1. The University of EdinburghSchool of Biological Sciences Honours Guide for the Academic Year2010-2011 A guide to the final year of the B.Sc. Biological Sciences degree programmes and the associated intercalated B.Sc. Medical Sciences and B.Sc. Veterinary Sciences degree programmes Produced by The Biology Teaching Organisation in association with the Honours Programme OrganisersTel:0131 650 8649 Email:BTO@ed.ac.uk

2. http://student.biology.ed.ac.uk/index.php Any updates and corrections to this guide will be given on http://student.biology.ed.ac.uk/undergraduate/courses/year4.php.All enquiries about individual programmes should initially be made to the appropriate Honours Programme Organiser or Secretary. Their contact details are given at the start of the section describing each programme. More general issues may be addressed to:For programmes based in the School of Biological Sciences, College of Science & Engineering:BTO Reception 0131 650 8649Technical Support Manager Mr. Brendan McGory0131 650 7196 E-learning Supportbtovle@ed.ac.uk For programmes based in the College of Medicine & Veterinary Medicine:BMTO Reception0131 650 3160 For programmes based in the School of Geosciences, College of Science & Engineering:Helen McKeating 0131 650 5430 DISCLAIMEREvery effort has been made to ensure the contents of this booklet are accurate at the time of printing. Unforeseen circumstances may, however, necessitate changes to the procedures, curricula and syllabuses described. The Biology Teaching Organisation undertakes to operate within the rules and regulations as set out in the Degree Regulations and Programmes of Study and the Examination Regulations. It will also honour undertakings made in writing to individual classes, insofar as these do not conflict with the Universitys regulations. 3. CONTENTS Semester 1...................................................................................................................1 Semester 2...................................................................................................................1 4. COMMON STRUCTURE OF THE SENIOR HONOURS YEAR The Senior Honours year of each Biological Sciences degree programme has a common structure with only minor variations. The common structure has the following features:Semester 1 50 points, generally 5 x 10 point courses:Some or all of these will be compulsory courses that must be taken by allstudents on a particular programme. Others may be elective courses, withguidance being given through programme-specific lists of recommendedand suitable courses. Semester 1 courses are generally examined at theend of the semester; for some there is in-course assessment as well.Semester 2 1 x 40 point research project. The assessment of the research project may be subdivided into component parts. For example, oral presentation, written work and laboratory performance may all be assessed separately. Students may be required to work on their research project during part of the Easter vacation. 30 points, generally 3 x 10 point courses including a synoptic exam. The nature of these courses varies between programmes. Some are electives (with choice guided as in Semester 1). Others are compulsory courses. In some programmes a compulsory course is linked to the project. Semester 2 courses are assessed through course work or otherwise within the course.The details of the courses you are required to take and possible elective courses are set out in this guide.University regulations mean that results from Junior and Senior Honours years contribute equally to your final degree class. For students who spent the Junior Honours year abroad and for students on the intercalated Bachelor of Medical Science with Honours and Bachelor of Science with Honours in Veterinary Science degree programmes; the degree class is based on the Senior Honours year only. Details of the assessment for the individual courses will be provided by the Honours Programmes.Please select up to four Honours programmes by going to http://student.biology.ed.ac.uk/ undergraduate/administration/prereg.php and selecting the relevant link. UPDATES AND CORRECTIONSAnyupdatesand correctionstothis guidewillbegivenon http://student.biology.ed.ac.uk/undergraduate/courses/year4.php.1 5. CRITERIA FOR ADMISSION TO THE SENIOR HONOURS YEARThis guide does not deal with this issue.B.Sc. Biological Sciences students should consult the appropriate BTO Guide. Offers of places in the final year are posted to students in early June once the Junior Honours exam results are known. If you are uncertain about your position, please consult your Director of Studies.Intercalating Bachelor of Medical Science with Honours and Bachelor of Science with Honours in Veterinary Science students will be told of their acceptance into the programme by their college. PRE-REGISTRATION FOR COMPULSORY COURSES ANDELECTIVESAll students admitted to a programme will be automatically registered for the relevant compulsory courses. However, it is necessary for all students to submit their choices for the electives. This guide explains the structure of the individual programmes and the decisions that have to be made regarding the electives. A course choice form will be sent to you with your offer letter. Make sure that you have provided an address to which the offer letter should be sent. You are asked to provide this when you submit your programme choices. Please inform the BTO (BTOhons@ed.ac.uk) if you wish to change this address. Intercalating medics and vets should make sure that their college office knows how to contact them.When you receive your offer of a place it is important that you reply with your acceptance and return your choice form for the electives by the date specified on the form. If you are away all summer you must arrange for someone to do this for you. Students who do not return their choice forms by the required date will miss out on the initial allocation of electives and will therefore have less chance of a place on their desired courses.When you return to the University for the start of Semester 1 you will automatically be enrolled for the compulsory courses for your honours programme. You will be informed through MyEd the electives to which you have been admitted.ADVICE ON CHOOSING ELECTIVES This is the final year of your degree programme and it is essential for your studies to be suitably focussed on your degree subject area. The section of the guide dealing with your honours programme explains the choices open to you. The advice in these sections varies from programme to programme; it has been specifically tailored to the subject areas.After a general introduction to the year, the compulsory courses are listed and you are told how you must choose elective courses to make up the 120 points. Please note the instructions carefully. Depending upon how many points are allocated to compulsory courses, you will be told how many points must be picked from one or two lists. These 2 6. are known as "List 1" which is a list of courses recommended for your programme, and "List 2" which is a list of courses also judged to be suitable for your programme. Full descriptions of these courses may be found starting on page 82.An important and valuable aspect of this system is that it opens up more avenues for students to shape their Senior Honours year to their specific interests. The instructions explain the freedom you may have to choose courses outside Lists 1 and 2 subject to the approval of your Honours Programme Organiser. If you are thinking of broadening your programme in this way, please bear in mind a number of points. Firstly consider how the subject adds 'academic value' to your programme. Secondly, remember that the courses must be at level 10 or 11 so, unless you have studied a subject in earlier years, this will limit your choice to biology and related areas. Even within biology you should consider whether you have the expected background needed for a specific elective. Thirdly, remember to check that you have fulfilled any specific requirements set out for each course.Each of the courses is "owned" by a specific honours programme. This means that the course comes under the control of the programme's Board of Examiners. Generally only the students registered for a specific programme are admitted to that programme's compulsory courses. However, if a course is compulsory for your programme you will be automatically admitted to it even if it is not owned by your programme. If you wish to do a compulsory course from another degree programme as an elective this may not be possible. Take note of any comments given in the course descriptions. If in doubt, contact the appropriate Honours Programme Organiser. The number of students admitted to electives is reasonably flexible and the course descriptions give an indication of maximum class sizes. Unnecessary restrictions will not be applied. However, there must be some limits as it is appreciated that honours teaching and learning is much more effective in smaller rather than larger classes. We also know that students look forward to smaller classes in their Senior Honours year after being in large classes in previous years. In allocating electives, Honours Programme Organisers will give preference to students for whom the course is particularly relevant but will do what they can to admit other students.Most of the courses build upon specific biology Junior Honours courses and this leads to courses having prerequisites in terms of requirements or recommended courses. Some prerequisites are prefaced by the word "normally"; this indicates that exceptions may be made, particularly for well qualified students. Students who spent their Junior Honours year abroad and intercalating medics and vets will be unable to meet requirements specified in terms of specific Junior Honours courses. These students will be excused these requirements by the Honours Programme Organiser.The course lists and descriptions indicate which programme owns the courses. The descriptions end with information on the requirements for admittance to the course.If you have any questions about the electives please direct these to the Honours Programme Organiser of the owning programme. The Organiser is responsible for the electives owned by their programme and controls admission to them. 3 7. HOW ELECTIVES WILL BE ALLOCATEDAccess to courses is controlled by the Honours Programme Organisers. Each organiser will allocate the students on their programme to appropriate electives, discussing this as necessary with other organisers.In an ideal world all students would get their top or other high choices but of course this is unlikely to happen as demand will be uneven. Honours Programme Organisers will take note of several issues when allocating the students on their programme to electives and when trying to place other students who wish to do courses 'owned' by their programme. These will include: 1) Whether the student is doing the 'owning' programme2) The ranking given to the elective by the student on their choice form3) Whether the elective is on the lists of recommended and suitable electives for the student's programme4) The student's background for courses that specify requirements5) The class size.A key aim will be to arrive at the 'best' overall solution taking account of the available information. The Board of Studies has agreed that if too few students wish to do a course it may be withdrawn.Allocations for semester two electives are made at the start of semester one, but these are preliminary and students must confirm their semester two courses towards the end of semester one. 4 8. BIOCHEMISTRY Programme Organiser: Programme Secretary: Dr. Paul McLaughlinMs Vicky Mactaggart Michael Swann Building Darwin Building Kings Buildings Kings Buildings Edinburgh EH9 3JREdinburgh EH9 3JU 0131 650 70600131 651 7052 Paul.McLaughlin@ed.ac.uk Biochem.hons@ed.ac.uk Biochemistry encourages the critical assessment of current developments and emphasises biochemical approaches to biological problems of current interest. Teaching takes the form of traditional lectures, specialised seminars in small and large groups, project work, and small-group tutorials.The programme is constructed around a set of compulsory courses. Some lectures emphasise the degree of understanding that already exists at the biochemical level; others seek to illustrate the need for a biochemical approach to particular problems. Students choose their courses as indicated below.Students pick a research topic in Semester 1. There are two parts to this aspect of the programme: Firstly, students prepare a Research Proposal in the form of a Grant Application. The topic of this proposal is linked to the Research Project when each student works independently in a research laboratory. Projects run during Semester 2, initially on a part-time basis (weeks 1-5) but ultimately with full-time commitment. Many of these projects are located in research institutes associated with the University, in addition to the SBS institutes contributing to the programme.A system of multiple assessments provides a broad view of each student's abilities and lessens the impact of final examinations. The compulsory lecture courses are assessed by examination. Electives are assessed either by examination or by essay immediately at the end of the period of study. Project work is assessed through the submission of a report and by an oral presentation. At the end of the year students will sit a synoptic exam which has the potential to cover any aspect of the course as it is focussed upon analysis of data and the interpretation of research literature.As an honours student studying Biochemistry:(a) You must do the following compulsory courses Points BICH10011 Biochemistry Project 40 BICH10014 Biochemistry Tutorials & Synoptic Examination20 BICH10010 Biochemistry Research Proposal 10 BICH10006 Biochemical Techniques 10TWO OF: BICH10007 Structural Biology 10 MLBI10009 Gene Expression10 BICH10009 Membrane Biology 10Points 1005 9. (b) In addition you must take further level 10 or 11 courses. These will normally* be from Lists 1 or 2 (below).20 Total points120Number of electives to be chosen: Semester 1: four, Semester 2: one. (Note that two of these electives must be chosen from the "Two of:" list of Biochemistry courses given under compulsory courses above.)*Students who wish a broader fourth year programme may choose, subject to the approval of the Head of School (i.e. Head of SBS, SBMS as appropriate), other level 10 or 11 courses from outside Biology. Students wishing to do this should first discuss it with their Director of Studies and their Honours Programme Organiser. Approval will only be given for courses that fit appropriately with the chosen honours specialisation and for which they are suitably qualified. The requirement for these courses to be at level 10 or 11 means that students wishing to take this option should plan for this early in their University career. Otherwise, earlier course choices may limit later choices.Compulsory Courses for the Biochemistry Honours Degree ProgrammeCode Course NameProgSem Time Slot BICH10006 Biochemical TechniquesBiochem 1Mon am Description: We aim to reinforce and extend your knowledge of biochemical techniques and to introduce you to new physical techniques in selected fields of current interest, especially those of relevance in structural biology. In the 'wet biochemistry' section the aim is to give you insight into selecting the simplest effective approach for solving the biochemical problem in hand. In the 'structural techniques' section we shall show how the answers to many fascinating questions in biology can be obtained by applying physical chemical techniques. Application of these techniques now in everyday use has improved in recent years so that the scientist is relatively free to concentrate on the biology of the problem rather than the collection of the data needed to consider the problem. A major advance in this regard is the relatively straightforward means by which an accurate 3-D structure can be obtained. The aim of this section, then, is to review some of the methods by which biomolecular structure is determined, how these methods combine to give a full picture of the structure and function of the biological system under study, which can be a single subunit, a whole molecule or a more complex assembly, and thereby show why such knowledge is an essential part of modern biochemistry, molecular biology and pharmacology. Requirements: Permission of the Curriculum Approval Officer. Normally Structures and Functions of Proteins 3 is required. Chemistry for Life Sciences 2 recommended. BICH10010 Biochemistry Research ProposalBiochem 1&2None Description: Preparation of an original Research Proposal. Requirements: Permission of the Curriculum Approval Officer. BICH10014 Biochemistry Tutorials & Synoptic Biochem 1&2Wed pmExam Description: Small group tutorial system covering all aspects of Honours Biochemistry (course work, topical biochemistry, data analysis, presentations) with particular emphasis on the preparation for the Synoptic Exam. Culminates in Synoptic exam. Requirements: Permission of the Curriculum Approval Officer. BICH10011 Biochemistry ProjectBiochem 2None Description: Honours Project: Lab Project - Thesis and Performance (35 points) Assessed Talk (5 points) Requirements: Permission of the Curriculum Approval Officer.6 10. List 1: Recommended elective courses for the Biochemistry Honours Degree Programme. As described above, students must take two of the following three courses. CodeCourse Name ProgSemTime SlotMaxClass MLBI10009 Gene ExpressionMolBiol 1 Thurs amNo limit Description: The aim of these lectures is to familiarise students with the variety of mechanisms responsible for regulating the expression of genetic information at the level transcription and post- transcription mechanisms. Teaching will focus on the organisation and packaging of the genetic material in eukaryotic cells and the implications this has for genetic expression. In addition, basic transcription control mechanisms will be examined in prokaryotes and eukaryotes. RNA processing will be studied at the level of splicing and its importance in the regulation of gene expression will be discussed. The special mechanisms which have evolved to operate within, and to take advantage of, a chromatin context will also be reviewed from a biochemical and developmental perspective. Requirements: Permission of the Curriculum Approval Officer. Structures and Functions of Proteins 3 and Molecular Genetics 3 recommended. BICH10009 Membrane Biology Biochem 1 Fri amNo limit Description: About a third of an organisms genes encode membrane proteins or enzymes involved in the biochemistry of membrane lipids, reflecting the fundamental importance of membranes in every living cell. Membranes serve to compartmentalise cell functions by isolating different biochemical processes, but membranes and lipids also function in cell signalling and regulation. Though much has been learned about biochemical pathways involved in membrane biogenesis, details of how organellar membranes assemble and achieve particular shapes and compositions remain elusive. The significant percentage of the genome associated with membrane biology implies likewise that we have only viewed the tip of the iceberg with regard to regulatory functions of lipids. The Membrane Biology module begins with a general overview of the breadth of membranes and associated proteins followed by allocation of the projects for the In Course Assessment. This will be essentially a 6-7 minute oral presentation by each student on a different mechanism for getting molecules across biological membranes followed by a question and answer/ discussion. This in-course assessment will be worth 25% of the course total. Most course lectures will combine textbook-style information with a description of methods used to gain that information. Using a combination of biochemical and cell biological approaches, we then explore emerging structures and mechanisms, including proteins involved in fusion and fission membrane interactions of viruses and the cells own endocytic and exocytic processes. Lipid modifications, membrane diffusion, and evolution of membrane bending mechanisms will also be discussed. The module also includes one Research Talk and three CPA (current paper awareness) sessions (titles to be announced). Requirements: Permission of the Curriculum Approval Officer. Structures and Functions of Proteins 3 or Molecular Cell Biology 3 is recommended. BICH10007 Structural Biology Biochem 1 Tues am No limit Description: The aim of this part of the course is to enrich your knowledge of cellular activities by providing you with structural details of the key molecular players and their interactions. Modern structural biology has shown us how numerous proteins are able to carry out their functions - in other words, how they actually work. It is not possible to appreciate just how far we have advanced in recent years in our understanding of cell and molecular biology without sampling the wealth of three-dimensional structures of proteins, protein-nucleic acid complexes, and macromolecular assemblies now available. In this course we have selected examples of structures that we consider to be most interesting and illustrative, or most important to fundamental processes such as DNA packaging and unpackaging, transcription, translation and correct folding of polypeptides to form proteins. We shall also provide some introductory material on protein and nucleic acid structures at the beginning of the course, and a bioinformatics perspective to engender 7 11. an appreciation of the role of structural biology in the post-genomics era. Requirements: Permission of the Curriculum Approval Officer. Normally Structures and Functions of Proteins 3.List 2: Suitable Elective Courses for the Biochemistry Honours Degree Programme. Further details may be found starting on page 82. CodeCourse nameProgSem Time SlotMax Class DEBI10023 Cell Biology: from CellBiol1 Tues pm 25 fundamental mechanisms to human disease. MLBI10017 Molecular Biology of Disease MolBiol 1 Fri am PYBM10025 Neurotransmitter Release and Physiol 1 Thurs pm 25 Vesicle Recycling DEBI10021 Patterning in DevelopmentDevBiol 1 Tues am BICH10002 Supercoiling in DNA andBiochem 1 Mon pm 12 Chromatin PLSC10019 The Growth of Plants PlantSci1 Fri pm BICH10016 Drug Discovery Biochem 2 Tues & Fri pm24 BICH10013 Signal TransductionBiochem 2 Mon & Thurs am 248 12. BIOTECHNOLOGY Programme Organiser:Programme Secretary: Dr. Bruce WardMrs Lesley Cochrane Darwin Building BTO Kings BuildingsDarwin Building Edinburgh EH9 3JU Kings Buildings 0131 650 5370 Edinburgh EH9 3JU B.Ward@ed.ac.uk 0131 651 8638 Biotech.hons@ed.ac.uk Biotechnology is concerned with applications of fundamental knowledge in biological. This covers many facets from making useful products using microbial, plant or animal cells (eg vaccines, antibiotics, enzymes etc) to using bioinformatics and structural biology to design new drugs. It covers a wide field from microarrays and gene therapy to biomining of genomic data to identify new drug targets for important diseases. The Honours course combines coverage of the basic principles and knowledge underpinning biotechnology and an appreciation of the processes involved in converting an idea into a product. Whilst the programme is centred round molecular biotechnology, students from different backgrounds taking third year courses in microbiology, biotechnology, molecular biology, genetics and biochemistry should find it an interesting and relevant option for Honours. Indeed the programme is closely integrated with Honours programmes in these related disciplines, providing flexibility and choice. Biotechnology is an exciting area with new developments each year in areas that affect us all. Examples include new drugs and vaccines to combat diseases, new enzymes for health care, biocontrol agents in the field and biosensors to monitor environmental pollution. We aim to keep up with new areas of interest as they emerge; for example we have introduced new lectures on synthetic biology, systems biology and microbial fuel cells.In Semester 1, students take 3 compulsory courses plus two elective courses. The compulsory courses are Enzymology & Biological Production, Novel Approaches, and Biotechnology Industrial Visits & Core Skills. These cover respectively: production of biotechnology products including antibiotics and recombinant proteins and drug design (Enzymology and Biological Production), emerging technologies for analysis, detection and product development in biotechnology (Novel Approaches) and industrial visits, topical seminars, career development, graduate skills, individual workshops, tutorials research analysis (Biotechnology Industrial Visits and Core Skills). Recommended electives are Genetic Approaches, and Gene Expression and Microbial Regulation. The former covers genetic techniques for cloning and expression and the latter covers regulation of microorganisms at the molecular level. However the opportunity to take electives from other Honours programmes is available and many students enjoy this opportunity to study in an area of choice, eg malaria, stem cell engineering etc.The objective is to provide a firm foundation in molecular and microbial biotechnology through compulsory sections dealing with topics such as expression vectors, microbial fermentation, protein structure, drug design, development of antimicrobials, vaccines etc. Whilst the course emphasises the science underpinning biotechnology, the principles of how biotechnology companies operate and topical issues are also covered. 9 13. In Semester 2 students take a further second elective course. This format allows students to tailor choices to suit their interests. For example there are electives to suit students with an interest in mammalian biology or plant biotechnology.Students undertake a major research project part-time in the second Semester. A wide choice of projects is available, as these are organised collectively within the School of Biological Sciences. One variation on this course is to take a degree in Biotechnology with Management. This requires students to have taken prerequisite courses in management in earlier years (see Biology with management elsewhere in this guide). As an honours student studying Biotechnology:(a) You must do the following compulsory courses Points BITE10004Biotechnology Project 40 BITE10006Biotechnology Synoptic Examination10 BITE10007Biotechnology Industrial Visits and Core Skills 10 BITE10005Biotechnology Literature Review 10 BITE10001Enzymology and Biological Production10 BITE10002Novel Approaches10 Points 90(b) In addition you must take further level 10 or 11 courses. These will normally* be from Lists 1 (below)10 (c) In addition you must take further level 10 or 11 courses. 20 These will normally* be from Lists 1 or 2 (below)Total points 120Number of electives to be chosen: Semester 1: two, Semester 2: one.*Students who wish a broader fourth year programme may choose, subject to the approval of the Head of School (i.e. Head of SBS, SBMS as appropriate), other level 10 or 11 courses from outside Biology. Students wishing to do this should first discuss it with their Director of Studies and their Honours Programme Organiser. Approval will only be given for courses that fit appropriately with the chosen honours specialisation and for which they are suitably qualified. The requirement for these courses to be at level 10 or 11 means that students wishing to take this option should plan for this early in their University career. Otherwise, earlier course choices may limit later choices.Compulsory Courses for the Biotechnology Honours Degree Programme Code Course NameProg Sem Time Slot BITE10005Biotechnology Literature ReviewBiotech1 None Description: A research-based course involving the preparation of a report covering the background to a chosen research topic and the formation of a research plan with milestones and objectives. Requirements: Permission of the Curriculum Approval Officer. 10 14. CodeCourse Name ProgSem Time Slot BITE10001 Enzymology and Biological Production Biotech 1 Tues am Description: An important feature of biotechnology is the use of enzymes and microorganisms to manufacture products useful to society. These products range from industrial alcohol, food additives and other bulk products, to antibiotics and recombinant therapeutic proteins. In this module we will consider important aspects of enzymes and microorganisms related to their use in industry, and methods for the discovery or generation of novel biocatalysts. We will also discuss technologies used in important commercial processes including the manufacture of antibiotics, monoclonal antibodies and recombinant proteins, as well as new approaches to drug discovery and the development of new therapeutic agents. Requirements: Permission of the Curriculum Approval Officer. BITE10002 Novel ApproachesBiotech1Thurs pm Description: Advances in scientific knowledge frequently allow development of new technologies or improvements to existing technologies. Recent examples in Biotechnology include knowledge of microbial genomes, the development of microarray and proteomic methods to examine how cells respond to various stimuli. This course examines examples of new technologies and their application to combating important diseases. Requirements: Permission of the Curriculum Approval Officer. BITE10007 Biotechnology Industrial Visits and Biotech 1&2Wed am Core Skills Description: This section will include visits to biotechnology companies in Scotland, seminars from industrial speakers of renown, discussion sessions on topical issues in biotechnology and an overview of how biotechnology companies translate scientific ideas into commercial products. During this course students will develop further career skills such as oral and written presentations, paper analysis and computer applications. Requirements: Permission of the Curriculum Approval Officer. BITE10004 Biotechnology Project Biotech2None Description: Honours Project: Lab Project - Thesis and Performance Presentation Requirements: Permission of the Curriculum Approval Officer. BITE10006 Biotechnology Synoptic ExaminationBiotech2None Description: Exam based on problem analysis and interpretation of data and information from scientific papers. Requirements: Permission of the Curriculum Approval Officer. List 1: Recommended Elective Courses for the Biotechnology Honours Programme. Further details may be found starting on page 82. Code Course Name Prog SemTime Slot MaxClass BITE10010Gene Expression and Microbial Biotech 1 Thurs amRegulation GENE10007Genetic ApproachesGenetics1 Mon am BITE10003Food-Borne Pathogens andBiotech 2 Tues & Thurs amFBPVaccines21 BITE10009Plant Biotechnology/Food- Biotech 2 Thurs & Fri am FBPborne Pathogens 21 BITE10008Vaccines/Human Genetics Biotech 2 Mon & Tues am 11 15. List 2: Suitable Elective Courses for the Biotechnology Honours Programme. Further details may be found starting on page 82. CodeCourse Name Prog Sem Time SlotMax Class GENE10004 Genetics of Host-Parasite Genetics1Fri am20 Interactions MLBI10017 Molecular Biology of DiseaseMolBiol 1Fri am GENE10015 The Cell Cycle: DNA Genetics1Thurs pm50 Replication, Segregation and Checkpoints GENE10001 Human Genetics/MammalianGenetics2HG - Mon am; HG Transgenesis and GenomeMTGE - Tues am30; Engineering MTG E 22 DEBI10017 Mammalian Stem Cell Biology DevBiol 2Tues & Fri am GENE10002 Molecular & Cellular AspectsGenetics2Mon & Thurs pm of HIV Infection12 16. CELL BIOLOGY Programme Organiser:Programme Secretary: Prof Hiro OhkuraMs Donna Wright Swann BuildingBTO Kings BuildingsDarwin Building Edinburgh EH9 3JR Kings Buildings 0131 650 7094 Edinburgh EH9 3JU h.ohkura@ed.ac.uk 0131 651 7051 Molbiol.hons@ed.ac.ukModern cell biology is a dynamic discipline that combines the interests and techniques of many scientific fields including molecular biology, genetics, developmental biology and biochemistry. Cell biologists investigate the basic structural and functional units of life: the cells that compose all living organisms. They aim to understand: cellular structure, composition and regulation; the organelles that cells contain; cell growth, nuclear and cellular division, and cell death. Understanding how cells work is fundamental to many areas of biology and is of particular importance to biomedical fields such as cancer research.Cell Biology Senior Honours is a new Programme, which shares many courses with the Genetics and Molecular Biology Programmes. It is taught by means of compulsory courses in Semester 1 and by elective courses in Semesters 1 and 2. Three of the compulsory courses are lecture-based. A further compulsory course (Data Interpretation) is specific to Cell Biology Honours, and includes paper presentations by students, essay writing and data analysis sessions to provide practice in data handling and problem solving. As described below, a wide range of elective courses is open to Cell Biology students, offered by Cell Biology, Molecular Biology, Genetics and other honours programmes. Semester 1 electives are generally assessed by exam, Semester 2 electives by essay or other continuous assessment.During Semester 2, each student conducts a research project in a field of his or her own choice. These are carried out under the supervision of a member of staff. Students present their findings for evaluation at the end of the course in the form of a short thesis and a 15 minute oral presentation. In addition to the research project, Cell Biology students undertake a library project of broad cell biological interest, writing a dissertation of 4000 words which is submitted in Semester 2.A synoptic exam at the end of the course examines the student's overall knowledge and understanding of cell biology, and ability to interpret cell biological data. Overall, examinations contribute about 50% to the final assessment.Note: The Cell Cycle course is normally required for Cell Biology Honours (see below) but some flexibility may be permitted. Students with a particular interest in molecular aspects of cell biology might consider taking the parallel programme in Molecular Biology.13 17. As an honours student studying Cell Biology:(a) You must do the following compulsory Courses Points Cell Biology Project 40 Cell Biology Data Interpretation & Synoptic20 Examination DEBI10023 Cell Biology: from fundamental mechanisms to10 human disease GENE10007 Genetic Approaches10 Cell Biology Library Project10 GENE10015 The Cell Cycle: DNA Replication, Segregation and10 Checkpoints Points 100(b) In addition you must take further level 10 or 11 Biological Sciences courses. These will normally* be from List 1 (below).20Number of electives to be chosen: Semester 1: one, Semester 2: one.*Students who wish a broader fourth year programme may choose, subject to the approval of the Head of School (i.e. Head of SBS, SBMS as appropriate), other level 10 or 11 courses from outside Biology. Students wishing to do this should first discuss it with their Director of Studies and their Honours Programme Organiser. Approval will only be given for courses that fit appropriately with the chosen honours specialisation and for which they are suitably qualified. The requirement for these courses to be at level 10 or 11 means that students wishing to take this option should plan for this early in their University career. Otherwise, earlier course choices may limit later choices.Compulsory Courses for the Cell Biology Honours Degree Programme CodeCourse NameProg SemTime Slot Cell Biology Data Interpretation & CellBiol 1 Wed am Synoptic Exam Description: Review of problem/practical papers. Requirements: Permission of the Curriculum Approval Officer DEBI10023 Cell Biology: from fundamental CellBiol 1Tues pm mechanisms to human disease. Description: This course will illustrate how fundamental research in cell biology is relevant to human disease. This will be done by consideration of how defects in basic biological processes, such as microtubule and chromosome structure and/or regulation, contribute to diseased states. The course begins with an introduction to microscopy and then focusses on specific areas of cell biology. A recurring theme is how a range of techniques (encompassing, imaging, proteomics and genetics) are used to identify and then dissect the function of complex multi-protein machines. When defective, these machines have significant impact on human diseases including ciliopathies, laminopathies, cancer, aneuploidy and ageing. Requirements: Permission of the Curriculum Approval Officer. Molecular Cell Biology 3 is recommended. 14 18. Code Course NameProg SemTime Slot GENE10007Genetic Approaches Genetics1Mon am Description: The aim of this course is to familiarise students with genetic, molecular genetic and bioinformatic approaches that are commonly used to study genes, their expression and their functions, and how transgenic organisms can be produced. The focus will be on the most frequently used model organisms, Plants, Escherichia coli, Saccharomyces cerevisiae and mouse, and will include classical as well very recent technological developments. The final lecture will discuss the need for computational methods to store, access and analyse genomic and functional genomic data. Requirements: Permission of the Curriculum Approval Officer. Molecular Genetics 3 is recommended. GENE10015The Cell Cycle: DNA Replication, Genetics1 Thurs pmSegregation and Checkpoints Description: The purpose of the cell division cycle is to ensure the accurate duplication of the cellular DNA and its partitioning into daughter cells. These lectures deal with the molecular mechanisms involved in the fundamental process of DNA replication and the controls regulating its occurrence during the cell cycles of prokaryotes and eukaryotes. In bacteria, cell growth and cell wall assembly are coordinated with cell cycle progress, and the assembly of a septum cross- wall is essential for cell division. Duplication of the genetic material becomes more complex in eukaryotic cells, as chromosomes are larger and DNA is tightly packed into chromatin. Controls called checkpoints prevent the cell from initiating late cell cycle events until earlier processes have been correctly completed. Failure of these checkpoints in vertebrate cells is implicated in some forms of cancer. Requirements: Permission of the Curriculum Approval Officer.Cell Biology Library Project CellBiol2 Description: Library Project - Dissertation Requirements: Permission of the Curriculum Approval OfficerCell Biology Project CellBiol2 Description: Lab Project - Thesis and Performance & Assessed Talk Requirements: Permission of the Curriculum Approval Officer List 1: Recommended Elective Courses for the Cell Biology Honours Degree Programme. Further details may be found starting on page 82. CodeCourse Name Prog Sem Time Slot MaxClass DEBI10020 Cellular Mechanisms inDevBiol1 Fri am Development MLBI10009 Gene Expression MolBiol1 Thurs am Nolimit GENE10004 Genetics of Host-Parasite Genetics 1 Fri am20 Interactions MLBI10017 Molecular Biology of DiseaseMolBiol1 Fri am BICH10007 Structural BiologyBiochem1 Tues amNolimit BICH10002 Supercoiling in DNA and Biochem1 Mon pm12 Chromatin GENE10001 Human Genetics/MammalianGenetics 2 HG - Mon am;HG Transgenesis and GenomeMTGE - Tues am 30; EngineeringMTGE 2215 19. CodeCourse Name Prog Sem Time SlotMax Class MLBI10004 Human Genetics/The RNAMolBiol 2HG Mon am;HG WorldRNA Thurs am30; RNA20 DEBI10017 Mammalian Stem Cell Biology DevBiol 2Tues & Fri am GENE10002 Molecular & Cellular AspectsGenetics2Mon & Thurs pm of HIV Infection BICH10013 Signal Transduction Biochem 2Mon & Thurs am24 MLBI10005 The RNA World/Mammalian MolBiol 2RNA Thurs am;RNA Transgenesis & GenomeMTGE Tues am20; Engineering MTG E 2216 20. DEVELOPMENTAL and CELL BIOLOGY Programme Organiser:Programme Secretary: Dr. Peter Doerner Mrs Lesley Cochrane Rutherford Building BTO Kings BuildingsDarwin Building Edinburgh EH9 3JH Kings Buildings 0131 650 7080 Edinburgh EH9 3JU Peter.Doerner@ed.ac.uk0131 650 8638 Devbiol.hons@ed.ac.uk Developmental and Cell Biology focuses on the molecular and cellular mechanisms that allow cells to form a complex adult organism in an exquisitely ordered sequence, so that the right cell types are formed in the right places at the right times. We study different organisms, which allows us to understand fundamental, conserved molecular mechanisms controlling patterning (the process of generating different cell types at the appropriate place and time) and growth.Developmental and Cell Biology is interdisciplinary: we cover embryology and patterning, cell interactions and differentiation, human genetics, transgenic animals, evolution, stem cell biology, developmental neurobiology, developmental anatomy and gene expression. We aim to understand the underlying molecular and genetic mechanisms that underpin these processes and focus on the way molecules control the properties of a developing organism and what goes wrong in congenital diseases.As recent publicity surrounding stem cells and regenerative medicine has shown, developmental and cell biology, genetics and molecular biology can impact directly upon our lives. Therefore, in addition to being informed about the basic science we encourage you to consider how these issues impact on society.In Semester 1, students in Developmental and Cell Biology take five courses, each worth 10 points. This includes three required courses: Cellular Mechanisms in Development, Patterning in Development and Professional Skills in Developmental and Cell Biology. The first two courses cover essential aspects of vertebrate, invertebrate and plant development, while the latter focuses on problem sessions relating to DB. Two further optional courses are selected from a recommended selection of five: Experimental Systems in DCB, Gene Expression in DB, Cell Biology: from fundamental mechanisms to human disease, Segmentation: Evolution and Development, Molecular Approaches to Disease but other Semester 1 SBS courses can be taken as well. The former two deal with basic aspects of Developmental Biology, whereas the latter are more specialised courses dealing with specific areas. The Semester 1 courses will be examined in December, however examination of Professional Skills in DB is deferred until May.In Semester 2, there is one optional 10-point course to choose from a large pool of specialised courses dealing with all biological subjects represented at the School of Biological Sciences. In addition, students will write a Research Proposal (10-points), relating to their projects. The research project (40 points) will make up most of Semester 2 and enables students to do research at MRC (Western General Hospital) and BBSRC (Roslin) units as well as in University departments. Students present seminars on their projects. The synoptic exam covers material from the entire course and will be taken in May.17 21. Teaching will include lectures, seminars and presentations of current papers. We place emphasis on transferable skills and our students have excellent verbal and written communication skills at the end of the courseDevelopmental and Cell Biology provides an exciting Honours programme with genuine career opportunities in, for example, the study of human genetic disease, transgenic plants and animals, etc. It would also be a valuable course for those planning to do a PhD, since many of the topics offered to students require the knowledge and expertise our students will have gained after their Honours year. As an honours student studying Developmental and Cell Biology:(a) You must do the following compulsory courses Points DEBI10024 Developmental and Cell Biology Project 40 DEBI10026 Developmental and Cell Biology Synoptic10 Examination DEBI10020 Cellular Mechanisms in Development10 DEBI10021 Patterning in Development 10 DEBI10028 Professional Skills in Developmental and Cell 10 Biology DEBI10025 Developmental and Cell Biology Research Proposal10 Points90(b) In addition you must take further level 10 or 11 Biological Sciences courses. These will normally* be from List 1 (below).10(c) In addition you must take further level 10 or 11 courses. These will normally* be from List 1 (below) or other Biological Sciences courses.20 Total points 120Number of electives to be chosen: Semester 1: two, Semester 2: one.*Students who wish a broader fourth year programme may choose, subject to the approval of the Head of School (i.e. Head of SBS, SBMS as appropriate), other level 10 or 11 courses from outside Biology. Students wishing to do this should first discuss it with their Director of Studies and their Honours Programme Organiser. Approval will only be given for courses that fit appropriately with the chosen honours specialisation and for which they are suitably qualified. The requirement for these courses to be at level 10 or 11 means that students wishing to take this option should plan for this early in their University career. Otherwise, earlier course choices may limit later choices. 18 22. Compulsory Courses for the Developmental and Cell Biology Honours Degree Programme Code Course NameProgSemTime Slot DEBI10020Cellular Mechanisms in Development DevBiol1Fri am Description: 1. Coping with Complexity: viewing life as a 'complex system', and why this is helpful. Self-assembly versus self-organization. Overview of developmental cell biology and of the rest of the module. 2. Gene expression: regulation, contingency and computation. 3. Genetic networks; spontaneous organization and emergence of high-level functions from connection of simple genes. Redundancy, robustness and graceful failure. 4. Connecting genetic networks to the rest of the body: signal sensing and cytoplasmic computation. 5. Controlling proliferation of cells and growth of tissues 6. Programmed cell death, the trophic theory 7. Adaptive self-organization as a key property of developing animals. 8. Cell movement: mechanisms and internal regulation 9. Navigation by cells: maps, mechanisms and the cell's internal 'compass'. 10. Embryonic origami: the bending and branching of epithelia. 11. Integration of development between different cells, tissues and organs 12. Revision and clinical perspective: cancer as mis-regulated development. Problem sessions; Computer sessions Requirements: Permission of the Curriculum Approval Officer. DEBI10021Patterning in DevelopmentDevBiol1Tues am Description: Key developmental processes will be considered: Polarity and patterning in embryogenesis, the evolution of development, and organogenesis and differentiation. The fundamental importance of these concepts will be underscored by discussing examples from plants and animals. 1 The Drosophila Embryo I Anterior-Posterior Pattern. L2 The Drosophila Embryo II Dorsal-Ventral Pattern. L3 Patterning the Vertebrate Embryo: Frog and Fish. L4 Very different Chordates: Tunicate and Mouse. L5 Left-Right Handedness. L5 Left-Right Handedness. L6&7 Patterning plant embryos. L8 Drosophila sensory bristle development the role of asymmetric cell division. L9 Pattern and Growth in the Drosophila Wing imaginal disc. L10 Sex and patterning: the Genital Disc. L11 Compound eye development eye field specification and growth. L12 Compound eye development retinal neurogenesis, cell division and cell death. L13&14 Patterning Vertebrate Limbs. L15 & 16 Patterning plant organs. L17&18 Stem cells in development and homeostasis. L19&20 Control of growth and size. Requirements: Permission of the Curriculum Approval Officer. DEBI10028Professional Skills in Developmental DevBiol1Wed amand Cell Biology Description: Paper Analysis; Use of Powerpoint and Bibliography programmes; Seminars; Research Seminars; Use of Organism Databases (Computer-lab); Proposal writing Requirements: Permission of the Curriculum Approval Officer. DEBI10024Developmental and Cell Biology DevBiol2NoneProject Description: Honours Project: Lab Project - Thesis, Performance and Project Talk (40 points) Lab Project - Thesis, Performance and Project Talk (40 points) Requirements: Permission of the Curriculum Approval Officer. DEBI10025Developmental and Cell Biology DevBiol2NoneResearch Proposal Description: Library Project - Grant Proposal; The Grant Proposal is intended to plan your project work. Requirements: Permission of the Curriculum Approval Officer. DEBI10026Developmental and Cell Biology DevBiol2NoneSynoptic Examination Description: Synoptic Exam Requirements: Permission of the Curriculum Approval Officer.19 23. List 1: Recommended Elective Courses for the Developmental and Cell Biology Honours Degree Programme. Further details may be found starting on page 82. CodeCourse NameProg Sem Time SlotMaxClass DEBI10023 Cell Biology: from fundamental CellBiol1Tues pm 25 mechanisms to human disease. DEBI10027 Experimental Systems inDevBiol 1Mon am Developmental and Cell Biology DEBI10014 Gene Expression in DevBiol 1Thurs am Development MLBI10017 Molecular Biology of Disease MolBiol 1Fri am ZLGY10008 Segmentation: Evolution andZoology 1Tues pm 25 Development GENE10001 Human Genetics/Mammalian Genetics2HG - Mon am;HG Transgenesis and Genome MTGE - Tues am30; EngineeringMTGE 22 MLBI10004 Human Genetics/The RNA MolBiol 2HG Mon am;HG World RNA Thurs am30;RNA 20 DEBI10017 Mammalian Stem Cell BiologyDevBiol 2Tues & Fri am GENE10002 Molecular & Cellular Aspects Genetics2Mon & Thurs pm of HIV Infection MLBI10005 The RNA World/MammalianMolBiol 2RNA Thurs am;RNA Transgenesis & Genome MTGE Tues am20; EngineeringMTGE 22 BITE10008 Vaccines/Human GeneticsBiotech 2Mon & Tues am 20 24. ECOLOGY Programme Organiser:Programme Secretary: Dr Richard EnnosMrs Helen McKeating Ashworth Building GeoSciences Kings BuildingsCrew Building Edinburgh EH9 3JT Kings Buildings 0131 650 5411 Edinburgh EH9 3JN rennos@ed.ac.uk 0131 650 5430 Helen.McKeating@ed.ac.ukThe word ecology comes from the Greek oikos, meaning a house or dwelling place. It is defined as the scientific study of organisms in relation to their physical and biological environment. The physical environment includes the soil, water and atmosphere; the biological environment includes influences that organisms have on one another. Although ecology is a relatively new science, it is becoming increasingly important as it provides ideas and conceptual tools that help in the protection, conservation and management of the environment and vital biological resources. It also feeds our natural human curiosity about how plants and animals survive and behave in the natural world.The B.Sc. Biological Sciences (Ecology) course is taught along side the related programme B.Sc. Ecological Science (Ecology). The two degree streams share many courses and the difference between them is one of emphasis and ethos. Those studying for Biological Sciences with Honours in Ecology will have more biological courses, and are likely to end up knowing more about such things as genetics, behavioural ecology and evolutionary ecology. In contrast, the B.Sc. in Ecological Science (Honours) in Ecology has more emphasis on the integration of biology with environmental sciences and management, and is selected especially by those heading for management-related careers in resource management.Whichever of our ecology degree streams you have chosen, you will attend vacation field courses and learn important practical skills. Ecologists have to be able to perform in the field as well as the laboratory, and to be skilled in the use of computers. Our overall aim is to offer you the best of ecology, within the degree stream that suits your aims and aspirations, and to provide the learning environment in which you can achieve individual excellence.When reading the following information you will find it helpful to consult the information provided to Ecology/Ecological Sciences students by the School of Geosciences.As an honours student studying Biological Sciences (Ecology):(a) You must do the following compulsory courses Points ECSC10001 Dissertation in Ecology [Project]40 ECSC10009 Ecological Science Field Course10 ECSC10017 Professional Skills in Ecological Science10 ECSC10010 Ecological Science Synoptic Paper [Examination]10 21 25. TWO OF ZLGY10007 Molecular Ecology 10 ZLGY10017 Biodiversity10 ECLG10003 Herbivory 10 ECSC10007 Ecological and Environmental Modelling10 ECSC10015 Plant Ecophysiology 10Points 90(b) In addition you must take further level 10 or 11 courses. These will normally* be from List 1 (below) or other Biological Sciences or GeoSciences courses.30 Total points 120Number of electives to be chosen: Semester 1: three, Semester 2: two. (Note that two of these electives must be chosen from the "Two of:" list of courses given under compulsory courses above.)*Students who wish a broader fourth year programme may choose, subject to the approval of the Head of School (i.e. Head of SBS, SBMS as appropriate), other level 10 or 11 courses from outside Biology. Students wishing to do this should first discuss it with their Director of Studies and their Honours Programme Organiser. Approval will only be given for courses that fit appropriately with the chosen honours specialisation and for which they are suitably qualified. The requirement for these courses to be at level 10 or 11 means that students wishing to take this option should plan for this early in their University career. Otherwise, earlier course choices may limit later choices.Compulsory Courses for the Ecology Honours Degree Programme CodeCourse NameProg SemTime Slot ECSC10009 Ecological Science Field CourseEcolSci Before Semester 1 Description: Ecological Science Field Course Requirements: ECSC10017 Professional Skills in Ecological ScienceEcolSci1 Mon am Description: Professional Skills in Ecological Science Requirements: ECSC10001 Dissertation in EcologyEcolSci2None Description: Dissertation in Ecology Requirements: ECSC10010 Ecological Science Synoptic PaperEcolSci2None Description: Ecological Science Synoptic Paper Requirements: 22 26. List 1: Recommended elective courses for the Ecology Honours Degree Programme. As described above, students must take two of the first five of these courses. Further details on the remaining courses may be found starting on page 82. Information on your choices will be considered along side any information you have already given to the Ecology Honours Programme Organiser. Code Course Name Prog Sem Time SlotMaxClass ECLG10003 HerbivoryEcology2 Mon & Wed am Description: The course will consider plant-herbivore community ecology; the responses of animals and plants to each other, and the effects of climatic variability on the dynamics of grazing systems. Although there will be discussion of management implications, the main emphasis will be on community, physiological and systems ecology. Requirements: Permission of the Curriculum Approval Officer. Normally Population & Community Ecology 3 or Behavioural Ecology 3 is required. ECSC10007 Ecological and Environmental EcolSci2 Tues & Fri pm Modelling Description: Along with observation and experimentation, modelling is a critical tool for scientific investigations, and it is becoming increasingly important in environmental management, from local to global scales. A model is a mathematical description of a system, necessarily simplified and only an approximation to the truth, but designed to describe and predict the behaviour of that system. Comparisons between model predictions and independent data provide a key test of scientific understanding, and a basis for refinement of hypotheses. In this course, we will explore the philosophy of modelling, and examine strengths and weaknesses of various modelling approaches. Then, using ecological and environmental models based on physical, chemical and biological principles, we will examine issues related to non-linear systems, dynamic simulation, feedback and control, and the problem of scaling. The course will emphasise problem-solving, and will provide training in mathematical formalisation of a problem, model construction and parametrisation, prediction and testing, and sensitivity and error analyses. Requirements: ECSC10015 Plant EcophysiologyEcolSci2 Tues & Thurs am Description: Plant ecophysiology is concerned with the function and performance of plants in their natural environment. It bridges the gap between plant physiology and ecology. The course will consider physiological and ecological aspects of adaptation to different environments. Plants are remarkably well adapted to growing in a range of environments from the Antarctic to hot dry deserts. Ecophysiology is the scientific study of the processes that enable them to do so. By the end of the unit you should be able to discuss analytically the key physiological processes affecting plants growing in the natural environment. Examples are drawn from forests, agricultural systems and the natural environment and most will relate to plants at the individual or stand scale. Sessions will cover plant water relations, stomatal physiology, transpiration, photosynthesis, global change, below-ground processes and predictive modelling. Assessment will be based on two Problem Based Learning (PBL) sessions at the end of the course, an essay and an oral presentation. Requirements: Evolution and Ecology of Plants 3 is recommended ZLGY10007 Molecular EcologyZoology1 Thurs am 25 Description: This course will look critically at how problems in ecology and conservation, such as measuring individual reproductive success and developing conservation policy, can be solved (or not) using molecular techniques. It will cover issues from the individual to the population level, including plant mating systems, gene flow and population history, identifying parentage, measuring relatedness, sex identification and the study of sex ratio, measuring inbreeding and the potential of molecular techniques in conservation. Requirements: Permission of the Curriculum Approval Officer. Normally Evolutionary & Ecological Genetics 3 or Behavioural Ecology 3 is required. 23 27. Code Course Name Prog Sem Time Slot Max Class ZLGY10017 Biodiversity Zoology 1 Mon pm 25 Description: This course seeks to uncover the scientific foundation of the study of biodiversity: what is it and what role does it play in ecological processes and ecosystem function? The existing science of biodiversity is overwhelmingly concerned with macroscopic as opposed to microscopic animals and plants. We will investigate whether this is appropriate. Typical units of biodiversity studies are species. We will explore both higher (ecosystem) and lower (genetic)levels of organisation. The material covered consists of both the most contemporary research as well as areas of classical ecology that have a renewed relevance. Requirements: Permission of the Curriculum Approval Officer. Normally Population & Community Ecology 3 is required.ECSC10025Effective Project PlanningGeoSci1 Mon & Wed amand Management ECSC10012Land Use and WaterEcology 1Resources ECSC10013Land Use Policy Ecology 1 Fri pm ECSC10014Land-Atmosphere Ecology 1 Wed amInteractions GEGR10039Principles of GeographicalGeography 1 Tues pmInformation Science PGGE11076Recent Global Environmental Ecology 1 Tues pmChange ECSC10022Conservation Management Ecology 2 Mon & Thurs pm ECSC10007Ecological andEcolSci 2 Tues & Fri pmEnvironmental Modelling ECSC10021Woodland Management Ecology 2 Fri am 24 28. EVOLUTIONARY BIOLOGY Programme Organiser: Programme Secretary: Prof Paul SharpMrs Pat Dougall Ashworth BuildingAshworth Building Kings Buildings Kings Buildings Edinburgh EH9 3JTEdinburgh EH9 3JT 0131 651 36840131 650 5464 paul.sharp@ed.ac.ukPat.Dougall@ed.ac.uk Evolutionary Biology is at the centre of modern biology, spanning the subject from genomes to whole organisms. All species, past and present, are related in a common phylogenetic tree; and all the diverse and extraordinary adaptations that allow organisms to function have evolved through natural selection. Our understanding of the history of life and the mechanism by which it has evolved has influenced virtually every aspect of human society - from literature to medicine. However, evolutionary biology is not simply a historical science. Information on evolution and the application of principles learned from the study of evolution also have many practical uses in diverse fields such as conservation biology, geology, computer science and epidemiology. This Honours Programme will give a thorough grounding in the principles of evolutionary biology, and will give an opportunity to study their application to a wide variety of questions. A leading American biologist of the 20th century, Theodosius Dobzhansky, wrote in 1973 that Nothing in biology makes sense except in the list of evolution: this seems more true today than ever before.The programme consists of three compulsory courses; a choice of up to four optional courses; and a substantial research project.Compulsory Courses: Population and Evolutionary Genetics builds on the third-year Evolutionary and Ecological Genetics course to develop the basic principles of population and evolutionary genetics. These are used to study different ways in which genetic variants can be useful in biology, including evolutionary biology, medicine, and the origins of human diseases, agriculture and conservation biology. Animal Evolution will cover several key areas, including phylogenetic analysis, selection and adaptation, evolution of development, coevolution and cospeciation, and the origin of life. This course will emphasise the conceptual basis of current research on these topics. In Semester 2, the Quantitative Zoology course provides training in experimental design and the analysis and interpretation of data. This is designed to provide the techniques necessary for analysing the project.Optional courses: Students take optional courses totalling 40 points, spread over Semesters 1 and 2. Note that some 20 point options are available. Various courses on specifically evolutionary topics are offered, including Biodiversity, Evolution and Climate Change, Evolution of Parental Care, Evolution of Sex and Breeding Systems, Evolutionary Ecology of Hosts and Parasites, Molecular Ecology and Molecular Phylogenetics. There are several other courses from a variety of Honours Programmes which would be appropriate: for example, Origins and Evolution of Language or Segmentation: Evolution and Development.25 29. Research projects are chosen towards the end of Semester 1 and run throughout Semester 2 (with appropriate work during the Easter 'vacation'). Edinburgh is exceptionally strong in evolutionary biology, and so a wide range of projects is offered: from ecological genetics to analysis of genomic data, and from experimental evolution with microbes to computer-based theoretical projects. Students are encouraged to suggest and discuss project topics. There may also be opportunities in external Research Institutes and the Royal Scottish Museum, which are co-supervised by members of staff. In the first half of Semester 2, students complete a literature review relevant to the project area, and the project itself is written-up and submitted as a thesis in April / May. As an honours student studying Evolutionary Biology:(a) You must do the following compulsory courses Points EVBI10002Evolutionary Biology Project40 EVBI10001Evolutionary Biology Synoptic Examination 10 ZLGY10001Animal Evolution10 ZLGY10003Quantitative Zoology10 EVBI10005Population & Evolutionary Genetics10 Points 80(b) In addition you must take further level 10 or 11 Biological Sciences courses. These will normally* be from List 1 (below).20(c) In addition you must take further level 10 or 11 courses. These will normally* be from Lists 1 or 2 (below).20Total points120Number of electives to be chosen: 40 points in total, over Semesters 1 and 2.*Students who wish a broader fourth year programme may choose, subject to the approval of the Head of School (i.e. Head of SBS, SBMS as appropriate), other level 10 or 11 courses from outside Biology. Students wishing to do this should first discuss it with their Director of Studies and their Honours Programme Organiser. Approval will only be given for courses that fit appropriately with the chosen honours specialisation and for which they are suitably qualified. The requirement for these courses to be at level 10 or 11 means that students wishing to take this option should plan for this early in their University career. Otherwise, earlier course choices may limit later choices.Compulsory Courses for the Evolutionary Biology Honours Degree Programme CodeCourse Name Prog SemTime Slot ZLGY10001 Animal EvolutionZoology1 Mon am Description: Evolutionary topics that are particularly relevant to zoology, such as phylogenetic analysis, evolution of developmental mechanisms, selection and adaptation, co-evolution and co- speciation, and major evolutionary transitions. Throughout, there is an emphasis on how modern biologists investigate these topics Requirements: Permission of the Curriculum Approval Officer.26 30. Code Course Name ProgSemTime Slot EVBI10005 Population & Evolutionary Genetics EvolBiol 1Tues am Description: This course will deal with several types of ways that genetic variants can be useful in biology, including evolutionary biology, medicine, agricultural production and conservation biology. We will critically discuss different approaches to analysing this genetic variation. The lectures will cover methods for finding and quantifying genetic variation for various types of markers that are currently important, together with illustrations of their uses. The basic principles of molecular evolution will include analysis of divergence between sequences of different species, phylogenetic tree estimation, the neutral theory of molecular evolution, polymorphism within species, and methods to detect natural selection acting on gene sequences. The principles of using markers in genetic analysis of quantitative characters will include some of the major current issues in this area, including the heritability of human IQ, and will provide concepts needed to understand the genetics of complex human diseases. Finally, the use of pedigree information to study selection in natural populations, including the effects of inbreeding on fitness and the maintenance of genetic diversity, will be covered. Requirements: Permission of the Curriculum Approval Officer. Evolutionary and Ecolgocial Genetics is recommended. EVBI10002 Evolutionary Biology Project EvoBiol2None Description: Honours Project: Lab or Field Project - Thesis and Performance (40 points) Requirements: Permission of the Curriculum Approval Officer. EVBI10001 Evolutionary Biology Synoptic Exam EvoBiol2None Description: Synoptic Exam Requirements: Permission of the Curriculum Approval Officer. ZLGY10003 Quantitative Zoology Zoology2Mon pm Description: A course teaching quantitative and statistical skills required for the study of zoology and evolution. Specific topics include: inference, experimental design and hypothesis testing; assumption behind statistical models and choice of statistical tests; analysis of variance and covariance; general linear models; regression and multiple regression. There will be lectures, tutorials and computer lab sessions. Requirements: Permission of the Curriculum Approval Officer.List 1: Recommended Elective Courses for the Evolutionary Biology Honours Degree Programme. Further details may be found starting on page 82. CodeCourse NameProg Sem Time SlotMaxClass ZLGY10017 Biodiversity Zoology1 Mon pm25 ZLGY10013 Evolution of Sex & BreedingZoology1 Fri am25 Systems ZLGY10024 Evolutionary Ecology ofZoology1 Fri pm 25 Hosts and Parasites ZLGY10007 Molecular EcologyZoology1 Thurs am 25 ZLGY10020 Animal-Plant Interaction Zoology2 Mon & Wed am 25 ZLGY10023 Evolution and ClimateZoology2 Mon&Thurs am 25 Change EVBI10003 Molecular PhylogeneticsEvoBiol2 Tue & Fri pm 27 31. List 2: Suitable Elective Courses for the Evolutionary Biology Honours Degree Programme. Further details may be found starting on page 82. CodeCourse Name Prog Sem Time Slot MaxClass ZLGY10022 Evolution of Parental CareZoology 1Wed am 25 ARCA10003 Human Origins Archaeol1Wed am ogy LASC10031 Origins and Evolution of1Mon pm Language PLSC10020 Plant Evolution PlantSci1Thurs am ZLGY10008 Segmentation: Evolution and Zoology 1Tues pm25 Development ECSC10007 Ecological andEcolSci 2Tues & Fri pm Environmental Modelling28 32. GENETICS Programme Organiser: Programme Secretary: Dr. Peter Fantes Ms Donna Wright Darwin BuildingBTO Kings Buildings Darwin Building Edinburgh EH9 3JUKings Buildings 0131 650 5669Edinburgh EH9 3JU P.Fantes@ed.ac.uk0131 651 7051Genetics.hons@ed.ac.uk Genetics is a biological discipline that underlies the majority of modern biological research. It is concerned with genes and the way in which they control the properties of cells and organisms. A different aspect of Genetics is the study of evolution, which has been revolutionised in recent years by the availability of large DNA sequence datasets, including full genome sequences for many species. This has also facilitated the study of many human traits, including diseases, which have a major genetic component but whose inheritance involves more than a single gene. Genetics impacts on almost every aspect of our lives from human genetics and health, infectious disease, what we eat and drink, how we live to how we think of ourselves and others in the scheme of things. It is involved in controversial areas such as the use of genetically engineered crops and the biological and ethical issues around human therapeutic cloning. It is unfortunately clear that many people involved in these debates do not understand the basic issues properly. Genetics students, in addition to being informed about the basic science, are encouraged to consider how these issues impact on society.Genetics Senior Honours is taught by means of compulsory courses in Semester 1 and by elective courses in Semesters 1 and 2. Three of the compulsory courses are lecture- based, some lectures being shared with other honours programmes. A further compulsory course (Data Interpretation) is specific to Genetics Honours, and includes paper presentations by students, essay writing and data analysis sessions to provide practice in data handling and problem solving. As described below, a wide range of elective courses is open to Genetics students, offered by Genetics and other honours programmes. Semester 1 electives are generally assessed by exam, Semester 2 electives by essay or other continuous assessment.During Semester 2, each student conducts a research project in a field of his or her own choice. These are carried out under the supervision of a member of staff. Students present their findings for evaluation at the end of the course in the form of a short thesis and a 15 minute oral presentation. In addition to the research project, Genetics students undertake a library project of broad genetical interest, writing a dissertation of 4000 words which is submitted in Semester 2.A synoptic exam at the end of the course examines the student's overall knowledge and understanding of Genetics, and ability to interpret genetical data. Overall, examinations contribute about 50% to the final assessment.Note: The Gene Expression course is normally required for Genetics Honours (see below) but some flexibility may be permitted. 29 33. Students with a particular interest in molecular aspects of genetics might consider taking the parallel programme in Molecular Genetics.As an honours student studying Genetics:(a) You must do the following compulsory coursesPoints GENE10010 Genetics Project40 GENE10016 Genetics Data Interpretation & Synoptic 20 Examination GENE10007 Genetic Approaches10 EVBI10005 Population & Evolutionary Genetics10 MLBI10009 Gene Expression 10 GENE10011 Genetics Library Project10Points100(b) In addition you must take further level 10 or 11 courses. These will normally* be from Lists 1 and 2 (below).20 Total points120Number of electives to be chosen: Semester 1: one, Semester 2: one.*Students who wish a broader fourth year programme may choose, subject to the approval of the Head of School (i.e. Head of SBS, SBMS as appropriate), other level 10 or 11 courses from outside Biology. Students wishing to do this should first discuss it with their Director of Studies and their Honours Programme Organiser. Approval will only be given for courses that fit appropriately with the chosen honours specialisation and for which they are suitably qualified. The requirement for these courses to be at level 10 or 11 means that students wishing to take this option should plan for this early in their University career. Otherwise, earlier course choices may limit later choices.Compulsory Courses for the Genetics Honours Degree Programme CodeCourse NameProg Sem Time Slot MLBI10009 Gene ExpressionMolBiol1 Thurs am Description: The aim of these lectures is to familiarise students with the variety of mechanisms responsible for regulating the expression of genetic information at the level transcription and post- transcription mechanisms. Teaching will focus on the organisation and packaging of the genetic material in eukaryotic cells and the implications this has for genetic expression. In addition, basic transcription control mechanisms will be examined in prokaryotes and eukaryotes. RNA processing will be studied at the level of splicing and its importance in the regulation of gene expression will be discussed. The special mechanisms which have evolved to operate within, and to take advantage of, a chromatin context will also be reviewed from a biochemical and developmental perspective. Requirements: Permission of the Curriculum Approval Officer. Structures and Functions of Proteins 3 and Molecular Genetics 3 recommended. GENE10007 Genetic Approaches Genetics 1Mon am Description: The aim of this course is to familiarise students with genetic, molecular genetic and bioinformatic approaches that are commonly used to study genes, their expression and their functions, and how transgenic organisms can be produced. The focus will be on the most frequently used model organisms, Plants, Escherichia coli, Saccharomyces cerevisiae and mouse,30 34. and will include classical as well very recent technological developments. The final lecture will discuss the need for computational methods to store, access and analyse genomic and functional genomic data. Requirements: Permission of the Curriculum Approval Officer. Molecular Genetics 3 is recommended. GENE10016 Genetics Synoptic/Data InterpretationGenetics 1Wed amExamination Description: Review of problem/practical papers Requirements: Permission of the Curriculum Approval Officer. EVBI10005 Population & Evolutionary Genetics EvolBiol 1Tues am Description: This course will deal with several types of ways that genetic variants can be useful in biology, including evolutionary biology, medicine, agricultural production and conservation biology. We will critically discuss different approaches to analysing this genetic variation. The lectures will cover methods for finding and quantifying genetic variation for various types of markers that are currently important, together with illustrations of their uses. The basic principles of molecular evolution will include analysis of divergence between sequences of different species, phylogenetic tree estimation, the neutral theory of molecular evolution, polymorphism within species, and methods to detect natural selection acting on gene sequences. The principles of using markers in genetic analysis of quantitative characters will include some of the major current issues in this area, including the heritability of human IQ, and will provide concepts needed to understand the genetics of complex human diseases. Finally, the use of pedigree information to study selection in natural populations, including the effects of inbreeding on fitness and the maintenance of genetic diversity, will be covered. Requirements: Permission of the Curriculum Approval Officer. Evolutionary and Ecolgocial Genetics is recommended. GENE10011 Genetics Library Project Genetics 2None Description: Library Project - Dissertation Requirements: Permission of the Curriculum Approval Officer. GENE10010 Genetics Project Genetics 2None Description: Honours Project: Lab Project - Thesis and Performance (35 points) Assessed Talk (5 points) Requirements: Permission of the Curriculum Approval Officer. List 1: Recommended Elective Courses for the Genetics Honours Degree Programme. Further details may be found starting on page 82. CodeCourse NameProg Sem Time SlotMaxClass DEBI10023 Cell Biology: from CellBiol 1 Tues pm 25 fundamental mechanisms to human disease. GENE10004 Genetics of Host-ParasiteGenetics 1 Fri am 20 Interactions MLBI10017 Molecular Biology of Disease MolBiol1 Fri am ZLGY10008 Segmentation: Evolution andZoology1 Tues pm25 Development GENE10015 The Cell Cycle: DNAGenetics 1 Thurs pm 50 Replication, Segregation and Checkpoints GENE10001 Human Genetics/Mammalian Genetics 2 HG - Mon am; HG Transgenesis and Genome MTGE - Tues am30; EngineeringMTGE 2231 35. CodeCourse NameProg Sem Time SlotMaxClass MLBI10004 Human Genetics/The RNA MolBiol 2HG Mon am;HG World RNA Thurs am30;RNA 20 DEBI10017 Mammalian Stem CellDevBiol 2Tues & Fri am Biology GENE10002 Molecular & Cellular Aspects Genetics2Mon & Thurs pm of HIV Infection MLBI10005 The RNA World/MammalianMolBiol 2RNA Thurs am;RNA Transgenesis & Genome MTGE Tues am20; EngineeringMTGE 22 List 2: Suitable Elective Courses for the Genetics Honours Degree Programme. Further details may be found starting on page 82. ZLGY10017 Biodiversity Zoology 1Mon pm25 ZLGY10013 Evolution of Sex & BreedingZoology 1Fri am25 Systems BICH10002 Supercoiling in DNA andBiochem 1Mon pm12 Chromatin EVBI10003 Molecular PhylogeneticsEvoBiol 2Tue & Fri pm BITE10008 Vaccines/Human GeneticsBiotech 2Mon & Tues am 32 36. IMMUNOLOGY Programme Organiser: Programme Secretary: Dr David CavanaghMs Alexandra Bedetti Ashworth LaboratoriesAshworth Laboratories Kings Buildings Kings Buildings Edinburgh EH9 3JTEdinburgh EH9 3JT 0131 650 54590131 650 5455 David.Cavanagh @ed.ac.uk a.bedetti@ed.ac.ukImmunology is a rapidly evolving subject that is at the forefront of many current advances in science and medicine. Immunology is fundamental to the diagnosis and treatment of important disorders including autoimmune and allergic diseases and immune deficiencies. It is also central to transplantation science, tumour biology and to vaccine development. This integrated programme aims to provide students with an advanced knowledge and understanding of the immune system, the ability to apply the knowledge to medical, veterinary, biological and biotechnological problems, and hands-on research experience.Immunology Honours is an inter-college programme for students of biological sciences and for medical students taking an intercalated Honours year, leading to B.Sc. Hons in either Biological Sciences (Immunology) or Medical Sciences (Immunology). The programme is taught by staff from the College of Science and Engineering and from the College of Medicine and Veterinary Medicine, as well as from Research Institutes in and outside Edinburgh. The teaching programme is run at the Institute for Immunology and Infection Research, Kings Buildings. Practical research projects are carried out in participating biomedical and clinical research laboratories in Edinburgh.Immunology Honours is a modular Programme of Courses. Of the seven 10 point courses required for an honours degree, three are compulsory; other courses (electives) are optional. Two of these electives must be from the Immunology list, while the other two can be taken from other programmes (eg. Infectious Diseases). Each course is taught on one day per week. In Semester 1 teaching consists of 2 core (compulsory) courses (Immunobiology and Molecular Immunology), as well as 4 electives (Inflammation and Inflammatory Disease, Immunity to Eukaryotic Parasites, Immunobiology of Malaria and Stem Cells, Haematopoesis and Immune Therapy). These titles only indicate the general areas of study; more specialised topics are selected for deeper study. Teaching includes lectures, student presentations and staff- led discussions, with about 2-3 hours/week contact time (running over 10 weeks). Reading of original scientific papers, preparation of oral and written presentations, and team-work are essential components of these modules. Semester 1 modules will be examined by exam in weeks 12-13 (December). In the first week of the course we take all the Immunology students for a reading party to FIRBUSH, the University Centre for Sport and Exercise Field Centre on Loch Tay. This provides an early opportunity for students and staff to get to know one another. In between the outdoor leisure activities at Firbush there are a few light academic sessions: for instance a talk given by a leading UK research immunologist.In Semester 2 only one Immunology elective course is offered (Autoimmune and Allergic Diseases), running along the same lines as Semester 1 courses. This will be 33 37. examined by in-course assessment (eg. closed-book test). Also running in semester 2 is a compulsory Immunology course, Experimental Immunology, which is only open to Immunology Honours students and is an adjunct to the Immunology Project. This course covers methods and techniques that are crucial to modern experimental immunology and will be examined by open-book assessment. The majority of time during Semester 2 will be occupied by a compulsory individual lab-based research project (worth 40 points: a wide variety of topics are on offer). The project provides a real flavour of how research is carried out, as the projects are all embedded in active research labs, contributing to the labs research programme. The work will be written up as a project report and this together with a project performance score will make up 33% of the final degree mark.Throughout the year, there are many relevant Immunology seminars either as part of the Edinburgh Immunology Group or the IIIR Seminar series. These seminars are regarded as an important extension of the teaching and student attendance is strongly advised.In May, there will be a final synoptic exam (worth 10 points) to test integrated immunological knowledge gained throughout the year.As an honours student studying Immunology:(a) You must do the following compulsory coursesPoints IMMU10008 Immunology Project40 IMMU10009 Immunology Synoptic Examination 10 IMMU10006 Experimental Immunology 10 IMMU10001 Immunobiology 10 IMMU10003 Molecular Immunology10 AT LEAST TWO OF: IMMU10002 Autoimmune and Allergic Diseases 10 IMMU10004 Inflammation and Inflammatory Disease10 IMMU10005 Immunity to Eukaryotic Parasites 10 IMMU10007 Immunobiology of Malaria 10 IMMU10011 Stem cells, haematopoiesis and immune therapy10Points 100(b) In addition you must take further level 10 or 11 courses. These will normally* be from Lists 1 and 2 (below).20Total points120Number of electives to be chosen: Semester 1: three, Semester 2: one (Note that two of these electives must be from the "TWO OF:" list of Immunology courses in the table above.). It is, of course, possible to take 4 Immunology electives.*Students who wish a broader fourth year programme may choose, subject to the approval of the Head of School (i.e. Head of SBS, SBMS as appropriate), other level 10 or 11 courses from outside Biology. Students wishing to do this should first discuss it34 38. with their Director of Studies and their Honours Programme Organiser. Approval will only be given for courses that fit appropriately with the chosen honours specialisation and for which they are suitably qualified. The requirement for these courses to be at level 10 or 11 means that students wishing to take this option should plan for this early in their University career. Otherwise, earlier course choices may limit later choices. Compulsory Courses for the Immunology Honours Degree Programme Code Course NameProgSemTime Slot IMMU10001ImmunobiologyImmunol1Tues am Description: This course will cover most aspects of the basic biology of the immune system. Initial lectures will consider the cells of the immune system, their function, the structure of lymphoid organs and how cells move around within and between lymphoid organs to bring about crucial interactions. The information provided is viewed as core knowledge for students wishing to gain an honours degree in Immunology; it will be useful, if not essential, for many of the other immunology electives. Following on from this orientation to the immune system, the course will narrow its focus onto 4 main areas of immune biology: 1. How the innate immune system (evolutionarily old) underlies and informs the adaptive immune system (lymphocytes). 2. How the immune system decides when (and how) to respond (issues such as co-stimulation, self versus non-self discrimination and danger). 3 How the immune system is prevented from responding to self (tolerance). 4. How the immune system remembers is has encountered an microorganism already (memory). These represent fields of very active current research and in which big, important questions remain. The course will involve a mixture of lectures and problem-based learning with an emphasis on discussion of the controversial aspects of the subject. Requirements: Permission of the Curriculum Approval Officer. Normally Immunology 3 (or Clinical Immunology & Haematology 3 at the discretion of the Honours Programme Organiser.) IMMU10003Molecular Immunology Immunol1Mon am Description: This course will introduce the structure and function of the families of molecules employed by the immune system to recognize and initiate a responses to antigen. It will provide an essential grounding for the understanding of the complex cellular interactions of the immune response. We will initially look at receptors involved in the recognition of antigens during the early phases of immunity. In particular we will examine Toll-Like Receptors (TLRs), components of the complement system, and receptors expressed on natural killer (NK) cells. In mammals, once an immune response is initiated, more complex families of molecules are used to deal with individual pathogens. A major focus of this course will be the molecules encoded by the MHC. Examination of the structure, polymorphism and intra-cellular trafficking of this family is essential to appreciate their role in 'presenting' antigenic peptides to activate the acquired immune response. MHC presentation of peptide antigens leads to activation T cells via the T cell receptor (TCR). This receptors ability to recognize an almost unlimited range of antigenic peptides associated with MHC molecules will be studied. B cells also recognize antigens via a specialized receptor (BCR). The structure of this receptor as well as the generation of a repertoire of capable of recognizing differing antigens will be examined. This course will conclude by looking at the molecules that transducing signals from antigen receptors. This will include both intracellular pathways, leading to cell activation, as well as the expression of accessory molecules. These include membrane- bound co-stimulation molecules and secreted molecules capable of relaying signals to other cells either locally (cytokines) or further away (chemokines). Requirements: Permission of the Curriculum Approval Officer. Normally Immunology 3 (or Clinical Immunology & Haematology 3 at the discretion of the Honours Programme Organiser). 35 39. Code Course Name Prog Sem Time Slot IMMU10006Experimental Immunology Immunol 2 Wed am Description: This course is a constituent part of the Immunology Honours project. During the first two weeks of the course there will be lectures, demonstrations and discussion sessions on commonly used immunological techniques, such as ELISA, Flow cytometry and FACS sorting, in vivo adoptive transfer, Western blots, immunoprecipitation. This will be augmented by the reading/discussion of papers illustrating the use of certain techniques (in particular, flow cytometry) and a session (in working groups) based around the solution of technical/experimental planning problems. In course assessment will take the form of questions set on a research paper given to students 24 hours previously and designed to probe practical knowledge and the ability to interpret results. Requirements: Permission of the Curriculum Approval Officer. Only open to Immunology Honours students. IMMU10008Immunology ProjectImmunol 2None Description: The Immunology Honours Projects are lab-based projects run in immunology-related research labs in and around Edinburgh. Projects are designed to be simple, but stimulating introductions to the process of scientific research. Placements are made in active research labs and the projects are usually an integral part of the labs' research effort. It is usual for students to be supe