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Module MSE-4084:
Genomics & Infectious Disease

Module Facts

Run by School of Medical Sciences

15 Credits or 7.5 ECTS Credits

Semester 1 & 2

Organiser: Dr David Pryce

Overall aims and purpose

From this module the student will understand how genomics can be used to provide more accurate diagnosis, predict which drugs are likely to be more effective and monitor treatment and control of infectious disease in individuals and populations.

Course content

  • Infection as a cause of national and global morbidity and mortality
  • Transmission of human infections: person to person, food and waterborne, sexually transmitted, vector-borne
  • Prokaryotes, their genome, replication and population genetics
  • Genomic characterisation of viruses: DNA and RNA genomes, single-stranded, double stranded, segmented
  • Genomic comparisons of microbial strains in the context of outbreaks and transmissions in hospitals and the community
  • Anti-infective drug action
  • Mutation rate & drug resistance
  • Genomic evidence of individual susceptibility to specific infection
  • Role of genomics in: infectious disease diagnosis, prognosis, drug selection, resistance, monitoring, epidemic control, drug research.

Assessment Criteria

good

Merit (B- to B+) (range 60-69%)

Primary criteria Good students demonstrate strong knowledge & understanding of most but not all of the subject area. Limited evidence of background study. The answers are focussed with good structure. Arguments are presented coherently, mostly free of factual/computational errors. Some limited original interpretation. Well know links between topics are described. Problems are addressed by existing methods/approaches. Good presentation with accurate communication

Secondary Criteria

B+ Good

  • Exceeds expectations for most primary criteria
  • Command of subject but with gaps in knowledge
  • Some ideas/arguments original

B Mid-level

  • Meets all primary criteria
  • Strong factual knowledge and understanding
  • Ideas/arguments are well presented by few are original

B- Meets requirements of class

  • Meets most but not all primary criteria
  • Strong factual knowledge with minor weaknesses in understanding
  • Most but not all ideas/arguments are well presented and few are original

threshold

Pass (C- to C+) (range 50-59%)

Primary criteria A pass level demonstrates knowledge and comprehension of key areas & principles, with understanding of the main elements of the subject area, although gaps and weaknesses in the argument are evident. No real evidence of background study and wider reading is evident. Answers are focussed on questions but also with some irrelevant material and weaknesses in structure & argument. Answers have several factual/computational errors. Lack of originality and interpretation. No links between topics are described. Limited problem solving skills. Some weaknesses in presentation accuracy & delivery.

Secondary Criteria

C+ Good within the class

  • Exceeds expectations for some primary criteria
  • Strong factual knowledge with some weaknesses in understanding
  • Ideas/arguments are limited but are well presented

C Mid-level

  • Matches all primary criteria
  • Moderate factual knowledge with some weaknesses in understanding
  • Ideas/arguments are limited presented with weaknesses in logic/presentation

C- Meets requirements of class

  • Matches most but not all primary criteria
  • Moderate factual knowledge with several weaknesses in understanding
  • Ideas/arguments are limited presented with weaknesses in logic/presentation

excellent

Distinction (A- to A) (range 70-100%)

Primary criteria Comprehensive knowledge & detailed understanding. Clear evidence of extensive background study & originality. Highly focussed, relevant and well structured answers. Arguments logically presented and defended with evidence and examples. Excellent presentation skills with very accurate communication.

Secondary Criteria A Outstanding

  • Exceeds expectations for most primary criteria
  • Complete command of subject and other relevant areas
  • Ideas/arguments are highly original

A+ Excellent

  • Exceeds expectations for some primary criteria
  • Complete command of subject
  • Ideas/arguments are highly original

A Good - Meets all primary criteria - Command of subject but with minor gaps in knowledge areas - Ideas/arguments are mostly original

A- Meets requirements of Class

  • Meets most but not all primary criteria
  • Complete command of subject but with some gaps in knowledge
  • Ideas/arguments are mostly original

Learning outcomes

  1. Demonstrate an in-depth knowledge of and explain the differences between prokaryote and eukaryote genomes

  2. Evaluate how sequencing of the genome of infective organisms can be used in infectious disease for assessing: diagnosis, sub-classification & strain identity, pathogenicity, drug resistance and drug selection; and for epidemic control.

  3. Critique the molecular basis of organism drug resistance in some infections and how this directs drug research

  4. Discuss and appraise how the genome sequence of pathogens can be used to track cross infection and outbreaks of infections among the population

  5. Review the emerging action of drugs in controlling infection e.g. HIV, TB

Assessment Methods

Type Name Description Weight
Report 35
Essay or coursework 65

Teaching and Learning Strategy

Hours
Private study
  • Self-directed study to develop in-depth knowledge and understanding, data processing/analysis and assessment preparation
126
Lecture
  • Lecture Lecture sessions will be held through first week of delivery period.
  • Lectures will be delivered in 4 x 3hr sessions, on days 1, 2, 3 and 4 of the teaching week
12
Seminar
  • Seminars sessions will present posters, or formal oral presentations or flash talks
  • Sessions will be delivered via 2 x 1.5hr sessions, on day 5 of the teaching week
3
Practical classes and workshops
  • Laboratory (wet lab), computer sessions or workshops.
  • Sessions will be delivered through first week of delivery period in 2 x 3hr sessions, on days 2 and 4 of the teaching week
6
Tutorial
  • Tutorials may vary in length, be conducted via individual or groups sessions and may utilise online conference facilities.
  • Timing are expected to be held within week 2 and 3 of the module (self study period).
  • Tutorial topics may be from any area of the module, including assessments, and/or from self-researched outside reading.
  • Students will supply topics for discussion and review.
3

Transferable skills

  • Literacy - Proficiency in reading and writing through a variety of media
  • Numeracy - Proficiency in using numbers at appropriate levels of accuracy
  • Computer Literacy - Proficiency in using a varied range of computer software
  • Self-Management - Able to work unsupervised in an efficient, punctual and structured manner. To examine the outcomes of tasks and events, and judge levels of quality and importance
  • Exploring - Able to investigate, research and consider alternatives
  • Information retrieval - Able to access different and multiple sources of information
  • Inter-personal - Able to question, actively listen, examine given answers and interact sensitevely with others
  • Critical analysis & Problem Solving - Able to deconstruct and analyse problems or complex situations. To find solutions to problems through analyses and exploration of all possibilities using appropriate methods, rescources and creativity.
  • Safety-Consciousness - Having an awareness of your immediate environment, and confidence in adhering to health and safety regulations
  • Presentation - Able to clearly present information and explanations to an audience. Through the written or oral mode of communication accurately and concisely.
  • Teamwork - Able to constructively cooperate with others on a common task, and/or be part of a day-to-day working team
  • Mentoring - Able to support, help, guide, inspire and/or coach others
  • Caring - Showing concern for others; caring for children, people with disabilities and/or the elderly
  • Management - Able to utilise, coordinate and control resources (human, physical and/or financial)
  • Argument - Able to put forward, debate and justify an opinion or a course of action, with an individual or in a wider group setting
  • Self-awareness & Reflectivity - Having an awareness of your own strengths, weaknesses, aims and objectives. Able to regularly review, evaluate and reflect upon the performance of yourself and others
  • Leadership - Able to lead and manage, develop action plans and objectives, offer guidance and direction to others, and cope with the related pressures such authority can result in

Resources

Resource implications for students

None foreseen

Reading list

PGT (level 7). A literature reading list will predominately be peer reviewed papers. The list will be dynamic and populated when module is active. Journals that are currently not available for direct access, will require digitising.