Module
Advanced Laboratory Skills
| Module title | Advanced Laboratory Skills |
|---|---|
| Module code | BIOM549 |
| Academic year | 2023/4 |
| Credits | 15 |
| Module staff | Dr Sam Stevens (Convenor) Dr Corin Liddle (Convenor) |
| Duration: Term | 1 | 2 | 3 |
|---|---|---|---|
| Duration: Weeks | 7 | 6 | 0 |
| Number students taking module (anticipated) | 22 |
|---|
Description - summary of the module content
Module description
In this module you will be trained in advanced techniques used in Biosciences research. You will perform advanced experiments and write-up the results in a scientific report. You will carry out an analysis on historical data to get experience in processing a range of data sets. This module will be invaluable to prepare you for the research project.
This module will commence in week 5 of term 1 with experiments running each week for the remainder of that term. Data analysis and write-up will take place in term 2. This content will be complementary for your research project. Please note that the timing of the laboratory sessions and the activities will be specific to each theme.
Module aims - intentions of the module
This module aims to ensure you are trained in the appropriate methodological skills to prepare you for your research project and will provide you with important skills of analysis of experimental data, scientific report writing and different ways of presenting data.
Intended Learning Outcomes (ILOs)
ILO: Module-specific skills
On successfully completing the module you will be able to...
- 1. Explain the principles of the advanced bioscience techniques covered, and have an awareness of the applications of these techniques in biosciences research
- 2. Collect your own experimental data in a subdiscipline of biosciences
- 3. Interpret experimental data obtained using experimental techniques
ILO: Discipline-specific skills
On successfully completing the module you will be able to...
- 4. Describe comprehensively some techniques applicable to research in a subdiscipline of the biosciences
- 5. With input from expert facility staff, deploy established techniques of analysis, practical investigation and enquiry within the biosciences
- 6. Critically evaluate experimental data
- 7. Develop scientific writing skills for reporting findings in appropriate formats.
ILO: Personal and key skills
On successfully completing the module you will be able to...
- 8. Collect and interpret appropriate data and complete research-like tasks with limited guidance
- 9. Work in a small team and deal proficiently with the issues teamwork requires (e.g. communication, motivation, decision-making, awareness, responsibility, and management skills, including setting and working to deadlines)
- 10. Communicate ideas, principles and theories fluently by written, visual and verbal means.
Syllabus plan
Syllabus plan
Whilst the module's precise content will vary year-on-year (dependent upon current specialist staff, equipment, skills availability, and interests), the expected format is given below.
Lectures and theoretical aspects
You will have the choice of one of the following three ‘tracks’:
Zebrafish track
- The use of model organisms in research
- Case studies that use transgenic Zebrafish as a model organism
- The issues of creating and using genetically modified zebrafish
- The considerations of setting up chemical exposures of embryo/larval zebrafish for environmental chemical assessments
- Approaches to imaging and quantifying organ-specific fluorescence in larval zebrafish subject to an environmental chemical exposure
Microbial track
- The use of agrochemicals in pest control
- The principles of the mode of action of antifungals
- The mechanisms of toxicity of pesticides
Plant track
- Plant-environment interactions and the concept of phenotypic plasticity.
- The genetics and molecular understanding of plant-environment interactions.
- The impact of environmental changes on plant life and its implications
Microscopy theory. As part of each of the tracks outlined above, you will undertake microscopy within the Bioimaging centre, covering:
- The key principles and concepts of light microscopy
- The key differences between widefield and confocal systems
- How to configure a confocal for different imaging objectives, such as spatial or temporal resolution
- Guidelines of how to prepare images for publication and how to conduct basic post capture data extraction and statistical analysis using R
Main practicals for report writing assessment
Within each track, you will generate data during full-day practicals that take place over a single week. Techniques covered within each track are outlined below:
- Zebrafish: Practicals will cover transgenic zebrafish larvae (ZFL) handling and grading, set up of chemical exposures, and mounting of sample for widefield fluorescence-imaging of ZFL organs.
- Microbial: Practicals will be themed around gathering data for testing the antifungal mode of action of fungicides. During this practical you will cover setting up fungicidal assays, live-imaging of fungal pathogens using widefield systems, and the assessment of mitochondrial potential.
- Plant: Practicals will be themed around applying molecular methods that will allow you to assess plant phenotypic and genetic responses to their environment. You will cover morphometric measurements of seedlings, RNA isolation and quantification, cDNA library preparation, and quantitative polymerase chain reactions (qPCR) and gene expression data analysis.
Confocal: The samples generated in the themed tracks will be imaged using advanced confocal systems.
Data analysis / tours / demonstrations for production of poster assessment
You will undertake workshops that are aligned with your research track, which will cover examples of the application of advanced biological methods, with a focus on the analysis of data output and interpretation, depending on your track you will either undertake:
- Mass spectrometry: Data sets will be examined and discussed that quantitate the uptake of compounds into zebrafish larvae.
- Flow cytometry: Data sets will be examined and discussed that cover fungal-themed biological questions.
- Sequencing: Data sets will be examined and discussed that explore genetic changes in plants due to environment interactions and climate-related factors.
Supporting seminars for production of scientific report
- Image data extraction and analysis workshops: These workshops will cover how to handle and prepare and extract data from images using sophisticated software packages, such as Zeiss’s Zen Blue and Black.
- Statistic support: Examples of suitable statistic tests for the data generated in your themes will be covered using R, such as linear regression and analysis of variance.
- Writing/Drafting support: The perils and tribulations of scientific writing will be discussed and explored, with an emphasis on dissecting the different parts of a scientific paper.
Accessibility statement:
As part of this module, you will undertake laboratory sessions in the large teaching laboratory that are up to the whole working day in duration. These sessions will be undertaken in groups and will involve fine laboratory work and chemical handling (with appropriate PPE and safety considerations). Breaks are possible and students are able to leave the laboratory for short periods. Please contact the convenor directly if you require further reasonable adjustments (provision of a computer, for example).
Learning and teaching
Learning activities and teaching methods (given in hours of study time)
| Scheduled Learning and Teaching Activities | Guided independent study | Placement / study abroad |
|---|---|---|
| 85 | 65 | 0 |
Details of learning activities and teaching methods
| Category | Hours of study time | Description |
|---|---|---|
| Scheduled learning and teaching | 33 | Laboratory practical activities |
| Scheduled Learning & Teaching activities | 52 | Lectures (10 hr), data handling (18 hr), writing and image processing (24 hr) sessions |
| Guided independent study | 20 | Reading around practical topics |
| Guided Independent Study | 45 | Preparation of coursework |
Assessment
Formative assessment
| Form of assessment | Size of the assessment (eg length / duration) | ILOs assessed | Feedback method |
|---|---|---|---|
| Lecturer/researcher feedback during contact sessions and practical activities | Ad hoc | 1-10 | Oral |
Summative assessment (% of credit)
| Coursework | Written exams | Practical exams |
|---|---|---|
| 90 | 0 | 10 |
Details of summative assessment
| Form of assessment | % of credit | Size of the assessment (eg length / duration) | ILOs assessed | Feedback method |
|---|---|---|---|---|
| Statistics report | 10 | 1 hour | 7-8 | Written |
| Drafting of laboratory write-up and tutorial engagement | 10 | 2,500 words | 1-10 | Written and lecture |
| Practical observation | 10 | During practical | 2, 5-9 | Written |
| Better poster | 15 | 1x A3 and digital supplement | 3,4,8,10 | Written |
| Laboratory write-up | 55 | 2,500 words | 1-10 | Written |
| 0 |
Re-assessment
Details of re-assessment (where required by referral or deferral)
| Original form of assessment | Form of re-assessment | ILOs re-assessed | Timescale for re-assessment |
|---|---|---|---|
| Statistics report (10%) | Statistics report | 7-8 | August Ref/Def |
| Drafting of laboratory write-up and tutorial engagement (10%) | Drafting of laboratory write-up and tutorial engagement | 1-10 | July, prior to August Ref/Def |
| Practical observation (10%) | Not applicable | Not applicable | Not applicable |
| Better poster (15%) | Better poster | 3,4,8,10 | August Ref/Def |
| Laboratory write-up (55%) | Laboratory write-up | 1-10 | August Ref/Def |
Re-assessment notes
Deferral – if you miss an assessment for certificated reasons judged acceptable by the Mitigation Committee, you will normally be either deferred in the assessment or an extension may be granted. The practical observation assessment is not deferrable due to its practical nature. The mark given for a re-assessment taken as a result of deferral will not be capped and will be treated as it would be if it were your first attempt at the assessment.
Referral – if you have failed the module overall (i.e. a final overall module mark of less than 50%) you will be required to submit a further assessment as necessary. The mark given for a re-assessment taken as a result of referral will be capped at 50%.
Resources
Indicative learning resources - Basic reading
- Some key reading materials specific to your research theme will be supplied.
Indicative learning resources - Web based and electronic resources
- ELE: BIOM549 ELE Page
https://vle.exeter.ac.uk/course/view.php?id=13271
Module has an active ELE page
| Credit value | 15 |
|---|---|
| Module ECTS | 7.5 |
| Module pre-requisites | None |
| Module co-requisites | None |
| Available as distance learning? | No |
| Origin date | 01/03/2021 |
| Last revision date | 20/10/2022 |