Module Catalogue 2024/25

Pre Requisite Comment

N/A

Co Requisite Comment

N/A

Aims

The module primarily aims to develop students' knowledge and hands-on experience in prokaryotic genomic science, enriching their understanding of microbial metabolism, diversity, structure, evolution, and the potential of microbes as a natural resource. It aspires to contribute to their development as independent researchers and to introduce the interdisciplinary nature of biological research.
Knowledge-based aims include key discoveries in genomic science; sequencing techniques, concepts and applications; and recognition and interpretation of connections between genotype and phenotype.
Skills-based aims include development of laboratory skills in microbiology, molecular biology and high-throughput DNA sequencing technologies (Oxford Nanopore technology); and bioinformatics skills in quality control, assembly, annotation, mining and phylogenomic inference of bacterial genome and metagenomic datasets;

Outline Of Syllabus

This is a student-led research module that combines practical learning through student-directed laboratory (wet and dry sessions) and inquiry-based learning in which posing questions, problems and scenarios related to genomic science are introduced by a facilitator and inquirers identify and research issues and questions to develop knowledge, or solutions.
The module consists of a series of workshops (including computer-based workshops) and student-driven practical sessions addressing two broad challenges: microbial diversity and functional genomics. An introductory workshop provide students with an overview to the concepts of student-led research and flipped learning. Students are then provided with information about the research goal i.e. genome sequencing and functional mining of bacterial plant endophytes. They are provided with details about the origin and preliminary data of provided endophytes and examples of biotechnological applications that rely on plant endophytes as well as insights into their ecology and metabolism. In the following workshops, students are introduced to sequencing technologies and hypothesis generation and experimental design in the field of genomics; and are encouraged to prepare and discuss their own research plans. After making a decision on their research direction, student-driven practical sessions in DNA extraction and purification, DNA library preparation and DNA sequencing are provided. Following those, students are provided with practical knowledge in genomic analysis and interpretation through workshops covering the topics:

•       Introduction to command line
•       Assembly and annotation of sequences
•       Genomic mining
•       Functional genomics
•       Metagenomics
•       Scientific writing –Genomic papers

All the workshops follow a flipped-classroom, active-learning model, with students working on the learning resources provided on Blackboard in their non-contact time (prior and after sessions) and on problem-solving and peer-discussion during the sessions. Those are designed to enable students to become familiar with the basic tools used for genomics and to develop their independent learning skills, teamwork and critical thinking. Ongoing formative feedback through dialogue with the academic facilitator is provided in each workshop and during practical sessions.

Intended Knowledge Outcomes

By the end of the course, students will be able to:
a. apply high-throughput DNA sequencing technologies in the field of microbial systematics, microbial ecology
and biotechnology.
b. recall, explain and apply the vocabulary used in genomics and molecular genetics of prokaryotes.
c. reconstruct and interpret microbial metabolism.
d. discuss techniques used to improve sequence assembly and annotation.
e. analyse, interpret and evaluate (meta)genomic data and establish genotype-phenotype links using standard
software packages.
f. Recognize, appreciate and evaluate practical implications of genomics studies, especially in the fields of
biotechnology, ecology and evolution.

Intended Skill Outcomes

By the end of the course, students will be able to:
a. demonstrate their ability in independent learning and teamwork.
b. collect and organise experimental results and analyse and interpret the data obtained
c. undertake independent practical research in the field of genomics.
d. create and interpret non-textual material.
e. apply theory into practise.
f. demonstrate critical and self-critical thinking.
g. search for, process and critically analyse information from a variety of sources.
h. communicate effectively scientific results in oral and writing formats.
i. produce data suitable for publication in research journals.

Teaching Rationale And Relationship

This module is designed to provide a pedagogical opportunity integrating hands-on research and core scientific competencies (i.e. experimental design, hypothesis generation, laboratory skills) with emerging next generation sequencing technologies to strengthen UG experiences in STEM education and contribute to their development as independent researchers.

Workshops based on problem-solving activities provide knowledge and help students develop awareness of key aspects of genomic science and critical analysis. Computer-based workshops gives students hands-on experience in analysing and genomic data interpretation.

Genomics is a rapidly evolving field – students are encouraged to read key papers from discovery and review journals to keep abreast of developments and to develop a critical appreciation of genomic science, its strengths and limitations. Private study prior sessions is therefore essential for students to fully understand and absorb material covered in workshops and to become familiar with genomic concepts, technologies and bioinformatics tools used for genome analysis and interpretation.

Assessment Rationale And Relationship

Summative assessments aim to assess different aspects of knowledge, understanding and integration of subject material obtained from workshops and practical sessions.
The research paper assess dry professional skills in sequencing and analysis of a bacterial genome and students' ability to interpret genomic data, in terms of technical limitations, genotype-phenotype correlations, evolutionary processes and potential biotechnological uses.
The practical/lab report assess general dry professional skills and students’ understanding in sequencing, assembly and annotation of a given genomic dataset.
Assessment lengths and required workload has been chosen to allow the students sufficient scope to explore and express the technical detail and the academic depth of the topics associated with the subject at this level and therefore to ensure they cover all learning outcomes associated.
Formative assessment and feedback are provided during sessions.

General Notes

Recommended Text Books
A list of recommended text books is provided in the Module Information folder on Blackboard site.

Further Help

If students identify problems which they cannot solve during their private study by reference to lecture notes, text books, etc., they should contact the Module Leader or lecturer by e-mail. If any student is experiencing great difficulty with the module they should request, by e-mail, an individual support session with the Module Leader.

Assessment Notes

To pass the assessment outright at the first attempt students must achieve 40% or more when all components of the assessment are combined together. Under certain circumstances students may “Pass by Compensation” with marks between 35 and 39%.