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GENETICS: Genetics, which can be said to have started with the rediscovery of Mendel’s rules in 1900, increasingly dominates biological science. What began as an esoteric field, concerned with minor variations and quirks, has become an indispensable component of enquiry into almost all aspects of biology and medicine. The increased scope of genetics arises through reinforcement of the classical genetic approach with newer and ever more sophisticated methods of molecular analysis. This partnership of classical and molecular approaches will be increasingly applied to revealing the secrets of nature.
The overall GENERAL AIMS are:
• To provide a thorough understanding of five major areas in genetics
• Genetic Analysis
• Molecular Genetics
• Medical Genetics
• Population Genetics
• Developmental Genetics
• To provide some fundamental, theoretical principles on which to form an integrated view of genetic processes.
• To enable you to experience at first hand some of the laboratory procedures, which have been introduced to genetic analysis. This will also serve the general function of increasing your level of experience at performing laboratory work.
• To demonstrate and emphasise, where appropriate, the relevance of academic science to the well-being of our species, i.e. the application of genetics to the benefit of mankind and the environment.
Students will also develop practical skills in genetic analysis and data interpretation, communication as well as interpersonal and team-working skills. These represent transferable skills that will benefit students across a range of disciplines.
The aims of the course will be achieved through a combination of lectures, tutorial and practical classes.
The strong impact of genetics on almost all aspects of biological and medical science is reflected in the subject matter covered in this course. The main aim is to provide a clear, comprehensive picture of genetic principles as they apply to a wide range of biological phenomena, attempting, where possible, to provide a molecular explanation for the observed phenotypic associations. The genetic composition of populations needs to consider the nature of the forces, selection and mutation, which helps to shape them. We also focus on the role of genes in the aetiology of different disease states and recognise the separate impact of chromosomal aberrations, single gene disorders and complex genetic traits in this respect. Isolating and characterising a gene is the ultimate aim of almost all genetic studies and this will be covered using human disease genes as examples. The ordering of gene function within a pathway will introduce you to the concept of epistasis. Finally, the need to feed an ever-growing world population underlines the importance of continued research in plant genetics, particularly in relation to disease-resistance and other important traits.
Subject: Genetic Analysis
No. of lectures: 6
Lecturer: Dr J Pettitt
The aim of these lectures is to provide an understanding of the way a biological process can be dissected using the tools of genetic analysis. The lectures will focus upon the principles involved, rather than specific facts, employing a wide-range of examples from different genetically-tractable experimental organisms.
Lecture 1: Mutations and mutant hunts
Genetic analysis requires mutations. This lecture will examine the different classes of mutations that can be produced, and how they can be used to begin the molecular dissection of a particular biological process.
Lecture 2: Complementation tests and what they can tell us
If two mutations affect the same gene, then they will “fail to complement”. This is the basis of the complementation test. This lecture will discuss the molecular basis of complementation tests, as well as situations when the test can “lie”, and the biological interpretation of such events.
Lecture 3: Genetic suppression and what it can tell you
Suppression of the phenotype of one mutation by another can tell us an enormous amount about the molecular basis of a gene products’ function. Such information is often invaluable in determining how a particular gene product contributes to a biological process.
Lecture 4: Building a pathway: epistasis
This lecture will demonstrate how genetic interactions between mutations can be used to assemble genes into pathways.
Lecture 5 & 6: Genetic redundancy and the limits of genetics
It is becoming increasingly clear that loss-of-function of many genes in eukaryotic genomes does not confer an obvious phenotype, at least within the laboratory. This means that some genes will be invisible to simple phenotype-based screens. However, there are tricks that can be employed to circumvent these problems.
Subject: Population Genetics
No. of lectures: 3
Lecturer: Professor Duncan Shaw
The aim of this series of lectures is to review the fundamental concepts of the Hardy-Weinberg theory as it applies to the genetic structure of populations. This provides a basis for the derivation of mathematical models describing the operation of selection in populations. Genetic polymorphisms are considered in relation to heterozygote advantage, artificial selection and natural selection in populations. In addition methods of measuring mutation rates, and their contribution to human gene frequencies are considered.
Subject: Medical Genetics
No. of lectures: 4
Lecturers: Dr A Schofield & Prof D Shaw
The general aim is to provide information on a range of genetic disorders and to expand their knowledge on the use of family studies including molecular analysis to provide appropriate genetic counselling.
Objectives: Students attending this course will have basic knowledge of the types of inherited disease, and the current state of our knowledge of their causes at the chromosomal or molecular level and the use of all of this information to counselling individuals in families.
Lecture 1: Major Groups of Genetic Disorders
Aim: To provide an overview of the role of genetics in multiple clinical disciplines.
Objective: As a result of attending this lecture, the student should understand the breadth of clinical areas on which clinical genetics now has an impact.
Lecture 2: Genetic Counselling
Aim: To provide an understanding of the basis of genetic counselling for a variety of types of disorders and, also, the ethical and legal considerations.
Objectives: Students should understand the nature of the non-directive counselling process and the need to educate the patient and family to make informed decisions relating to complex genetic situations.
Lecture 3: Localization and Characterisation of Genes
Aim: To provide an understanding of linkage analysis and its significance in pinpointing the localization of genes, their identification and further characterisation and use in risk analysis.
Objectives: Students should understand the nature of the processes involved in gene identification and characterisation and how to use this information.
Lecture 4: Cancer Genetics
Aim: To provide an understanding of the genes involved in cancer initiation and progression.
Objectives: Students should understand the role of oncogenes, tumour suppressor genes and DNA repair defects in cancer and in inherited predisposition.
Subject: Complex Genetic Disorders
No. of lectures: 3
Lecturer: Dr Lynne Hocking
The general aim of these lectures is to provide an overview of our current understanding of the genes involved in multifactorial diseases and the strategies being utilised in an effort to gain insight into the specific genes involved in the aetiology of such diseases.
Lecture 1: The role of genetics in the aetiology of complex genetic disorders; monogenic, oligogenic and polygenic inheritance of traits in relation to disease susceptibility in cancer, coronary heart disease and diabetes.
Lecture 2: The search for genes involved in complex genetic disorders – the ‘candidate’ gene approach; the selection of candidate genes based through knowledge of metabolic pathways and the pathology of the disease; genetic variation, phenotypic association and disease susceptibility.
Lecture 3: Searching for genes using the non-parametric sib-pair approach; concordance, discordance, allele identity by descent and state. Transmission/disequilibrium testing and haplotype relative risk. Genome scans using sib-pairs and microsatellites for the identification of disease susceptible regions for NIDDM, IDDM, age related macular degeneration and multiple sclerosis.
Subject: Genes and Genomes
No. of lectures: 3
Lecturer: Dr Jonathan Pettitt
The availability of large amounts of sequence data arising from genome sequencing projects has revolutionised genetics, but the key to these innovations has been the concurrent development of computational tools and associated databases. These lectures and the accompanying tutorials will investigate the development and application of “bioinformatics” tools to the understanding of gene function.
Subject: Gene Hunting and Human Genetics
No. of lectures: 4
Lecturer: Prof D Shaw
The general aim of these lectures is to outline the methodological approaches to finding human genes in the absence of knowledge of their structure and function.
Lecture 1: Introduction to genetic diseases and gene identification strategies, types of genetic disease, types of inheritance, linkage mapping, LOD scores, multipoint mapping
Lecture 2: Polymorphism in human DNA and how to analyse it, RFLP’s, mirosatellites, SNP’s and DNA arrays (chips) for rapid genotyping, genome scans, identifying genes in candidate regions using genome databases.
Lecture 3: Proving the candidacy of a gene; methods of mutation detection – large scale, based on gel electrophoresis – small scale using PCR – single-strand conformation polymorphism, heteroduplex analysis and direct DNA sequencing, dHPLC, examples: myotonic dystrophy and Huntington’s disease.
Lecture 4: The Human Genome Project. Expressed Sequence Tags and Sequence Tagged Sites, cDNA sequencing programmes, X-ray hybrid mapping, clone contigs, combining physical and genetic maps of the genome. Large - scale sequencing technology
Subject: Vertebrate Development
No. of lectures: 4
Lecturer: Dr A MacKenzie
Lecture 1: The evolutionary conservation of vertebrate and invertebrate genes involved in body patterning.
Lecture 2: The role of gene expression in vertebrate segmentation; somites and rhombomeres.
Lecture 3: Cranio-facial formation and the neural crest; the 4th vertebrate germ layer.
Lecture 4: The genetic regulation of vertebrate limb development
Subject: Fungal Genetics
No. of lectures: 4
Lecturer: Dr I Stansfield
Aims: to describe the structure and function of genetic materials in fungi, and to describe the molecular mechanisms of fungal genome dynamics and evolution.
Lecture 1: Chromosomes; structure function and inheritance; chromosomal components, their molecular biology and role in hereditary; telomeres and position effects; rDNA and its inheritance.
Lecture 2: Extrachromosomal inheritance in fungi; mitochondrial DNA, petite mutations in yeast: fungal plasmids, natural and artificial; protein based inheritance – yeast prions.
Lecture 3: Genome dynamics I: homologous recombination in yeast; gene conversion; using homologous recombination in yeast molecular genetics.
Lecture 4: Genome dynamics II: Site-specific recombination in yeast; inheritance of mating type, the MAT locus, and epigenetic inheritance.
As part of the course all students will fully participate in three practicals. The first is a wet-based exercise in molecular genetics involving genotype identification and analysis using PCR and RFLP methodologies. Individual students are responsible for the acquisition of genotype information on specific samples. Further haplotype analysis can only be carried on the total class sample. At the end of the practical, a report will be submitted as part of the continuous assessment. The second practical exercise is paper-based, using C.elegans as model system to dissect genetic pathways involving genes in sex determination. A short report will be submitted on the practical. The third exercise is computer-based and utilises WWW resources to investigate the likely functional role of a DNA sequence. A short report is also required for this exercise. Full information on these practicals is provided in the course manual.
At the start of the practical exercise all students will be instructed on the correct behaviour and level of safety expected in carrying out laboratory experiments. All students are expected to possess and wear a laboratory coat while attending practical classes. Additional forms of personal protection including safety glasses and disposable gloves will be provided. Students will also be instructed on the correct handling of chemicals and biological materials used during the practical.
Each student should own a personal copy of the book below; the course cannot be studied satisfactorily from lecture notes alone.
Griffiths A. J. F., Gelbart W. M., Miller, J. H., Lewontin, R. C. Modern Genetic Analysis
W H Freeman, London, 2nd ed (2002) (£35.99)
Books strongly recommended for reference and for further reading on selected aspects of the course. All books are available from the University library.
Strachan, T. & Read, A. (1999) Human Molecular Genetics
Dale, J. W. (1998) Molecular genetics of Bacteria
Hawley, R. S. & Walker, M. Y. (2003) Advanced Genetic Analysis
Wolpert, L. (1998) Principles of Development
The University has strict regulations on plagiarism. If you are unsure about what constitutes plagiarism read the University guide on plagiarism at:
http://www.abdn.ac.uk/writing
Copying or plagiarising another persons work, either from other students or published material in books or papers and submitted as your own for assessment is considered a form of cheating. This is considered by the University to be a serious offence and will be penalised according to the extent involved and whether it is decided there was an attempt at deliberate deception, or whether bad practice was involved. If you do use information or ideas obtained from textbooks or other published material you must give a precise reference to the source both at the appropriate point in your narrative and in a list of references at the end of your work. Direct quotations from published material should be indicated by quotation marks and referenced in the text as above.
This will consist of:
1. CONTINUOUS ASSESSMENT (30% of total): This will be made up of marks from the written reports of:
ASSIGNMENT VALUE OF FINAL MARK
1
2
3 C. elegans RNA interference Practical
Bioinformatics Report
Genetic Analysis Problems 10%
10%
10%
Assignments must be handed in before the deadlines specified.
Coursework Deadline for handing in Work Assessed by
Genetic Analysis Problems 12.00 pm Friday 18th February Dr Pettitt
C. elegans RNAi Practical 12.00 pm Friday 25th March Dr Pettitt
Developmental Genetics Practical 12.00 pm Friday 25th March Dr Pettitt
All items of course work should be handed in by the time and dates specified above to the secretaries in the School of Medical Sciences Office, Room 2:62.3, located on Level 2, IMS. Work appearing after this time will be deemed to be late and there will be an automatic deduction of marks.
Work handed in late must be deposited with the Year Co-ordinator with a written explanation attached. Note: without a medical certificate only exceptional reasons will be acceptable so that no penalty will be incurred.
Please inform your Year Co-ordinator immediately if you anticipate problems with handing in your course work.
COLLECTION OF COURSEWORK ONCE IT HAS BEEN ASSESSED
All work may be collected from Room 2:62.3. The staff will endeavour to return your work within two weeks after receipt.
2. WRITTEN EXAMINATIONS (70% of total): This will be of three hours duration and will be held at the end of the second semester in May/June. The examination paper will be divided into three parts, the first two parts consisting of essay type questions, while the third part will consist of problem/data analysis type questions. There will be 9 questions in total, 3 in each part. You will be requested to answer 4 questions, one question from each part plus one other. All questions have an equal weighting and questions may be based on any part of the course.
Details regarding Time and Place will be given to you in plenty of time.
EXAMINATION RESULTS
The results will be posted on the 3rd year notice board, and sent by email approximately 10 days after the examination. The criteria used for marking examination questions are given on the following page of the manual. Similar considerations apply to marking your other assessed written work.
ORAL EXAMINATIONS may be arranged for a few students who fall close to the borderlines of Pass/Fail or possibly the Honours entry standard. The list of students for oral examination will be contacted by email and posted on the 3rd year notice board within 5 working days after the written examination in June, and the oral examinations will be held shortly thereafter. Each exam will last for 15-20 minutes and will normally be conducted by Mr Alastair Cumming and another member of staff who taught on the course. Any aspect of the course may be discussed. The outcome of this oral examination will be posted on the 3rd year notice board and by personal email the following day.
IMPORTANT NOTES
Students are responsible for checking whether they will be required for an oral examination by regularly monitoring the notice board and or checking their email messages in the days following the written examination. The staff has three working days to mark examination questions, so oral lists are unlikely to appear until at least 3 days after the written examination.
Students should also note that candidates asked to attend for oral examination and failing to do so will be assigned their pre-oral (failing) CAS assessment. It is important, therefore, that you do not plan to take a holiday at this time unless you can be certain that you will not be required to attend an oral examination.
REQUIREMENTS FOR PASSING THE COURSE
The total assessment of the course, recorded as a single CAS mark, is based on two elements of the course as follows: Continuous assessment marks contributing 30% of the total and the written examination contributing 70%. To achieve an overall pass for the course you MUST obtain a CAS score of 9 or better for the entire course AND you must pass the written examination with a score of 9 or better. Failure to pass the written exam will mean a fail for the course.
ENTRY INTO HONOURS
The criteria for entering the Honours classes 2010/11 are:
• achievement of a CAS mark of 12 or more for all four 30 credit courses at Level 3; and
• no outstanding courses at Levels 1 and 2.
The Chairs of Microbiology, Biochemistry and Genetics try to welcome as many students as possible into the Honours year, but it must be recognised that it will only benefit the more able students. In addition to the general rules for Honours entry published in the University Calendar, a CAS mark of 12 or better in each 3rd year module is taken as a reasonable sign that the student has reached an appropriate standard for acceptance into the Honours year. Exceptions can be made if there is a good reason, and a mixture of excellent results and one or two lightly poorer ones may sometimes be acceptable.
EXTERNAL EXAMINER
The external examiner plays a major, over-seeing role in the setting and marking of the written examination, in decisions about candidates to be entered for oral examination, in oral examinations themselves, and in the ultimate decisions about awards of passes and of CAS marks. He/she also has a strong input into the format and content of the course itself.
With regard to the written examination papers the external examiner will check for a sensible balance of questions, that they reflect the course content, that they are written in good English and that they are "do-able" i.e. questions should be neither too difficult or too easy.
The external examiner may wish to meet informally with the class representatives.
FIRST AND SECOND CLASS MERIT CERTIFICATES
First and Second Class Merit Certificates are normally awarded to students achieving CAS scores (collated from coursework and written examination marks) of 18-20 and 15-17 inclusive, respectively (see the CAS descriptors). Award of the certificates is made by the Registry on receipt of the CAS marks from the Department, and the award is entered in student records. No "certificates" as such are actually distributed. Students re-sitting the degree examination are not eligible for an award of a merit certificate.
Dr Alasdair MacKenzie
Dr Jonathan Pettitt
Dr Andrew Schofield
Dr Ken Forbes, Medical Microbiology; Dr Zosia Miedzybrodska, Medical Genetics; Dr Adam Price, School of Biological Sciences, Plant & Soil Science; Dr David Stephenson, Medical Genetics
The University is keen to help you successfully complete your studies. If at any time you feel you need assistance, there is a range of support services available to help you. These include support to help with unexpected and/or exceptional financial difficulty, support for disabled students and academic learning support through the Student Learning Service. Further details about all these services are available at;
http://www.abdn.ac.uk/studenthelpguide/.
We value student’s opinions in regard to enhancing the quality of teaching and its delivery; therefore in conjunction with the Students Association we support the operation of a Class representative system.
The students within each course, year, or programme elect representatives by the end of the fourth week of teaching within each half-session. In this course we operate a system of course representatives. Any students registered within a course that wishes to represent a given group of students can stand for election as a class representative. You will be informed when the elections for class representative will take place.
What will it involve?
It will involve speaking to your fellow students about the course you represent. This can include any comments that they may have. You will attend a Staff Student Liaison Committee and you should represent the views and concerns of the students within this meeting. As a representative you will also be able to contribute to the agenda. You then feedback to the students after this meeting with any actions that are being taken.
Training
Training for class representatives will be run by the Students Association. Training will take place in the fourth or fifth week of teaching each semester. For more information about the Class representative system visit www.ausa.org.uk or email the VP Education & Employability vped@abdn.ac.uk
The University operates a system for monitoring students' progress to identify students who may be experiencing difficulties in a particular course and who may be at risk of losing their class certificate. If the Course Co-ordinator has concerns about your attendance and/or performance, the Registry will be informed. The Registry will then write to you (by e-mail in term-time) to ask you to contact their office in the first instance. Depending on your reason for absence, the Registry will either deal directly with your case or will refer you to your Adviser of Studies or a relevant Support Service. This system is operated to provide support for students who may be experiencing difficulties with their studies. Students are required to attend such meetings with their Adviser of Studies in accordance with General Regulation 8.
Set criteria are used to determine when a student should be reported in the monitoring system. You will be asked to meet your Adviser if any of the following criteria apply for this course:-
either (i) if you are absent for a continuous period of two weeks or 25% of the course (whichever is less) without good cause being reported;
or (ii) if you are absent from two small group teaching sessions (e.g. tutorial, laboratory class) without good cause;
or (iii) if you fail to submit a piece of summative or a substantial piece of formative in-course assessment by the stated deadline'
If you fail to respond within the prescribed timescale (as set out in the e-mail or letter), you will be deemed to have withdrawn from the course concerned and will accordingly be ineligible to take the end-of-course assessment or to enter for the resit. The Registry will write to you (by e-mail in term-time) to inform you of this decision. If you wish consideration to be given to reinstating you in the course you will require to meet with the Convener of the Students' Progress Committee.
Students who attend and complete the work required for a course are considered to have been awarded a ‘Class Certificate’. Being in possession of a valid Class Certificate for a course entitles a student to sit degree examinations for that course. From 2010/11 class certificates will be valid for two years and permit a total of three attempts at the required assessment within that two year period i.e. the first attempt plus up to two resits.
You will receive a University e-mail account when you register with the University Computing Centre. The University will normally use e-mail to communicate with you during term-time. These e-mails will be sent to your University e-mail account, which you can access using Eudora or SquirrelMail.
It is your responsibility to check your e-mail on a regular (at least weekly) basis and to tidy the contents of your e-mail inbox to ensure that it does not go over quota (see http://www.abdn.ac.uk/diss/email/mailquota.hti for guidance on managing your e-mail quota). It is recommended that you use your University e-mail account to read and respond to University communications. If you already have a non-University e-mail account that you use for personal correspondence, it is possible to set up automatic forwarding of messages from your University e-mail account to your personal e-mail address (see http://www.abdn.ac.uk/studentmail/about.shtml) but, should you do so, it is your responsibility to ensure that this is done correctly. The University takes no responsibility for delivery of e-mails to non-University accounts.
You should note that failure to check your e-mail or failure to receive e-mail due to being over quota or due to non-delivery of an e-mail forwarded to a non-University e-mail account would not be accepted as a ground for appeal. For further information on appeals procedures, please refer to;
http://www.abdn.ac.uk/registry/quality/appendix5x18b.pdf
Tutorials
During the course students are required to attend four tutorials, focusing particularly, on topics in the general area of genetic analysis (twins, pedigrees, complex diseases). Students should come to the tutorial having attempted to answer the tutorial questions in advance and be fully prepared to contribute to the discussion which will arise during the tutorial session. Although no formal assessment mark will be awarded for the tutorial, student attendance will be recorded.
External Examiner
Professor John Quinn, Department of Human Anatomy and Cell Biology, University of Liverpool
