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BSc Biotechnology with Industrial/Professional Experience / Course details
Year of entry: 2023
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Course unit details:
Molecular Biology RSM
|Unit level||Level 2|
|Teaching period(s)||Semester 2|
|Available as a free choice unit?||No|
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 hypotesis 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 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.
This unit aims to increase the students understanding of the following:
1. Specific skills associated with molecular biology
- the use of an array or online bioinformatics tools to develop hypothesis regarding protein glycosylation.
- design of gene-specific chain reaction (PCR) primers and amplification of DNA.
- agarose gel electrophoresis of PCR products d) plasmid construction using state of the art cloning approaches
- plasmid transformation into Esherichia coli
- production of protein lysates and analysis of proteins by Western blotting
2. How to design and plan experiements 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 proetin based molecular biology techniques. The potential for identification of novel Campylobacter or Helicobacter N-linked glycoproteins will allow students insight into hw new scientific knowledge emerges in the life sciences from hypotheses to experimental verification. Students will also learn to appreciae how careful experimental design interpretation combined with good laboratory practce is vital for the advance of knowledge.
In the Molecular Biology RSM students learn specifc DNA and protei-based labratory 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 genomesequence 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 indentified 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 PCRfrom 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 undertanding and practical experiences of a number of moecular 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 hte genes cloned in week 3 encode glycoproteins. This will involve determining th eglycosylation status of the putative glycoproteins by Western blotting experiments using N-linked glycan specific antiserum from vectors in glycocompentent E. coli strainsthat have complete function C. jejuni N0linked glycosylation systems encoded on a second vector.
Teaching and learning methods
Practical sessions including some bioinformatics.
Knowledge and understanding
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
Transferable skills and personal qualities
- work as a team
- problem solve
- present data
- project manage
- time manage
- 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.
- Students have 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.
- 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.
- 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.
|Written assignment (inc essay)||50%|
A weekly set of short answer questions will be provided each Thursday teting 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 provid rapid feedback that be used to improve subsequent assessments where possible. (50%) The RSM will be written up as a short research publication no longr 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 an 2 there are drop-in sessions for students to ask questions as they work through the bioinformatics programme. In additioan to feedback on assessments, informal formative feedback will be provided in the laboratory by staff and demonstators throughout the 2 week practical component.
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:
|Scheduled activity hours|
|Practical classes & workshops||60|
|Independent study hours|
|James Linton||Unit coordinator|