Molecular Biology RSM

BIOL20352 Molecular Biology RSM 10 Semester 2 Undergraduate Level 2 James Linton Unit coordinator School of Biological Sciences 1 FHEQ level (Framework for Higher Education Qualifications) ' Middle part of Bachelors ' European Credit Transfer & Accumulation System Rating : 5.0 This Research Skills Module is an example of research-informed teaching and will develop your experimental design, report writing and practical skills. You will be introduced to modern molecular biology research techniques in a laboratory-based project in which you will investigate the N-linked glycosylation of proteins fin species from the genera Helicobacter and Campylobacter. You will use a range of online bioinformatics tools to identify putative previously uncharacterised N-linked glycoproteins from Campylobacter/Helicobacter species. In the second part of the RSM you will experimentally test the hypothesis that these proteins are indeed N-glycosylated. This will involve PCR amplification of the corresponding gene and cloning into a suitable plasmid that will allow you to express the protein and test whether it is glycosylated using Western blotting. Successful experiments will identify novel Campylobacter or Helicobacter N-linked glycoproteins. This Research Skills Module is an example of research-informed teaching and will develop your experimental design, report writing and practical skills. You will be introduced to modern molecular biology research techniques in a laboratory-based project in hybrid online bioinformatics and laboratory-based project in which you will investigate the N-linked glycosylation of proteins in species from the genera Helicobacter and Campylobacter. Following the bioinformatics-based identification of potential N-linked glycoproteins the corresponding genes will be PCR amplified, cloned, expressed and tested for glycosylation using Western blotting thereby identifying novel glycoproteins. This unit aims to increase the students understanding of the following: 1. Specific skills associated with molecular biology <ul> <li> the use of an array or online bioinformatics tools to develop hypothesis regarding protein glycosylation.</li> <li> design of gene-specific chain reaction (PCR) primers and amplification of DNA.</li> <li> agarose gel electrophoresis of PCR products d) plasmid construction using state of the art cloning approaches</li> <li> plasmid transformation into Escherichia coli</li> <li> production of protein lysates and analysis of proteins by Western blotting</li> </ul> 2. How to design and plan experiments and work independently 3. How to analyse, interpret and record data 4. How to present data in a research paper format Students will develop an understanding of an array of online bioinformatics tools. The hypotheses generated will be tested using DNA and protein based molecular biology techniques. The potential for identification of novel Campylobacter or Helicobacter N-linked glycoproteins will allow students insight into how new scientific knowledge emerges in the life sciences from hypotheses to experimental verification. Students will also learn to appreciate how careful experimental design interpretation combined with good laboratory practice is vital for the advance of knowledge. Understand the utility of diverse online bioinformatics tools. Understand the basis of several commonly used DNA and protein-based molecular biology techniques. Be able to design experiments to test a hypothesis and to analyse and interpret the data obtained. Be able to apply online bioinformatics tools as appropriate to analyse sequence data including genome sequences and specific proteins. Develop skills in several experimental methodologies relevant to molecular biology. <ul><li>Work as part of a team</li><li>Problem solving</li><li>Presenting data</li><li>Project management</li><li>Time management</li></ul>  Analytical skills Students must describe and analyse the results of PCR and cloning, transformation, and Western blots. These practical approaches are underpinned by bioinformatic analyses. Transformation, Western blots and SDM experiments. These practical approaches are underpinned by bioinformatic analyses. Group/team working Students work at the bench in pairs. Innovation/creativity Students have to input into how they approach the analysis and presentation of their data. Problem solving If students do not get the 'expected' results then they will employ problem solving skills to identify what might explain this. The bioinformatics and lab-based work have elements of independence to allow students to try out different approaches. Research Students carry out a structured four-week mini project involving hypothesis generation (identification of putative glycoproteins) and subsequent testing. If successful students will add to existing knowledge and there is even potential for eventual publication of data. Students will learn theoretical and practical aspects of a number of molecular biology techniques. Written communication Students will be required to, and be advised on how to keep a thorough record of their experiments in a lab book. Weekly short answer questions will test their knowledge and understanding. Students will write up their results in the form of a short scientific paper. Other Students gain confidence working in a laboratory, making solutions, researching protocols, following protocols, setting up experiments, and analysing the results. Importantly students will have the opportunity to generate novel data and see how their experiments will add to scientific knowledge and consider how this might be disseminated. In the Molecular Biology RSM students learn specific DNA and protein-based laboratory techniques to investigate protein glycosylation status. Students work in pairs. Weeks 1 and 2. Students will follow an online Softchalk-based programme of Bioinformatics enabling identification of putative N-linked glycoproteins from bacterial genome sequence data. This involves accessing proteins via UniProt, BLAST analysis, sequence alignment, accessing genome sequence data and analysing via SignalP. In this way students will develop their hypotheses for subsequent experimental testing in weeks 3 and 4. Week 3. Putative glycoprotein encoding genes identified in weeks 1 and 2 will be PCR amplified and verified by agarose gel electrophoresis. Following purification, PCR products will be ligated into suitable vector for expression in Escherichia coli using state-of-the-art- In-Fusion cloning method. Following transformation PCR from E. coli colonies will be used to verify cloning and colonies will be inoculated into LB broth for plasmid minipreps These approaches will provide theoretical understanding and practical experiences of a number of molecular biology techniques. Students will also use bioinformatics to identify putative glycoproteins and will be asked to consider the experimental design aspects of the RSM. Week 4. In week 4, students will test their hypothesis that the genes cloned in week 3 encode glycoproteins. This will involve determining the eglycosylation status of the putative glycoproteins by Western blotting experiments using N-linked glycan specific antiserum from vectors in glycocompentent E. coli strains that have complete function C. jejuni N0linked glycosylation systems encoded on a second vector. Practical sessions including some bioinformatics. 0 Other 50% 2 Written assignment (inc essay) 50% A weekly set of short answer questions will be provided each Thursday testing students understanding of the previous week's work. Feedback provided as annotated assessment sheets returned within 15 work days of submission although we will attempt to provide rapid feedback that be used to improve subsequent assessments where possible. (50%) The RSM will be written up as a short research publication no longer than 5 pages in length, submitted in Blackboard and feedback provided via Turnitin within 15 work days of submission (50%). An initial 1 hour intro session given by the course coordinator will prove the necessary background and discuss the bioinformatics approach - students are encouraged to ask questions here. Each Thursday of weeks 1 and 2 there are drop-in sessions for students to ask questions as they work through the bioinformatics programme. In addition to feedback on assessments, informal formative feedback will be provided in the laboratory by staff and demonstrators throughout the 2 week practical component. BIOL10221 Molecular Biology Pre-Requisite Compulsory BIOL10221 is a mandatory pre-requisite for BIOL20352This unit is compulsory for Molecular Biology honours students and may be selected by Biology, Biomedical Science or Biotechnology students. It is important that students not registered on the Molecular Biology Degree programme consult their Programme Director or the Unit Coordinator. BSc(Hons) Biology BSc(Hons) Biology Second Year Optional BSc (Hons) Biology with IE/PE BSc (Hons) Biology with IE/PE Second Year Optional BSc(Hons) Biology w Mod Lang BSc(Hons) Biology w Mod Lang Second Year Optional BSc(Hons) Biology w Mod Lang BSc(Hons) Biology w ML (Asian) Second Year Optional BSc (Hons) Biomed Sci w IE/PE BSc (Hons) Biomed Sci w IE/PE Second Year Optional BSc(Hons) Biomedical Sciences BSc(Hons) Biomedical Sciences Second Year Optional BSc (Hons) Molec Biol w IE/PE BSc (Hons) Molec Biol w IE/PE Second Year Mandatory BSc(Hons) Molec Bio w Mod Lang BSc(Hons) Molec Bio w Mod Lang Second Year Mandatory BSc(Hons) Molec Bio w Mod Lang BSc(Hons) Mol Bio w ML (Asian) Second Year Mandatory BSc(Hons) Molecular Biology BSc(Hons) Molecular Biology Second Year Mandatory BSc(Hons) Biomed Sci w Mod Lan BSc(Hons) Biomed Sci w Mod Lan Second Year Optional BSc(Hons) Biomed Sci w Mod Lan BSc(Hons) Bio Sci w ML (Asian) Second Year Optional BSc (Hons) Biotechnology BSc (Hons) Biotechnology Second Year Optional BSc (Hons) Biotech w IE/PE BSc (Hons) Biotech w IE/PE Second Year Optional MSci Biology MSci Biology Second Year Optional MSci Biomedical Sciences MSci Biomedical Sciences Second Year Optional MSci Biotechnology MSci Biotechnology Second Year Optional MSci Molecular Biology MSci Molecular Biology Second Year Mandatory BSc(Hons) Biol with Entrepren BSc(Hons) Biol with Entrepren Second Year Optional BSc(Hons) Biomed Sci W Entrepr BSc(Hons) Biomed Sci w Entre Second Year Optional BSc(Hons) Biotech w Entre BSc(Hons) Biotech w Entre Second Year Optional BSc(Hons) Molec Biol w Entrepr BSc(Hons) Mol Biol w Entre Second Year Mandatory N Nothaft H & Szymanski CM (2010) Protein glycosylation in bacteria: sweeter than ever. Nature Reviews Microbiology (8) 765–778. For information and advice on Link2Lists reading list software, see:http://www.library.manchester.ac.uk/academicsupport/informationandadviceonlink2listsreadinglistsoftware/ Practical classes & workshops 60 0 40