BIO3019 : Genomics
- Offered for Year: 2019/20
- Module Leader(s): Dr Maria Del Carmen Montero-Calasanz
- Lecturer: Professor Frank Sargent, Dr Jon Marles-Wright, Dr James Stach
- Owning School: Natural and Environmental Sciences
- Teaching Location: Newcastle City Campus
|Semester 1 Credit Value:||10|
The module aims are to develop students' knowledge of Prokaryotes genomic science, including its key discoveries, concepts and applications, and to recognise and interpret connections between genotype and phenotype.
Outline Of Syllabus
Lectures will cover the following topics:
• Introduction to the course and History of prokaryotic genome
• Insight of prokaryotes genetics
• How to sequence, assemble and annotate a genome
• Genome mining
• From genome to phenome
• Prokaryote genome evolution
• Evolutionary and comparative genomics
The aims of these practical sessions is to give students first-hand experience in structural, functional and comparative genomics gaining practical understanding of the basic tools used for genome mining, genome evolution, connections between genotype and phenotype and potential biotechnological applications.
The practical sessions are designed to enable students to become familiar with working with the basic tools used for genome mining and develop their independent learning skills, teamwork and their critical thinking. Those follow a student-centred learning approach, it is therefore expected that students be active part and responsible in their own learning and with their own pace of learning.
During the first practical session, students will learn how to use and interpret the basic tools used for genome mining by working on guided self-study exercises. Students will be allocated in pairs in the computer cluster and provided with a handbook (containing general information about practical sessions, lab assessment details, a microbial genome analysis tutorial and a glossary of terms), the worksheets and a document detailing what is expected to include in the final report (all of them can also be downloaded from Blackboard). During the session students are encouraged to work on your own pace in the proposed exercises. Support and formative feedback will be provided.
During the second and third practical sessions it is expected students work on their assigned bacterial genomes applying the knowledge and practical skills already acquired in the first session. The bacterial genomes assignations will be advertised on Blackboard after the first practical session. In these sessions, students will be allocated in groups working on the same set of genomes. During the session students are encouraged to work as a team, i.e. planning the research, distributing tasks to minimise the individual workload, sharing ideas, solving problems, etc. Support and formative feedback will be provided in both sessions.
A Discussion Board forum will be created on Blackboard to share and discuss ideas inter/intra groups and solve doubts related to genome mining tools and the final report. The forum will be organised by threads around each set of genomes and general thread for sharing ideas inter-groups and general clarifications. The forum will be moderated by the module leader.
A seminar will be delivered to cover genome mining in practical terms.
|Guided Independent Study||Assessment preparation and completion||1||0:30||0:30||Self and peer assessment|
|Guided Independent Study||Assessment preparation and completion||1||2:00||2:00||Practical worksheet|
|Guided Independent Study||Assessment preparation and completion||1||38:00||38:00||Practical Report|
|Scheduled Learning And Teaching Activities||Lecture||10||1:00||10:00||N/A|
|Guided Independent Study||Assessment preparation and completion||1||1:00||1:00||MCQs Exam|
|Guided Independent Study||Assessment preparation and completion||10||0:30||5:00||Exam Revision|
|Scheduled Learning And Teaching Activities||Practical||3||3:00||9:00||Computer practicals|
|Scheduled Learning And Teaching Activities||Workshops||1||0:30||0:30||Seminar|
|Guided Independent Study||Independent study||1||20:00||20:00||Student selected study of lectures, recap, blackboard, websites, etc. to enhance understanding|
|Guided Independent Study||Independent study||1||4:00||4:00||Practical follow up|
|Guided Independent Study||Independent study||10||1:00||10:00||Routine lecture follow up to identify areas requiring further more detailed study.|
Teaching Rationale And Relationship
Lectures impart knowledge and help students develop awareness of key aspects of genomic science. The computer practical gives students supervision and guidance in analysing genomic data. Genomics is a rapidly evolving field – students will be 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 is necessary for students to absorb information presented in lectures and for self-assessment, to deepen their knowledge and understanding through directed reading, to become familiar with the web and its resources for genome analysis, and to complete the computer analysis.
The format of resits will be determined by the Board of Examiners
|Practical/lab report||1||M||50||lab report on analysis of genomic data (1500 words)|
|Practical/lab report||1||M||10||Practical Worksheet|
|Reflective log||1||M||10||Self and Peer assessment|
Assessment Rationale And Relationship
The exam assesses knowledge, understanding and integration of subject material obtained from lectures and additional reading. The computer practical report tests students' ability to analyse and interpret genomic data, correlate genotype-phenotype and hypothesise potential biotechnological uses of genomes. The report length 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.
Study Abroad students may request to take their exam before the semester 1 exam period, in which case the format of the paper may differ from that shown in the MOF. Study Abroad students should contact the school to discuss this.