BIO3045 : Bioprospecting
- Offered for Year: 2018/19
- Module Leader(s): Dr Thomas Howard
- Lecturer: Dr James Stach
- Owning School: Natural and Environmental Sciences
- Teaching Location: Newcastle City Campus
|Semester 1 Credit Value:||20|
The primary aim of this module is to familiarise students with conducting independent research within an overall project area - the isolation and screening of plant fungal endophytes for properties of biotechnological relevance. It aims to provide students with the knowledge, confidence and skills that they need to become independent researchers.
Knowledge-based aims include an appreciation of fungal and chemical diversity; an understanding of the important role endophytes play in plant physiology and cellular metabolism; and an understanding of the processes of repurposing natural systems to biotechnological applications.
Skills-based aims include continued development of their laboratory skills in microbiology (aseptic technique) and molecular biology; the application of sequencing and bioinformatics to research; and an ability to infer phylogenetic relationships.
Broader aims of the module are to enhance the research skills of students in preparation for both their research projects and their ability to conduct independent research after graduation, as well as improving the student learning experience. Finally, the module aims to introduce the students to the necessity of inter-disciplinary research in modern life-sciences. As such the module spans aspects of botany and ecology, microbiology, molecular analysis, biochemistry, bioassays and, potentially, chemical analysis.
Outline Of Syllabus
Lectures and independent study:
These provide students with an introduction to the concepts of student-led research, including a discussion of the teaching philosophy. Students are provided with information for the broad research goal i.e. isolation and screening of plant fungal endophytes for properties of biotechnological potential. They are provided with examples of natural products that are of interest, and of biotechnological processes that rely on natural systems for their operation. The example of antimicrobial drug discovery is given and is used as the exemplar structure for module learning and practical work. However, the module provides students with the opportunity to innovate new approaches based on the antimicrobial screening paradigm. Students are expected to use their non-contact time to read around the subjects and a reading list comprised of relevant scientific papers is provided. These are introduced during the lectures and workshops. Examples include the discovery of plastic degrading enzymes and the production of biofuel molecules by fungal species.
The workshop elements are student-centred and encourage both peer-discussion and ongoing formative feedback through dialogue with the academic facilitators. The workshops focus on the following topics, though students propose areas they wish to discuss.
Endophytes: What are endophytes? Why are they important? Where are they found? Methods for isolation. Students begin to explore the methodology that they will in their practical elements.
The scientific process: Proposing and researching ideas; constructing a hypothesis; developing a collection strategy. Researching and understanding methods. Antimicrobial screening – review of methods and approaches. Developing a research plan to test a hypothesis. Modifying questions/hypothesis to ensure they are testable and falsifiable with the resources. How a manuscript/scientific paper differs from a report that the students are likely to be familiar with. Expectations for the report format.
Data management and analysis: Species concepts – phylogenetic approaches to defining species. How to create phylogenetic trees – phylogeny concepts. Handling DNA sequencing data. The importance of accession numbers and database curation (both for biological samples and data).
These sessions provide the students with the opportunity to cement within the laboratory the understanding they are gaining in the ‘dry-lab’ sessions. Over the course of the semester the practical sessions encompass: inoculation of media with plant sections; purification of endophytes (streaking/sub-culture); DNA extraction; PCR; PCR clean-up and sequencing; antimicrobial screening; use of reporter gene constructs to indicate antimicrobial mode-of-action. Students may, to some extent, work at their own pace through these sessions, and with agreement they may undertake novel assays in place of the antimicrobial screening assays.
|Scheduled Learning And Teaching Activities||Lecture||1||2:00||2:00||Introductory lecture – lecture split into 1hr of intro. material and 1 hr of Q&A.|
|Guided Independent Study||Assessment preparation and completion||1||10:00||10:00||Project proposal|
|Guided Independent Study||Assessment preparation and completion||1||15:00||15:00||Prof skills assessment|
|Guided Independent Study||Assessment preparation and completion||1||60:00||60:00||Journal paper|
|Scheduled Learning And Teaching Activities||Practical||7||4:00||28:00||Practical sessions: x6 lab sessions, x1 sample collection|
|Guided Independent Study||Directed research and reading||20||2:00||40:00||Students will be given research papers relevant to workshops to read prior to attending workshop|
|Scheduled Learning And Teaching Activities||Workshops||10||2:00||20:00||To discuss student hypotheses, answer questions, test student understanding & introduce concepts|
|Guided Independent Study||Independent study||25||1:00||25:00||Students to independently read in order to complete practicals & assessments (summative & formative)|
Teaching Rationale And Relationship
A recent review of teaching in biological sciences - Innovations in Teaching Undergraduate Biology and Why We Need Them (Wood, 2009 Annu. Rev. Cell Dev. Biol. 2009. 25:5.1–5.20) – has highlighted the need for research-based teaching, as opposed to the more traditional practice of learning facts and recalling them. This module is designed to address this issue, and provides students with the opportunity to undertake their own research. The fact that the final outcomes of the module are unknown (i.e. we don’t know what will be discovered) places students at the centre of the module and gives them ownership and responsibility for their learning. Specifically, the module requires students to think critically and synthesise information (the upper tiers of Bloom’s levels of understanding). The teaching methods require students to formulate their own hypotheses and to subject them to peer review. They are required to undertake the practical testing of their hypotheses, and will be assessed on their research skills. The teaching methods remove the traditional student-lecturer relationship as both parties can gain from the outputs of the module e.g. novel species and enzymes may led to further research. The teaching methods have been designed to reflect the steps that are required to achieve successful research outcomes: students formulate hypotheses; critically evaluate their ideas; undertake practical research to test their hypotheses and/or to generate novel data using established techniques; and present their work for appraisal.
The format of resits will be determined by the Board of Examiners
|Prof skill assessmnt||1||M||15||Observation of practical skills - isolation of pure cultures, microscopy, DNA extraction and quantification; PCR and sequencing.|
|Written exercise||1||M||80||Student produce a written report in the style of a journal paper (including methods, results and discussion section) 4000 words max|
|Written exercise||1||M||5||Project proposal (500 words)|
|Oral Presentation||1||M||Plant identification: Students provide a taxonomic description of their target plant species.|
|Oral Presentation||1||M||Student short talks on aspects of methodology/theory used in the module-feedback is given on presentation and on methods/processes.|
Assessment Rationale And Relationship
The assessments are designed to be student-centred and research-based. In order for students to be engaged in their practical work, it is important that they do not feel that they are simply following a recipe. This module assesses their individual ideas, and their ability to perform research in the lab. Students are therefore assessed on the skills required for research biologists, not on the recall of factual information. The study by Wood, cited above, has shown that this form of teaching improves student engagement and satisfaction and provides students with transferable skills. Assessments are weighted such that their understanding and hypotheses count more than their lab abilities; intended so as to relieve pressure in the lab, and let students enjoy the experience of research without a fear of failure. This module is in response to extensive discussions with third-year undergraduates regarding their preferences for learning. For many years, feedback (multiple sources) from School of Biology students has expressed a desire for a greater degree of research-based/practical teaching.
There are three aspects to the assessment that fit and complement this structure:
1. A 500-word project proposal (5%) - this is an early assessment in which the student is required to detail their project proposal. Specifically, why it is important (with reference to the wider literature), the rationale for their collection strategy, an outline of their screening strategy and expected outcomes. The value in this assessment is to provide an early check on their understanding of the module and to prevent any student progressing on a flawed prospectus. There will be formative feedback in advance of this assessment on construction of the proposal.
2. Professional skills (15%) - this is assessed on the quality of the following laboratory skills: genomic DNA extraction, PCR and sequencing data. These data are provided by the student in the form of Supporting Information appended to the final report.
3. Final report (80%) - the students are tasked with writing a clear and coherent scientific manuscript following the Instructions for Authors for the Proceedings of the National Academy of the Sciences, USA. This report does not have to cover all of the practical work they have done and can be assembled using their own data, class data, or a combination of both. Full attribution is however required for data sources. Students are tasked with providing between three and six main figures as appropriate, with extra information appearing in Supplementary Information. Student reports are assessed for their ability to clearly and concisely summarise their research, from the literature required to introduce their research, data collected, analysed and discussed, conclusions drawn and the methods used to reach these conclusions. As such the final report requires the student to synthesise the entire module learning.