegant molecular machines to catalyse efficient and accurate duplication of their genetic material. However, no biochemical process occurs in isolation and DNA replication must occur concurrently with many other essential metabolic processes. These lectures will analyse the nature of barriers to genome duplication within cells, and the consequences of blocks to DNA replication in terms of genome stability and cell viability. The multiple accessory replication systems that are needed to underpin genome duplication in complex intracellular environments will be outlined, and the close interplay between DNA replication, recombination and repair will be highlighted.
Subject: Microbial interactions
Lecturer: Dr D McLaggan
The study of bacterial communication systems is an extremely active area of microbiology. Bacteria can communicate with each other through small ‘hormone-like’ organic signalling compounds. There is a huge diversity of different signals and this microbial chatter has altered the way we now perceive and examine microbial populations. These lectures will explore the many languages of bacteria, how and why microbes communicate with each other, and how inhibition of these communication mechanisms can have therapeutic potential.
Subject: Secondary metabolism/antimicrobial agents
Lecturer: Dr D MacCallum
Secondary metabolites are produced by many microbial species at certain stages of growth and can be associated with changes in morphology or help to promote survival of the microbe. These lectures will discuss the synthesis of secondary metabolites by microbes; some of which are antibiotics. These naturally produced agents, synthetic modifications, their modes of action and antimicrobial resistance mechanisms will also be discussed.
Lecture 1: Microbial secondary metabolism. What are secondary metabolites? When and why are they produced? Synthesis of secondary metabolites.
Lecutre 2: Antimicrobial agents (1). Antimicrobial drug discovery. Assessment of antimicrobial activitiy. Classes of antibiotics and modes of action.
Lecture 3: Antimicrobial agents (2). Antimicrobial drug resistance; mechanisms and spread of resistance. Antiviral agents.
Lecture 4: Antimicrobial agents (3). Antifungals: antifungal agents, modes of action and clinical use.
As part of the course all students will follow a single practical exercise which is spread over the first three weeks of the course. The practical will involve the genetic manipulation to disrupt specific gene(s) in Candida albicans, a diploid yeast. During the practical students will have the opportunity of applying the techniques of genetic manipulation and examining the outcome of the genetic manipulations. Full details of the practical exercise will be provided during the course. An important aspect of the practical in this course is that students are expected to maintain a detailed laboratory notebook to record protocols and data as required. At the end of the practical the work will be written up in the format of a typical research paper. The work will be assessed on the basis of the final written presentation as well as the laboratory notebook written and maintained during the practical classes.
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.
As part of the course all students will be expected to complete a 1500 word essay. Students will be able to select their preferred essay topic from a list distributed during the introductory lecture of the course and the final assignments of the topics will be distributed shortly after. For each essay topic a key reference is provided and this will form the starting point for the student to research the essay topic. Guidance will be provided during the Introductory lecture on the preparation of the essay. The marks for this essay will form part of the Continuous Assessment for this course. The marks awarded for the practical exercise will also contribute towards the course continuous assessment.
The dates for the submission of the course work are noted in the course timetable and students are expected to follow these submission dates without exception. You will be penalised if you do not submit the course work on time. Students will be advised by email as to the location where course work should be handed in. This box will be removed at 12.30 p.m. on the day the course work is to be handed in and work appearing after this time will be deemed to be late. This will incur a penalty i.e., 50% reduction in marks for every day or part of a day the work is late. Work handed in late must be handed directly to a member of the secretarial staff. Please take special care to ensure that your work is placed in the correct collection box as you will incur the same penalty if your work is placed in the wrong collection box. Seek the advice of a secretary if you realise that you have placed your work in the wrong box as the boxes are tamper-proof and you should not attempt to recover the work yourself.
Each student should own a personal copy of the following book; the course cannot be studied satisfactorily from lecture notes alone.
Madigan, M., Martinko, J. & Parker, J Brock’s Biology of Microorganisms, Pearson Education 10th Ed (2002) (£39.99)
The following books are strongly recommended for reference and for further reading on selected aspects of the course. Many of these books are available from the University library.
Dixon, B. (1994) Power Unseen: How Microbes Rule the World (75 vignettes of microbes, very approachable)
Gow, N.A.R. & Gadd, G.F. (1995) The Growing Fungus
Postgate, J.R. 4th Ed Microbes and Man (A very approachable book-for bedtime reading)
Postgate, J.R. (1994) The Outer Reaches of Life
Prescott, L.M. et al. (2001) Microbiology
Douglas, A.E. (1994) Symbiotic interactions
Agrios (1997) Plant Pathology
Atlas & R.M. Bartha (1998) Microbial Ecology: Fundamentals & application
Kjelleberg, S. (1993) Starvation in Bacteria
Schmidt, GD (2000) Foundations in Parasitology
Cox FEG (1993) Modern Parasitology
The course is assessed by two means which are continuous assessment and written examination. The continuous assessment represents 35% of the total mark and is made up of marks from the written reports of your laboratory work and the essay. The practical carries 25% of the final mark. The essay carries 10% of the marks. The written examination provides 65% of the total mark and is of three hours duration and will be held at the end of the 12 week second half-session in May/June. The examination paper will contain 7 questions of equal weighting, from which you must answer 4. Details regarding time and place will be given to you in plenty of time.
Oral examinations may be arranged for a few students who fall close to the borderlines of Pass/Fail or possibly the Honours entry standard. The list of students for oral examination will be posted on the 3rd year notice board within 7 days of the written examination in June, and the oral examinations will be held shortly thereafter. Each exam will last for 20 minutes and will be conducted by Dr Cash and another member of staff who taught on the course. The outcome of this oral examination will be posted on the 3rd year notice board the following day.
A resit examination in the same format as the main examination will be provided for those students who are unsuccessful in the June examination. This resit examination may contain material from both the practical and lecture components of the course.
The total assessment of the course, recorded as a single CAS mark, is based on two elements of the course as follows: Continuous assessment marks contributing 35% of the total and the written examination contributing 65%. 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 written examination with a score of 9 or better. Failure to pass the written examination will mean a fail for the course.
Prof Ian Booth
Prof Neil Gow
Prof Peter McGlynn
Prof Maggie Smith
Dr Phil Cash, Medical Microbiology (Course Co-ordinator); Dr Alex Brand, SMS; Dr Ken Forbes, Medical Microbiology; Dr Gail Ferguson; Dr Debbie McLaggan, SMS; Dr Carol Munro, SMS; Dr Meggan Lenardon
If you are absent from one or more practical classes these will be discounted from the total mark spreadsheet ONLY if a medical certificate or acceptable self-certification form has been submitted. If your reason for absence is unacceptable or if you do not submit an “absence from class form” you will be awarded a zero mark for each practical missed. The re-sit examination will be based on the written paper as above and the previous continuous assessment marks achieved during the course.
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.
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, which you can access using Eudora or SquirrelMail.
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/diss/email/mailquota.hti 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/local/mail.forward/) 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/appendix5x18b.pdf
Tutorials
During the course students are required to attend three tutorials covering topics in Mycology, Bacteriology and Virology. Each essay is based around either a review or primary research paper. Students should come along to the tutorials and be prepared to discuss the issues raised in the paper provided. Specific areas will be highlighted for discussion during the tutorial session. Be prepared to contribute towards the discussion! Although no formal assessment mark is given for the tutorials, student attendance will be recorded.
Horizon Lectures
Two Horizon lectures are included as part of the course. These lectures are presented by Research Fellows form the School of Medical Sciences and cover topics of general Microbiological interest. These lectures give students the opportunity to hear about Microbiological relevant research not covered by the normal lecture course as well as being able to discuss future careers in Microbiology with young scientists.
External Examiner
Prof Judith Armitage, University of Oxford
