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  • 1. UNIVERSITY OF ABERDEEN SCHOOL OF MEDICAL SCIENCES DEGREE PROGRAMMES IN: BIOCHEMISTRY BIOMEDICAL SCIENCES (Molecular Biology) BIOTECHNOLOGY (Applied Molecular Biology) GENETICS IMMUNOLOGY MICROBIOLOGY MOLECULAR BIOLOGY MOLECULAR MICROBIOLOGY HONOURS MANUAL 2006-2007 Name ...........................................................
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  • 3. CONTENTS Honours Year - General Info: p Tutorials: p 5 59 Welcome The tutorial system Structure of the Honours Year and Timetable Tutorial topics The Role of the Honours Co-ordinators Project: p What to do if you have a problem or question 60 Responsibilities of Honours students and Laboratory/ Literature based research project Teaching staff (Safety in the laboratory) Honours Project list 2006-2007 Other useful information: About this Guide on laboratory or literature assessment manual; Points of contact; Seminars; Use of and laboratory notebook assessment the Library; Careers / Entrepeneurship information; Postgraduate studies; University Support; Staff contacts Thesis including “Instructions and Guidance Coursework Summary Form for authors” Attendance and Performance requirements Brief guidelines on writing conventions Class Representatives Assessment of thesis Mission statements; University and School; Timetable for projects Statement on Standards Expected for Students Project seminars and oral presentations Assessment: p Assessment forms for lab/ literature performance, 26 thesis and oral examination Submission of written work Essays: p Examinations 70 Marking Essays 1, 2 and 3: Submission dates and guidelines for essay titles Honours Degree Classification Plagiarism Course elements Titles for Essays 1 and 2 Requirements for the award of an Honours Degree Guide on essay writing Marking scheme Assessment of essays and assessment forms The Lecture Course: p 31 Research Tutorials: p List of modules for each course 79 Timetables for first semester Preparation Course synopses Evaluation forms 3
  • 4. Tutorial Synopses Past Examination Papers: p 88 Papers 1 - 4 available at www.abdn.ac.uk/diss/library/examdb/ and WebCT Paper 5 ~ Data analysis ~ available from School office on request Plagiarism sheet (to be completed and handed in with all course work) This manual can also be found on WebCT (MB4050) 4
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  • 6. WELCOME TO THE HONOURS COURSE We are pleased to welcome you into the Honours Course, the final year of your undergraduate programme. We believe that you will find this course stimulating and challenging. We know that you will have to work hard, and hope that you will see it as rewarding, even though this may only be with hindsight! The primary aim of our Honours teaching is to develop your powers of critical analysis and communication. By the end of the year it will have become second nature for you to structure your ideas and information such that there is an orderly development of the argument that you are presenting. Ultimately this involves the cross-referencing of information from different sources, eg reviews, lecture notes and original papers, and integrating the material around a central theme or set of themes. There are several ways in which we try to stimulate the development of these abilities: eg essays, seminars, project work. Regular tutorials act as an aid to the orderly revision of lecture material, the discussion of problems and the development of your understanding of your subject. Structure of the Honours Year The teaching in the Honours year involves fewer lectures and more input from you than in previous years. You will take 1 core course in Advanced Cell and Molecular Biology (45 hours) and 2 options modules, each of 15 contact hours comprising a mix of lectures, tutorials and seminars running over 3 weeks. Considerable additional reading on your part is needed to support both the core and options courses and is an integral part of the structure of the options modules. The options modules for each degree are fixed, with the exception of Biotechnology, where a mix of any two modules can be taken as long as they are in two different subject areas (Biochemistry, Microbiology, Genetics or Immunology). During the first semester you will also write three essays, which form part of the course continuous assessment. The research project, lasting 10 weeks, is undertaken in the second semester. Alongside the project run two research tutorials, where the scientific literature is carefully studied with the help of a member of staff acting as tutor. First and second semester material is examined in May. Honours continuous assessment and course work account for 7 elements of assessment, with formal examinations accounting for 17 elements out of a total of 24 elements of the degree assessment (see assessment section for more details). You will be kept busy throughout the year and it is important that you develop a well-structured plan for the optimal organisation of your time. The tasks to be completed are all important but none should be allowed to dominate your effort. You must learn to set priorities and to apportion a set time to any particular piece of work. When the time has elapsed, move on to the next task and accept that you cannot do everything perfectly. This is not, of course, a set of excuses to try to get by on the minimum of effort, which is not consistent with undertaking an Honours degree. A quick guide to the structure of the honours year is included in this section. A form on which you should summarise all your work, including essay titles etc, is enclosed. Please fill this in and hand it in with your thesis, the last piece of work submitted. The form is of particular help to the external examiners. 6
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  • 8. TIMETABLE FOR 2006-2007 HONOURS Week Week beginning 11 18 September 2006 Kindrogan 21-22 September 06 12 25 September 2006 MB4050 Careers Talk (28 September 06) Advanced 13 02 October 2006 Option Molecular Library Visit (29 September 06) 14 9 October 2006 Course and Cell 15 16 October 2006 No. 1 Biology Essay 1 hand-in (17 October 06) 16 23 October 2006 Core 17 30 October 2006 Option Course 18 06 November 2006 Course 19 13 November 2006 No. 2 Essay 2 hand-in (15 November 06) 20 20 November 2006 21 27 November 2006 22 04 December 2006 Revision and assimilation Careers & Entrepreneurship talks 23 11 December 2006 time (date to be confirmed) (15TH END OF TERM ) Essay 3 hand-in (12 December 06) CHRISTMAS HOLIDAYS 27 08 January 2007 28 15 January 2007 Laboratory Project 29 22 January 2007 (starts 15 January 07) 30 29 January 2007 Research tutorial advice session and 31 05 February 2007 Project thesis writing tutorial 32 12 February 2007 } 33 19 February 2007 } Research tutorial 1 34 26 February 2007 } 35 05 March 2007 } 36 12 March 2007 } Research tutorial 2 37 19 March 2007 Advice session ~ University } (23rd END OF TERM) Finish Lab Work by 16th March 07 Evaluation Form to be filled in Project Presentations (21-23 March 07 – to be confirmed) EASTER HOLIDAYS 41 16 April 2007 Project Thesis hand-in (18 April 07) (TERM BEGINS) 42 23 April 2007 43 30 April 2007 44 07 May 2007 Papers 1 and 2 (9th & 11th Exams (EXAM PERIOD BEGINS) May 07 – to be confirmed) 45 14 May 2007 Papers 3, 4 and 5 (14th, 16th Exams & 18th May 07) – to be confirmed 46 21 May 2007 47 28 May 2007 48 04 June 2007 Oral exams 6-8 June 07 (8th END OF TERM) (to be confirmed) 52 Thurs 5 July 2007 PROVISIONAL GRADUATION & SCHOOL GRADUATION RECEPTION 8
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  • 10. THE ROLE OF THE HONOURS CO-ORDINATORS Welcome to your level 4 courses in the School of Medical Sciences. We are the level 4 Co-ordinators and are responsible for the administration of Honours courses within the disciplines of Biochemistry, Genetics, Immunology and Microbiology. You will also have a Module Organiser for each of the 2 options modules of the taught course, and you should approach them if you are having difficulties with a specific module. For all other issues, we are your main points of contact on the academic staff. We will also be available to discuss any general points relating to the modules. Please feel free to let us know about any problems, either directly or via your class representatives. It saves a lot of time if suggestions not requiring discussion, are made by leaving notes in our pigeon-holes/sending emails; the same route is often a useful first step in matters where you do want to discuss a problem. You can contact us either directly, BM in IMS room 2:18; tel 55826; KD in IMS room 4:30; tel 55769; AS in Polwarth room 4:015; tel 53006; or via Lucy Meldrum, in the School Office (IMS room 2.62.3, tel 55872). In our role as Honours Co-ordinators we are formally responsible for: • The smooth running of all Honours courses, including the essays, allocation of projects and tutors, teaching timetable, and dealing with any problems arising • Preparation and distribution of the course manual • Monitoring records of attendance, medical certificates and other reasons for absence • Recording any failure to hand in work on time and interviewing any student who fails to do so • The Assessment Form in this manual and the University Course Assessment Form you will receive at the end of each half-session. • Responding to suggestions for changes to the Honours courses. In practice, our duties are not limited by this list. We will do all we can to make your experience of the Honours year as happy and fruitful as possible. Remember that you also have an individual tutor (see Tutorial section), who is there to help you. Kevin Docherty, Berndt Mueller and Andy Schofield WHAT TO DO IF YOU HAVE PROBLEMS OR QUESTIONS ABOUT THE COURSE OR WISH TO SEE ONE OF THE HONOURS CO-ORDINATORS One of the Honours Co-ordinators will be available every Wednesday from 5.00–6.00pm throughout term time for consultations. You may book an appointment by signing up on the diary available from Lucy Meldrum in the School Office. These consultations will be held in the office of one of the co-ordinators. You should make every effort to restrict your enquiries to the Honours Co-ordinators to these allocated times unless it is an emergency. Remember that most of the information you will need about the course and the deadlines is in your manual. You may want to discuss other matters with your Tutor as your first port of call. Also, remember to direct any comments you may have on the course content and/or organisation to the relevant Class Representative who will channel your comments to the appropriate member of staff or Course Co-ordinator. 10
  • 11. RESPONSIBILITIES OF HONOURS STUDENTS 1. You must ensure that you are available, without exception, during term time throughout the year to fulfil course requirements; this includes the post-exam period. 2. You must read the manual carefully and familiarise yourself with the contents. 3. You should establish a good working relationship with your Tutor, part of which will involve attendance at all tutorials scheduled. Remember that your Tutor and your Project Supervisor may be asked to speak on your behalf at the final Examiner’s Meeting in June. 4. You must bring any difficulties you are having with the course or any other problem that may affect your academic performance and progress to the attention of your Tutor immediately. 5. You must establish a rigorous programme of study and manage your time carefully. 6. You must meet deadlines without fail. 7. You must ensure that any absence from the course during term time is covered by a medical certificate which should be lodged with Lucy Meldrum in the School Office immediately upon return to study. Retrospective medical certificates will not be accepted. RESPONSIBILITIES OF TEACHING STAFF 1. Tutors must establish and maintain contact with their tutees throughout the year: they must bring any problems individual students are having to the attention of the Honours Co-ordinators (BM, KD, AS). 2. Teaching staff should encourage and seek to develop the full academic potential of every student. 3. Honours Project Supervisors should ensure that the students are adequately supervised and that progress during the project is monitored frequently. 4. Staff must discuss any changes to the Modules with the relevant Student Representative and the Honours Co-ordinators BEFORE making any changes. 11
  • 12. HONOURS PROJECTS 2006-2007 PROJECT TITLE SUPERVISOR TUTOR BIOCHEMISTRY Chaudry, Samir Factors promoting genetic stability in E. coli Dr P McGlynn Prof N A Booth MacNeish, Kelly The role of chromatin remodelling in the Prof K Docherty Dr A Donaldson expression of the endogenous PDX1 gene in non-islet cells McCrimmon, Angela Food Microbes: The Good, The Bad & The Drs J Perkins / C Dr I J McEwan (library based) Beautiful! Fraser Paget, Jane The kinetics of hyphal gene regulation in Prof A J P Brown Dr B Mueller Candida albicans Shay, Gemma Biomarker discovery using proteomics Dr P Cash Prof N A Booth (Med Micro) Sheils, Emma Allosteric Regulation of Transcription by DNA Dr I J McEwan Dr A Donaldson binding BIOMEDICAL SCIENCES (MOLECULAR BIOLOGY) Liaros, Angela An analysis of the regulatory systems Dr A MacKenzie Dr I J McEwan controlling the expression of the MSX1 gene in the developing heart McClure, Christina Localisation and function of RNA processing Dr B Mueller Prof M C M Smith factors in animal model systems Morrison, Emma Mechanisms of fibrin stabilization to lysis Prof N A Booth Dr P van West BIOTECHNOLOGY Cheyne, Richard Isolation of fully human antibodies specific for Prof A J R Porter Prof F Odds peptide targets Tan, Pei Xin Building Blocks of the Cell Nucleus: Dr A Donaldson Prof N A R Gow Identifying Molecules that Position Chromosomes in the Nucleus GENETICS Kennedy, Stuart Biosynthesis and secretion of a novel SPFH Dr K I J Shennan Dr I Stansfield protein (mORF) McKenzie, Christopher Directional growth of Candida albicans Prof N A R Gow Prof D Shaw Rattray, Alexander Mitochondrial DNA polymorphism and MLST Profs D Shaw/ F Dr I Broadbent in Candida albicans Odds/ N A R Gow Reichmann, Judith Learning about colorectal cancer by studying Dr J Pettitt Dr A MacKenzie worms 12
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  • 14. GENETICS (IMMUNOLOGY) Abdullah, Ahmad Do heparan proteoglycans act as signalling co- Dr W F Long Prof D Shaw (library based) receptors during HIV infection? Harman, Laura Does CD200/CD200R signalling bias the Dr J Liversidge (O) Prof N A R Gow Th1/Th2 balance in inflammation? Hector, Beverley Protein synthesis in yeast; mistakes on the Dr I Stansfield Dr I Broadbent assembly line Kastl, Lena Chemotherapy drug resistance in breast cancer Dr A C Schofield Dr I Stansfield Murdoch, Suzanne Bcl-2 involvement in CD69 induced Eosinophil Dr G Walsh Dr A MacKenzie apoptosis (M&T) MOLECULAR MICROBIOLOGY Molecular Basis of Antibiotic Resistance in Prof I R Booth Dr P van West Shewring, Dawn Bacteria Med Mic = Medical Microbiology; M&T = Medicine & Therapeutics; O = Ophthalmology This Manual This manual is designed to give you all the information you will need. We have tried to make it complete but accept that you may identify some omissions (please let us know of these). It is structured so that all information on one topic, e.g. Projects or Essays, is together. There are a number of important general issues that are dealt with in this introductory section. We also need some information from you. We ask you to fill in a registration form with local and home addresses and telephone numbers. It is essential that the information we have is up-to-date, so do not forget to advise us of changes. Also for safety reasons, we must make sure that you have read the Safety Manual before you are allowed to start your project 14
  • 15. Points of Contact Messages for individuals will be left in the Honours Class pigeon hole (round the corner from the School Office, Room 2:62.3). Messages for the class as a whole will also be sent to University e-mail addresses; this facility depends on your giving us details of your e-mail number. Please do not delay in giving us this information (see Registration Form). It is your responsibility to check these sources of information. All important notices will be sent by e-mail; check these frequently [emails will be sent to your University email account, not any hotmail.com etc accounts you might have]. Seminars The School of Medical Sciences runs a seminar programme with research seminars that focus on topics in Microbiology, Cell and Developmental Biology and Immunology. These seminars normally take place on Mondays, Thursdays and Fridays. In addition a high profile Institute of Medical sciences seminar programme will bring well-known speakers to Aberdeen. These seminars take normally place each, on a Wednesday. All seminars are widely advertised and you are strongly encouraged to attend relevant seminars. Immunology degree programme students are also expected to attend the Aberdeen Immunological Association Seminar series. These are widely advertised throughout the IMS and are usually held twice a month at 12:30pm on a Thursday. As well as their research content, well-presented Research Seminars are clear lessons on how to present complex data in a form readily assimilated by non-experts, and are useful for picking up tips on how to present your own seminars. They also give you a feel for science research as a career option. You are also welcome to attend any seminar series offered by other departments; information on these will be circulated throughout the IMS. Use of the Library Students should make themselves aware of all the services available in the University library, including use of the CD-ROM system. The Library staff have agreed to give a seminar and tour for you, attendance at which is compulsory. This will be on Friday 29th September. From 10:30-11:30am, the whole class will attend a library information session commencing in the Library Project Room. For the computer classroom part of the session, the class will be divided as follows – 29.09.06 1:30-2:30pm ~ Genetics, Genetics (Immun), Immunology, Micro, Molecular Micro 29.09.06 3:00-4:00pm ~ Biochem, Biochem (Immun), Molecular Biology, BMS (Molecular Bio), Biotech You will be provided with one photocopy card (which can be collected from the School Office), sufficient for 140 copies. Further cards can be purchased from the School Office (£6.00). Focus on Careers On Thursday 28th September, Peter Fantom from the University Careers Service will give a talk on careers at 10:00am in the Foresterhill Lecture Theatre for all Honours students. In December 06/ January 07 there will be a visit from industry representatives. They provide a forum where interested undergraduates and postgraduates can hear about opportunities for jobs as industrial scientists. A group of scientists representing a range of industries will present short talks on the work of scientists in their companies, together with a question and answer session. There may be an opportunity for you to have a one-to-one meeting with the visitors. The School office will contact you nearer the time with details. This is a great opportunity for all students to hear about careers in industry from people already engaged in one. 15
  • 16. Post-Graduate Study Many of our graduates go on to become research students either here in Aberdeen or in other universities. If you are interested in the possibility of studying for a PhD, discuss the position early in the year with Duncan Shaw, the Postgraduate Supervisor, Berndt Mueller, Kevin Docherty or Andy Schofield, the Honours co- ordinators, in the first instance. We can usually suggest suitable departments in other universities for you to approach. Early application is recommended if you wish to be considered for quota Research Council Awards or if special application (eg for CASE or University Studentships) is to be made on your behalf. Should you have any queries regarding availability of funding for study please enquire in the Graduate School, College Office (Christine Bain: ext 59970), about Postgraduate admissions. Entry to the IMS Entry can be gained by using your Student ID Card. University Support In addition to the academic advice that your supervisor, tutor and all academic staff can give you, it may be that you require additional professional help. The University has a Counselling service, which provides personal support. There is also advice available on financial problems. University Counselling Service Tel: 27-2139 William Guild Building, Old Aberdeen Money Advice Centre for Students Tel: 27-2965 c/o SRC Office, Room 23 Luthuli House, 50/52 College Bounds, Old Aberdeen 16
  • 17. STAFF CONTACTS Teaching Staff E-mail Office Room Lab Lab …….@abdn.ac.uk Ext Number Ext Room No Booth, Prof Ian R i.r.booth 55852 5:30 55851 6:51 Booth, Prof Nuala A n.a.booth 55818 3:17 54575 1:32/1:33 Brown, Prof Alistair JP al.brown 55883 3:25 55888 2:50 Connolly, Dr Bernadette b.connolly 55825 4:31 55922 4:59 Cumming, Mr Alastair a.cumming 55722 5:16 - 6:55 Docherty, Prof Kevin k.docherty 55769 4:30 55830 4:42/4:43 Donaldson, Dr Anne a.d.donaldson 50975 2:17 55770 2:01 Glover, Prof L Anne l.a.glover 55799 2:32 55800 2:39/2:40 Gow, Prof Neil AR n.gow 55879 3:26 55878 2:50 Long, Dr Bill F * w.f.long (76)4175 Ed Wr - - Anx G01 MacKenzie, Dr Alasdair Alasdair.mackenzie 55893 5:27 55922 4:59 McEwan, Dr Iain J iain.mcewan 55807 2:34 55810 2:06 McGlynn, Dr Peter p.mcglyn 55183 2:31 55770 2:01 Mueller, Dr Berndt b.mueller 55826 2:18 55887 2:04 Odds, Prof Frank f.odds 55828 3:27 59536 2:50 Perkins, Dr Joy j.perkins 51934 5:17 - - Pettitt, Dr Jonathan j.pettitt 55737 4:38 55922 4:59 Porter, Prof Andy JR a.porter 55870 5:31 59482 SS1 Schofield, Dr Andy** a.schofield 53006 4:015 - WFR1/2/6 Shaw, Prof Duncan d.shaw 55891 6:21 - 6:55 Shennan, Dr Kathy IJ k.i.shennan 55827 2:20 55810 2:06 Smith, Prof Maggie maggie.smith 55739 5:32 55794 6:58 Stansfield, Dr Ian i.stansfield 55806 2:19 55887 2:04 Wright, Dr Matthew C m.c.wright 55880 3:16 55830 4:42 Crane, Dr Isabel i.j.crane 53783 5:19 Liversidge, Dr Janet j.liversidge 59548 4:22 Sternberg, Dr Jerry*** j.sternberg (76)2272 308 Walsh, Dr Garry g.m.walsh 54533 4:19 Ward, Dr Frank f.j.ward 55948 4:63 * based in Edward Wright Annexe ** based in Polwarth Building ***based in Zoology Building School Co-ordinator Maureen Carr (e-mail: m.carr@abdn.ac.uk) 55871 Rm 2:62.1 IMS Senior Secretary Lucy Meldrum (e-mail: l.meldrum@abdn.ac.uk) 55872 Rm 2:62.3 IMS Secretary Jill Reid (e-mail: jill.reid@abdn.ac.uk) 55717 Rm 2:62.3 IMS Safety Mrs Diane Massie 55922 Dr Kath Shennan 55827 DIALING Internal from IMS to Old Aberdeen: 76 + ext no (last 4 digits):: from IMS to IMS/ Polwarth: 5 digit ext no (beginning with 5) from Old Aberdeen to Foresterhill: 76 + 5 digit ext no (e.g. 76 55xxx) External to Old Aberdeen: 27 + ext no (last 4 digits) to IMS/ Polwarth: 5 + 5 digit ext no (beginning with 5) 17
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  • 19. HONOURS COURSEWORK SUMMARY NAME DISCIPLINE TUTOR PROJECT SUPERVISOR CORE MODULES ADVANCED MOLECULAR BIOLOGY OPTION MODULE 1 OPTION MODULE 2 PROJECT TITLE ESSAY 1 ESSAY 2 ESSAY 3 This form is required by the External Examiners. Please complete and submit with your thesis. 19
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  • 21. ATTENDANCE AND PERFORMANCE REQUIREMENTS: Students are expected to attend ALL lectures, tutorial and practical classes and to submit ALL written assignments by the specified time. Attendance and submission information will be recorded. ABSENCE FROM CLASSES ON MEDICAL GROUNDS Candidates who wish to establish that their academic performance has been adversely affected by their health are required to secure medical certificates relating to the relevant periods of ill health (see General Regulation 17.3). The University’s policy on requiring certification for absence on medical grounds or other good cause can be accessed at: www.abdn.ac.uk/registry/quality/appendix7x5.pdf You are strongly advised to make yourself fully aware of your responsibilities if you are absent due to illness or other good cause. In particular, you are asked to note that self-certification of absence for periods of absence up to and including eleven weekdays is permissible. However, where absence has prevented attendance at an examination or where it may have affected your performance in an element of assessment or where you have been unable to attend a specified teaching session, you are strongly advised to provide medical certification (see section 3 of the Policy on Certification of Absence for Medical Reasons or Other Good Cause). Medical certificates are to be submitted to the School Office immediately on return to classes after an absence or non-submission of assignments due to medical reasons. The School reserves the right to reject medical certificates issued or submitted an excessive time after the period of absence. Other reasons for absence or non-submission of assignments must be presented in writing to the School Office. Students who do not present adequate reasons for failure to submit written work on time will be awarded zero marks for the assignment concerned. MONITORING STUDENTS’ PROGRESS 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 21
  • 22. 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. CLASS CERTIFICATES A class certificate is defined as “a certificate confirming that a candidate has attended and duly performed the work prescribed for a course”. The period of validity for a class certificate is limited to the academic year in which it is awarded and the academic year immediately following. Hence, candidates have a maximum of four opportunities to take the end-of-course assessment without re-attendance i.e. the normal (January or May) diet and the August resit diet in the year in which the course is taken and the year immediately following. Students who have been reported as ‘at risk’ through the system for monitoring students’ progress due to their failure to satisfy the minimum criteria (as outlined above) may be refused a class certificate. If you are refused a class certificate, you will receive a letter from the Registry (e-mail in term-time) notifying you of this decision. Students who are refused a class certificate are withdrawn from the course and cannot take the prescribed degree assessment in the current session, nor are eligible to be re-assessed next session, unless and until they qualify for the award of a class certificate by taking the course again in the next session. If you wish to appeal against the decision to refuse a class certificate should do so in writing to the Head of School within fourteen days of the date of the letter/e-mail notifying you of the decision. If your appeal is unsuccessful, you have the right to lodge an appeal with the relevant Director of Undergraduate Programmes within fourteen days of the date you are informed of the Head of School’s decision. As this course forms part of an Honours programme, you should be aware that if you are refused a class certificate, you will be awarded the equivalent of a No Paper (NP) for the course, i.e. a CAS mark of zero when applied to the Grade Spectrum used for determining degree classification. This will mean that, normally, you would be unable to gain a higher class of degree than Lower Second Class Honours. IF YOU WISH TO CHANGE YOUR CURRICULUM: YOU MUST OBTAIN THE APPROVAL OF YOUR ADVISER AS SOON AS POSSIBLE AND TELL THE DEPARTMENT/SCHOOL CONCERNED. CLASS REPRESENTATIVES 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 year representatives. Any students registered within a year 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 year 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 in conjunction with SPARQS (Student Participation in Quality Scotland). 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 22
  • 23. the VP Education & Employability vped@abdn.ac.uk . For further information on class representation and student involvement in Quality visit www.sparqs.org.uk MISSION STATEMENTS THE UNIVERSITY OF ABERDEEN MISSION STATEMENT The University of Aberdeen aims to create, develop, apply and transmit through the work of all its members, knowledge, skills and understanding at the highest levels of excellence. SCHOOL OF MEDICAL SCIENCES (MCB) MISSION STATEMENT 1. Provide high quality educational programmes which stimulate and foster interest and enthusiasm in Biochemistry, Genetics, Immunology and Microbiology and provide a training for a career in these and related disciplines. 2. Encourage and support the dissemination of research in Biochemistry, Genetics, Immunology and Microbiology through publications and participation in conferences. 3. Promote and develop excellent research programmes in pure and applied aspects of Biochemistry, Genetics, Immunology and Microbiology and encourage collaboration within the University and, externally, with industry and government research institutes. 4. Develop and provide high quality programmes of training and development for research staff. 5. Encourage and facilitate training for academic staff to optimise their teaching and research skills and performance. AIMS With regard to education, we aim to: 1. continue to provide courses and Degree programmes in Biochemistry, Biotechnology, Genetics, Immunology, Microbiology, Molecular Biology and Biomedical Sciences which are attractive to students and provide high quality education in these topics; 2. provide the conditions and facilities which optimise the potential for students to gain an understanding and appreciation of Biochemistry, Genetics, Immunology and Microbiology; 3. foster and encourage curiosity, originality, creativity and critical appraisal associated with the study of Biochemistry, Biotechnology, Genetics, Immunology, Microbiology, Molecular Biology and Biomedical Sciences in particular and scientific study in general; 4. maintain and develop procedures for entry of mature and other non-standard students to undergraduate courses and Degree programmes in Biochemistry, Biotechnology, Genetics, Immunology, Microbiology, Molecular Biology and Biomedical Sciences; 5. encourage the development of personal and transferable skills to equip students for careers and situations which are not specific to their chosen subject; 6. optimise the allocation and utilisation of resources to maintain the facilities required for delivery of high quality teaching; 7. provide the facilities and procedures necessary for continual review and modification of aims, curricula and course content necessary to achieve the above aims, including seeking and considering the opinions of students and extra-departmental experts; 8. provide an atmosphere and procedures which make the learning process enjoyable, stimulating and challenging; OBJECTIVES AND LEARNING OUTCOMES 23
  • 24. We intend that students attending our courses and Degree programmes should: 1. acquire factual, up-to-date knowledge and practical skills required for a career in Biochemistry, Biotechnology, Genetics, Immunology, Microbiology, Molecular Biology and Biomedical Sciences; 2. for students taking Degree courses outwith the School of Medical Sciences , acquire the fundamental factual knowledge and understanding of Biochemistry, Genetics, Immunology and Microbiology required for their particular Degrees; 3. develop personal transferable skills required for scientific study, including numeracy, information retrieval, computer literacy, presentation skills, group work, essay and thesis writing; 5. develop general conceptual skills, including problem solving, creative and original thought, hypothesis generation and testing, interpretation and critical evaluation of experimental data and published work. SUBJECT SPECIFIC STANDARDS EXPECTED FOR STUDENTS COMPLETING HONOURS COURSES IN BIOCHEMISTRY, GENETICS, IMMUNOLOGY AND MICROBIOLOGY (a) Biochemistry (BC4012), Biochemistry (Immunology) (BC4013), Biotechnology (BT4005), Genetics (GN4007), Genetics (Immunology) (GN4008), Microbiology (MC4012), Molecular Microbiology (MC4013), Molecular Biology (MB4004), Biomedical Sciences (Molecular Biology) (BM4008), Immunology (IM4002) The aims of the course are to enable students: (a) to establish a knowledge of aspects of advanced molecular and cell biology, including protein structure and function, the regulation of gene expression, genome organisation and analysis, and development and form at the cell and whole organism level. (b) to establish a knowledge at advanced level of specific aspects of biochemistry, microbiology, immunology or genetics appropriate to the degree course being studied. The core course-specific learning outcomes are such that, at the end of the course, students should be able to: (a) describe the current state of understanding of molecular genetics, in the context of genome structure and evolution, using data emerging from the microbial and eukaryote genome sequencing projects; understand methods and approaches being used to understand function of novel genes. (b) understand major principles that determine the three-dimensional structure of proteins, evolution of proteins, how evolution has shaped protein structure and function, the contribution of structure to function, and the physical and chemical constraints on protein structure and function. (c) describe the processes and mechanisms determining bacterial, yeast and animal gene expression (using specific examples), ranging from transcription regulation to mRNA degradation. Students will be aware of the role of control of gene expression in the context of differentiation, development and the adaptation to changes in the environment. (d) understand the ways in which cells and groups of cells in tissues establish shape, polarity and undergo morphogenesis, giving an overview of how form and function is generated at the cell and molecular level, and how form contributes to function. Students will be aware of the contribution of cell morphogenesis to the generation of diversity of forms in complete simple and complex cellular life forms. The subject-specific learning outcomes are such that, at the end of the course; Biochemistry students and those students combining either of the two biochemistry options should be able to: 24
  • 25. For Option 1 (Receptors and Cell Signalling) and Essay 1 (RNA catalysis and modification) (a) describe using examples from specific families of receptors, the ways in which receptor proteins transmit information from the extra-cellular environment to the intracellular site of action and the mechanisms by which cross-talk between different signalling pathways can be achieved. (b) Describe the role of rRNA and tRNA molecules in gene expression; understand RNA-based catalysis and the role of RNA modifications. For Option 2 (Mechanisms of Human Disease) and Essay 2 (Nucleo-cytoplasmic transport) (a) use examples of key infectious human diseases to analyse the molecular mechanisms underlying the subversion and exploitation of the biochemistry of the human host; describe the nature of the disease- causing agents and their how their activities contribute to pathogenicity at the molecular level. (b) understand the molecular basis of nucleo-cytoplasmic transport, a fundamental cell biological process. Microbiology students and those students combining either of the two microbiology options should be able to: For Option 1 (Molecular Genetic Evolution in Micro-organisms) and Essay 1 (Microbiology) (a) using well studied microbial groups the students will gain understanding of the molecular methods used to analyse species formation in microorgansims and of the insights gained by these approaches. (b) describe, using a range of examples, the complexities of the molecular basis of host-microbe interactions, and their relevance to symbiosis and pathogenicity For Option 2 (Antibiotic Synthesis and Resistance) and Essay 2 (Microbiology) (a) describe the molecular principles that underlie the molecular mechanisms of resistance to antimicrobial compounds or the development and evolution of resistance to anti-microbial drugs. (b) describe the theory and importance of metabolic flux in bacteria, and the importance of genome sequencing in anti-microbial drug design. Genetics students and those students combining either of the two genetics options should be able to: For Option 1 (Human Medical Genetics) and Essay 1 (Dynamic Genomes) (a) describe the role of cytogenetics in gene mapping and identification of congenital defects; understand the role of animal models in elucidating the role of the gene products and the role of epigenetic phenomenon in modifying gene expression. Lastly, the student will be able to describe the operation and workings of a DNA Diagnostic laboratory. The student will be aware of the ethical dimension to diagnosis of human medical conditions. (b) understand the forces, both directed and random, that shape the formation and reformation of genomes, including transposon activity, and examples of programmed genome re-arrangements. For Option 2 (Population Genetics) and Essay 2 (Genetic Analysis) (a) understand how population genetic composition is controlled by mutation rates and selection, how human genetic disease incidence is directed by genetic epidemiological factors including gene polymorphism-phenotype association; describe the relationship of population structure to evolutionary history. (b) analyse the role of modern molecular genetic methodologies in genome analysis, genetic disease diagnosis and forensics. Immunology students and those students combining the immunology option should be able to: For Option 1 (Infection, Immunity and Inflammation) and Essay 1 (Immunology) 25
  • 26. a) understand and describe the interaction of cells cytokines chemokines and other immune mediators that regulate leucocyte trafficking and migration during inflammation and how these processes may lead to autoimmune or allergic disease. b) describe the complex cellular and molecular processes underlying the co-ordinated series of events linking the innate and adaptive immune response to infection. c) understand how modern imaging technologies and emerging disciplines such as immuno- epidemiology can be used to understand molecular and cellular processes underlying disease. For Option 2 (Molecular Immunology) and Essay 2 (Immunology) (a) describe the human adaptive immune response and the role inheritance genes of the immune system play in disease susceptibility; and how immunological homeostaisis is maintained by regulatory cells, and how immunological dysfunction can lead to disease. (b) understand how specialized antigen receptors of T and B lymphocytes function to induce immunity, tolerance or disease. (c) describe the role of phage display technologies in elucidating immuno-generic repertoires and understand the contribution of MHC structure to its function in T cell recognition. In addition, for all students, intellectual skills consolidated comprise: (a) recognition that for all cell types, from prokaryotes and archaea to higher eukaryote cells, form and phenotype, and dynamic processes such as development and evolution, are governed ultimately by the physical and chemical properties of the molecular components of cells, principally proteins and nucleic acids. (b) ability to apply subject-specific knowledge and understanding to address problems in molecular and cell biology Practical skills advanced comprise: (a) ability to search for and access bioscience literature resources using Web-based search programs (b) ability to use protein and nucleic acid search and comparison algorithms; (c) ability to communicate effectively in writing in the form of essays and the Honours thesis. Numeracy and communication skills are encouraged by opportunities to: (a) analyse literature-derived numerical data and discuss scientific papers during tutorials; (b) verbally address topics during tutorials; Interpersonal and teamwork skills are encouraged by opportunities to: (a) work productively with others in tutorials and class computer program tutorials; (b) recognise and respect the views and opinions of others during tutorials; Self management skills are needed in: (a) balancing the various demands of this and other courses you are studying. For the following course codes; (b) Biochemistry (BC4512), Biochemistry (Immunology) (BC4513), Biotechnology (BT4505), Genetics (GN4507), Genetics (Immunology) (GN4508), Microbiology (MC4512), Molecular Microbiology (MC4513), Molecular Biology (MB4504), Biomedical Sciences (Molecular Biology) (BM4508), Immunology (IM4502) The aims of these courses are to enable students: (a) to develop practical research expertise by undertaking a laboratory research project, a literature research project, or a computer-based bioinformatics-type project. (b) to establish a knowledge, at advanced level, of specific aspects of biochemistry, genetics, immunology or microbiology appropriate to the student's degree title, through study of the scientific literature. 26
  • 27. The subject-specific learning outcomes are such that, at the end of the course. Biochemistry and related students should be able to: (a) describe, understand and evaluate suitable experimental approaches appropriate to the study of DNA repair recombination and replication. (b) describe, understand and evaluate suitable experimental approaches appropriate to such fundamental cell biological processes as secretion, and vesicle trafficking Microbiology and related students should be able to: (a) describe, understand and evaluate suitable experimental approaches appropriate to the study of cell motor proteins such as kinesins, and the dynamic processes they participate in, and describe our current understanding of kinesin structure/function relationships in different fungal species. (b) describe, understand and evaluate suitable experimental approaches appropriate to the study of molecular epidemiology, and describe our current understanding of epidemiology of bacterial pathogens. Genetics and related students should be able to: (a) describe, understand and evaluate approaches for studying the evolution and history of human populations, based on molecular genetic analysis; gain an appreciation, in outline form, of the mathematical techniques used for this analysis. (b) describe, understand and evaluate suitable experimental approaches appropriate to the study of complex phenotypes such as schizophrenia, and describe our current understanding of schizophrenia aetiology. Immunology and related students should be able to: a) Demonstrate a broad knowledge and understanding of immunology at the cellular, molecular and physiological levels, and show an appreciation of the importance of immunology in medicine, agriculture, biotechnology and industry. b) Apply their knowledge and skills acquired during the course to the solution of practical and theoretical problems and be able to proceed to further studies in specialised areas of immunology or multi- disciplinary areas involving immunology. c) Describe, understand and critically appraise experimental approaches appropriate to the study of molecular and cellular immunology in health and disease. In addition, intellectual skills consolidated comprise: (a) ability to carry out research, derive results, process these and using this information, to design subsequent experiments (b) ability to reach justifiable and logical conclusions based upon acquisition of primary research data. (c) ability to apply subject-specific knowledge and understanding to address problems (during tutorials); Practical skills advanced comprise: (a) in the case of literature research projects, the ability to search for specific literature resources using Web-based search programs (b) in the case of bioinformatic research projects, the ability to use protein and nucleic acid search and comparison algorithms; (c) in the case of lab-based research projects, the ability to undertake specific project specific techniques and protocols. (d) generally, the ability to plan, execute, and present the results of a 9 week project (e) the ability to place the results of that project in context, and suggest further lines of investigation. Numeracy and communication skills are encouraged by opportunities to: (a) analyse literature-derived numerical data and discuss scientific papers during tutorials; (b) verbally address topics during tutorials; 27
  • 28. (c) processing and manipulation of data derived from the research project (d) presentation of research project data to lab. research meetings, and as part of the Honours thesis presentation exercise. Interpersonal and teamwork skills are encouraged by opportunities to: (a) work productively with others in tutorials and research groups; (b) recognise and respect the views and opinions of others during tutorials and research lab. meetings. Self management skills are needed in: (a) balancing the various demands of this and other courses you are studying. HONOURS ASSESSMENT Submission of written work All written work (theses, essays) must be submitted to the School Office (not to individual staff members). The submission of your work will be recorded and distribution to members of staff undertaken. You are responsible for recovering the work, again from the office, once the marking process is complete. It is vital that the deadlines given are adhered to. Submit an incomplete piece of work rather than miss a deadline. Work not submitted on time will not be accepted unless accompanied by either a medical certificate or a written explanation justifying this Deadlines are: 17.10.06 Essay 1 (3 copies) (hand in completed plagiarism sheet with essay) 15.11.06 Essay 2 (3 copies) (hand in completed plagiarism sheet with essay) 12.12.06 Essay 3 (3 copies) (hand in completed plagiarism sheet with essay) 18.04.07 Thesis (2 copies) (hand in completed work sheet with thesis) Examinations Five papers are taken in May. The exams will comprise three 3 hour papers, one on the Advanced Molecular Biology core course (Paper 1; answer 2 questions from 4 in section A, 2 questions from 4 in section B), another on the options lecture course (Paper 2; 2 sections with 3 questions each, answer 2 questions per section); and the third will examine the research tutorials material (paper 3, 3 hours; 4 questions, no choice). One 2 hour paper and one 4 hour paper, test general essay writing (paper 4, 2 hours; write two essays from a choice of 10) and data analysis skills (paper 5, 4 hours; no choice of question). The Data Analysis paper will have the following format: • There will be one common paper for all students, relying on common elements of the course. • At the start of the examination each student will be handed a slightly modified copy of a research paper from which the title, abstract, discussion and references have been deleted and the examination paper. • You should set aside 30 minutes at the start of the exam to study the paper and make notes. • At the end of the 30 minutes each student should answer the questions in the exam paper from their own knowledge of their discipline and from the information in the research paper they have studied. • The paper contains three sections: Section A is primarily concerned with the Methods section of the research paper; Section B is primarily concerned with analysis of the results presented in the paper, but may also call for interpretation and for suggestions for further experimentation; 28
  • 29. Section C requires that the student suggest, in response to specific questions, ways in which the research described in the paper could be extended in future. The student is also required to write a 150 word scientific summary of the paper. • Students will be allowed a total of 4 h for the Data Analysis exam. • Students will not be allowed to remove the examination papers from the examination room. • Students are permitted to bring a calculator to the examination. The examination timetable will be posted on student portals and emailed to all students, as soon as it is available. Marking Marking of examination scripts is carried out on coded scripts, so that the identity of the student is unknown to the marker. Please co-operate in this by giving no information that would identify you on your examination scripts; only your student ID number is necessary. Marking is carried out independently by two members of staff, and marks agreed if they differ. A copy of the CAS (Common Assessment Scale) scheme used is included in this section. All work (continuous assessment and examinations) will be marked using this scale, and you will be told the CAS marks attained in your written submissions (essays, etc.). All work is marked by two members of staff, using the same rules of agreement as for examination scripts. Detailed information on how laboratory performance, theses and project seminars and examination are assessed is included in the Project section. Similarly, there is specific information on assessment of essays in the relevant section of the manual. Oral examination and interviews Once papers 1-5 are done the examination process is not complete. You may be called for an oral examination (viva), where you will meet the external examiner accompanied by an internal examiner. These will take place on either 7th or 8th June. This is officially term time, and you have a duty to be available at that time. Please make sure therefore that you are in Aberdeen and in contact with the School Office. A list of candidates to be examined will be put up outside the office as early as possible that week, as soon as we have the agreement of the external examiners. This list will make clear who is being asked for a viva because their performance is borderline for a particular degree class (you may not want to know that, but it is a current University regulation). In addition to this, the external examiners will want to meet (interview) some students in order to assess how good the courses are, how well the students enjoyed the courses. If your are asked for a viva because you are borderline, try not to be nervous (!), and definitely do not be despondent; a viva is a great opportunity to go up a degree classification, since students are asked if their marks lie close to, but below, a particular borderline between two degree classes. A good viva performance will impress the external examiner, who may recommend you be pushed up a grade. Remember that this is an opportunity to improve and that your grades cannot go down. External examiners often like to talk about your project - you should be able to give an informed account of what you did, what it all means, and what the background is. Externals also often ask what you enjoyed most on the course - i.e. an opening to talk about a molecular and cell biology subject that enthuses you. A bad thing to do is to suggest a favourite subject, and then 'dry up', not having revised it - pick a subject beforehand, and prepare it well so you can talk about it, again in an informed way. You should expect a range of questions over different parts of the course. If you know that you did badly in a particular area during the exams, revise that part. 29
  • 30. 30
  • 31. Honours Degree Classification All Honours Degrees are classified using the University’s Grade Spectrum which is available at http://www.abdn.ac.uk/registry/quality/appendix7x4.pdf. The Grade Spectrum, an extract of which is outlined below, is used to determine degree classification on the basis of the CAS mark awarded for each element of Honours Degree Assessment. First: Marks at 18 or better in elements constituting half the total elements; and Marks at 15 or better in elements constituting three quarters of the total elements; and Normally marks at 12 or better in all elements. 2i: Marks at 15 or better in elements constituting half the total elements; and Marks at 12 or better in elements constituting three quarters of the total elements; and Normally marks at 9 or better in all elements. 2ii: Marks at 12 or better in elements constituting half the total elements; and Marks at 9 or better in elements constituting three quarters of the total elements. Third: Marks at 9 or better in elements constituting three quarters of the total elements. The Grade Spectrum defines the threshold standards against which the different classes of honours degree are awarded. The Examiners, however, have discretion (in the circumstances defined in Note 4 of the Grade Spectrum) to depart from this and may choose to award a higher degree than that indicated by the Grade Spectrum. The course elements used to determine honours classifications are: Individual questions in Paper 1 1 element per question answered, 4 elements in total Individual questions in Paper 2 1 element per question answered, 4 elements in total Individual questions in Paper 3 1 element per question answered, 4 elements in total Individual questions in Paper 4 1 element per question answered, 2 elements in total Paper 5 (Data analysis) 3 elements in total Project: Laboratory work 1 element Thesis 2 elements Project seminar and oral examination 1 element Individual essays (Essays 1, 2 and 3) 3 elements in total Total elements 24 Note that assessment of the honours degree programmes is summarised in 3 final marks: One for the core course (Paper 1 and essay 3), one for the options module (Paper 2 and essays 1 and 2), and a third mark for the honours project, the written thesis, the thesis defence and papers 3, 4 and 5. Credit Requirements for the award of an honours degree. All students who are admitted to an Honours programme, in or after 2004/05, will be required to achieve 480 credit points, including at least 180 at levels 3 and 4, of which at least 90 must be at level 4. This change to the requirements for the award of an Honours Degree was made by the Senate to ensure that Honours degrees are awarded in compliance with the Scottish Credit and Qualifications Framework (SCQF). Further information is available at www.scqf.org.uk. Accordingly, students failing to meet this credit requirement at the first attempt will require to make up this credit shortfall before graduating. How this can be achieved is summarised below. Note that in these degree programmes “element” refers to one of the 3 final course marks, and not to a single element of 31
  • 32. assessment. In case that one of these course marks is a fail, candidates may have to resit relevant exams for a degree to be awarded. Note that this, except in case of illness or other good cause, will only result in the award of sufficient credits, but will not affect the degree classification. General Regulation 21, as outlined below, sets out the procedures available to enable students to make up this credit shortfall. In the case of a candidate who has failed to complete satisfactorily an element of Honours degree assessment1 at the time prescribed by Regulation 9.3, then the appropriate procedure from (a) to (e) below shall apply: a) If, but only if, the failure is on account of illness or other good cause, the candidate shall be required to submit themselves for assessment at the next available opportunity, and shall be permitted to count the result of that assessment towards Honours classification. b) If the failure is the result of absence or non-submission for any other cause, the candidate shall be awarded zero for the assessment concerned and shall be required to submit themselves for assessment at the next available opportunity, but shall not be permitted to count the result of that assessment towards Honours classification. c) For courses at level 4 and above only, if the candidate has completed the assessment but been awarded a mark on the Common Assessment Scale between 6 and 8 inclusive, they shall be awarded the same amount of unnamed specific credit, not exceeding 30 credit points in total, at level 1. d) If the candidate has completed the assessment, but the course is at level 3, or the course is at level 4 or above and the mark awarded on the Common Assessment Scale is less than 6, the candidate shall be required to submit themselves for assessment at the next available opportunity, but shall not be permitted to count the result of that assessment towards Honours classification. Alternatively, for courses at level 4 and above only, such candidates may elect to attend and submit themselves for assessment in another course or courses of equivalent credit value, which may be at any level. e) If any of options (a), (b) or (d) above would normally apply, but medical advice indicates that it would be unreasonable to require a candidate to appear for assessment on a subsequent occasion, and if the candidate’s past record provides sufficient evidence that they would have obtained Honours, the examiners may recommend the award of an Aegrotat degree, but only after obtaining the consent of the candidate. The award of an Aegrotat degree will debar candidates from counting towards Honours degree assessment any result achieved thereafter. Notes (i) For courses at level 4 and above, the timing and format of the assessment required under any of sub-sections (a), (b) or (d) above shall be determined by the Academic Standards Committee (Undergraduate) on the recommendation of the Head of the relevant School. (ii) The options to achieve or be awarded credit under (b), (c) and (d) above shall not be available to candidates who have accumulated less than 90 credit points at level 4 or who have failed to complete satisfactorily the assessment for a course which, on the recommendation of the Head of the relevant School, has been prescribed by the Academic Standards Committee (Undergraduate) as compulsory for the award of a degree with Honours. Such candidates will be able to qualify for a non-Honours degree only. Further guidance is also available in the Guidance Note for Students who either Fail, or who Fail to Attend or Complete, an Element of Prescribed Degree Assessment which can be accessed at: http://www.abdn.ac.uk/registry/quality/appendix7x6.pdf 1 Note that “element” refers to one of the 3 final course marks, and not to a single element of the 24 elements of assessment. 32
  • 33. SCHOOL OF MEDICAL SCIENCES (MOLECULAR & CELL BIOLOGY) LEVEL 3 AND 4 MARKING SCHEME AND PERCENTAGE/CAS CONVERSION STUDENTS SHOULD NOTE THAT SPECIFIC FORMS ARE USED FOR PARTICULAR ASSESSMENTS, FOR INSTANCE ORAL PRESENTATIONS; THE FORMS FOR THESE SHOW WHAT IS CONSIDERED IMPORTANT. DESCRIPTION PERCENTAGE CAS FIRST: OUTSTANDING WORK, SHOWING THOROUGH UNDERSTANDING; 91-100 20 DISCRIMINATION IN THE USE OF INFORMATION AND STRONG ANALYTICAL ABILITY; EVIDENCE OF EXTENSIVE USE OF ORIGINAL LITERATURE (ESPECIALLY FOR CAS 19/20). CAS 18 FOR WORK SHOWING 81-90 19 EXCELLENT SYNTHESIS OF CONCEPTS, IN ITSELF EVIDENCE OF CRITICAL READING 70-80 18 Answer/essay well-structured with good style and appropriate diagrams integrated with the text. Good integration of material from different elements of the course. UPPER SECOND: WORK SHOWING GOOD UNDERSTANDING OF THE CRITICAL CONCEPTS; 67-69 17 WORK DRAWN LARGELY FROM LECTURE MATERIAL AND FROM A LIMITED SELECTION OF THE LITERATURE; GOOD USE OF EXAMPLES 64-66 16 Marks at the upper end of the scale for integration of material from different elements 60-63 15 of the course. Marks deducted for minor errors. LOWER SECOND: REASONABLE ATTEMPT AT ADDRESSING THE QUESTION BUT SHOWING 57-59 14 LIMITED UNDERSTANDING AND/OR KNOWLEDGE 54-56 13 Few illustrative examples; important facts omitted or lacking breadth. 50-53 12 THIRD: A POOR ANSWER THAT SHOWS SOME RELEVANT KNOWLEDGE BUT 47-49 11 LACKS FOCUS ON THE CENTRAL QUESTIONS 44-46 10 Other major shortcomings, such as inaccuracy, random rather than selected content, material largely irrelevant to the question, poor presentation. 40-43 9 FAIL: 37-39 8 SERIOUSLY LACKING IN CONTENT AND ACCURACY 34-36 7 30-33 6 Marks are given for any relevant material using the full range shown: 25-29 5 CAS 6-8 for some material relevant to the set question 20-24 4 CAS 1-5 for minimal content 15-19 3 CAS 0 for no answer 10-14 2 5-9 1 0-4 0 The CAS scale is not linear. CAS scores are indicators of performance and cannot be averaged or mathematically-manipulated in any way. 33
  • 34. PRESCRIBED MODULES FOR HONOURS DEGREES 2006-2007 ALL HONOURS DEGREES ATTEND THE FOLLOWING ADVANCED MOLECULAR AND CELL BIOLOGY CORE MODULES - 1. Genome organisation and analysis 3. Control of gene expression 2. Evolution of protein structure and function 4. Form and development DEGREE COURSE CODE OPTION MODULES Research Tutorials Biochemistry BC4012 / Receptors and Cell Signalling & MB4050 / BC4512 Biochemisty of Human Diseases Res. Tutorial; Biochem. 1 and 2 Biochemistry BC4013 / Receptors and Cell Signalling & (Immunology) MB4050 / BC4513 Molecular Immunology Res. Tutorial; Biochem. 1 and Immunol. 2 Biotechnology (Appl. Mol. BT4005 / 2 modules from the following list of general subject Biol.) MB4050 / BT4505 categories: biochemistry, genetics, microbiology and immunology Research Tutorials corresponding to Options in semester 1; e.g. if options choice is Biochem 1 + Genetics 2, then Res. Tutorials will be Biochem 1 + Genet. 2 Genetics GN4007 / MB4050 Medical Genetics & / GN4507 Population Genetics Res. Tutorial; Genetics. 1 and 2 Genetics (Immunology) GN4008 / MB4050 Medical Genetics & / GN4508 Molecular Immunology Res. Tutorial; Genetics. 1 and Immunol. 2 Immunology IM4002 / Infection, Immunity and Inflammation & MB4050 / IM4502 Molecular Immunology Res. Tutorial; Immunology 1 and 2 Microbiology MC4012 / MB4050 Population and Environment & / MC4512 Antibiotic Synthesis and Resistance Res. Tutorial; Microbiology 1 and 2 Molecular Microbiology MC4013 / MB4050 Receptors and Cell Signalling & / MC4513 Antibiotic Synthesis and Resistance Res. Tutorial; Biochem. 1 and Microbiol. 2 Molecular Biology MB4004 / MB4050 Medical Genetics & / MB4504 Biochemisty of Human Diseases Res. Tutorial; Genetics. 1 and Biochem 2 Biomedical Sciences BM4008 / MB4050 Receptors and Cell Signalling & (Molecular Biology) / BM4508 Biochemisty of Human Diseases (for students having taken Res. Tutorial; Biochem. 1 and 2 BC3804) Biomedical Sciences BM4008 / MB4050 Receptors and Cell Signalling & (Molecular Biology) / BM4508 Molecular Immunology (for students having taken Res. Tutorial; Biochem. 1 and Immunol 2 IM3802) 34
  • 35. CORE COURSE SESSION 2006-2007 Genome Organisation and Analysis - Dr Jonathan Pettitt Week Date Time Title Staff Venue 12 M 25.9 9-10 The Honours Year Prof Docherty, Dr Mueller, & Dr Schofield FLT Tu 26.9 9-10 Yeast Genome 1 Prof Brown FLT 12-1 Yeast Genome 2 Prof Brown FLT W 27.9 9-10 Yeast Genome 3 Prof Brown FLT 10-11 Animal Genomes 1 Dr Pettitt FLT Th 28.9 9-10 Animal Genomes 2 Dr Pettitt FLT 13 Tu 3.10 9-10 Animal Genomes 3 Dr Pettitt FLT 4-5 Animal Genomes 4 Dr Pettitt FLT W 4.10 3-4 Comparative genomics in mammals 1 Prof Shaw FLT 4-5 Comparative genomics in mammals 2 Prof Shaw 1:032/033 Evolution of Protein Structure and Function - Professor Nuala Booth Week Date Time Title Staff Venue Th 5.10 9-10 Protein Evolution Dr Pettitt FLT 4-5 Protein Evolution: constraints Dr Pettitt FLT Fr 6.10 12-1 Protein Evolution: modular proteins Dr Pettitt FLT 14 M 9.10 9-10 Protein folding: pathways Dr McEwan FLT Tu 10.10 9-10 Protein folding: flexibility and conformation Dr McEwan FLT W 11.10 3-5 Tutorial - Protein structure Dr Stansfield Comp Rm 3 Th 12.10 9-10 Protein folding: aberrant folding Dr McEwan FLT 15 M 16.10 9-10 Proteolysis Prof NA Booth FLT Tu 17.10 9-10 Proteolysis: protease families Prof NA Booth FLT 10-12 Tutorial – Folds and function Prof IR Booth Comp Rm 3 W 18.10 9-10 Proteolysis: protease inhibitor families Prof NA Booth FLT F 20.10 3-5 Tutorial – paper presented and discussed Prof IR Booth, Prof NA Booth, Dr McEwan, Dr Pettitt & 1.032/033, 1.034, Dr Stansfield 1.039, 1.040 35
  • 36. Control of Gene Expression - Dr Berndt Mueller Week Date Time Title Staff Venue Th 19.10 12-1 Transcription and Chromatin structure (1) Dr McEwan FLT 16 M 23.10 9-10 Transcription and Chromatin structure (2) Dr McEwan FLT 4-5 Transcription and Chromatin structure (3) Dr McEwan FLT Tu 24.10 9-10 Transcription and Chromatin structure (4) Dr McEwan FLT 1-2 Transcription and Chromatin structure (5) Dr McEwan FLT 17 M 30.10 9-10 Myogenesis and sex differentiation (1) Dr Shennan FLT 4-5 Myogenesis and sex differentiation (2) Dr Shennan FLT Tu 31.10 9-10 Myogenesis and sex differentiation (3) Dr Shennan FLT 1-2 Myogenesis and sex differentiation (4) Dr Shennan FLT Th 02.11 1-2 Post-transcriptional control of gene expression (1)Dr Mueller FLT 2-3 Tutorial 1 Dr Mueller 1:040 Fr 03.11 11-12 Tutorial 1 Dr McEwan 1:032/033 1-2 Tutorial 1 Dr Shennan 1:039 18 Tu 07.11 1-2 Tutorial 2 Dr Mueller 1:032/033 1-2 Tutorial 2 Dr McEwan 1:040 3-4 Post-transcriptional control of gene expression (2)Dr Mueller FLT 4-5 Tutorial 2 Dr Shennan 1:040 W 08.11 2-3 Post-transcriptional control of gene expression (3)Dr Mueller FLT F 10.11 12-1 Post-transcriptional control of gene expression (4)Dr Mueller FLT Development and Form - Professor Neil Gow Week Date Time Title Staff Venue 19 M 13.11 11-12 Tutorial Dr Pettitt FLT Tu 14.11 10-11 Yeast cell and cell polarity (1) Prof Gow 1:032/033 1-2 Yeast cell and cell polarity (2) Prof Gow 1:032/033 3-4 Yeast cell and cell polarity (3) Prof Gow FLT W 15.11 11-12 Embryonic polarity (1) Dr Pettitt FLT Th 16.11 1-2 Tissue polarity and animal morphogenesis (1) Dr Pettitt FLT F 17.11 9-12 Tutorial Prof Gow, Dr Pettitt & Project Room, Dr Hoppler Medical School Library 20 M 20.11 9-10 Tissue polarity and animal morphogenesis (2) Dr Pettitt FLT Tu 21.11 12-1 Tissue polarity and animal morphogenesis (3) Dr Pettitt FLT Th 23.11 9-10 Axis establishmentin embryogenesis (1) Dr S Hoppler FLT 12-1 Axis establishmentin embryogenesis (2) Dr S Hoppler FLT F 24.11 2-4 Tutorial Prof Gow, Dr Pettitt & Dr Hoppler FLT 36
  • 37. BIOCHEMISTRY OPTION 1 - RECEPTORS AND CELL SIGNALLING SESSION 2006-2007 Biochemistry Biochemistry (Immunology) Biomedical Sciences (Molecular Biology) Molecular Microbiology Week Date Time Class Staff Venue 13 Tu 03.10 1-2 Receptor Structure and Cell signalling (1) Prof Docherty 1:039 W 04.10 1-2 The Wnt signalling pathway (1) Dr Hoppler 1:040 Th 05.10 11-12 The Wnt signalling pathway (2) Dr Hoppler 1:040 F 06.10 9-10 The Wnt signalling pathway (3) Dr Hoppler 1:040 14 W 11.10 11-12 Receptor Structure and Cell signalling (2) Prof Docherty 1:040 1-2 Receptor Structure and Cell signalling (3) Prof Docherty 1:040 Th 12.10 10-11 Receptor Structure and Cell signalling (4) Prof Docherty 1:040 F 13.10 9-10 Receptor Structure and Cell signalling (5) Prof Docherty 1:040 15 Tu 17.10 1-2 Nuclear receptor superfamily (1) Dr McEwan 1:040 W 18.10 11-12 Nuclear receptor superfamily (2) Dr McEwan 1:040 1-2 Nuclear receptor superfamily (3) Dr McEwan 1:040 Th 19.10 11-12 Nuclear receptor superfamily (4) Dr McEwan 1:040 F 20.10 9-10 Tutorial Dr McEwan 1:040 Module Organiser - Dr Iain McEwan (55807; 55887; e-mail iain.mcewan@abdn.ac.uk) 37
  • 38. BIOCHEMISTRY OPTION 2 – BIOCHEMISTRY OF HUMAN DISEASES SESSION 2006-2007 Biochemistry Biomedical Sciences (Molecular Biology) Molecular Biology Week Date Time Class Staff Venue 17 M 30.10 12-1 Towards an understanding of human prions (1) Dr Stansfield 1:032/033 W 01.11 12-1 Towards an understanding of human prions (2) Dr Stansfield 1:034 1-2 Towards an understanding of human prions (3) Dr Stansfield 1:034 Th 02.11 12-1 The molecular biology of HIV and AIDS (1) Dr Long 1:039 3-4 Towards an understanding of human prions (4) Dr Stansfield 1:040 18 M 06.11 12-1 The molecular biology of HIV and AIDS (2) Dr Long 1:032/033 W 08.11 12-1 The molecular biology of HIV and AIDS (3) Dr Long 1:034 1-2 The molecular biology of HIV and AIDS (4) Dr Long 1:034 Th 09.11 12-1 Virus-cell interactions during virus-induced transformation (1) Dr Cash 1:039 F 10.11 2-3 Virus-cell interactions during virus-induced transformation (2) Dr Cash 1:032/033 19 M 13.11 10-11 Virus-cell interactions during virus-induced Dr Cash 1:032/033 transformation (3) 3-4 Virus-cell interactions during virus-induced Dr Cash 1:034 transformation (4) 20 Tu 21.11 2-5 Tutorial Dr Cash, Dr Long & Dr Stansfield 1:032/033 Module Organiser – Dr Bill Long (e-mail: w.f.long@abdn.ac.uk ~ tel: (27) 4175) 38
  • 39. GENETICS OPTION 1 – MEDICAL GENETICS SESSION 2006-2007 Molecular Biology Genetics Genetics (Immunology) Week Date Time Class Staff Venue 13 M 02.10 10-12 Controversies in medical genetics Dr Schofield 1:032/033 Tu 03.10 10-11 Cytogenetics (1) Mr Stevenson 1:032/033 W 04.10 9-11 Tutorial Group 1: Stem cell research Dr Schofield 1:034 Th 05.10 10-12 Tutorial Group 2: In vitro fertilisation and imprinting Dr Kelly 1:039 2-3 Cytogenetics (2) Mr Stevenson FLT F 06.10 9-11 Tutorial Group 3: Genetic testing Dr Schofield 1:032/033 3-4 Cytogenetics (3) Mr Stevenson 1:032/033 14 M 09.10 2-3 Cytogenetics (4) Mr Stevenson 1:032/033 3-4 Medical Genetics (1) Dr Schofield 1:032/033 Tu 10.10 10-11 Medical Genetics (2) Dr Schofield FLT 11-12 Medical Genetics (3) Dr Schofield FLT Th 12.10 10-11 Medical Genetics (4) Dr Schofield 1:032/033 F 13.10 9-10 DNA Diagnostics Dr Kelly 1:032/033 10-11 Medical Genetics (5) Dr Schofield 1:032/033 15 F 20.10 10-1 Group presentations: Controversies in medical genetics Dr Schofield & 1:032/033 Dr Kelly Mr David Stevenson (50931; email: david.stevenson2@nhs.net) Dr Kevin Kelly (53888; email: gen182@abdn.ac.uk) Module Organiser – Dr Andy Schofield (53006; email: a.schofield@abdn.ac.uk) 39
  • 40. GENETICS OPTION 2 - POPULATION GENETICS SESSION 2006-2007 Genetics Week Date Time Class Staff Venue 17 M 30.10 12-1 Population Genetics (1) Mr Cumming 1:039 2-3 Population Genetics (2) Mr Cumming 1:040 W 01.11 11-12 Population Genetics (3) Mr Cumming 1:039 Th 02.11 11-12 Genetic Epidemiology (1) Mr Cumming 1:032/033 F 03.11 9-10 Population Genetics (4) Mr Cumming 1:039 3-4 Genetic Epidemiology [Tutorial 1] Mr Cumming 1:032/033 18 W 08.11 10-11 Immunogenetics (1) Mr Cumming FLT 11-12 Immunogenetics (2) Mr Cumming FLT 3-4 Ecogenetics (1) Dr Dallas 1:040 Th 09.11 11-12 Ecogenetics (2) Dr Dallas 1M:003 19 M 13.11 12-1 Genetic Epidemiology (2) Mr Cumming 1:032/033 2-3 Ecogenetics (3) Dr Dallas 1:040 W 15.11 1-2 Ecogenetics (Tutorial) Dr Dallas 1:040 Th 16.11 10-11 Population Genetics [Tutorial] Mr Cumming 1:032/033 Fr 17.11 2-5 Genetic Epidemiology [Tutorial 2] Mr Cumming 1:040 Module Organisers - Mr Al Cumming (555722); e-mail a.cumming@abdn.ac.uk 40
  • 41. IMMUNOLOGY OPTION 1 – INFECTION, IMMUNITY AND INFLAMMATION SESSION 2006-2007 Immunology Week Date Time Class Staff Venue 13 M 02.10 4-5 Leucocyte trafficking 1: in health Dr Liversidge 1:040 Tu 03.10 12-1 Leucocyte trafficking 2: blood-brain barrier Dr Liversidge 1:040 Dysfunction and retinal autoimmunity W 04.10 10-11 Leucocyte diapedesis and migration Dr Liversidge 1:039 Th 05.10 2-3 Regulation of leucocyte function in tissues Dr Liversidge 1:039 F 06.10 9-10 Myeloid cells in innate and adaptive immune Dr Liversidge 1:039 responses 14 M 09.10 4-5 Tutorial: In vivo and ex-vivo imaging technologies Dr Xu 1:040 Tu 10.10 12-1 Principals and practice of flow cytometry and Dr Blaylock 1:040 Application in immunological research W 11.10 10-11 Tutorial: Practical aspects of FACS analysis Dr Blaylock 1:039 And quality control for cytometry Th 12.10 2-3 Allergy Dr Walsh 1:039 F 13.10 9-10 Asthma 1 Dr Walsh 1:039 15 M 16.10 4-5 Asthma 2 Dr Walsh 1:040 Tu 17.10 12-1 Resolution of asthmatic and allergic Dr Walsh 1:040 Inflammation - Apoptosis W 18.10 10-11 Immuno-epidemiology (1) Dr Sternberg 1:039 Th 19.10 2-3 Immuno-epidemiology (2) Dr Sternberg 1:039 F 20.10 9-10 Immuno-epidemiology (3) Dr Sternberg 1:039 Module Organiser: Dr Janet Liversidge: tel 59548; e-mail: j.liversidge@abdn.ac.uk) 41
  • 42. IMMUNOLOGY OPTION 2 - MOLECULAR IMMUNOLOGY SESSION 2006-2007 Biochemistry (Immunology) Genetics (Immunology) Immunology Biomedical Sciences (Molecular Biology) Week Date Time Class Staff Venue 17 M 30.10 10-11 Immuneregulation: self-tolerance Dr Ward 1:034 Tu 31.10 2-3 Immuneregulation: MHC molecules and disease Dr Ward 1:034 Th 02.11 9-10 Immuneregulation: Regulatory T cells Dr Ward 1:034 F 03.11 10-11 Molecular mechanisms of immune evasion Dr Vickers 1:034 2-3 T-cell activation – how much provocation does a T-cell need? Dr Barker 1:034 18 M 06.11 10-11 Immuneregulation: T-cell polarisation Dr Ward 1:034 Tu 07.11 2-3 T-cell regulation – cytokine cascades Dr Wilson 1:034 W 08.11 10-11 Immuneregulation: Fc receptors and disease Dr Ward 1:034 11-12 Immuneregulation: AID Dr Ward 1:034 F 10.11 2-3 Immunotechnology (1) Dr I Broadbent 1:034 19 M 13.11 10-11 Immunotechnology (2) Dr I Broadbent 1:034 Tu 14.11 9-10 Immunotechnology (3) Dr I Broadbent 1:034 2-3 Immunotechnology (4) Dr I Broadbent 1:034 Th 16.11 9-10 Immunotechnology (5) Dr I Broadbent 1:034 F 17.11 2-3 Tutorial Dr I Broadbent 1:034 Module Organiser: Dr Frank Ward (55948; e-mail f.j.ward@abdn.ac.uk) 42
  • 43. MICROBIOLOGY OPTION 1 - POPULATION AND ENVIRONMENT SESSION 2006-2007 Microbiology Week Date Time Class Staff Venue To be confirmed Module Organiser: Dr Ian Stansfield (55806; 55887; e-mail i.stansfield@abdn.ac.uk) 43
  • 44. MICROBIOLOGY OPTION 2 - ANTIBIOTIC SYNTHESIS AND RESISTANCE SESSION 2006-2007 Microbiology Molecular Microbiology Week Date Time Class Staff Venue 16 W 25.10 9-10 Antibiotic resistance in bacteria (1) Prof I R Booth 1:034 Th 26.10 2-3 Antibiotic resistance in bacteria (2) Prof I R Booth 1:034 F 27.10 12-1 Antibiotic resistance in bacteria (3) Prof I R Booth 1:032/033 17 M 30.10 10-11 Antibiotic synthesis pathways (1) Prof M Smith 1:040 3-4 Antibiotic synthesis pathways (2) Prof M Smith 1M:003 Tu 31.10 10-11 Antibiotic synthesis pathways (3) Prof M Smith 1:040 18 M 6.11 12-1 Antibiotic resistance in fungi (1) Prof Frank Odds 1:029 T 7.11 9-10 Antibiotic resistance in fungi (2) Prof Frank Odds 1:034 W 08.11 10-11 Antibiotic resistance in fungi (3) Prof Frank Odds 1:040 Th 09.11 2-3 Antiviral resistance in viruses (1) Dr P Cash 1:040 4-5 Antiviral resistance in viruses (2) Dr P Cash 1:039 F 10.11 11-12 Antiviral resistance in viruses (3) Dr P Cash 1:039 1-2 tbc Dr F McKenzie / IRB 1:040 3-5 Tutorial various staff (tbc) 1:040 Module Organiser: Professor Ian Booth (55852; 55851; e-mail i.r.booth@abdn.ac.uk) 44
  • 45. CORE MODULE - GENOME ORGANISATION AND ANALYSIS SESSION 2006-2007 The genome is the primary source of information for building and maintaining an organism. We now have complete access to this 'raw' information, in the form of DNA sequence, for several organisms, and within ten years several other genomes, including that of humans, are expected to be similarly available. There is a problem, though. To make full use of this data we have to determine the rules used to convert it into biological function. This is a challenge far greater than that required to produce the genome sequences in the first place. The aim of this module is to describe the current progress in these studies with reference to the data emerging from the various genome projects. ANALYSIS OF GENOMES FROM 'HIGHER ORGANISMS' Comparative genomics in mammals I Duncan Shaw Comparative genomics in mammals II Duncan Shaw THE GENOME PROJECT PARADIGM Animal genomes I: The discovery of microRNAs Jonathan Pettitt Animal genomes II: Analysis of microRNA function Jonathan Pettitt Animal genomes III: Ome sweet ome? Jonathan Pettitt Animal genomes IV: Evolution of animal genomes Jonathan Pettitt FUNCTIONAL GENOMICS Yeast genome I: discovery of orphans Al Brown Yeast genome II: functional genomics Al Brown Yeast genome III: towards an understanding of the system Al Brown Module Organiser: Dr Jonathan Pettitt (55737;55922); e-mail j.pettitt@abdn.ac.uk) 45
  • 46. CORE MODULE – EVOLUTION OF PROTEIN STRUCTURE AND FUNCTION SESSION 2006-2007 Proteins are central to all biological processes, and understanding them is essential for all molecular life scientists. This core course will explore current knowledge of protein structure and function. The objective of the course is to give students an appreciation of the relationships between primary sequence and final structure, consequences for function, including interactions, as well as insights into mutations that cause disease and into the evolution of biological systems. Dr Jonathan Pettitt (3 lectures) "Biology only makes sense in the light of evolution." Theodosius Dobzhansky. Despite much talk about the gene as unit of selection, most of the actual selection process is occurring at the level of the protein. The aim of these lectures is to describe how evolution has shaped protein structure and function, as well as illustrating the physical and chemical constraints on this process. Protein-protein interactions are an important consideration. • Evolution of proteins: Concept of homology. Mutation and its consequences. Conservative and non-conservative amino-acid substitutions. • Constraints upon protein evolution: Physico-chemical properties of protein structure and function. Protein folding as an evolutionary constraint. • The modular nature of proteins: The hierarchical view of protein structure. Concept of module as an autonomous folding unit. Examples of commonly found protein modules. Ancient conserved regions. Theories of domain shuffling. Protein families. Dr Ian Stansfield and Professor Ian Booth (tutorials on understanding structure) The objective of these tutorial exercises is to familiarize students with key concepts regarding the folding and function of proteins: • The importance of amino acid side chains in controlling the interaction of the protein with its environment and with ligands; • The conservation of folds among diverse protein sequences; • The role of amino acid side chains in catalysis; • Static versus dynamic views of proteins. Students will be expected to supplement the tutorials with extra work at computer terminals. Dr Iain McEwan (3 lectures) These lectures will consider how the linear sequence of amino acid residues in a polypeptide chain is folded to adopt the final protein structure. Recently it has become clear that some proteins or protein domains are intrinsically unstructured and that this degree of flexibility is crucial for function. This series of lectures will examine: • Protein folding pathways, including the concept of the ‘molten globule’ and methods for investigating protein folding. • Flexibility in protein structure and the role of macromolecular interactions in inducing protein conformation. • What happens when protein folding goes wrong? What is the cell’s response? We will consider some pathological conditions that have been linked to protein misfolding. 46
  • 47. Prof Nuala Booth (3 lectures) These lectures will examine families of proteins and the insights they provide. The main examples chosen are proteases and their inhibitors, including the serpin family (which you heard about at Kindrogan). These will develop the themes of evolution and folding of proteins to achieve their functional forms. We will examine other modules in proteases and their roles in protein-protein interaction. A particular theme will be understanding structure-function relationships by studying mutants, both naturally-occurring and experimental. • Proteases - key roles in all organisms. Proteolysis has to be appropriately controlled in different environments. • Serine proteases are not just active sites but modular structures capable of other interactions. A new family of membrane–associated serine proteases is emerging. • Serpins are a family of inhibitors in which a reactive centre loop mimics the normal target for the protease. Other inhibitors, including the Kunitz inhibitors, E coli inhibitor, ecotin, and elafin, have quite different structures but all similarly present a reactive centre loop. NAB, IRB, IMcE, JP, IS (tutorial) This final tutorial will require you to have read, and to be ready to discuss, a paper that illustrates important concepts covered in the core course. The paper will be provided early in October, together with particular points that you should consider in advance. Module Organiser: Professor Nuala Booth (e-mail n.a.booth@abdn.ac.uk) 47
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  • 49. CORE MODULE – CONTROL OF GENE EXPRESSION SESSION 2006-2007 This core module will provide insights into the processes and mechanisms that control gene expression in the context of differentiation, development and the adaptation to changes in the environment, using examples from bacteria, yeast and animal systems. We will provide information about the molecular mechanisms of transcriptional, post-transcriptional and translational control. Specific examples will include transcriptional control by the bacterial CAP protein and during myogenesis, post-transcriptional control of sex determination in Drosophila and control of translation. Two tutorials will supplement the lectures by bridging different aspects of the course. The overall aim of the module is to gain an understanding and appreciation of the complexity of the mechanisms that control gene expression in simple and complex life forms. Module Organiser: Dr Berndt Mueller (b.mueller@abdn.ac.uk ~ tel: 55826) 49
  • 50. CORE MODULE – DEVELOPMENT AND FORM SESSION 2006-2007 This core module will examine the ways in which individual cells and groups of cells in tissues establish shape, polarity and undergo morphogenesis. We intend to provide information illustrative of general principles at various levels and then use a tutorial exercise to allow you to develop a global vision of how these principles are related to key systems in which form and development have been studied. The course will consider systems at three levels. [i] The establishment and maintenance of cell polarity in yeasts; [ii] The regulation of polarity during embryogenesis in worms, frogs and flies; [iii] Tissue development and pattern formation in whole body plans. Together these topics will create an overview of how form and function is generated at the cell and molecular level. The course will consist of lectures in these three areas and a series of three tutorials in which groups of students will create a web-based resource of information that describes how key model systems from bacteria to Drosophila, frogs, Zebra fish and mice have contributed to our understanding of developmental biology. The overall aim of the lectures and tutorials is to gain an understanding of what cells have to accomplish to generate the diversity of forms represented in simple and complex cellular life forms. Module Organiser: Professor Neil Gow (55879; 55878; e-mail n.gow@abdn.ac.uk) 50
  • 51. BIOCHEMISTRY OPTION 1 – RECEPTORS AND CELL SIGNALLING SESSION 2006-2007 Cell signalling and communication is of crucial importance to the development and survival of multicellular organisms. For example, during animal development signalling pathways have to co-ordinate cell patterning in both time and space. The aim of this module is to consider the ways in which receptor proteins transmit information from the extra-cellular environment to the intracellular site of action and the mechanisms by which the effects of ligand binding are achieved. The structural and functional features of the different families of receptors will be discussed and the cell signalling pathways of some of these, such as the insulin receptor and wnt, will be covered in detail. The mechanism of action of members of the steroid-thyroid hormone-retinoic acid superfamily, which represent a large family of intracellular receptor proteins, will be discussed. The Option will include lectures, tutorials and reading of original literature. Professor Kevin Docherty: Receptor Structure and Cell signalling (7 hours) • 7-Helix receptor family and G-protein coupled signalling. • Cytokine receptors: JAKs, STATs and SMADs. • Tyrosine kinase receptors. • Insulin signalling pathway. • Calcium signalling in the cytoplasm. • Inhibitiors of protein kinases and phosphatases and their uses. Dr Stefan Hoppler: The Wnt signalling pathway (3 hours) • Would the real Wnt receptor please step forward? • Flies, frogs and cancer. • Neither straight nor narrow. Dr Iain McEwan: Nuclear receptor superfamily (5 hours) • Receptor structure-function studies: ligand-binding, DNA-binding and transactivation functions. • Positive mechanisms of receptor-dependent gene regulation. • Negative mechanisms of receptor-dependent gene regulation. • Cross-talk between different signalling pathways. • Receptor knock-out studies and clinical disorders of hormone action. • Towards an integrated understanding of cell signalling (paper discussion) 51
  • 52. Module Organiser - Dr Iain McEwan (55807; 55810; e-mail iain.mcewan@abdn.ac.uk) BIOCHEMISTRY OPTION 2 – BIOCHEMISTRY OF HUMAN DISEASES SESSION 2006-2007 Biochemistry is profoundly influencing medicine in a number of ways. One of these involves the molecular explanation of events occurring when disease-causing organisms infect man. A clear understanding of the structure and replication of such organisms opens ways to a rational design of methods for preventing and treating illness. In this module, a selection of important human diseases is explored: the causative agents are viruses and prions. A theme running through the module is the way in which the infecting organism subverts and exploits the biochemistry of the human host. Building on previous knowledge of molecular biology, an understanding of the nature of the disease-causing agents and their activities will be constructed. 20% of the module involves informal class presentation and discussion of work from the primary literature that illustrates themes common to the various module elements. Dr Ian Stansfield: Towards an understanding of human prions: yeast proteins as signposts The PrP protein is encoded by a human gene, but has the ability to adopt a conformation that enables it to act as an infectious agent (prion). The molecular bases of the infectivity and propagation of this agent are beginning to be explored. In particular, instructive comparisons may be made between PrP and similar proteins isolated from a genetically tractable yeast – Saccharomyces cerevisiae. • Nature and properties of mammalian prions. • Propagation and infectivity mammalian prions: Creutzfeld-Jacob and Gerstmann-Straussler-Scheinker syndromes. • Yeast prions: the eRF3 protein; nature and properties of the PSI prion. • Yeast prions: propagation and inheritance; in vitro prion conversion; host factors required for propagation. Dr Bill Long: The molecular biology of HIV and AIDS HIV has become one of the best explored of all viruses, but many aspects of its activity remain mysterious. It is clear that much of its infectivity and replication involves the subtle subversion of host cell functions. This subtlety, together with the hypermutability of the virus, make its control a formidable task. Nevertheless, particular aspects of HIV replication may themselves be susceptible to attack. • Interaction of the virus with susceptible cells: gp120, gp41, CD4, chemokine receptors. • Reverse transcription and integration of the provirus. • The regulation of virus gene expression, tat, nef and rev. • Towards a molecular basis for treating and preventing AIDS. Dr Phil Cash: Virus-cell interactions during virus-induced transformation Virus infection can result in a variety of outcomes including the development of chronic diseases and neoplastic transformation of cells. Viruses, in fact, are one of the major causes of human cancer. The intimate interaction of viruses and host cell during virus replication provides a number of options by which viruses subvert the normal growth of cells. • The development of chronic virus infection and the transformed phenotype. • DNA viruses and cancers. • Papillomaviruses, the role of the virus T antigen, E6 and E7 in deregulating cell growth. The cellular p53 and retinoblastoma genes. • Retroviruses as the original transforming viruses, oncogenes, the role of HTLV in human cancer. 52
  • 53. Module Organiser – Dr Bill Long (e-mail: w.f.long@abdn.ac.uk ~ tel: (27) 4175) GENETICS OPTION 1 – MEDICAL GENETICS SESSION 2006-2007 The aim of this module is to consider three aspects of medical genetics providing a brief overview of the breadth and scope of the area. The first topic will cover cytogenetics and the role this area has played in gene mapping, in understanding the nature of sexual development, cancer genetics and many congenital abnormalities and its likely role in future research into human disease. In the second topic, we will cover molecular genetics of a variety of disorders including haemoglobinopathies and single-gene disorders such as Duchenne muscular dystrophy, cystic fibrosis and Huntington’s disease. We will also look at the role of epigenetic phenomenon in modifying the expression of genes, and examine some of the genetic events involved in cancer. Lastly, we will look at the use of these findings in the DNA diagnostic laboratory and the factors that have to be taken into account in setting up such a laboratory. Common themes in these topics will be the ethical problems which can arise and the need for expert counselling for individuals before they choose to be involved in either research or diagnostic procedures which may be used to predict future predisposition’s. In addition, there will be three topics based on controversies in medical genetics covering stem cell research, genetic testing and problems associated with in vitro fertilization. The class will be divided into three groups, one group per topic, to discuss the scientific and ethical issues relating to each topic. Each group will make a presentation and write a brief group report. Mr David Stevenson: Cytogenetics • Chromosome mapping and molecular cytogenetics • The clinical significance of microdeletions, balanced rearrangements and marker chromosomes • The cytogenetics of sexual development and dysmorphology • The cytogenetic aspects of prenatal diagnosis • Cancer cytogenetics Dr Andy Schofield: Medical Genetics • Haemoglobinopathies • The clinical and molecular features of single-gene disorders • Complex disease analysis • Genomic imprinting • Mitochondrial inheritance • Genetics of cancer Dr Kevin Kelly: DNA Diagnostics • DNA diagnostics in human disease • Models of service provision • Targeting techniques to mutations 53
  • 54. Module Organiser – Dr Andy Schofield (53006; email: a.schofield@abdn.ac.uk) GENETICS OPTION 2 - POPULATION GENETICS SESSION 2006-2007 The application of Mendel's Laws and other genetic principles to entire populations constitutes the subject matter of population genetics. The genetic composition of a given population reflects its current and past history in relation to different forces which have helped to shape it. Important 'forces' include - selection, mutation, migration and drift. A major objective of this series of lectures is to examine population genetic structure in relation to such influences. In particular, we wish to:- • Examine population genetic composition in relation to mutation rates, selection, migration & genetic drift • Evaluate gene polymorphism-phenotype association in relation to disease susceptibility. • Use genetic data for the study of population parameters in animal, insects and plant ecology. • Gain insight into human disease mechanisms using a genetic epidemiological approach. • Use coalescence theory to study the relationship of population structure to evolutionary history MR AL CUMMING • measurement of gene frequencies - Hardy-Weinberg equilibrium • linkage disequilibrium and haplotye frequencies. • selection and heterozygous advantage for globin mutants in malarial endemic regions: recessive diseases - selection or drift? • migration and population admixture • genetic polymorphism/phenotypic association & population genetic structure • Immunogenetics - MHC complex and disease; extended haplotypes and selection. Tutorial: Detection of the signature of natural selection in humans: evidence from the Duffy Blood Group locus (2000) Hamlin, MT & Di Rienzo, A. Am J Hum Genet 66: 1669-79 • Genetic epidemiology of complex diseases. • Interaction of genetic and environmental factors in the disease etiology. • Gene-gene interaction. Tutorial: The “Thermolabile” variant of Methylenetetyrahydrofolate Reductase and Neural Tube defects: An evaluation of genetic risk and the relative importance of the genotypes of the embryo and the mother (1999) Sheilds DC et al. Am J Hum Genet 64:1045-55 DR JOHN DALLAS • Population genetics meets ecology; forces which shape genetic composition; theoretical models and real populations. • Use of genetic data for stabilising population parameters in insects and plants. Tutorial: papers yet to be selected 54
  • 55. Module Organiser - Mr Al Cumming (55722); email a.cumming@abdn.ac.uk 55
  • 56. MICROBIOLOGY OPTION 1 – MOLECULAR GENETIC EVOLUTION MICRO-ORGANISMS SESSION 2006-2007 Microbial Populations in Natural Environments This module will consider the nature of speciation, through a consideration of microorganisms. In non- microorganisms, species definitions are based upon easily observable differences, visible characteristics and behaviours. In microorganisms, there are frequently no visible differences between closely-related species, and historically, researchers have relied upon biochemical differences in bacterial metabolism to differentiate between species e.g. their differential abilities to metabolise a range of sugars. More recently, rRNA sequences have been used as a tool for differentiating species. However, related strains of the same species can exhibit profound differences in genome structure and composition. This module will attempt to address the question ‘How different do two strains need to be before they are considered distinct species?’. The molecular mechanisms that drive speciation will be considered in the context of whole genome sequences. Module Organiser: Dr Ian Stansfield (55806; 55887; e-mail i.stansfield@abdn.ac.uk) 56
  • 57. MICROBIOLOGY OPTION 2 – ANTIBIOTIC SYNTHESIS AND RESISTANCE SESSION 2006-2007 This option will explain the pathways of synthesis of antibiotics as a necessary background to understanding the risks and opportunities provided by antibiotic resistance. Lectures will cover the basis of antibiotic resistance in bacteria, fungi and viruses and will consider the factors leading to the emergence of antibiotic resistance. The course will consist of lectures and tutorials based on published literature. Module Organiser: (Professor Ian Booth (55852; email: i.r.booth@abdn.ac.uk) 57
  • 58. IMMUNOLOGY OPTION 1 – INFECTION, IMMUNITY AND INFLAMMATION SESSION 2006-2007 This option will focus on immune function at the organismal level. We will look in detail at the complex cellular and molecular immune mechanisms underlying the co-ordinated series of events linking the innate to the adaptive immune response and how immunological dysfunction can lead to a pathological inflammatory response and disease. The future for new immuno-therapeutic strategies and how emerging disciplines such as immuno-epidemiology can be used to understand the mechanisms underlying population immunity to disease will be explored. Organ specific autoimmunity often presents as a mononuclear cell inflammatory response to tissue antigens. The functional consequences of chemokine and adhesion molecule driven monocyte and T lymphocyte trafficking and migration that drives disease will be studied using autoimmune uveoretinitis as a model. This will include the significance of myeloid cell differentiation into functionally disparate subsets and cognate interactions between antigen specific T lymphocytes and antigen presenting cells within the autoimmune lesion. The pathological consequences of a Th1 versus a Th2 inflammatory response compared, and the potential for macrophages and tissue resident cells to drive resolution of disease will be considered. Allergies are usually driven by immediate hypersensitivity responses to common environmental proteins and chemicals rather than infection. Immunoglobulin-E, mast cells, eosinophils and basophils are central to the pathology and the mechanisms governing recruitment and, the effects of mediators produced decribed. Asthma will be used to illustrate how a chronic inflammatory disorder can develop. This will include the signals controlling the accumulation of cells such as eosinophils, the contribution of the broncial epithelium and other structural lung tissues to asthma pathogenesis and the significance of apoptosis in the respolution. How disease is initiated and ultimately controlled by underlying Th1/Th2 cell activity and the potential for allergen de-sensitisation will be described. Opportunities for “hands-on” experience with new and emerging technologies that are being used and developed in Aberdeen will be provided. This will give students a critical understanding of the proper use and potential of essential core facilities for immunological research such as multicolour fluorescence activated cell sorting and analysis, in vivo live cell imaging, and four dimentional confocal imaging Module Organiser: Dr janet Liversidge: tel 59548; e-mail j.liversidge@abdn.ac.uk) 58
  • 59. IMMUNOLOGY OPTION 2 - MOLECULAR IMMUNOLOGY SESSION 2006-2007 The aim of the molecular immunology module is to focus on recent discoveries that have shaped our understanding of how the adaptive immune system (mainly comprised of B and T lymphocytes) discriminates and functions at a molecular level. T-cells are of fundamental importance to the adaptive immune system and require interaction with polymorphic major histocompatibility molecules (MHC). The genomic organisation and molecular composition of MHC, and their significance in autoimmune disease, will be explored. T-cell mediated immunological tolerance is of great interest because it could be harnessed for therapies to suppress damaging inflammatory responses in immune-mediated disorders. We will review immunological tolerance and elaborate proposed models to explain how the immune system discriminates harmful from non-harmful challenges. CD4+ regulatory T-cells contribute to immunological tolerance, and their function and potential as therapeutic agents will be explored. Some pathogens evade the immune system by inducing artificial and inappropriate host tolerance. Understanding immune evasion strategies at a molecular level is of prime importance especially in tumour immunology where there are clear links between tumour formation and persistence of particular microbial pathogens. A second theme overviews the decision-making processes that permit T-cells to generate an appropriate response after antigen encounter. Naïve and memory T-cell activation, effector cell differentiation, and the molecular signalling mechanisms behind them are reviewed. Finally, up to 20% of emerging clinical pharmaceutical therapies are based on engineered monoclonal antibodies. The final theme in this course is to evaluate the strategies that have been successfully employed in antibody-based technology from elucidating antibody structure through to designing antibodies and antibody fragments that form a basis for new therapies. Material for the course will be drawn from a wide range of sources and in particular, cutting edge publications will be covered in lectures. T-cells and immunological tolerance • MHC and autoimmune disease • The tolerance hypothesis • Regulatory T-cells • Immune evasion Decision-making for T-cells • Activation requirements for T-cells • Th1/Th2/Treg subsets – mechanisms of differentiation • Regulation of T-cells at the cytokine level – targets for intervention? Receptors and disease • Fc receptors and their role in shaping the antibody repertoire • Killer immunoglobulin receptors – another adaptive immune system? Antibody based technology • AID - its role in promoting effective antibody responses • Structure of the antibody binding site of immunoglobulins • Chimeric and re-shaped antibodies • Human germ-line repertoires • Therapeutic antibodies and antibody fragments Module Organiser: Dr Frank Ward ((01224 5)55862, f.j.ward@abdn.ac.uk 59
  • 60. COURSE EVALUATION FORMS To assist in the development and future operation of courses, the University seeks your views on the effectiveness of the teaching-learning process. A University Course Evaluation Form is used to gain information about how you viewed the process in general: essentially the same form is used for all courses at all levels. Computer-readable forms will be given out towards the end of the course (a copy is shown overleaf). Bear in mind that we would also like written verbal comments about the element(s) of teaching. We are very keen to know both what you liked and what you did not like regarding any particular aspect of the course. If you wish to criticise something it would be helpful to have specific comments regarding what you think is wrong and suggestions for improving that aspect. The comments you make will be collated and discussed at a Student-Staff Liaison Committee meeting, at which your Class Representatives will be present and asked for their views. At that meeting, the proceedings of the corresponding meeting for the previous year will be reviewed, so that progress made in course development as a result of previous student comment can be checked. The Head of School has to report to the University Academic Standards Committee on the results of the student evaluation of each course run by the School. Your comments, then, are taken seriously, and the School’s reaction to them is monitored – in part by the succeeding generation of students. For a more immediate response, we encourage you to make critical (or other) comments, if you have them, directly to a member of the teaching staff, to the course co-ordinators, or to a class student representative – whichever seems the most appropriate. We hope that you enjoy the Honours course. Thank you for contributing to its evaluation. 60
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  • 64. TUTORIALS Tutorials and their purpose You are each assigned a tutor (see list in general section), whose responsibility it is to ensure that progress is being maintained throughout the year, who will develop your individual potential and in whom you should confide any problems. In addition the tutor will provide a reference for the Head of School if asked, will act as a referee in job applications and may be called upon to speak on your behalf at the Examiners Meeting in June. It is thus essential that each student establishes a good working relationship with his/her tutor, and contacts him/her at the beginning of the session in order to arrange meetings on a regular basis (about every 3 weeks). Do not wait for your tutor to seek you out. Take the initiative and make contact at Kindrogan or by early October at the latest. This is of particular importance with regard to advice on Essay Writing as the deadline for Essay 1 is October 17th . The object of tutorials is not to provide you with more information, but to help you to organise and use your knowledge effectively. Problems of understanding are often overcome through discussion. A list of suggested topics for tutorials is included in this section, although you should feel free to ask for help on topics other than those listed. Generally, tutorials require you to do some preparation in advance. Failure to prepare will mean you get much less out of the tutorial; remember, tutorials are held exclusively for your benefit. Tutorials are often held in a group with 2-3 other students, although of course, any problems of a personal or course work nature can be addressed on a one-to-one basis with you tutor. Tutorial topics Managing your work • organising your time and dealing with deadlines Writing Essays • structure, organisation and referencing the literature • plagiarism and how to avoid it (see http://www.abdn.ac.uk/diss/ltu/resources/plagiarism.hti ) The scientific literature • reading and critical analysis of scientific papers Thesis writing • approach, organisation and pitfalls Presentation skills • scientific writing; abstracting information and writing synopses • preparing for oral presentations; content of talk and visual aids • critical evaluation of seminars (eg a recent Departmental Seminar) Preparation for examinations • planning revision • apportioning time in the examination • data analysis papers The future • career options, preparation of CV and interviewing techniques 64
  • 65. LABORATORY-BASED RESEARCH PROJECTS Laboratory-based research projects are undertaken in the second semester and last for 10 weeks, starting on Monday 15th January 2007. This includes 9 weeks of lab work. The final 10 th week is for preparation of your project seminar, which takes place at the end of this week. Make sure that you see your supervisor early during the first semester, in order to discuss the project and its aims. You will also need to discuss a title for Essay 3, which will be a literature-review type essay based around the research interests of your supervisor. Laboratory work will occupy 25-30 hours per week but this may vary slightly according to the nature of the project. You must not work in the lab outside normal working hours without first arranging with your supervisor what work you will be undertaking, so that suitable supervision is assured. All students should consult supervisors frequently on their progress and must present up-to-date laboratory records to him/her. Contact should preferably be daily but twice a week is the absolute minimum. Research tutorials, tutorials or seminars run during the same term should not be missed in order to devote more time to research. Safety in the Laboratory It is very important that safe working procedures are adhered to at all times. The IMS Safety Manual is available on the web at http://www.abdn.ac.uk/ims/safety/manual.shtml and there is also a copy in each laboratory. You must read the guide carefully. Your particular attention is drawn to the sections on radioactivity, cell culture and genetic manipulation. If your project uses any of these, you must make certain that you understand what you may and may not do, and whether you need direct supervision during certain procedures. You must read and sign appropriate COSSH forms in the laboratory before you begin experimental work. If these are not offered to you, ask for them. You must not start work until you have signed them. LABORATORY ASSESSMENT Project work will be assessed by your supervisor (1 element) and is based on your laboratory work and the keeping of a laboratory notebook with equal weight being given to both (assessment form in this section). Remember that all elements on the assessment are not equally important. Marks will be given for organisation, approach, technique, interpretation and accurate and detailed record keeping, and not simply for good attendance or generating a large body of data. Projects that yield few successful results can be judged to be excellent if approached intelligently and good results do not in themselves guarantee high marks. Some projects turn out to be easier than others and the students performance will be judged in the light of this. Laboratory Work • Motivation and attendance. We expect good students to show interest and enthusiasm in their work and to be able to maintain this attitude when setbacks are experienced. You are expected to be in the lab for about 25 h per week. The time cannot be more than a recommendation, but clearly you should be there whenever your experiment demands it (within normal hours). Similarly, you must be there when a particular arrangement has been made to show you a technique or to discuss your data. • Organisation of time. This is even more important than mere attendance. A good student will fit in the experiments to be done in an effective way, will be prepared for experiments to come, and will not get into a position where he/she is confused by the experimental programme. • Experimental design & execution. This includes thinking about the aims of an experiment and planning it accordingly, with good planning of controls and appreciation of what purpose they will serve. It also covers technical ability and the capacity to take instruction. 65
  • 66. • Data analysis & interpretation. This asks how well you handle data. Do you make appropriate calculations, without error? Students are expected to be able to draw some conclusions from the experiments performed, and not to be reliant on others to point out the significant findings. Do you understand what information can be drawn from the data from further calculations, graphical methods and statistics? • Contribution. This is a measure of your understanding of your work and of how it might be extended. This is divided into two sections, to distinguish between technical improvements and more radical suggestions for using new approaches. • Achievement. This comments on what you actually achieved. Did you make reasonable progress and go some way towards achieving the aims of the project. Laboratory Notebook The keeping of an accurate and up-to-date record is essential in scientific research. The laboratory notebook is a permanent record of the experiments performed and also contains details of experimental design and analysis and interpretation of results. It is the basis for writing your thesis and care should be taken to see that it is well organised and complete. The laboratory notebook remains the property of the laboratory head and must be returned to him/her (or the School Office), once your thesis has been handed in. • Organisation. Each page should be numbered and entries dated. Records should be in ink (do not use pencil), be clearly legible and well organised. The layout should be easy to follow and experiments cross-referenced where appropriate. • Experimental detail. Records will include the date on which each stage of the work was performed, the rationale for the experiment and the details of the experiment including reagent concentrations and volumes (identify the source of special reagents or those not prepared by yourself), conditions like temperature and time, and instrumentation. • Results. These will be presented clearly and properly labelled. It should be clear to which experiment they belong and controls should be easily identified. Figures, tables, graphs etc. will be included with the experiment to which they belong. Analysis and interpretation of the results will be included with proposal for possible follow-up experiments THESIS Your thesis represents an important component of your training output in the Honours year. Plan and write it carefully. We strongly recommend "A guide to scientific writing" by David Lindsay, (Longman Cheshire). This will help you with the planning of essays and seminars, as well as with your thesis. Your Honours thesis is a document which should be entirely your own work. Before starting to write it you should discuss with your supervisor in detail issues of thesis structure, content and style. You should also discuss experimental interpretation and analysis, so you can be sure you are on the right track before putting pen to paper. Two other sources of help are also available. Firstly, a thesis writing tutorial will be organised by the Honours co-ordinators in the second semester, week 30, which will cover in detail the mechanics of constructing a well-written thesis. Secondly, you should ensure that thesis writing is one of the topics covered in one of your tutorials. Your supervisor may comment on a draft of your thesis but this will be restricted to a single draft only. Neither your tutor, nor the post-doctoral/PhD researcher who may have acted as a lab supervisor, will be able to give you any feedback, written or otherwise, on any thesis draft document. Please do not embarrass them by asking for such help. The thesis is an examined piece of work, and should be your own effort. Instructions and Guidance for Authors All theses must conform to the format described in this section. Please take the time to read this section carefully and refer to it often when writing your thesis. The thesis should take the form of a paper submitted for publication to a journal, whose instructions for authors are given below. Also consult the assessment form, which indicates what are the attributes of a good thesis. Length of the thesis 66
  • 67. The text of an honours thesis should be no more than 5000 words in length. A word count should be included on the front (title) page of the thesis. Note: the 5000 word limit does not include the following. • Tables, diagrams, photographs and figure legends • References The individual sections may vary considerably in length depending on the particular project. As with any submission of a paper to a journal, students are expected to keep to this size. Please note that these recommendations, and the thesis format, have changed in recent years; previous theses are not a good guide in terms of length or structure. Sections of the manuscript Honours theses should all contain the following sections in the order shown. Sections should be presented in the order shown, with each new section beginning on a new page: * Title page * Abstract * Introduction * Aims * Materials and methods * Results * Discussion * Acknowledgements * References General format An original should be legibly typed on A4. The manuscript must be double-spaced. Margins of at least 25 mm (1 inch) should be left at the sides, top and bottom of each page. Please note the left-hand margin will need to be deeper to allow the manuscript to be read once bound. Number each page at the bottom (Title page is 1). Clearly identify unusual or hand-written symbols and Greek letters. Differentiate between the letter O and zero, and the letters I and l and number 1. Figures and tables, with their legends, should be included at the appropriate point in the manuscript where their corresponding text lies. The thesis should be typed (not less than 12 point) and should be bound in spiral binding or stapled into a cover. The student's name and the title of the thesis should be on the cover. Two copies of the thesis should be handed into the School Office by 18.04.2006. Title Page. The title should be short and informative, and should not contain any abbreviations. The total length of the title should not exceed 100 characters (including spaces). Abstract. The Abstract should be a single paragraph not exceeding 200 words. Please abide strictly by this limitation of length. The Abstract should be comprehensible to readers before they have read the paper, and abbreviations and reference citations should be avoided. The overall aims of the paper should be briefly stated in this section. Introduction. This introduces the historical background to the research and outlines the current state of knowledge. It points to the questions that remain to be answered and the specific question your study tackles. It therefore should include, and lead naturally to, a clear statement of the Aims of the project. Aims. The aims should be described on a separate page and should be a brief (50-150 word) summary of the question(s) the research sets out to answer. Materials and Methods. This section describes how to perform the methods used; it must not give the rationale for doing the experiments but it is permissible to mention what it is used for. Remember that published methods must be referred to, and that these only need a brief description identifying modifications made to published methods. The materials and methods used should be presented in a logical order. Materials, which may include cells, organisms, specialist chemicals etc, should be described. Give only essential details of preparation of reagents and solutions. Avoid recipe-type lists. It is essential that readers of the thesis be able to repeat your work from the description given but avoid excessive detail; your supervisor will guide you on this. Do not 67
  • 68. forget to mention the statistical methods you have used. Include brief comments, as appropriate, on safety procedures that are necessary for the safe conduct of the experiments. Results. This section tells the story of what you did, with enough explanation of each result to show why you did the next experiment. The reader will only notice trends in Figures and Tables that you bring to his/her attention so make sure you explain what to look out for. In general, make no references to the literature in this section, except where it is essential to explain why you moved on to another approach. The text in the results section must be continuous i.e. do not insert page breaks after each Results sub- section. Remember that the reason for doing an experiment is always to answer a question. Stress the question and refer to the technique chosen in terms of how appropriate it was to the question. Do not create the impression that the technique was central, unless that happens to be the case in your project. Figures and Tables go on separate pages, following as closely as possible after first mention in the text. Figure legends are an important component. Figures themselves should be printed on a separate page with their corresponding figure legends. Legends should give all keys to symbols and should also explain error bars. If an experiment was done 4 times, this should be stated, as should information on whether all data were averaged to give the graph shown etc. The reader should be able to see what kind of experimental error is shown. It is vital to distinguish between different sources of variation. For instance you will need to consider assay variation, well-to-well variation in a cell culture experiment, and variation between different experiments. Controls are central to experimentation. Avoid value judgements in your choice of term. Your view of positive or negative controls may not be the same as the reader's, so explain what is present or absent in any particular control. Most systems could have several controls; as with blanks, it is important that the reader understands what you mean by the term. In particular, never talk of the control; it suggests that you can only think of one. If at all possible keep this section to a statement of results, with supporting figures and tables, but provide linking paragraphs to say why you did experiments and to show how one led on to the next. It is not necessary to present this section in the order in which you performed the work. Remember not to quote data to more significant figures than is justified. Finally, remember it is critical that the results section communicates well to the reader. It is strongly suggested that you consult examples of well-written papers, perhaps in EMBO Journal, to see how experienced researchers communicate their findings (try taking a look at Templin et al., (1999) EMBO J 18; 4108-4117, or Endres et al., (1999) EMBO J 18; 3214-3221). Note the EMBO J. format is different to that required for your thesis; nevertheless, these papers represent good examples of clear scientific description. Discussion. This is where you make connections with the literature, speculate on overall mechanisms and suggest extensions of your experiments. Make certain your Discussion is not a reiteration of results. You must discuss what your results mean and place them in the context of published material. Include suggestions for possible future work. It is usually best to incorporate these into the body of the Discussion, each appearing at the most appropriate place. You may prefer to keep it separate but, if you do, make sure it follows directly; if it appears as a new section it may be missed by the reader. Note that if your practical work yields few results, you should still contribute a full and thoughtful discussion section; why might experiments not have worked; how can your (negative) results be interpreted in the context of the literature. Acknowledgements. Proper reference should be made to those who helped you with your project. References. Make sure that you have read the references you quote and that the reference list is accurate. Avoid excessive reliance on reviews. Where appropriate cite the most up-to-date references possible. The numbered system of references is not to be used. 68
  • 69. In the text a reference should be cited by author and date, eg 'Water is known to boil at 100°C (Jones and Brown, 1872; Brown et al, 1873) and freeze at…'. Not more than two authors may be cited per reference; if there are more than two authors use et al. References should be listed alphabetically according to the initial letter of the surname of the first author. Where the same authors have published more than one paper, list them in the order in which their papers appeared. If necessary use a and b eg 1990a., with the authors' surnames and initials inverted. References should include, in the following order: authors' names; year; article or chapter title; editors (books only); journal or book title; name and address of publisher (books only); volume number and inclusive page numbers. The name of each journal should be abbreviated according to the World List of Scientific Periodicals (see an EMBO J. paper for reference) and italicized. References should therefore be listed as follows: Tugendreich, S., Bassett, D.E., Jr, McKusick,V.A., Boguski, M.S. and Hieter, P. (1994) Genes conserved in yeast and humans. Hum. Mol. Genet., 3, 1509-1517 Gehring, W. (1994) A history of the homeobox. In Duboule, D. (ed.), Guidebook to the Homeobox Genes. Oxford University Press, Oxford, UK, pp. 1-10 Lewin, B. (1994) Genes V. Oxford University Press, Oxford, UK. Nomenclature, abbreviations and units Authors should follow internationally accepted rules and conventions. The Nomenclature sections of the current `Instructions to Authors' of the Biochemical Journal and Journal of Bacteriology are useful sources of information. Particular care should be taken with genetic nomenclature. The international system of units (SI) should be used; ml is acceptable in place of cm3 for liquid measures. The preferred form for units is g ml-1 and not g/ml. Multiplication of numbers should be indicated by a multiplication sign with spaces either side (e.g. 6.2 x 108) and of units by a space (e.g. mg l-1). A space should be inserted between numbers and the units (e.g. 10 mM) The correct abbreviations are as follows and none of them ever takes an s to make them a plural. Remember to use the correct case and subscripts/superscripts as necessary. Base b (as in kb) kilo k Dalton Da (as in kDa) litre l (American journals use L) Hour h molar M (means mole per litre) Minute min mol mol Minimum min. millimolar Mm Second s Svedberg S (as in 18 S RNA) KD Dissociation constant (note that this is an equilibrium constant, unit is M) ka Association rate constant (unit is M-1s-1). This can also be called a kon kd Dissociation rate constant (unit is s-1). This can also be called koff Absorbance The term optical density should be used only to describe the measurement of turbidity, e.g. bacterial growth. In every other situation, the correction word is absorbance (not absorbency). If you need a plural, say absorbance values. The abbreviation Ax nm is correct. TECHNICAL NOTES ON THESIS PRODUCTION 1. It is important to produce clear, well-planned diagrams. All graphs and diagrams should be clearly visible, preferably in black & white. Photocopies can be made if you require a reduced size copy. If you intend to reduce the size of diagrams to half the size of the original, lines and lettering in the original must be twice the size you require in the final copy. Avoid fine shading or stippling that will not reproduce well. Note that large areas of solid black do not copy well. 2. Allow enough time for writing your thesis. Make an early start and be realistic about your speed of production. 69
  • 70. 3. Make back-up copies of your computer files/disks as you go along. Computer problems will not be accepted as an excuse for late submission. 4. You should prepare photographic work as soon as possible, preferably as the research proceeds; your supervisor will guide you as to which results should be recorded photographically. 5. Be careful of your use of punctuation. In general, titles and headings do not require full stops. Use a spellchecker on your computer where possible. Use British spellings. ASSESSMENT OF THESIS Your thesis is assessed independently by two staff members. They will use the form included in this section. This assessment is not open to negotiation. If you are unhappy with the assessment you must approach the assessors to gain further information, not the Course Supervisors who will not have read your thesis. Your supervisor will be asked to provide comments on the final submitted form of the thesis, the mastery of the literature, whether the writing is entirely your own or is plagiarised from other sources, the correctness of reference citations etc. and will be asked to confirm that he/she has commented on a single draft, but he/she will not give a mark. Remember that plagiarism is considered a serious offence by the School and the University and will be dealt with accordingly; if you are at all unsure what constitutes plagiarism, please see this web site; [The Web site will explain what is and is not acceptable. ] http://www.abdn.ac.uk/diss/ltu/resources/plagiarism.hti TIMETABLE FOR PROJECTS 1. Experimental work must be completed by Friday 16th March 2007. 2. Project seminars are provisionally arranged for, 21st-23rd March 2007. 3. Three copies of your thesis should be prepared for binding. Two copies of your bound thesis must be submitted for examination by 18th April 2007. One copy will be retained for the School Library collection, and the second copy is donated to your supervisor. The third copy is for your own use. 4. Any departure from this timetable will be agreed only in exceptional circumstances. Such a request must be supported in writing by your supervisor and must have the agreement of the Course Co- ordinators and the Head of School. PROJECT SEMINARS AND ORAL PRESENTATIONS You are required to give a formal presentation on your project; this is given in March (21st-23rd March 2007). Each student presentation should be timed to last for TEN MINUTES, and will be followed by a 20 minute discussion and examination by a panel of 3 staff members, who will ask questions arising from the oral presentation. The general advice on preparation of theses is equally applicable to seminar preparation. Remember that your aim is to inform your audience about the research project. Think of what they need to know to understand what is to be presented. Try to forget the assessment of the seminar; setting out to impress the audience often gets in the way of communication. Your tutor, your project supervisor and your classmates will all give you useful advice on presentation. Seek it in good time, so that you have the opportunity to use it well. The criteria used to assess seminars are shown. In essence two aspects are particularly important: “Content” (content of the talk) and “Presentation” (clarity of communication). Marks for Lab work, thesis and oral presentation will be made available after the exams. 70
  • 71. CONTENT Introduction: A short talk leaves little time for the audience to get to grips with the topic. Consequently a valuable use of time is to tell the listeners at the start what the talk is about. The introduction should contain the following information: what was being investigated, why it was being investigated. Experimental work: What experimental system was being used and why. In 10 min you must limit yourself to only the essential details and you are entitled to assume an understanding of basic technology. You may also have to select which of your data to present. You must select those experiments that are most critical and informative and present these. Make sure that those presented are sufficiently clear to allow your audience to understand them readily. Conclusions: Make sure that the conclusions can be drawn from the data presented. PRESENTATION Effectiveness of communication: Be professional, prepare well, do not be flippant. Speak clearly and look directly at your audience. Practice your talk and try to use your own words Avoid reading your talk from a prepared script. Overheads and slides: Write legibly and with a large enough size of letter that it can be read clearly; do not put too much information on one overhead. Only use photocopied figures when they are simple and clear. Time keeping: You only have 10 mins so practice your talk with a view to keeping to time. Do not assume that you will speed up on the day allowing you to cram 20 min into 10. QUESTIONS Spend some time thinking about possible questions, and try to prepare yourself for this part of the seminar. A frequent problem is that the student is so prepared to view the question as a challenge, he/she fails to notice how simple and even how helpful the question actually is. Try to listen calmly, and don’t rush your answer. Be prepared to answer technical questions on protocols etc., since not all examiners will be familiar with the methods you have used. 71
  • 72. Assessment of Laboratory Work Student: Project title: Supervisor: STANDARD ACHIEVED 1 2 3 4 5 LABORATORY WORK Motivation, attendance Keen, eager to learn, regular attendance less interested, irregular attendance Organisation of time Effective time management less well organised or poorly focused Experimental design & Good understanding of experimental design, good limited understanding of experimental design, limited execution technical ability technical ability Data analysis & Capable of manipulating experimental data & required major assistance in data handling, lacked interpretation understanding results understanding of results Contribution Able to suggest modifications & different approaches did not show much interest or ability to make suggestions Achievement Well above expectation for project below average expected LABORATORY NOTEBOOK Organisation Clear, legible, easy to follow Disorganised, illegible Experimental detail Precise details, sufficient for reproduction Insufficient detail, incomplete record Results Accurately recorded, tables, graphs etc annotated No results recorded, poorly labelled, tables etc absent Specific Comments Laboratory work Laboratory notebook CAS mark = 1. Excellent; hard to improve upon 2 3 4 5; needing major improvement to reach an acceptable Honours standard
  • 73. Assessment of Thesis Student: Project title: Marker: STANDARD ACHIEVED 1 2 3 4 5 CONTENT Introduction – style Clear, concise, focused rambling, confused, poorly focused Introduction – content Good knowledge of relevant literature rather superficial knowledge Aims and objectives Aims clearly identified aims not clearly stated Methods Clearly and concisely explained confused and ill-organised Results – presentation Experimental rationale clearly presented rationale not clear Figures and Tables Experimental data clearly presented data poorly presented Results – analysis Significance of data clearly explained explanation poor or absent Results – conclusions Valid conclusions drawn conclusions inadequate or incorrect Discussion Results discussed in context of literature limited attempt to place results in context Future work Clear statement of possible future work future work limited or poorly argued References Appropriate literature cited correctly references lacking or format inconsistent Specific Comments CAS mark = 1. Excellent; hard to improve upon 2 3 4 5; needing major improvement to reach an acceptable Honours standard PRESENTATION Sentence construction Good, readability high poor, less coherent Spelling & Grammar Correct many errors Organisation Visually attractive, well-organised, legible untidy, badly organised, illegible Figures & Tables Neatly drawn/constructed, properly labelled untidy, poorly labelled
  • 74. Research Project Presentation and Oral Examination Assessment Form Student: Project title: Markers: STANDARD ACHIEVED 1 2 3 4 5 CONTENT Introduction and aims Good relevant knowledge, aims clear rather superficial knowledge Experimental work Experimental data and rationale clearly presented rationale not clear Analysis and conclusions Valid conclusions and analysis conclusions inadequate or incorrect PRESENTATION Effectiveness of communication Clear effective presentation Presentation unclear or difficult to understand Time keeping Kept to 10 minutes allowed Poor time keeping ORAL EXAM Defence and reasoning Able to discuss and defend work done Poor quality defence Understanding Comprehensive, clear grasp of concepts Poor grasp of fundamental concepts Knowledge relevant to project Thorough, detailed Superficial knowledge Specific Comments CAS mark = 1. Excellent; hard to improve upon 2 3 4 5; needing major improvement to reach an acceptable Honours standard
  • 75. ESSAYS Essay writing is an important scientific skill. Its function in the Honours course is to provide you with training in researching the literature and in judging what are the central issues. It also serves as part of your continuous assessment (3 elements in total). You will write three essays. The first 2 essays will be chosen on the basis of the options modules dictated by your degree designation. For instance if you are doing Biochemistry Option module 1, with Microbiology Option module 2, essay 1 title will be chosen from the Biochemistry essay 1 list, with an essay 2 title from Microbiology essay 2 list. Each should be 2000 words (excluding the reference list), which requires you to be disciplined in its preparation; being able to write to a required length is a very useful skill, so we expect you to stay within the limit set. Essays more than 10% over the word count will be returned for shortening. Your word-processor will give you a word count; this must be included on the cover (title) page of the essay. The third essay is again 2000 words (reference list extra), and will focus on a topic of research interest in your assigned project lab. Your supervisor will provide a title early in semester 1. You should discuss the content and subject area of your third essay with your supervisor when you are at the essay planning stage (although your supervisor will not be offering written comment on any drafts of your essay 3). If you are doing a literature based-project, your essay 3 will be based on a free choice of question from the 2005 Molecular and Cell Biology Honours paper 4. The essays will be assessed by two members of staff, using the same criteria for agreement on marks as outlined in the Assessment section (see below). This assessment is not open to negotiation, although if asked, the markers will clarify any points of constructive criticism. The assessment form for essays is included in this section. Please read it with care; the notes that accompany it give you guidance on what we judge to be important in a good essay. If you have particular doubts about your ability to write essays, either in terms of organising material or in the mechanics of good scientific writing, seek help from your tutor during the first term. Do not wait until your first essay is causing you anxiety. All your essays should make reference to the latest literature on the subject you have chosen. While you may be guided through an unfamiliar subject area by reference to a review, your essay should specifically not paraphrase the review article, but should be a synthesis of your own views of the subject, written in your own words arrived at by reading of the original research papers indicated by resources like Web of Science/Medline/review articles. This will give insight into how information is derived (one criteria assessed) as well as helping in preparation for the Paper 5 Data Analysis exam at the end of the year, where understanding of a research paper is examined. In your essays, credit will be given for citing, where appropriate, up-to-date references published within the last 6 months. PLAGIARISM The definition of Plagiarism is 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. The instruction given above to write essays in your own words and not to copy whole sentences from articles is crucially important to avoid plagiarism. If you are unsure what constitutes plagiarism, you must consult the following Web site; click on ‘Self Test’ to see if you know what is / is not acceptable; http://www.abdn.ac.uk/diss/ltu/resources/plagiarism.hti 75
  • 76. The University views this offence extremely seriously indeed; it can have dire consequences, including the awarding of no higher than a pass degree. On the subject of plagiarism, please see; http://www.abdn.ac.uk/registry/quality/disccode.doc for a note of the University Code of Conduct. The University Code of Conduct states: "For the purpose of this Code 'cheating' includes plagiarism. Plagiarism is the substantial use, without acknowledgement and with intent to deceive the examiners or knowing that the examiners might be deceived, of the intellectual work of other people by representing, whether by copying or paraphrase, the ideas or discoveries of another or of others as one's own in work submitted for assessment. The mere inclusion of the source in a bibliography shall not be considered sufficient acknowledgement." All hand-in work should be accompanied by a ‘Plagiarism Front Cover Sheet’, which you will find at the end of the manual and which should be copied as required. FEEDBACK As for all elements of continuous assessment, you will be given feedback on the Honours classification your essay has attained, with the grading on the University CAS scale. Feedback is normally given within 3 weeks of essay submission. Latest Submission dates: Essay 1: 17.10.06 (3 copies to be submitted) Essay 2: 15.11.06 (3 copies to be submitted) Essay 3: 12.12.06 (3 copies to be submitted) Note that computer failure is not accepted as a reason for late submission - it is good practice to maintain at least two copies of computer files. 76
  • 77. TITLES FOR ESSAY 1 (2000 WORDS) The essay topics offered are given below. You should select one title from the following lists according to the options Modules you are taking i.e. if you are taking Biochemistry Option 1, select from the Biochemistry essay 1 list; if you are taking Genetics Option 1, select from the Genetics essay 1 list etc. (3 COPIES TO BE HANDED INTO THE SCHOOL OFFICE BY 17 th OCTOBER 2006). BIOCHEMISTRY ESSAY 1 RNA catalysis and modification 1. The ribosome is a ribozyme. Discuss the evidence for this statement and compare the putative reaction mechanism of this marcomolecular catalyst with more simple ribozymes. 2. Discuss mechanisms of rRNA and tRNA modification in the cell, and the physiological roles of such modifications. GENETICS ESSAY 1 Dynamic Genomes: 1. L1 retrotransposons have a profound effect on the expansion, permutation and evolution of other, non-L1, DNA sequences in the human genome: discuss. 2. Several mammalian genomes, including human, chimpanzee, rat and mouse, have been sequenced. What has this told us about the mechanisms of genome evolution? MICROBIOLOGY ESSAY 1 Host Microbial Interactions: 1. There are many types of host-microbe interactions. Where the interaction is pathogenic in nature, describe how the microbe coordinates its gene expression to maximise the impact of its attack on the host. 2. Most host-microbe interactions exhibit a degree of specificity. Describe, at the molecular level, the different recognition events that occur between a microbe and its designated host which ensure a successful interaction. IMMUNOLOGY ESSAY 1 1. Leucocytes are programmes for different functions and express distinct patterns of chemokines and chemokine receptors. Give examples of this, and discuss why these patterns are important for an efficient immune response. 2. The brain is an immune privileged organ. Fact or Fiction? Discuss with reference to the requirement to maintain immune surveillance of the central nervous system in health and disease. 77
  • 78. TITLES FOR ESSAY 2 (2000 WORDS) The essay topics offered are given below. You should select one title from the following lists according to the options Module you are taking i.e. if you are taking Biochemistry Option 2, select from the Biochemistry essay 2 list; if you are taking Genetics Option 2, select from the Genetics essay 2 list etc. (3 COPIES TO BE HANDED INTO THE SCHOOL OFFICE BY 15th NOVEMBER 2006). BIOCHEMISTRY ESSAY 2 Nucleo-Cytoplasmic Transport 1. The transport of molecules and complexes between the nucleus and cytoplasm is critical for eukaryotic cell function. This process is specific in terms of the cargo that is transported and the direction of transport. Discuss how the Ran-GTPase cycle contributes to nucleo-cytoplasmic transport 2. Control of nucleo-cytoplasmic transport plays a key role in the regulation of many cellular processes including cell division, stress responses and carbon assimilation. Using one specific example from yeast and a second example from mammalian cells, describe the molecular mechanisms by which nucleo-cytoplasmic transport can be regulated. GENETICS ESSAY 2 Genetic analysis: 1. DNA microarrays have been used to monitor global gene expression patterns in cells. Describe how this technology is now being exploited to study the molecular basis of disease. 2. Discuss the merits and limitations of using genetically manipulated mouse models in the study of genetic polymorphisms and human disease. MICROBIOLOGY ESSAY 2 1. Using original research papers as reference material, describe and discuss the contribution of flux control analysis to the production of aromatic amino acid precursors in enteric bacteria. 2. Describe the impact made by the knowledge of whole genome sequences on rational design of new antimicrobial drugs. IMMUNOLOGY ESSAY 2 1. Describe the mechanisms of innate and adaptive immune responses initiated by dendritic cells and discuss how dendritic cells might be used therapeutically to induce tumour rejection or to induce tolerance to organ transplants. J Liversidge/ S Wong 2. Activated T cells play a critical role in the pathogenesis of multiple sclerosis. Discuss the experimental evidence supporting this concept, with specific reference to the site(s) at which T cell activation must occur to initiate an inflammatory response in the central nervous system. 78
  • 79. ESSAY 3 Essay 3 for students carrying out a laboratory-based project Essay 3 is a 2000 word essay whose title will be provided for you early in the first semester by your project supervisor. The essay will be on a subject based upon the research interests of the lab in which you will be carrying out your project, although it will specifically not describe the exact research background to your project. Your supervisor has been given guidance on this matter and will provide you with a title during semester 1. The purpose of essay 3 is to get you reading around the broader subject of the research area of your assigned research lab, before you actually begin the project. You should discuss your project and the content of this essay with your supervisor before you start to actually write it. Essay 3 for students carrying out a literature-based project Those of you who have been assigned a literature-based project will write a 2000 word essay 3 on one of the titles from the 2005/2006 Molecular and Cell Biology Paper 4 (General Essay paper; http://www.abdn.ac.uk/diss/library/examdb/). (3 COPIES TO BE HANDED INTO THE SCHOOL OFFICE BY 12th DECEMBER 2006). 79
  • 80. GUIDE ON ESSAY WRITING AND ASSESSMENT Students should refer to "A Guide to Scientific Writing" by David Lindsay (Longman Cheshire) for more general guidance on writing essays. What follows is not a substitute for reading this book, but gives general guidance on writing essays and on how we assessment them. PLANNING AND WRITING AN ESSAY 1. Think What does the title mean? What do I know already? What are my views on this question? Where can I find more information? What are the best examples to illustrate the points that I want to make? How many words do I devote to each example? 2. Prepare Devise a set of themes and ideas. Organise evidence under the theme headings: remember that arguments pro and contra are equally important. Select illustrations (diagrams/schemes) that reflect the themes and ideas. 3. Plan Place themes in a logical order, and have a clear, and planned, introduction and conclusion. Start simply and develop towards more complex arguments. Do not hop from one theme to another and then back again. Identify the links between themes as a mechanism of ensuring continuity. 4. Execute Write short sentences and keep clauses simple. Use appropriate tenses. Be consistent in the organisation of sections. Have diagrams in front of you when writing about them. Support statements with evidence, usually a citation; ensure your citation style is consistent 5. Complete Read over what you have written - can you read it out loud without stumbling? Have you answered the question? Have you done what you said you would do at the start of the essay? Have you checked it carefully for typographical errors? ASSESSMENT OF ESSAYS The assessment form ensures that you get useful feedback on your written work. When there is a mixture of tick positions you may wish to discuss with the marker how the final mark was reached. CONTENT and PRESENTATION Each essay will be judged on content and also on style of presentation. An essay must always be more than a collection of facts and ideas. Good presentation is central to clear communication. Knowledge: It is expected that any essay will contain a substantial body of facts gleaned from appropriate literature, which should be cited within the text (Citations). The length of the essay will dictate how many facts can be given in support of a given statement, and allowance will be made for this by the staff. 80
  • 81. Analysis: Students are expected to develop their analytical skills. This is most readily demonstrated by use of carefully selected examples, which should show a good understanding of the material. Remember that examples may either support or undermine an argument. A balanced essay will consider the relative strengths of the arguments for and against a particular point of view (Viewpoint). Structure: A good essay will be clearly structured by division into appropriate sections, including an introduction, which provides a clear and concise statement of the issue to be discussed, and a conclusion, which briefly sums up the issues discussed. Viewpoint: Students should form a view on the subject about which they are writing and should be able to support their views with balanced use of appropriate examples. Figures: An argument can often be supported by Figures or Tables that present information more effectively than text alone. Figures and Tables should not be an add on, but must be an integral feature of the text and must be described and discussed. A poor or inappropriate figure or table will usually detract from the essay. Hand-drawn figures are preferred to reproductions of complex diagrams from other people's work (if used, make sure you acknowledge the source). Citations: Papers and reviews used as source material should be cited in the text. Direct quotes should be indicated by quotation marks, although their use should be kept to a minimum (see University Web page on plagiarism). Use of the EMBO Journal style of citation is essential and a list of citations should be presented at the end of the essay. The reference list does not have to be included in your count of 2000 words. In the text a reference should be cited by author and date; not more than two authors may be cited per reference; if there are more than two authors use et al. References should be listed alphabetically according to the initial letter of the surname of the first author. Where the same authors have published more than one paper, list them in the order in which their papers appeared. If necessary use a and b eg 1990a., with the authors' surnames and initials inverted. References should include, in the following order: • authors' names; year; article or chapter title; editors (books only); journal or book title; name and address of publisher (books only); volume number and inclusive page numbers. The name of each journal should be abbreviated according to the World List of Scientific Periodicals (see an EMBO J. paper for reference) and italicized. References should therefore be listed as follows: Tugendreich, S., Bassett, D.E., Jr, McKusick,V.A., Boguski, M.S. and Hieter, P. (1994) Genes conserved in yeast and humans. Hum. Mol. Genet., 3, 1509-1517. Gehring, W. (1994) A history of the homeobox. In Duboule, D. (ed.), Guidebook to the Homeobox Genes. Oxford University Press, Oxford, UK, pp. 1-10. Lewin, B. (1994) Genes V. Oxford University Press, Oxford, UK. Techniques: Scientific information is derived from experimentation. It is important to understand how information is derived. For example what technique was used, how was the experiment conducted etc. Sentence construction, spelling, grammar: Students are expected to spell correctly and to follow the basic rules of grammar. Short, clear sentences are preferable to complex, tortuous, rambling constructions. You should be able to pick up the eight clear grammatical, punctuation and spelling errors in the sentence that follows. If you can’t, then revise your grammar/spelling rules! “Its clear to 81
  • 82. the company that there commercial targetted young people of the same age as Johns friends who where clearly able to recieve it’s message.” Organisation: An essay is easier to read if it is attractively set out on the page (wide margins, double spaced, font size ≥12). For this reason the Department encourages the use of word processors for essays. Specific comments: This section is provided for the staff to make comments that amplify the box assessments in the top half of the form. Note that computer failure is not accepted as a reason for late submission - it is good practice to maintain at least two copies of computer files. 82
  • 83. Assessment of Essays Student: Essay title: 1st Marker: STANDARD ACHIEVED 1 2 3 4 5 CONTENT Introduction Clear, concise, focused rambling, confused, poorly focused Knowledge Deep, thorough, detailed knowledge superficial knowledge Analysis Selective use and analysis of information restricted to facts Understanding Clear grasp of fundamental concepts less grasp of fundamentals Structure Clear logical structure confused order of topics Viewpoint Clearly expressed little view expressed or lacking logical approach Figures Well integrated with text poorly integrated with text Citations Range of current sources used & accurately cited citations out of date/lacking, format inconsistent Techniques Clear recognition of how information derived lacking in technical insight Conclusions Concise and reflecting content of essay poorly defined, not always relevant to essay Specific Comments CAS mark = PRESENTATION Sentence construction Good, readability high poor, incoherent Spelling & Grammar Correct many errors Organisation Visually attractive, well-organised, legible untidy, badly organised, illegible Figures & Tables Neatly drawn/constructed, properly labelled untidy, poorly labelled 1. Excellent; hard to improve upon 2 3 4 5; needing major improvement to reach an acceptable Honours standard 83
  • 84. RESEARCH TUTORIALS The research tutorials are a series of second semester small group teaching exercises at which, supported by a staff member, you will discuss a specialist subject, based upon self-directed reading of the literature. Five papers have been chosen that reflect the development of a particular topic, and you must have read the five papers before attending the first research tutorial. You will be required to develop an understanding of what constitutes a key and important paper, how the information is derived (techniques and their application), the design of those experiments, an understanding of the crucial data and an appreciation of what in the field is controversial. You are also expected to read outside the prescribed five papers, and such 'use of extensive original literature' (CAS marking scheme) will be taken as an indicator of a first class student. You will thus build up a set of your own notes on two particular subject areas. For each of the Research tutorials, you will be divided into small groups and attend two tutorials, each of 1-2 hours. You will subsequently be examined on your knowledge and understanding of the subjects, in particular how they are studied and how given practical techniques function, what are the merits of different approaches, and in what situation their application is appropriate. In addition, your understanding of the biology described in the five papers will be tested. Preparation The time spent with the tutors for each Research tutorial is very limited (3-4 hours). For this reason, it is important to 'hit the ground running' and go into the first of your two 2-hour sessions fully prepared. It is thus essential that you read the appropriate notes page(s) which follow describing each Research tutorial, and prepare by reading any supporting review recommended by the tutors, as well as the 5 papers listed. This reading of the papers should be thorough, making sure in particular you understand the rationale of the results sections, how all the techniques work that are described, how the results lead to the main conclusions of the paper. If anything is not clear, bring those questions along to the tutorial with you; if you are critical of anything in the papers, bring these discussion points along as well. Remember, the tutors are there to support your learning, not to spoon-feed you with the answers. You should therefore go to the tutorial prepared to ask questions, to think, and to contribute to the group discussion subjects suggested in the tutorial notes (following pages). The tutorials are spaced so as to allow time to prepare for each of the two 2 hour sessions, each of which will have a different focus and address a different set of questions. 84
  • 85. BIOCHEMISTRY TUTORIAL 1 THE 3 RS OF GENOME STABILITY: DNA REPLICATION, RECOMBINATION, AND REPAIR Tutors: Dr Anne Donaldson and Dr Peter McGlynn Introduction In this tutorial we will discuss our understanding of the processes ensuring DNA replication initiation and continuity, and how cells cope with the inevitable blocks to replication progression. This topic will be explored in the first session by discussing techniques used to investigate genome stability. In the second tutorial, groups of students will present and discuss the importance of recent cutting-edge publications in this area. Papers to be covered are: Sangrithi MN, Bernal JA, Madine M, Philpott A, Lee J, Dunphy WG, Venkitaraman AR. Initiation of DNA replication requires the RECQL4 protein mutated in Rothmund-Thomson syndrome. Cell. 2005 Jun 17;121(6):887-98. (PMcG/AD) Takeda DY, Shibata Y, Parvin JD, Dutta A. Recruitment of ORC or CDC6 to DNA is sufficient to create an artificial origin of replication in mammalian cells. Genes Dev. 2005 Dec 1;19(23):2827-36. (AD) Luke B, Versini G, Jaquenoud M, Zaidi IW, Kurz T, Pintard L, Pasero P, Peter M. The cullin Rtt101p promotes replication fork progression through damaged DNA and natural pause sites. Curr Biol. 2006 Apr 18;16(8):786-92. (AD) Davies AA, Masson JY, McIlwraith MJ, Stasiak AZ, Stasiak A, Venkitaraman AR, West SC. Role of BRCA2 in control of the RAD51 recombination and DNA repair protein. Mol Cell. 2001 Feb;7(2):273-82. (PMcG) Boddy MN, Gaillard PH, McDonald WH, Shanahan P, Yates JR 3rd, Russell P. Mus81-Eme1 are essential components of a Holliday junction resolvase. Cell. 2001 Nov 16;107(4):537-48. (PMcG) 85
  • 86. BIOCHEMISTRY RESEARCH TUTORIAL 2 MECHANISMS OF EUKARYOTIC PROTEIN SECRETION Tutors: Kath Shennan and Bernadette Connolly Soluble factors destined for the classical pathway of eukaryotic protein secretion typically contain N- terminal signal peptides that mediate co-translational translocation into the lumen of the endoplasmic reticulum and from there the proteins are packaged into vesicles for transport to the cell surface via the Golgi apparatus. Alternative mechanisms exist and these include post-translational translocation and ER/Golgi independent secretion. This research tutorial focuses both on the methods and methodology used to investigate the molecular basis of the various secretory pathways and how to distinguish between classical and non-classical mechanisms. It will cover specific peptide signals that target proteins to individual pathways, post- and co-translational modification and current controversies in the field. Tutorial 1 Objective: The main objective of this tutorial is to gain an understanding of the mechanism of classical protein secretion and the biochemical, molecular and cellular methods used in its study. Preparation: All members of the class will read the mini review and research paper (to be decided) and be prepared to discuss the research paper in terms of: • Experimental methodologies • Data interpretation from each figure • Conclusions drawn Tutorial 2 Objective: The main objective of this tutorial is to explore non-classical mechanisms of protein secretion and the methodology involved. Preparation: The class will be split into small groups. Each group will: • Be allocated a research paper (from a list to be decided) • Focus on their paper, but read the other papers too. • Meet as a group to discuss the content of their paper. • Present the paper to the whole class, highlighting the experimental approaches that were used and the key conclusions. 86
  • 87. GENETICS RESEARCH TUTORIAL 1 MOLECULAR ANTHROPOLOGY Tutors: Duncan Shaw Format: • Introductory talk to whole class • Drop-in session for help • 2nd Tutorial - Presentation by class Synopsis: Traditionally, the study of human evolution relied on the use of morphological characteristics of fossils, together with archaeological evidence of behaviour such as tools, art, remains of food, types of dwelling, etc. Over the last 15 years it has become possible to use DNA sequence variation to answer many fascinating questions, such as where modern humans came from, whether we are derived from types such as Neanderthal man, how farming and other cultures were spread across the world, and whether or not the histories of peoples as described in their oral traditions are supported by scientific evidence. Much of this investigation is done using the DNA of modern humans (we focus on the use of Y-chromosome and mitochondrial markers) supplemented in some cases with rare (and very precious) DNA from human fossils. Main points: • Appreciation of the technical/methodological issues involved. • Go beyond the set 4 papers and identify literature that further addresses certain points. • Resolution of the major theories concerning the origins of modern man and related questions concerning population movements. • Limitations of this kind of approach. • Major conclusions that can be drawn concerning the original research questions addressed by these investigations. Papers (4 set): Capelli C, Redhead N, Abernethy JK, Gratrix F, Wilson JF, Moen T, Hervig T, Richards M, Stumpf MP, Underhill PA, Bradshaw P, Shaha A, Thomas MG, Bradman N, Goldstein DB. (2003) A Y chromosome census of the British Isles. Curr Biol. 13:979-84. Ovchinnikov I. V., Götherström A., Romanova G. P., Kharitonov V M., Lidén K & Goodwin W. (2000). Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404 (no 6777) 490-493. Thomas MG, Parfitt T, Weiss DA, Skorecki K, Wilson JF, le Roux M, Bradman N, Goldstein DB. (2000). Y chromosomes traveling south: the cohen modal haplotype and the origins of the Lemba--the "Black Jews of Southern Africa". Am J Hum Genet. 66:674-86. Caramelli D, Lalueza-Fox C, Vernesi C, Lari M, et al. (2003). Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. Proc Natl Acad Sci USA 100, 6593-6597. 87
  • 88. GENETICS RESEARCH TUTORIAL 2 COMPLEX PHENOTYPES Tutors: Al Cumming and Andy Schofield Very few diseases conform to the “one gene-one disease” rule. The majority of common diseases, such as cancer, heart disease, epilepsy, manic depression and diabetes are determined by the interaction of numerous genetic factors together with environmental factors. It is the additive effect and interplay between these components that eventually produces the final disease phenotype. In order to understand the interactions of genetic and environmental influences on complex diseases, we will consider the example of Alzheimer’s disease (AD). AD is a disorder which is relatively uncommon in those aged less than 65yr, but becomes an increasing cause of morbidity and mortality in older populations. The illness is characterized by memory loss and by impairment of cognitive function, followed by changes in personality. Data from family and twin and indicate a genetic basis for the disease and rare single gene families have provided insight into the precise cellular mechanisms involved in the disease process. The aim of the research tutorial will be to understand the nature of a complex disease trait, and gain an understanding of how genetic and environmental factors influence the disease phenotype. An appreciation of the different analytical methods used to study complex disease traits will be required, together with a critical appraisal of the relative merits and limitations of each approach. List of suggested papers to be studied: 1. Mattson MP (2004) Pathways towards and away from Alzheimer’s disease. Nature 430: 631-638 2. Blennow K, de Leon MJ & Zetterberg (2006) Alzheimer’s disease. Lancet 368: 387-399 3. Kamboh ML (2004) Molecular genetics of late-onset Alzheimer’s disease. Annals of Human Genetics 68: 381-404 4. Mudher & Lovestone (2002) Alzheimer’s disease – do tauists and baptists finally shake hands? Trends in Neurosciences 25:22-25 5. Lesné S et al (2006) A specific amyloid-ß protein assembly in the brain impairs memory. Nature 440: 352-7 88
  • 89. MICROBIOLOGY RESEARCH TUTORIAL 1 : THE CELL BIOLOGY OF KINESINS AND MYOSINS IN FUNGI Tutors: Prof. Neil Gow Introduction The cytoskeleton, composed of actin microfilaments (F-actin) and microtubules is responsible for mechanical work processes in eukaryotic cells. It has a defined architecture connecting the cell surface to the cell interior and it directs how cells move, grow and divide. Together the actin and microtubule-based cytoskeleton directs vesicle traffic, constricts or expands the cell surface, moves, orientates, divides and segregates nuclei and other organelles during cell division. The cytoskeleton can also influence RNA transport in the cell. Actin and microtubules function as railroad tracks along which vesicles and organelles can move by hooking them on to unidirectional motor proteins that translocate themselves and their cargo along the rails. This tutorial is concerned with the cell and molecular biology of these critical motor proteins. Myosins are a family of actin-based motor proteins that have a range of specific functions. Kinesins are one class of microtubule motor. In this tutorial we will examine in detail how the roles of individual myosins and kinesins can be dissected. Importantly the tutorial will also encourage you to consider the integrated functions of the cytoskeleton as it drives the growth and division of eukaryotic microorganisms. Our objectives are three fold. [i] We want you to understand the concept of “hypothesis driven research” as applied in this case to the study of myosins. [ii] You will learn to analyse in detail the rationale and methodology of some key experiments. [iii] You will be asked to critically evaluate and interpret data that has been published. You will find the following review a helpful introduction to the area of myosins and kinesins; Steinberg, G. (2000) The cellular roles of molecular motors in fungi. Trend. Microbiol. 8; 162-168. This must be read before the first tutorial. Tutorial 1 will introduce some of the important concepts in this subject area. It will discuus the concept of hypothesis-driven research, illustrated through discussion of one of the five papers. Please come to the first tutorial having done the following; - Carefully read the review by Steinberg (2000). - Critically read, and made notes on, the paper by Geli et al; be prepared to discuss this paper in detail at the tutorial. Make notes for your own benefit about the key experiments, and if necessary consult reference books or your tutor about scientific terms and methods that you are not familiar with. In the tutorial you will be expected to have a firm grasp of the content of this paper, so be prepared. - Tutorial 2 will focus on the techniques that are used to study the cell biology of molecular motors such as myosin. Through student-lead study of the remaining four papers, including paper-review style presentations of data in the papers, the tutorial will focus on the following key questions; How can protein function be studied in (i) intact cells (ii) intact living cells? What specific techniques allow study of dynamic or spatially constrained processes; what are the drawbacks of these techniques? There are four more papers to read. You will be tackling one of these yourself but you must also read the three others in this group and be prepared to ask informed questions of the presenter. Papers for study: Wedlich-Soldner R et al (2002). A balance of KIF1A-like kinesin and dynein organizes early endosomes in the fungus Ustilago maydis. EMBO J. 21:2946-57. Seiler, S. et al. (1999) Kinesin and dynein mutants provide novel insights into the roles of vesicle traffic during cell morphogenesis in Neurospora Curr. Biol. 9: 779-785 Geli, M.I. and Riezman H. (1996) Role of type I myosins in receptor mediated endocytosis in yeast Science 272; 533-535 Schott D. et al. (1999) The COOH-terminal domain of Myo2p, a yeast myosin V, has a direct role in secretory vesicle targeting. J. Cell Biol. 147; 791-807 Wedlich-Soldner R et al. (2002) Dynein supports motility of endoplasmic reticulum in the fungus Ustilago maydis. Mol Biol Cell. 13:965-77. 89
  • 90. MICROBIOLOGY RESEARCH TUTORIAL 2 BACTERIOPHAGES AND VIRULENCE FACTORS IN PATHOGENIC BACTERIA Tutor: Maggie Smith Introduction Pathogenic bacteria cause disease because they encode virulence factors that usually work combinatorially to enable them to multiply in the human/animal/ plant enviromnet. Virulence factors are extremely varied in nature causing adherence to certain cell types, secretion of effector proteins and toxins, inhibition of innate immune responses, etc. Many virulence genes are known to be encoded on so-called pathogenicity islands and some of these have been shown to be phage. In these tutorials we will examine the role that bacteriophages have in the spread of virulence factors between pathogen bacteria. First we will examine studies where they have shown that a toxin gene is encoded by a phage genome and where a phage has been shown to mobilise a pathogenicity island. We will then look in detail at how some of the toxin genes are expressed and how they link in with the phage life cycle. Finally we will look at the in vivo interaction between commensal bacteria and lysogens in vivo. . The background to phage encoded virulence is given in the review article; Boyd and Brussow (2002) ‘Common themes among bacteriophage-encoded virulence factors and diversity among the bacteirophages involved. Trends in Microbiology 10: 521. The papers to be studied are: 1. Waldor and Mekalanos (1996) Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272: 1910. This paper demonstrates that the cholera toxin is encoded by a phage. 2. Ruzin, A., Lindsay, J. and Novick, R.P. (2001) Molecular genetics of SaPI – a mobile.pathogenicity island in Staphylococcus aureus. Molecular Microbiology 41:365-377 3. Wagner et al, (2002) Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli. Molecular microbiology 44: 957-970. 4. Livny and Friedman (2004) characterising spontaneous induction of Stx encoding phages using a selectable reporter system. Molecular microbiology 51, 1691-1704. 5. Gamage, S.D., Patton, A.K., Strasser, J.E., Chalk, C.L. and Weiss, A.A (2006) Commensal bacteria influence E. coli O157:H7 persistence and shiga toxin production in the mouse intestine. Infection and Immunity, 74: 1977-1983. 90
  • 91. IMMUNOLOGY RESEARCH TUTORIAL 1: THE ROLE OF PHAGOTIC REMOVAL OF APOPTOTIC CELLS IN THE RESOLUTION OF INFLAMMATION Tutor: Garry Walsh Introduction Apoptosis or programmed cell death is a central and essential process in the resolution of inflammation, the control of tissue remodelling and is vital for a viable immune system. It is a tightly controlled specific process by which damaged or unwanted cells are removed without spillage of their contents. While much attention has rightly been paid to the study of the mechanisms by which pro-inflammatory cells can be induced to become apoptotic - it must be remembered that removal of cellular corpses by phagocytosis is as vital a process as apoptosis itself. There has therefore been a great deal of work aimed at understanding the processes responsible for apoptotic cell recognition and removal by phagocytes. Phagocytic removal of apoptotic cells is a rapid event controlled by a complex array of receptors that phagocytes use to recognise changes in the membranes of apoptotic cells. Once recognised apoptotic cells are engulfed and digested. Importantly, the process of recognition has a profound effect on the phagocyte. For example, engulfment of apoptotic cells by macrophages “re-programmes” them to an anti-inflammatory secretory profile. Good reviews of the area are: Savill J & Fadok V 2000 Nature 407 784-788; and Fadok et al., J Clin Invest, October 2001;108: 957-962 Tutorial 1 The first tutorial will serve as an overview of the area. All tutorial members will read the first paper, i.e. Fadok et al. J Immunol 1992;148:2207-16. Please come to the tutorial having: • Read the background reviews and the paper by Fadok et al • Understand the methodology used in the study • Be able to interpret the data in the paper • Recognise the significance of the findings of the paper • Note any questions you may have regarding the area or the paper. Tutorial 2 This will focus on the recognition pathways used by phagocytes to recognise apoptotic cells and the effect that engulfment of apoptotic cells has on macrophage cytokine secretion. Fadok et al. CD36 is required for phagocytosis of apoptotic cells by human macrophages that use either a phosphatidylserine receptor or the vitronectin receptor (αvβ3). J Immunol 1998; 161: 6250-6257. Brown et al. Apoptosis disables CD31-mediated cell detachment from phagocytes promoting binding and engulfment. Nature 2002; 418: 200-203. Huynh et al. Phosphatidylserine-dependent ingestion of apoptotic cells promotes TGFβ-1 secretion and the resolution of inflammation. J Clin Invest 2002; 109:41-50 Lucas M et al. Requirements for Apoptotic Cell Contact in Regulation of Macrophage Responses. J Immunol. 2006 Sep 15;177(6):4047-4054 • The class will be split into four groups • Each will be allocated one of the above papers to read in detail • Each group will discuss the paper in detail but the other papers must be read also • Present the findings to the whole class discussing methods used and key findings – there will then be a general discussion. 91
  • 92. IMMUNOLOGY RESEARCH TUTORIAL 2 IMMUNE SUBVERSION BY AFRICAN TRYPANOSOMES Tutor: Dr Jerry Sternberg African trypanosomes have been the subject of intense interest amongst immunologists and parasitologists for many years, and every immunology text book uses the trypanosome antigenic variation system as a paradigm for immune evasion by parasites. Yet the interactions between trypanosomes and the immune system extend beyond antigenic variation and recent research has demonstrated the role of the immune system in pathogenesis, possible direct interactions between these protozoan parasites and cytokines, and the difficulties in extrapolating from in vitro and animal models to an actual human disease. This tutorial will focus one such interaction, namely that between trypanosomes and TNF. As you will read, it is a topic not without controversy. Through a critical reading of the selected papers on this topic, you will gain an understanding of methods and data interpretation in the immunology of trypansomiasis . You will be able to bring this understanding to evaluate the biological relevance of trypanosome-TNF interaction in parasitic disease. Tutorial 1 Tutorial 1 will set the scene and provide a general background to the biology of African trypanosomes. All members of the class should read: • Stich et al (2002) Brit.Med.J. 325:203-206 and at least one of the following reviews: • Donelson, (2003) Antigenic variation and the African trypanosomes genome. Acta Tropica. 85:391-404 • Vanhamme et al (2001) An update on antigenic variation in African trypanosomes. Trends Parasitol 17:338-343 • Pays and Nolan (1998) Expression and function of surface proteins in Trypanosoma brucei. Mol. Biochem Parasitol. 91:3-36 In this tutorial we will discuss first the disease caused by African trypanosomes and antigenic variation. Then the evidence for more extensive interactions with the host immune system will be introduced. Tutorial 2. In this tutorial we will discuss the role of TNF in African trypanosome infections. We will work with the following set of papers. You must read them before the tutorial and make notes on the methodologies used, conclusions, and areas of contradiction or consensus between each study. In the tutorial we will critically review the papers and come to a general conclusion on the role of parasite-cytokine-host relationships in trypanosomiasis. • Lucas et al (1994) Mapping the Lectin-like activity on Tumor Necrosis Factor. Science. 263:814-817. • Kitani et al (2002) Recombinant TNF –alpha does not inhibit the growth of African trypanosomes in axenic cultures. Infect Immun 70:2210-2214. • Magez et al. (1998) The glycosyl-inositol-phosphate and dimyristoylglycerol moieties of the glycosylphosphatidylinositol anchor of the trypanosome variant-specific surface glycoprotein are distinct macrophage-activating factors. J Immunol 160:1949-56. • Magez et al (1999) Tumor necrosis factor alpha is a key mediator in the regulation of experimental Trypanosoma brucei infections. Infect Immun 67:3128-32. • Daulouede et al. (2001) Human macrophage tumor necrosis factor (TNF)-alpha production induced by Trypanosoma brucei gambiense and the role of TNF-alpha in parasite control. J Infect Dis 183:988-9. • Magez et al (2004) P75 TNF-receptor shedding occurs as a protective host response during African trypanosomiasis. J. Infect. Dis. 189:527-539. 92
  • 93. PAST EXAMINATION PAPERS 2001 – 2005 Data Analysis papers available from School Office on request. 2003 – 2006 Papers 1-4 are available at www.abdn.ac.uk/diss/library/examdb/ and on WebCT (MB4050 course) --------------------------- 93
  • 94. School Of Medical Sciences Molecular and Cell Biology Front Cover Sheet Please complete for every piece of work submitted Name:______________________________________________________________ ID PLAGIARISM I confirm this work is my own, that work from other sources is acknowledged, and that nothing in this work constitutes plagiarised material. I understand the meaning of the term plagiarism, and I have read and understand the University guide on plagiarism at http://www.abdn.ac.uk/writing I have read, and understand, the University regulations and advice on cheating, including plagiarism http://www.abdn.ac.uk/registry/quality/appendix5x15.pdf Signed: ____________________________________ Date: _________________________________ 94