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The “Frontiers of Molecular Medical Sciences" course, SM3001, runs in parallel with the courses MB3006 and DB3005 during the 12 weeks of the first half-session.
The modern biologist, if (s)he wishes to completely understand a biological process, must employ a wide range of tools and methodologies drawn from several disciplines. This course is designed to provide students with an understanding of how biological information is obtained drawing on the full range of techniques currently employed in biological research. It will provide students with core knowledge facilitating effective study of all fields of modern biology.
The General Aims of the course are to enable students:
• to establish an understanding of the molecular technologies used by biologists to gain knowledge of molecular cell systems;
• to establish an appreciation of the advantages and disadvantages of different molecular biological tools, the appropriateness of their application to a given biological problem and how the information from each technique can be integrated;
• to analyse primary experimental results.
Some lectures in this course, particularly those that span 2 hours, will be interactive using group discussion and PRS to aid analysis of primary research data. The tutorials enable further group work and allow discussion of a topic in an informal setting. The laboratory class gives you practical experience of some of the basic cloning techniques that are the basis of many research papers. The computer class (laboratory simulation) allows you to generate and analyse a large body of data that would be impossible to produce in the timescale of this course. It also provides an opportunity to improve your computer skills.
Attendance at all classes is compulsory and is monitored.
At the end of the course students should be able to:
• Describe the basic ‘tools’ and techniques used in molecular biology, such as enzymes, vectors, recombinant DNA methods, gene cloning, PCR etc;
• Describe techniques used for gene mapping to identify the basis of a given mutant phenotype;
• Describe computer techniques used to handle the wealth of nucleic acid and protein sequence data that is becoming available;
• Describe RNA structure, synthesis, degradation, isolation and characterisation techniques;
• Describe techniques that can be used to study (a) sub-cellular localisation of proteins and (b) global patterns of protein expression in different tissues and cell types;
• Describe techniques to analyse gene function. This to include classical genetic analysis, using mutants as a basis for cloning, sequencing and characterising a wild type gene, together with various genetic screening methods;
• Describe methods to obtain function information about a gene from a knowledge of only the gene sequence;
• Describe procedures for expressing foreign genes in appropriate hosts such as bacteria, yeast, insect and mammalian cells (to include transgenic mice in biological research);
• Describe a variety of methods for purifying proteins from tissues or from gene expression systems and also the criteria for selecting particular methods;
Subject: Gene cloning
No of Lectures: 4
Lecturer: Dr C Munro
These lectures give an account of the techniques employed in the manipulation of DNA and the cloning of specific DNA sequences and complement the Cloning practical. Topics to be covered include:
• Cutting and Joining DNA: restriction endonucleases, ligases, polymerases, gel electrophoresis
• Cloning vectors: plasmids and expression vectors
• Cloning: constructing gene/cDNA libraries
• Selection strategies: DNA homology, antibody screening, functional complementation
Subject: Genomics
No of Lectures: 4
Lecturer: Dr J Pettitt
Genomics is a term that refers to the global analysis of an organism's gene function. The first step involves the large scale application of gene cloning techniques. The aim of these lectures is to give an overview of techniques employed in genome projects; from the generation of the raw DNA sequence to the computational analysis of this sequence. Examples from human, C. elegans and Drosophila genome projects will be used to illustrate key experimental approaches. Topics to be covered will include:
• Genome sequencing strategies: The special problems created by genome projects; generating whole genome physical maps; Clone-by-clone Vs shotgun assembly approaches
• Deciphering the genome: Identifying protein coding genes; the combined use of experimental approaches such as computational gene finding and cDNA projects.
• Assigning function to genes: Using sequence similarity as a tool to provide functional information.
Subject: Gene expression analysis
No of Lectures: 4
Lecturer: Dr A MacKenzie
How the one-dimensional information contained within the DNA of the genome is changed into a four dimensional organism, remains one of the biggest questions in biology. This process starts with transcription. The instructions for where and when a gene is switched on are found in the regulatory regions (enhancers and promoters) that surround the gene and identification of these regions is critical. Once transcription has been initiated selected gene sequences are transcribed into mRNA that is then able to leave the nucleus. How a cell interacts with its environment and assumes a specific identity is reflected by the specific identity, amounts and timing of the expression of mRNA. These lectures explore current methods of identifying the promoter regions of genes and subsequently detecting specific mRNA species.
• Promoter analysis: bioinformatics approaches, reporter gene assays, transgenics
• Quantitative RNA detection Methods: Northern blots, RNAse protection Assay, rtPCR Differential display, macroarrays and microarrays
• Qualitative RNA detection Methods: In Situ Hybridisation; Sense and Antisense probes; Radioactive and non radioactive RNA detection methods
Subject: Functional Genomics: what does our gene do?
No of Lectures: 4
Lecturer: Dr J Pettitt
Classical genetic analysis in both microorganisms and higher eukaryotes has typically started with the isolation of a mutant with a given phenotype, on the basis of which the wild-type gene can be cloned, sequenced and characterised. However, we now know the complete (or nearly complete) gene complement for a variety of organisms; although the function of most of these genes is not known. Gene function can be studied by observing the effect of altering the activity of a given gene on an organism’s phenotype. These lectures will first describe the basis of the forward genetics approach to gene cloning and go on to describe reverse genetics strategies, using examples from several model organisms.
• Forward genetics: from mutant to cloned gene
• Reverse genetics: RNA interference in C. elegans, Drosophila and mammalian cells
• Transgenics: creation of knock-out mice
Subject: Foreign gene expression & protein purification
No of Lectures: 6
Lecturer: Dr John Barrow
Recombinant DNA technology enables directed transfer and expression of DNA from one species to another. For some time now biologists have been able to harness this technology for the production of both pharmaceutically and scientifically important foreign proteins from a variety of species including man. The aim of these lectures is to explain the principles behind expression of foreign proteins. But in order to study the structure and function of a protein, it is necessary to purify the protein. This is true both for foreign proteins expressed in cells and for proteins derived from their natural source. These lectures will discuss the range of methods available for this purpose and the criteria for selecting particular methods.
• Why we purify proteins and what influences our choice of methods.
• The theory and practice behind commonly employed chromatographic methods.
• The use (and misuse) of protein fusions, such as His tags and maltose binding protein to facilitate protein purification.
Subject: Antibodies as tools
No of Lectures: 2
Lecturer: Dr F Ward
Antibodies are incredibly useful both in basic research, as diagnostics, and are increasingly being introduced as sophisticated therapeutics for a range of difficult to treat disorders including cancer.
• A basic overview of the adaptive immune response that underlies the production of antibodies will be introduced along with the principles of monoclonal antibody technology.
• Antibodies as research tools or in diagnosis: antibodies can be used in a number of techniques including ELISA, flow cytometry and immunocytochemistry. Even "everyday" tests such as the pregnancy test kit rely on antibody technology.
• Finally, while at a relatively early stage, antibody therapeutics are gaining market share year-on-year and several are now multi-billion pound blockbuster products. Notable examples of such therapies in cancer and autoimmune disease will be covered in detail.
Subject: Protein localisation (& PRS revision session)
No of Lectures: 4
Lecturer: Dr B. Mueller
Protein function is usually tightly linked to sub-cellular localisation i.e. growth factor receptors are targeted to the plasma membrane while transcription factors are localised in the nucleus. In some instances the sub-cellular localisation of a protein is subject to regulation i.e. the transcription factor NFB upon activation translocates from the cytoplasm (inactive) to the nucleus (active). The aim of these lectures is to consider methods that can be used to determine the sub-cellular localisation of a specific protein.
• Cell extracts & fractionation techniques: Preparation of whole and fractionated cell extracts, including nuclei, cytosol, mitochondria and membrane fractions.
• Microscopy: use of tags, e.g. GFP; live cell imaging
Subject: Proteomics
No of Lectures: 2
Lecturer: Dr D Stead
Proteomics is a term that refers to the analysis of the proteins expressed by an organism, tissue or cell (the proteome). Because of the high complexity and wide dynamic range within a proteome, large scale proteomic studies tend to provide information about the more abundant proteins. The aim of these lectures is to provide an overview of the main techniques used in proteomics and the strategies for their application. Topics to be covered will include:
• Protein identification: Peptide mass fingerprinting and tandem mass spectrometry.
• Quantification: 2-D gel electrophoresis and mass spectrometric techniques.
• Post-translational modifications: How they may be detected and characterised.
Subject: Protein:Protein interactions
No of Lectures: 4
Lecturer: Dr K I J Shennan
Proteins often form protein complexes in order to carry out their particular function. The aim of these lectures is to describe different experimental approaches to studying protein:protein interactions, using primary data to illustrate the advantages/disadvantages of each method.
• Yeast two hybrid: basic principle involved and use for identification of previously unknown protein:protein interactions
• pull-down assays: using affinity purification of GST or His-tagged proteins to pull down interacting partners.
• Co-immunoprecipitation: the use of antibodies to one protein to pull down interacting proteins
Subject: Protein:DNA interactions
No of Lectures: 4
Lecturer: Dr B. Mueller
A subset of proteins within the cell play a crucial role in controlling gene expression by interacting with DNA, e.g. transcription factors, and a number of powerful techniques are available with which to analyse such protein:DNA interactions. The aim of these lectures is to introduce you to some of these techniques and show you how to analyse the data that these methods can generate.
• Yeast one-hybrid: rapid detection of transcription factors interacting with a specific DNA sequence
• EMSA: gel electrophoretic mobility shift assay
• ChIP: chromatin immunoprecipitation
There will be two assessed practicals, a “wet” laboratory Cloning Practical and a computer simulation on Protein Purification. The Cloning Practical involves a continuous experiment which runs over seven sessions in the first half of the course (including a tutorial in session 6).
Attendance at all of these sessions is compulsory and is monitored.
1. CLONING PRACTICAL: Zoology Teaching Labs B013/B014
Cloning and propagation of restriction fragments in Escherichia coli using the plasmid pBR322.
The main aim of this practical is to teach you some of the basic methods that are central to most gene cloning strategies. A summary of the planned work is shown below and the complete practical manual is available on the course MyAberdeen site; a hard copy of the practical manual will be given out at the first practical session. You are encouraged to read each session’s practical work in advance of the practical so that you can work more effectively.
1. You will use the restriction enzymes EcoRI and BamHI to digest DNA from both phage (lambda), to make inserts, and from the vector pBR322.
2. The products of digestion will be analysed using agarose gel electrophoresis.
3. After cleavage, the restriction enzymes will be inactivated by heat treatment; the DNA fragments will be mixed and then ligated together using T4 DNA ligase.
4. The sequence specificity of the ends generated in the two populations of DNA fragments (lambda and pBR322) by BamHI and EcoRI allows only those DNA fragments to be ligated to form circles which have one end terminated by a BamHI cleavage site and the other terminated by an EcoRI cleavage site (see Fig.1). Many of the lambda DNA sequences have such a structure and can therefore combine with BamHI/EcoRI-cut pBR322 to form a mixture of circular recombinant DNA molecules of the type indicated.
5. These circular forms are able effectively to transform competent bacterial cells and propagate within them.
6. Cells that acquire plasmids can be selected on the basis of their resistance to ampicillin, resulting from the presence of the AmpR gene located on fragment 1 of pBR322. Since, on average, cells are unlikely to receive more than one recombinant DNA molecule, DNA plasmids in the mixture are "cloned" in individual cells which are separated by plating on nutrient medium containing ampicillin.
7. Those bacterial colonies containing recombinant plasmids which have a target DNA segment inserted between the EcoRI and BamHI cleavage sites of pBR322 are identified by their sensitivity to tetracycline, since the TetR gene of pBR322 is interrupted and inactivated by insertion of DNA at this position.
8. Finally, you will investigate the structure of the recombinant plasmid DNA's isolated from three individual transformed clones. Restriction of a recombinant plasmid DNA with EcoRI and BamHI removes the lambda DNA insert from the plasmid, allowing the size of the insert to be determined by agarose gel electrophoresis. Further digests will confirm the identity of the cloned fragments.
A template for word processing your report is available on the SM3001 MyAberdeen site.
2. COMPUTER AIDED LEARNING PRACTICAL: Zoology Teaching Labs ZG9
Protein Purification.
The aim of this practical is to enable you to apply your theoretical knowledge of protein structure and properties to explore various scenarios for purifying proteins. The programme allows you to choose the most effective methods from a number of laboratory procedures and gives you “on screen” results of your chosen method. In this manner you can explore different scenarios much more quickly than would be possible in the laboratory.
Each student will attend one timetabled 3 hour session. This practical will be assessed by a test that will be available on MyAberdeen.
Report Deadlines:
ASSIGNMENT CONTRIBUTION TO FINAL MARK DEADLINE
1 DNA cloning practical report 25% Midday on 16th November
2 CAL protein purification report 5% Midday on 4th December
BEHAVIOUR AND SAFETY IN LABORATORIES
Please read these notes carefully. Laboratories are potentially dangerous places, and certain codes of conduct must be observed to maximise the chances of you and everyone else working safely. These notes are not designed to be comprehensive, since rules and notices themselves cannot ensure safety. You have an important part to play in ensuring your own and others’ safety. Think carefully before you undertake any task, and if in doubt about safety, ask the supervisory staff.
Protective Clothing
You must possess and wear a laboratory coat during practical classes. Do not carry sharp objects in your clothing. Ensure that footwear is non-slip and is able to protect your feet from falling glassware, etc.
Safety spectacles are available and should be worn at all times in practical classes. Disposable safety gloves are also available: make sure that they are worn whenever chemical reagents of any sort are being used.
Fire and Accident Precautions
During the first classes of the session, the class supervisor will tell you where the fire extinguishers, fire alarm, fire exits and first-aid equipment are located in the main rooms in which you will be working. If you enter an unfamiliar room, note where these facilities are before starting work.
Any accident involving personal injury must be reported to the member of staff supervising the class.
GENERAL SAFETY ASPECTS
1. Arrive on time in order to listen to the instructions for the practical class.
2. Leave bags, etc. under the bench, not blocking the aisles, or cluttering the benches.
3. Do not shout or run in the laboratory.
4. Do not eat, drink or put anything into your mouth in the laboratory. Smoking is banned in the School of Medicine and Medical Sciences.
5. Never pipette anything by mouth; safety pipettes are available. Be especially careful when fitting a pipette controller to a glass pipette not to use excessive force as this may result in the pipette snapping and being driven into your hand.
6. Check that you know where the laboratory fire extinguisher, fire blanket, eye-wash bottle, safety spectacles, gloves and shower are located, and how to use them. Note the locations of the teaching laboratory fire exits, fire alarm and preparation room first-aid box.
7. Fume hoods are present in all laboratories; use them whenever necessary, e.g. when handling volatile or toxic chemicals of any kind.
8. Make sure when lighting Bunsen burners that there are no flammable or volatile chemicals nearby.
9. Label clearly all vessels containing liquid or solid.
10. Mix solutions in test-tubes by securely sealing the tube top with flexible plastic sheet and gently inverting the tube once or twice.
11. Do not throw water-immiscible solvents down the sink; bottles for collection of solvent waste are available in the preparation room.
12. Do not throw solid waste into the sink; waste boxes are available.
13. Do not use cracked or broken apparatus, or leave it lying about. Inform a member of the supervisory staff.
14. If you suspect malfunction of any instrument, do not attempt to dissemble it; inform the supervisory staff.
15. Do not connect electrical apparatus without permission.
16. Apparatus left operating outside normal working hours must be labelled.
17. Laboratory work outside time-tabled hours without permission of supervisory staff is forbidden. At no time work alone in the laboratory.
18. When leaving, switch off gas, water and electrical supplies, and wash your hands.
COSHH Regulations
In accordance with the Control of Substances Hazardous to Health Regulations (1988), risk assessments have been made for these classes. Copies are held by Mrs Cath Clark, Teaching Laboratory Supervisor. Safety information, specific to each class, is set out before each individual set of practical instructions, and must be read before work is begun.
Health
If you have difficulties such as epilepsy, diabetes, a heart condition, or colour blindness, which might affect your performance or safety in the laboratory, please tell the Course Co-ordinator (Dr. Kath Shennan) at the start of the session. The information, if desired and where practicable, can remain confidential.
There is no single text that covers the contents of this course. Most general biotechnology texts will provide relevant information. Some additional texts are also detailed below.
Lodish H et al., Molecular Cell Biology (Freeman, San Francisco 6th Ed) 2008
ISBN: 0-7167-7601-4
Alberts et al., Molecular Biology of the Cell (Garland, 5th Ed) 2008 ISBN: 978-0-8153-4105-5
Brown T A, Gene Cloning and DNA analysis: An Introduction (Blackwell, 6th edition) 2010 ISBN: 978-1-4051-8173-0
Primrose & Twyman, Principles of Gene Manipulation and Genomics (Wiley-Blackwell, 7th Ed) 2006 ISBN: 978-1-4051-3544-3
Turner, McLennan, Bates & Whyte. Molecular Biology (Instant Notes) (Taylor & Francis, 3rd Ed) 2005. ISBN: 0415351677,
This contains very useful notes on techniques and is particularly useful as background reading for the cloning lab.
Notes
(a) The University Library system has copies of all the books on the list.
(b) If buying any of these books, make sure you buy the most up to date version. Past editions of these books can substitute to some extent but be aware that as technology advances rapidly, outdated versions may give incomplete information.
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 person’s work, either from other students or published material in books or papers, and submitting it 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.
Course assessment for SM3001 consists of continuous assessment (30%) and the end of course written exam (70%).
• CONTINUOUS ASSESSMENT - This will comprise the following assignments:
ASSIGNMENT VALUE OF
FINAL MARK DEADLINE
1 DNA cloning practical report 25% Midday on 16th November
2 CAL protein purification report 5% Midday on 4th December
All coursework should be handed in to the Zoology Basement Teaching Laboratories. Take care to ensure that your work is placed in the correct collection box (labelled SM3001) as failure to do so may incur the same penalty as if your work was handed in late. Seek the advice of a member of staff if you have placed your work in the wrong box as the boxes are tamper-proof and you should not attempt to recover the work yourself. The box will be removed at 12.30 pm on the day the course work is to be handed in, and work appearing after this time will be deemed to be late, and there will be an automatic deduction of marks. Please inform the course co-ordinator (Dr Berndt Mueller) immediately if you have any problems handing in your coursework.
Work handed in late must be deposited with the course co-ordinator with a written explanation attached. Note: without a medical certificate only under exceptional circumstances will be no penalty will be incurred.
Penalty for late hand-ins
If you fail to hand in coursework by the deadlines given above without a justifiable reason (i.e. illness confirmed by a medical certificate) there will be an automatic deduction of 25% of the mark for each day, or part of a day that the work is late. Please inform the course co-ordinator (Dr. Berndt Mueller) immediately if you have any problems in this respect.
Collection of work once it has been assessed
All work may be collected from the appropriate box outside the Zoology Basement Teaching Labs. Staff will endeavour to return your work about two weeks after receipt.
• WRITTEN EXAMINATIONS (70% of total):
This will be of three hours duration and will be held in the January diet of exams. The paper is a combination of essay-style questions and problem solving/data analysis-type questions. Past papers will be available on the course MyAberdeen site. Questions may be based on any part of the course. The re-sit examination will be based on the written paper as above and the previous continuous assessment marks achieved during the course.
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. The external examiner may wish to meet informally with the class representatives.
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.
Guidance on examination regulations:
• Arrive at the examination venue in good time. Your student ID card should be placed on your desk.
• Bring all necessary pens, rulers and a calculator. Put all these materials on your desk. Everything else should be put away in your bag or jacket, normally stored at one end of the examination hall.
• Basic scientific calculators are allowed but graphical or programmable ones are forbidden, since they can be used to store information.
• Mobile phones are prohibited. They must be switched off before the examination begins and put away in your bag.
• Dictionaries (English to other language and vice versa) are allowed but not electronic ones. Your dictionary will be checked by the invigilators; make sure that it contains no additional notes or writing. So-called scientific dictionaries, which explain the meaning of scientific terms, are not allowed. Inappropriate dictionaries or calculators will be confiscated and taken away to be checked.
• Eating and drinking are formally forbidden by University regulations. We do not object to students having water or other non-alcoholic drink, or mints etc, but nothing noisy is allowed.
Examination results: The results will be posted on the student portals as soon as possible (approx 3 weeks) after the examination. The criteria used in marking examination questions are given later in 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 drawn up, and students contacted by email, as soon as possible after the written exam, and the oral examinations will be held shortly thereafter. Each exam will last for 15-20 minutes and will normally be conducted by the Course Co-ordinator 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 student portal.
Important notes
Students are responsible for checking whether they will be required for an oral examination by regularly monitoring their University email in the days following the written examination.
Students should also note that candidates asked to attend for oral examination, but 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 in the three weeks or so after the exam unless you can be certain that you will not be required to attend an oral examination. Following the exam therefore, if you intend to be absent from Aberdeen, please check with the School of Medical Sciences office to see if you are to be called for a viva exam. This advice also applies to the August re-sit examinations.
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 examination will mean a fail for the course.
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 John Barrow
Prof Alistair Brown
Dr Alasdair MacKenzie
Dr Berndt Mueller
Dr Carol Munro
Dr Jonathan Pettitt
Dr Kath Shennan
Dr David Stead Dr Frank Ward
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 students’ 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 student registered within a course who 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 will 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 half-session. For more information about the Class representative system visit www.ausa.org.uk or email the VP Education & Employability vped@abdn.ac.uk . Class Representatives are also eligible to undertake the STAR (Students Taking Active Roles) Award; further information about the co-curricular award is available at: www.abdn.ac.uk/careers .
The University operates a system for monitoring students' progress to identify students who may be experiencing difficulties in a particular course. If the Course Co-ordinator has concerns about your attendance and/or performance, the Registry will be informed and you will have "C6" entered on your student record. The Registry will then write to you (by e-mail in term-time) to ask you to contact them. Depending on your reason for absence, 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 any e-mail or letter), you will be deemed to have withdrawn from the course concerned and "C7" will be entered on your student record. If this occurs you will 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 be required to meet with the Convener of the Students' Progress Committee.
Students who attend and complete the work required for a course are considered to have been awarded a ‘Class Certificate’. Being in possession of a valid Class Certificate for a course entitles a student to sit degree examinations for that course. From 2010/11 class certificates will be valid for two years and permit a total of three attempts at the required assessment within that two year period i.e. the first attempt plus up to two resits.
You will receive a University e-mail account when you register with the University Computing Centre. The University will normally use e-mail to communicate with you during term-time. These e-mails will be sent to your University e-mail account.
It is your responsibility to check your e-mail on a regular (at least weekly) basis and to tidy the contents of your e-mail inbox to ensure that it does not go over quota (see http://www.abdn.ac.uk/diss/email/mailquota.hti for guidance on managing your e-mail quota). It is recommended that you use your University e-mail account to read and respond to University communications. If you already have a non-University e-mail account that you use for personal correspondence, it is possible to set up automatic forwarding of messages from your University e-mail account to your personal e-mail address (see http://www.abdn.ac.uk/local/mail.forward/) but, should you do so, it is your responsibility to ensure that this is done correctly. The University takes no responsibility for delivery of e-mails to non-University accounts.
You should note that failure to check your e-mail or failure to receive e-mail due to being over quota or due to non-delivery of an e-mail forwarded to a non-University e-mail account would not be accepted as a ground for appeal (for further information on appeals procedures, please refer to
http://www.abdn.ac.uk/registry/quality/appendix5x18b.pdf)
MYABERDEEN (THE UNIVERSITYS VIRTUAL LEARNING ENVIRONMENT)
MyAberdeen replaces WebCT as the students’ Virtual Learning Environment. This is where you will find learning materials and resources associated with the courses you are studying. MyAberdeen also provides direct access to TurnitinUK, the originality checking service, through which you may be asked to submit completed assignments.
You can log in to MyAberdeen by going to www.abdn.ac.uk/myaberdeen and entering you University username and password (which you use to access the University network). Further information on MyAberdeen including Quick Guides and video tutorials, along with information about TurnitinUK, can be found at: www.abdn.ac.uk/students/myaberdeen.php
Information about academic writing and how to avoid plagiarism can be found at: www.abdn.ac.uk/sls/plagiarism
The SM3001 site on “MyAberdeen” that contains a wealth of information and material to support the course. Lecture material will be put onto this site usually, but not always, in advance of the lecture. Accessing lecture material on MyAberdeen is no substitute for attending lectures; there may be information given during lectures that is not on the slides so if you miss lectures you may well miss important explanatory information. Bear in mind that to go over a lecture that you have not attended takes a lot more time, and generally gives less understanding, than if you had attended in the first place.
ENTRY INTO HONOURS
The criteria for entering the Honours classes 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 slightly poorer ones may sometimes be acceptable.
STUDENT RESPONSIBILITIES REGARDING ATTENDANCE AND MEETING DEADLINES
Attendance is compulsory at all lectures, tutorials and practical classes. Attendance is recorded at tutorials and practicals, and may also be noted at lectures. Practical Reports must be handed in by the dead-lines set out in the timetable. Failure to attend classes and/or failure to submit Practical Reports by the specified dead-lines may lead to the School reporting you to the Senate Office by recording a ‘C6’ on your student record.
ABSENCE FROM CLASSES ON MEDICAL GROUNDS
Candidates who wish to establish that their academic performance has been adversely affected by their health are required to secure medical certificates relating to the relevant periods of ill health (see General Regulation 17.3).
The University’s policy on requiring certification for absence on medical grounds or other good cause can be accessed at:
www.abdn.ac.uk/registry/quality/appendix7x5.pdf
You are strongly advised to make yourself fully aware of your responsibilities if you are absent due to illness or other good cause. In particular, you are asked to note that self-certification of absence for periods of absence up to and including eleven weekdays is permissible. However, where absence has prevented attendance at an examination or where it may have affected your performance in an element of assessment or where you have been unable to attend a specified teaching session, you are strongly advised to provide medical certification (see section 3 of the Policy on Certification of Absence for Medical Reasons or Other Good Cause).
PLAGIARISM
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 person’s work, either from other students or published material in books or papers, and submitting it 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.
STUDENT PORTAL
Your computer i.d. and password also enable you to access the University of Aberdeen Student Portal, through which you can view and check your personal details, course enrolments, timetable, accommodation fees, library loans and exam results. Log on at http://www.abdn.ac.uk/studentportal.
COURSE EVALUATION
Towards the end of the course you will be asked to fill in an electronic course evaluation form. This will give you an opportunity to tell us what you thought of the course, and highlight any aspects that you think could be improved for next year’s course. This is a really important tool that will help us decide on any changes or improvements for next year, and so we encourage you to be as open and honest as possible – this process is completed anonymously.
TRANSITION INTO LEVEL 3
As students progress through their degree programme, they will notice a change in the style and approach of teaching and the expectations upon them as learners. This is particularly marked as students move into level 3 and beyond. To help with this transition into level 3, a number of activities will be planned to address any new challenges faced by students at level 3. The level 3 co-ordinator - Dr Steve Tucker (s.j.tucker@abdn.ac.uk; 01224 437491) will organise such events and should be a first point of contact for any level 3 SMS students facing any kind of difficulty. Regular activities and workshops will be designed around key issues faced by new level 3 students e.g. new exam format, time management, but guidance and support will also be provided on request for individuals or groups with any other problem relating to level 3. In addition, Dr Tucker will hold regular, advertised drop-in surgeries for students to raise any issues face to face and all level 3 SMS students will have access to a MyAberdeen site that will offer information, feedback, guidance and discussion forums designed to enable all students to achieve the most from level 3.
FEEDBACK ON ASSESSMENT
The University recognises that the provision of timely and appropriate feedback on assessment plays a key part in students learning and teaching. The guiding principles for the provision of feedback within the University are detailed in the Institutional Framework for the Provision of Feedback on Assessment available at:
www.abdn.ac.uk/registry/quality/appendix7x8.pdf
Enhancing Feedback
The University recognises both the importance of providing timely and appropriate feedback on assessments to students, and of enabling students to voice views on their learning experience through experience through channels such as Student Course Evaluation Forms and Class Representatives. FAQ’s, guidance and resources about feedback can be found on the University’s ‘Enhancing Feedback’ website at: www.abdn.ac.uk/clt/feedback
APPEALS AND COMPLAINTS
The University’s appeals and complaints procedures provide students with a framework through which to formalise their concerns about aspects of their academic experience or to complain when they feel that standards of non-academic service have fallen short of that which they expect.
The process has been designed to make the appeals and complaints process as accessible and simple as possible and to provide a robust, fair mechanism through which to ensure that all appeals and complaints are considered in the appropriate way at the appropriate level.
A major feature of the process is the emphasis it places on early or informal resolution. All students should note that there is an expectation that they will take responsibility for seeking resolution of their academic or non-academic concerns by raising and discussing them at the earliest possible stage with the relevant individuals in an academic School or Administrative Service.
Further details of the processes for making an appeal or complaint, including where to find further help and support in the process, is given at:
www.abdn.ac.uk/registry /appeals
TRANSCRIPTS AT GRADUATION
It is anticipated that students who commenced their studies in, or, after, 2009/10, will receive a more detailed transcript of their studies on graduation. The increased details will include a record of all examination results attained. For students graduating in 2012/13 transcripts will show details of all CAS marks awarded, including marks which are fails. Where a resit has been required as a result of medical circumstances or other good cause (MC/GC) this will not be shown, but all other circumstances (i.e. No Paper ‘NP’) will be included.
ABERDEEN GRADUATE ATTRIBUTES
Graduate Attributes are a wide-ranging set of qualities which students will develop during their time at Aberdeen in preparation for employment, further study and citizenship.
There are four main areas of the Graduate Attributes:
• Academic excellence
• Critical thinking and communication
• Learning and personal development
• Active citizenship
Students have many opportunities to develop and achieve these attributes. These include learning experiences on credit-bearing courses and co-curricular activities such as work placements, study abroad and volunteering. In accordance with the University’s commitment to Equality and Diversity, students can request support with any aspect of the Graduate Attributes framework.
The ACHIEVE website offers resources that enable students to assess and reflect upon their present skills and development needs. The website also contains resources to help students to improve their skills and links to a range of university services such as the Careers Service and the Student Learning Service. Students can access ACHIEVE from their MyAberdeen site in ‘My Organisations’ section. More information about Aberdeen Graduate Attributes and ACHIEVE can be found at www.abdn.ac.uk/graduateattributes .
THE CO-CURRICULUM
The co-curriculum enhances a student’s employability and provides opportunities to develop and achieve Aberdeen Graduate Attributes. Co-curricular activities complement a student’s degree programme and include: work placements, study abroad, enterprise and entrepreneurship activities, the BP Student Tutoring Scheme, career mentoring and the STAR (Students Taking Active Roles) Award initiative. Below are examples of credit-bearing co-curricular activities. It is anticipated that these types of activity will be included on an enhanced transcript for students graduating in, or after, 2012/13
ERASMUS is an exchange programme funded by the European Commission which enables students to study or work in another European country as part of their degree programme. Eligible students will receive a grant to help with extra costs while abroad and a number of our partner institutions teach through English. For more information, visit www.abdn.ac.uk/erasmus/ . The University also has opportunities for students to study in a non-European country as part of their degree through the International Exchange Programme. International partners include universities and colleges in North America, Hong Kong, and Japan (www.abdn.ac.uk/undergraduate/international-exchange.php). The University aims to ensure full academic recognition for study periods abroad; therefore the credits gained from study abroad will count towards the Aberdeen degree programme for students participating in both ERASMUS and the International Exchange Programme.
Work placements can also form and integral parts of a degree programme and attract academic credit. Placements are available locally, internationally and internationally, lasting from a few weeks to a full year and are generally paid. Visit the Careers Service website for further placement information and to find available work placements.
Further information about the co-curriculum is available at: www.abdn.ac.uk/careers
