2020-2021 Biomedical Sciences Options - Course Details

Biomedical Sciences Options – 2020-2021, Semester 2
Title: BIOL5238 – Animal Models of Disease

Credits: 10
Course Coordinator: Prof Margaret Harnett
Course Duration: 3 Weeks (Weeks 29-31)
Programmes Applicable
• MSc in Immunology and Inflammatory Disease, Optional

• MSc Infection Biology, Optional
• MSc Biomedical Sciences, Optional
Course Description
The course aims to provide students with a critical understanding of the technologies and techniques used to
develop animal models of human inflammatory and infectious disease. Students will understand the place of
animal models in exploring disease pathogenesis and therapy, and will discuss the ethical issues relating to
the use of animals in medical research.
Course Aims
The course aims to provide students with the opportunity -
• To develop an understanding of comparative anatomy and the technical approaches used in
evaluating and developing animal models of disease (e.g. imaging, transgenesis, polyomics, flow
cytometry)
• To develop a working knowledge of animal models of human inflammatory and infectious diseases
• To discuss the ethical basis for the use of animals in medical research and role of animal models in
drug discovery and development.
Intended Learning Outcomes
By the end of this course students will be able to:
• Explain the anatomy of the immune response in relevant animal models;
• Discuss technologies used in the development of new animal models for human inflammatory and
infectious diseases;
• Critically evaluate recent developments in analytical approaches, such as imaging, cytometry and
‘omics and their impact on the value animal models of disease;
• Critique widely used animal models of human inflammatory (e.g. rheumatoid arthritis, Crohn’s
disease, multiple sclerosis, asthma) and infectious disease (e.g. malaria);
• Critically review how animal models have provided insight into the critical points in pathogenesis of
inflammatory and infectious disease;
• Critically review the contributions of animal models within the drug discovery and development
process;
Course Summative Assessment
Report (100%): Students will be provided with relevant papers on the use of a particular animal model of
infectious or inflammatory disease. They will individually produce a report (2000 words max) critiquing the
approaches and techniques used and suggesting improvements, for example in terms of the principles of the
3Rs, the question being addressed, and the quality of the data derived.
Page 1
Title: BIOL5199 – Current Trends and Challenges in Biomed Research & Health
Credits 10
Course Coordinator: Dr Kirsty Hacking
Course Duration: 3 Weeks (Weeks 29-31)
MSc in Infection Biology, Optional MSc Biomedical Sciences, Optional

MSc in Immunology and Inflammatory Disease,
Optional
Course Description
During this course students will select a current topical issue in biomedical research or health, and working in
small groups, will critically research the topic, develop a plan to address the challenge, and present their
research and conclusions as a poster.
Course Aims
The course aims to provide students with an opportunity to research a current topical issue or challenge of
their choice in biomedical research or health. Students will select an area of recent global or national
importance, and working in groups, will plan and perform research of the scientific background of the issue,
analysing and synthesising the available information to draw conclusions, and/or develop possible solutions
to the issue.
By the end of this course, students will be able to:
• select and critically investigate a current topical issue or challenge in biomedical research or health;
• critically analyse, evaluate and summarise the literature and other factual information on the
current topical issue or challenge;
• develop and appraise solutions to resolve, control or contain the current challenge, or explanatory
hypotheses and plans for further research, as appropriate to the topic chosen;
• summarise and present their conclusions in poster form in a style appropriate for a target audience
of stakeholders, end-users or the general public;
• work effectively in autonomous groups, and reflect critically on their role and performance within
the group
• Students are assessed individually with a reflective portfolio, summarising their participation and
contribution to the group work, and an assessment of the skills developed during the course (30%).
• Each group of students is assessed through a poster showing the results of their research, and their
solutions to resolve, control or contain the current challenge, or explanatory hypotheses and plans
for further research, as appropriate to the topic chosen. The poster will be aimed at a specific and
appropriate target audience (e.g. stakeholders, public health officials, general public) (70%). A group
mark will be awarded for the poster that is the same for all students in the group.
Co-requisites/Excluded Courses
None
Page 2
Title: BIOL5303 – Endocrinology in Health and Disease

Credits: 10
Course Coordinator: Dr Michelle Bellingham/Dr Michelle Welsh
Course Duration: 3 Weeks (29-31)
• MSc Biomedical Sciences

Course Description
The course will discuss the importance of hormones in coordinating and regulating normal physiology and
how this can be altered in disease states. This will require integrating knowledge, skills and basic concepts
from a variety of disciplines including physiology, pharmacology and anatomy. Students will discuss how the
endocrine system can be used to develop new clinical therapies. .
Course Aims
The aim of this course is to provide insight into how the endocrine system regulates the body in health and
disease. Students will learn to critically evaluate published data surrounding current research and clinical
practice in the field and appraise the current research and strategies.
• Give detailed explanations of normal endocrine anatomy and physiology.
• Critically discuss how the endocrine system is altered in examples of diseased states.
• Critically evaluate current research and/or clinical therapies in endocrinology.
• Design possible strategies for utilising the endocrine system to develop new therapies
• Paper Analysis and lay summary – 30% (350 words approx.)

• Written Assignment – 70%
Page 3
Title: BIOL5354 – Bioinformatics using R for Biologists
Credits: 10
Course Coordinator: Dr Kirsty Hacking/Dr John Cole

• MSc Cardiovascular Science, Optional
• MSc Precision Medicine, Compulsory
Course Description
This course will provide life sciences students with an introduction and practice in bioinformatic data
analysis with a focus on programming in R.
Course Aims
This course aims to introduce students to bioinformatic data processing with a focus on R programming,
using a common package and statistical analysis. This course will introduce the basics of cleaning data and
the general qualities of small/big, and low/high dimensional data. This course will provide practice in using
these methods to provide a foundation understanding for future project and industry placements
• Demonstrate fundamental principles of coding in R, with particular focus on manipulating large files,
statistical analysis and generating plots.
• Demonstrate a critical awareness of how omic and clinical datasets are generated, processed, quality
controlled, cleaned and corrected.
• Critically explore and communicate the biological results from big and high dimensional datasets
using statistics and visualisation techniques appropriate to their own field.
• Critically appraise omic and/or clinical data of a type that is now ubiquitous in biological research.
• Critically assess the role of bioinformatics in their own field
• Analysis of dataset– 80%

• Written assignment– 20%
Page 4
Title: BIOL5346 – Introduction to Next Generation Sequencing Bioinformatics
Credits: 10
Course Coordinator: Dr Thomas Otto
• MSc in Immunology and Inflammatory • MSc in Biotechnology, Optional

Disease, Optional • MSc Biomedical Sciences, Optional
• MSc in Infection Biology, Optional • MSc Stem Cells, Optional
Course Description
This course will provide students with a holistic understanding of bioinformatics and how it can be used to
analysis next generation sequencing data. The learnt skills will provide a good understand for future dry lab
project or to understand bioinformatics analysis. Also, the learnt skill set will be transferable, e.g.
visualization and abstraction of data.
Course Aims
The aim of this programme is to introduce the concepts of bioinformatics and give participants the
opportunity to understand and undertake next generation sequencing analysis
• Critically explain the use bioinformatics in life sciences
• Use of command line tools (Linux / R) to perform bioinformatics analysis
• Critically evaluate the step of quality control in next generation sequencing experiments
• Critically understand the visualization possibilities of next generation sequencing results
• Evaluate approaches to analysis genomic and transcriptomic experiments
• Critically discuss bioinformatics analysis in scientific publication
• Set exercise with short discussion of a genomic NGS dataset. Write up should be screenshots and a
short (100-500 words) discussion on the main findings. (33%.)
• Analysis of transcriptomics NGS data in Linux and R. Students need to quality control the NGS data,
map them in Linux, analysis them in R in two different manners and finally discuss the results by
comparing the results to data presented in the lectures. Write up can be screenshots (with short
description) of the different steps and around 500-1000 words to discuss the findings. (66%)
Page 5
Title: BIOL5200 – Technology Transfer & Commercialisation of Bioscience Research
Credits: 10
Course Coordinator: Dr Elaine Huston
• MSc in Infection Biology (including • MSc Biotechnology, Optional

specialisms), Optional • MSc Biotechnology & Management,
• MSc in Immunology and Inflammatory Optional
Disease, Optional • MSc Stem Cells for Regenerative
• MSc Biomedical Sciences, Optional Medicine, Optional
Course Description
During this course, students will evaluate the technology transfer of bioscience research and the
commercialisation of research ideas. Working in small groups, they will design and evaluate a market
research strategy and business plan for a small company planning to commercialise a recent bioscience
discovery.
Course Aims
This course aims to provide students with an opportunity to assess the nature of businesses based on
bioscience knowledge and research, their opportunities for innovation, and constraints related to regulatory
requirements, intellectual property and ethical issues and the market. Students will study a range of
biotechnology industry topics in depth, including the fundamental concepts of business structures, business
plans and models related to the biotechnology industry. In addition, they will evaluate the ethical, legal,
professional, and social issues raised by biotechnology.
• critically analyse and evaluate the fundamental concepts of business structures, business plans and
models related to the biotechnology industry;
• design and critically evaluate a market research strategy for a small company planning to
commercialise a recent bioscience discovery;
• draft a business plan for a small company involved in the commercialisation of a recent bioscience
discovery, including appropriate SWOT (strengths, weaknesses, opportunities & threats) and PEEST
(political, environmental, economic, societal, technical) analysis;
• evaluate and analyse data relating to the biotechnology industry and present research findings in the
form of written reports;
• summarise and present clear, well-constructed oral presentations and written reports on areas of
the biotechnology industry and specific biotechnology companies.
• Written Assignment including Essay (35%).

• Report (50%)
• Oral Assessment & Presentation (15%)
Page 6
Title: BIOL5291 – Neuroinflammation in Health & Disease
Credits: 10
Course Coordinator: Prof Jonathan Cavanagh
• MSc in Immunology and Inflammatory Disease, Optional

• MSc Brain Sciences, Optional
Course Description
Innate and adaptive immunity play central roles in nervous system development, as well as the pathogenesis
of many neurological and psychiatric diseases. The pathways involved not only provide targets for novel
therapeutics for diseases affecting the nervous system, but also new insights into fundamental mechanisms
involved in normal brain development and function. Students taking this course will be given opportunities
to study the research into the diverse roles of neuroinflammatory processes in health and disease and gain a
detailed understanding of their involvement in inflammatory, neurodegenerative and neuropsychiatric
disorders.
Course Aims
The specific aims of this course are:
• to enable students to evaluate critically research pertaining to the involvement of immune
mechanisms in nervous system development, homeostasis and repair
• to provide students with the opportunity to learn of how adaptive and innate immunity contribute
to the pathogenesis of inflammatory, neurodegenerative and neuropsychiatric diseases
• to provide students with the opportunity to learn how recent technical advances are used to
investigate innate and adaptive immunity within the nervous system
• summarise and critically evaluate research pertaining to the functional outcome of
neuroinflammatory mechanisms in the developing and adult nervous system
• critically evaluate how adaptive and innate immunity contribute to development and resolution of
specific neurological diseases
• critically appraise recent technical advances used to investigate innate and adaptive immunity within
the nervous system
Page 7
Title: BIOL5314 – Emerging Viruses
Credits: 10
Course Coordinator: Dr Sam Wilson
• MSc Infection Biology, Optional

• MSc Immunology and Inflammatory Disease, Optional
• MSc Stem Cells Engineering for Regenerative Medicine
Course Description
Emerging viral diseases of humans and animals such AIDS, influenza, MERS, Zika and Schmallenberg pose
significant threats to public health and food security. Understanding the factors that drive viral emergence is
essential to design proper intervention measures that aim to predict, prevent or control the emergence of
new epidemic viruses. This course will cover basic concepts of viral emergence, research approaches to
determine their underpinning mechanisms, as well as current topics in emerging viral diseases.
Course Aims
The specific aims of this course are:
• to provide students with fundamental knowledge and intellectual skills to critically analyse the
factors involved in viral emergence
• to give students up-to-date knowledge of the current burden of emerging viral diseases and the
methods employed to study and contain them

• critically analyse the factors that drive emergence of viral diseases in new host populations
• construct an overview of current emerging viruses and the threats they pose to humans and animals
• discuss the application of current technological developments in the study and containment of
emerging viruses
Page 8
Title: BIOL5197 – Omic Analyses for the Biomedical Sciences: From Genomics to Metabolomic
Credits: 20
Course Coordinator: Dr Richard Burchmore
• MSc Cancer Research & Precision • MSc in Biotechnology, Optional

Oncology, Optional • MSc (Med Sci) in Medical Genetics and
• MSc in Immunology and Inflammatory Genomics, Optional
Disease, Optional • MSc Biomedical Sciences, Optional
• MSc in Infection Biology (including • MSc Stem Cells, Optional
specialism), Optional
Course Description
An introduction to workflows for the resolution and characterisation of complex mixtures of biomolecules,
from DNA to small molecule metabolites. The course will emphasize the potential and challenges of omic
approaches and will include data handling tasks and demonstration.
Course Aims
The course aims to provide students with a critical understanding of a range of modern “omics” technologies
and applications. The course will introduce students to genomic, transcriptomic, proteomic and
metabolomic techniques, and the analytical approaches that can be employed to examine the data output
from these approaches. The relative benefits and challenges of each -omic approach will be presented, with
exemplar data sets. Examples of the application of omic approaches in a variety of relevant biological
systems will be presented, to give students an appreciation of the type of output generated and of typical
strategies for data analysis and interpretation.
• critically discuss information flow in biology, and evaluate the benefits of the different levels of omic
data collection;
• discuss challenges to omic data collection;
• evaluate strategies to characterise a genome/transcriptome/proteome/metabolome;
• critically evaluate and summarise workflows that are exploited to identify, quantify and characterise
molecules in a complex mixture;
• explain the importance of validating proteomic data, and evaluate strategies available to do this;
• compare and contrast data from different “-omic” data collection approaches (genomics,
transcriptomics, proteomics, metabolomics).
• Identify appropriate applications for different omic approaches.
• Design an experimental strategy to exploit an omic analysis
• Critically discuss the importance of controls and validation in ‘omics strategies’
• Produce effective written communication in the form of a grant application
Written Assignment including Essay (100%). Students will prepare a mock grant proposal of 3000-3200
words, to address a specified biomedical question, using a combination of omic and
reductionist/conventional approaches, and following a prescribed structure:
Page 9
Title: BIOL5261 – Bioimaging for Research Scientists

Credits: 20
Course Coordinator: Dr Francis Burton
• MSc Immunology & inflammation, • MSc in Biotechnology & Management,

Optional Optional
• MSc Infection Biology, Optional • MSc Bioinformatics
• MSc Biomedical Sciences, Optional • MSc Stem Cells Engineering for
• MSc in Biotechnology, Optional Regenerative Medicine
Course Description
An introduction to the science of imaging and image analysis in life sciences. The course includes lectures
and practical classes covering range of imaging modalities.
Course Aims
The course aims to provide students with both knowledge and practical skills in biological image analysis
(Bioimaging). Students will be introduced to a wide range of techniques and technologies for collecting
images of cells and biological tissues. Tuition will be given in the appropriate design of protocols and
appropriate methods of quantitative image analysis.
• Use ImageJ for 2D and 3D image processing and analysis.
• Design effective and appropriate imaging experiments and analysis protocols.
• Critically appraise the structure, capture and storage of digital images.
• Critically evaluate the use of fluorescent probes and issues surrounding their selection.
• Critically assess the advantages and disadvantages of different imaging modalities
Page 10
Title: BIOL5312 – Plant Biotechnology
Credits: 20
Course Coordinator: Dr Joel Milner

• MSc in Biotechnology, Optional
• MSc in Biotechnology & Management, Optional
Course Description
An introduction to the science of imaging and image analysis in life sciences. The course includes lectures
and practical classes covering range of imaging modalities.
Course Aims
The course aims to provide students with both knowledge and practical skills in biological image analysis
(Bioimaging). Students will be introduced to a wide range of techniques and technologies for collecting
images of cells and biological tissues. Tuition will be given in the appropriate design of protocols and
appropriate methods of quantitative image analysis.
• Use ImageJ for 2D and 3D image processing and analysis.
• Design effective and appropriate imaging experiments and analysis protocols.
• Critically appraise the structure, capture and storage of digital images.
• Critically evaluate the use of fluorescent probes and issues surrounding their selection.
• Critically assess the advantages and disadvantages of different imaging modalities
Page 11
Title: MED5425 – Clinical Genomics
Credits: 20
Course Coordinator: Prof Ed Tobias
• MSc in Genetic and Genomic Counselling • MSc Cancer Research and Precision Oncology
(compulsory) • MSc Biomedical Sciences
• MSc in Medical Genetics (option)
Course Description
This course will provide an overview of the clinical applications of genomic approaches to human disorders, particularly
in relation to clinical genetics, discussing the methods and capabilities of the new technologies. Tuition and hands-on
experience in data analysis will be provided, including the interpretation of next generation sequencing reports.
Course Aims
The aims of this course are to facilitate an understanding of the following topics:
• Structure and function of the human genome (e.g. enhancers, epigenetics, chromatin remodelling, non-coding
regions and the ENCODE project)
• Diagnostic analysis of the human genome (and exome and genome sequencing) – standard and high-
throughput technologies
• Clinical bioinformatics - making sense of the data (“PHREDs, PEDs and BEDs”), with practical hands-on
experience in data analysis and evaluating the pathogenicity of single nucleotide variants (SNVs).
• Terminology (e.g. PHRED scores, PED and BED files, BAM files, CRAM files, BCFs, VCFs, SNVs, CNVs, and many
more)
• Ethical aspects of whole genome analysis (including incidental findings)
• Stratified medicine & pharmacogenomics.

• Structure and function of the human genome
o Critically appraise what is known and what is not, including literature regarding transcriptional control
at a distance, epigenetics and chromatin remodeling.
o Critically discuss the purpose and implications of the ENCODE Project.
• Diagnostic analysis of the human genome
o Critically evaluate the purpose of current standard techniques (e.g. MLPA & aCGH) in comparison with
the new massively parallel sequencing techniques and technologies
o Critically discuss the capabilities and limitations of these available technologies
• Bioinformatics - making sense of the data:
o Demonstrate critical awareness of quality checks, trios and gene panel filtering (“PHREDs, PEDs and
BEDs”)
o Critically discuss the evaluation of variants using online prediction algorithms, based on
▪ biophysical amino acid properties (e.g. using Grantham matrix to examine molecular volume
and polarity) and
▪ evolutionary sequence conservation
• Stratified medicine & pharmacogenomics
o Critically discuss examples of effects of genomic variants upon:
o drug responses and
o adverse effects

Students will analyse and interpret clinical next generation sequencing data from patient investigations and then
generate a critical report of 2,000 words which presents their analysis in the context of relevant literature and provides
guidance on how the information should be presented to the patient (or their family) and to the referring clinician.
Page 12
Title: BIOL5342 – Immunotherapy and Precision Oncology

Credits: 20
Course Coordinator: Dr Laura Richmond / Dr Seth Coffelt

• MSc (Med Sci) in Medical Genetics and Genomics, Optional
• MSc Cancer Research and Precision Oncology, Optional
• MSc Immunology & Precision Oncology, Optional
• MSc Immunology & Inflammatory Disease, Optional
• MSc Stem Cells, Optional
Course Description
The course will enable the students to gain in depth knowledge on the use of state of the art ‘omic’
technologies in stratifying patients into prognosis and treatment groups, the use of personalised medicine,
latest targeted treatment regimens and the rapidly developing field of immunotherapy to target cancer.
Course Aims
This course aims to provide students with an in-depth knowledge and understanding of latest approaches in
treating cancer patients. It will explore the latest diagnostic techniques used to stratify patients for precision
medicine treatment approaches.
• Critical evaluate the use of precision oncology and its application for personalized medicine and
patient care;
• Critically discuss the use of targeted therapies used in the cancer field.
• Develop knowledge and expertise in immunotherapy strategies and their application in the cancer
field.
• Critically evaluate the literature and demonstrate scientific writing skills by effectively writing an
essay on one of the taught topics and gain skills in communicating with impact
• Compile a structured essay 2500-3000 words approx. (80%)

• Oral Presentation (20%)
Page 13

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Biomedical Sciences Options – 2020-2021, Semester 2

Title: BIOL5238 – Animal Models of Disease

• MSc in Immunology and Inflammatory Disease, Optional

MSc in Infection Biology, Optional MSc Biomedical Sciences, Optional

Title: BIOL5303 – Endocrinology in Health and Disease

• MSc Biomedical Sciences

• Paper Analysis and lay summary – 30% (350 words approx.)

• MSc Biomedical Sciences, Optional

• Analysis of dataset– 80%

• MSc in Immunology and Inflammatory • MSc in Biotechnology, Optional

• MSc in Infection Biology (including • MSc Biotechnology, Optional

• Written Assignment including Essay (35%).

• MSc in Immunology and Inflammatory Disease, Optional

• Written Assignment including Essay (100%).

• MSc Infection Biology, Optional

Intended Learning Outcomes

• Written Assignment including Essay (100%).

• MSc Cancer Research & Precision • MSc in Biotechnology, Optional

Title: BIOL5261 – Bioimaging for Research Scientists

• MSc Immunology & inflammation, • MSc in Biotechnology & Management,

• Written Assignment including Essay (100%).

• MSc Biomedical Sciences, Optional

• Written Assignment including Essay (100%).

Intended Learning Outcomes

Course Summative Assessment

Title: BIOL5342 – Immunotherapy and Precision Oncology

• MSc Biomedical Sciences, Optional

• Compile a structured essay 2500-3000 words approx. (80%)

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