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Module

BIO2033 : Bioprospecting: chemical and biological diversity of endophytic bacteria

  • Offered for Year: 2020/21
  • Module Leader(s): Dr Thomas Howard
  • Lecturer: Dr Maria Del Carmen Montero-Calasanz, Dr James Stach
  • Owning School: Natural and Environmental Sciences
  • Teaching Location: Newcastle City Campus
Semesters
Semester 2 Credit Value: 20
ECTS Credits: 10.0

Aims

The aim of this module is to allow participants to conduct independent research within a specified project area - the isolation and subsequent screening of microbial species to identify properties of biotechnological relevance. Specifically, the research is focussed on the discovery of endophytic microbes with novel antimicrobial properties. Within this topic area, participants gain knowledge about the microbial and chemical diversity of plant endophytes and the important role they play in plant physiology. Participants will also learn about the function of microbial culture collections in curating and preserving microbial diversity. Participants will understand how bioprospecting is the start of a processes of discovery and ultimately re-purposing of natural systems for biotechnological applications. Further, the module aims to enhance the independent research skills of participants in preparation for subsequent research projects. This includes the development of laboratory skills common in microbiology and molecular biology, the application of computational skills for the analysis of DNA sequences and bioinformatics to infer phylogenetic relationships, and the deployment of scientific skills such as the formation of hypotheses, null-hypotheses, experimental plans, data analysis, figure presentation, and writing for scientific manuscripts.

Outline Of Syllabus

This module follows an inquiry-based learning format. The broad challenge is to isolate and screen plant endophytes for their biotechnological potential, a process known as bioprospecting. We focus on the discovery of microbes with novel antimicrobial properties. Topics covered within the module include:
•       Bioprospecting (methods for the discovery of natural products of biotechnological interest),
•       The antibiotic discovery pipeline,
•       The plant microbiome,
•       Microbial culture collections,
•       Bioinformatics tools and phylogenetic relationships,
•       The development of hypotheses, aims, objectives and research plans,
•       Writing and presenting for scientific papers.

Where it is possible to conduct practical sessions, they will include: surface sterilisation of plant material and the inoculation of media with plant sections, isolation of microbial endophytes and the generation of axenic cultures, media preparation, light microscopy, colony PCR, PCR clean-up, DNA sequencing, antimicrobial screening, and the use of reporter constructs. Participants may work at their own pace through these sessions, and with agreement from the module leader may undertake different assays in place of the antimicrobial screening assays.

Teaching Methods

Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion120:0020:00Preparation for submission of project proposal
Guided Independent StudyAssessment preparation and completion130:0030:00Professional skills assessment
Structured Guided LearningLecture materials91:009:00Asynchronous online material
Guided Independent StudyAssessment preparation and completion150:0050:00Preparation for final report
Scheduled Learning And Teaching ActivitiesPractical43:0012:00PiP - Practical sessions
Guided Independent StudyDirected research and reading34:0012:00Reading prior to three workshops
Guided Independent StudyDirected research and reading46:0024:00Preparation and writing around practicals
Structured Guided LearningStructured non-synchronous discussion110:0010:00Discussions of projects proposals
Scheduled Learning And Teaching ActivitiesWorkshops124:0024:00PiP (or non-synchronous) - Phylogenetic analysis activities/plant collection
Scheduled Learning And Teaching ActivitiesModule talk91:009:00Online synchronous seminars
Total200:00
Teaching Rationale And Relationship

BIO2033 has been modified to fit within the shorter semester, the interuption to learning caused by the inclusion of a buffer week in the timetable and it contains plan B assessments for the professional skills component and the final report. These latter changes have been made to ensure that - in the event of labs being stopped, or some students not being able to attend labs - data can be provided (for the report) and an online assessment can be made of the students professional skills. This online professional skills assessment is an augmented version of a succesful assessment that has been running for the last three years as part of this module. The following rationale remains core to the module: A 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.

Assessment Methods

Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.

The format of resits will be determined by the Board of Examiners

Other Assessment
Description Semester When Set Percentage Comment
Report2M10Project proposal - students provide a 500-word proposal for the work they intend to undertake in the subsequent lab sessions
Prof skill assessmnt2M20Three data sheets for three different bacterial strains isolated
Report2M70A written report in style of a journal paper, 2500 words. To include introduction, methods, results and discussion sections.
Formative Assessments
Description Semester When Set Comment
Oral Presentation1MShort presentation
Assessment Rationale And Relationship

There are three aspects to the assessment that fit and complement this structure:

1. A 500-word project proposal (10%) - 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 (20%) - assessed on the quality of the following laboratory skills: inc. genomic DNA extraction, PCR and sequencing data. These data are provided by the student in the form of data sheets for their isolated microbes or B. if lab work is curtailed they will be assessed through a comparative exercise for writing and presentation skills (formerly an additional part of this module), and will complete a mock data sheet using supplied data.

3. Final report (70%) - the students are tasked with writing a clear and coherent scientific manuscript following the Instructions for Authors provided during the module. 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 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.

Reading Lists

Timetable