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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
Semester 2 Credit Value: 20
ECTS Credits: 10.0


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 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 microbial 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 development of 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 their research projects and their ability to conduct independent research after graduation. 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

This is a student-led research module that follows an inquiry-based learning format. The module delivers a broad challenge to the students: specifically, they must isolate and screen plant endophytes for properties of biotechnological potential, known as bioprospecting.
They must research and propose a testable hypothesis. They must design and execute an experimental plan within the resources of the module. Finally, they must assemble their data into a clear and coherent body of work. Class data is shared at each stage allowing students the opportunity to progress through the learning experience even if individual components fail. Students are not penalised for undertaking ambitious work.
The course is a combination of practical learning through student-directed laboratory work and other inquiry-based learning elements including reading the literature, discussions within the peer-group and with facilitators, and the synthesis, critical analysis and presentation of data.
Lectures and independent study elements of the module.
These elements provide students with an introduction to the concepts of student-led research, including a discussion of teaching philosophy, and the value of student-centred teaching. Students are provided with information for the broad research goal i.e. isolation and screening of plant endophytes. 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 the module learning and practical work. However, the module provides students with the ability to apply their ideas and innovate new approaches based on the antimicrobial paradigm. Students use their non-contact time to read the subject and relevant scientific papers are provided. These are introduced during the seminars.
The workshop elements are student-centred and encourage both peer-discussion and ongoing formative feedback through dialogue with the academic facilitators. The workshops loosely focus on the following topics, though students are expected to propose areas they wish to discuss.
Endophytes: What are endophytes? Why are they important? Where are novel endophytes found? Methods used to isolate endophytes – students begin to explore the methodology that they will in their practical elements. Including techniques used to identify endophytes and plants.
The scientific process: Proposing and researching ideas; constructing a hypothesis and null-hypothesis; developing a collection strategy. Researching and understanding methods. Antimicrobial screening. Developing a research plan to test a hypothesis. Modifying questions/hypothesis to ensure they are testable and falsifiable. Writing research reports for submission to journals. How a manuscript/scientific paper differs from a report that the students are likely to be familiar with. Expectations for the report.
Data management and analysis: Species concepts – phylogenetic approaches to defining species. How to create phylogenetic trees. Handling DNA sequencing data. The importance of accession numbers and database curation (both for biological samples and data).
Practical sessions
These sessions provide the students with the opportunity to cement within the laboratory the understanding they gain in the ‘dry-lab’ sessions. Over the course of the semester the practical sessions encompass: inoculation of media with plant sections; isolation of endophytes; DNA extraction; PCR; PCR clean-up and sequencing; antimicrobial screening; use of reporter gene constructs. Students may, work at their own pace through these sessions, and with agreement they may undertake novel 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 completion140:0040:00Students prepare a project proposal for assessment
Guided Independent StudyAssessment preparation and completion54:0020:00No more marking exercise
Guided Independent StudyAssessment preparation and completion65:0030:00Reading prior to practicals
Guided Independent StudyAssessment preparation and completion120:0020:00Project Proposal
Guided Independent StudyAssessment preparation and completion120:0020:00short presentation
Guided Independent StudyDirected research and reading33:009:00Find and read material prior to workshops
Scheduled Learning And Teaching ActivitiesPractical64:0024:00Practical sessions
Guided Independent StudyDirected research and reading115:0015:00PC Cluster Follow Up
Scheduled Learning And Teaching ActivitiesWorkshops12:002:00PC Cluster for phylogenic analysis exercises
Scheduled Learning And Teaching ActivitiesWorkshops102:0020:00Introduction lecture & seminars with mixed exercises.
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.

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
Report2M5Project proposal - students provide a 500-word proposal for the work they intend to undertake in the subsequent lab sessions
Prof skill assessmnt2M20Observation of practical skills
Prof skill assessmnt2M15Student-led marking exercise (NMM). 5 exercises of equal weight to assess ability to judge writing and figure preparation skills.
Report2M60A 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 (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 (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 Supporting Information appended to the final report and 15% assessed through a no more marking exercise for writing and presentation skills.
3. Final report (60%) - 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