MSc Molecular Medicine

[15 Credits]

This module illustrates the connection between identifying a gene by its position, discovering single gene defects and investigating the function of genes and proteins.

• Detecting gene defects within the modern framework of the Human Genome Project
• Contemporary methods to study human gene function
• Source high-throughput databases from human and model species

This module will be assessed by an essay assignment.

Martin Nicklin
Module Leader
School of Medicine & Biomedical Sciences
Beech Hill Road
Sheffield
S10 2RX
Tel: +44 (0)114 215 9541
Email: m.nicklin@sheffield.ac.uk

2019/20 timetable

[10 Credits]

This module introduces you to recent developments in immunity and recombinant molecules that are used to modulate the human immune system therapeutically.

• Introduction to innate and adaptive immunity
• Control of immune responses
• Making recombinant proteins
• Examples of recombinant proteins as immune therapeutics
• New strategies for vaccine generation

Assessment will be by an assignment.

Dr Helen Marriott
Module Leader
School of Medicine & Biomedical Sciences
Beech Hill Road
Sheffield
S10 2RX
Email: h.m.marriott@sheffield.ac.uk

2019/20 timetable

[15 Credits]

This module offers you training in critical analysis of the literature and in writing a review of a field of work.

Learning aims:

In this module, students will develop a variety of scientific literacy skills such as effective bibliography searches, critical reading, essay planning and writing without inadvertently plagiarising sources. They will be expected to learn or improve these skills through practicing them under supervision.

In addition, students will learn specialised background scientific knowledge in the subject area of their future MSc laboratory project.

Module contents

The module starts at the beginning of October and ends at the beginning of February. It is split into 6 teaching and study periods, or calendar blocks. Each block focuses on the development or reinforcing of specific skills or on the completion of definite tasks.

The first three blocks are short periods of less than one week each in October and November. In this part of the module, learning of basic scientific literacy skills takes place mainly in taught sessions. The classes are a mix of lectures and tutorials in which students carry out bibliographical searches, essay planning and writing tasks.

In the second part of the module (Blocks 4 to 6, November to February), students will put to use the skills learned previously by writing a review of the scientific literature relevant to their research project. They will be expected to carry out a bibliographical research on the background to their MSc laboratory project and to write a review of the scientific articles that they will have read. The students will complete these tasks on their own but under guidance of their laboratory project supervisors, who will provide advice and feedback at two important stages in the preparation and writing of the review.

Assessment

The module will be assessed through the marking of the literature review, which the students will submit at the beginning of February.

The marking of the review will take in account the bibliographic searching and writing skills as well as the scientific knowledge and understanding of the topic.

Dr Lisa Parker
Module Leader
Department of Infection, Immunity and Cardiovascular Disease
School of Medicine
Beech Hill Road
Sheffield
S10 2RX
Tel: +44 (0)114 215 9544
Email:l.c.parker@sheffield.ac.uk

2019/20 timetable

[10 Credits]

This module  illustrates the principles underlying recent research that has uncovered genetic components in several common diseases.

• Genetics in cancer
• Genetics in cardiovascular diseases
• Genetics in endocrine disorders
• Genetics in arthritis
• Chromosomal disorders
• Genetics in coagulation disorders
• Genetics in neurological diseases
• Genetics in bone diseases
• Pharmacogenetics

Assessment will be by an assignment

Professor Sheila Francis
Module Leader
School of Medicine & Biomedical Sciences
Beech Hill Road
Sheffield
S10 2RX
Email: s.francis@sheffield.ac.uk

2019/20 timetable

[15 credits]

This module is a computer practical class, teaching you how to extract, manipulate and interpret DNA and protein sequence from public sources using web-based software.

The module is a practical guide to web-based sequence analysis.  We focus on human genes and web-based genome browsers.

You will learn:

• how to obtain and analyse genomic, mRNA and protein sequences
• how to compare individual data with public data
• ways to present sequences and sequence alignments
• to design primers for PCR for sequencing cDNA and genomic DNA
• to differentiate unknown from known variants in human sequences
• to impute functional similarity and loss of function from sequences
• to create simple bacterial expression clones
• to design tools (currenlty CAS9/CRISPR) to disrupt genes in cells

Assessment will be by a written assignment, divided into (probably ten) discrete tasks, based on an individualised set of data.  You will present the results of your analysis of your sequences, your proposals for discovering mutations and for manipulating specific DNA sequences.

Learning consists of discovering why these tasks are useful and how to do them.  I will give brief explanatory talks for each topic and provide an up-to-date booklet that explains how to do the tasks and their relevance.  Expert demonstrators will help you to learn how to perform the tasks.  You will work with shared practice data sets in 40 hours of computer classes.  We will encourage you to assemble into learning groups.

Dr Martin Nicklin
Module Leader, School of Medicine & Biomedical Sciences
Beech Hill Road
Sheffield
S10 2RX
Email: m.nicklin@sheffield.ac.uk

2019/20 timetable

[15 credits]

This module offers you training in essential laboratory operations, lab safety and etiquette, keeping records and statistical analysis.

This unit aims to introduce the student to the basic practical laboratory techniques that they will need to undertake a laboratory based MSc project in biomedical science.

The unit will involve training in safety, record keeping, the use of the common laboratory equipment, basic techniques and important principles. It will also include training and practice in common maths and statistics. The unit consists of lectures, tutorials, practical exercises, problem solving classes and self directed learning.

Dr Gareth Richards
Module Leader
School of Medicine & Biomedical Sciences
Beech Hill Road
Sheffield
S10 2RX
Email:g.richards@sheffield.ac.uk

[10 credits]

This module teaches you about how we investigate the abnormal molecular processes that lead to pathologically deviant cell biology.

How do failed molecular control pathways – all of which are features of cancer – contribute to cell proliferation, errors in DNA repair, loss of cell cycle control, and the loss of the essential pathways for cell suicide?

How are molecularly targeted therapies starting to transform treatment?

Dr Will English
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: w.english@sheffield.ac.uk

[10 credits]

This module will show you how genomics and proteomics are providing new ways of detecting important molecular-level defects in cancer cells.

Which new techniques and methodologies are currently revolutionising the molecular understanding of cancer? From classic tumour biology to the recent use of genomics and the even more recent use of proteomics, how can we identify the molecular lesions that are essential for the survival and progression of different cancers? We will use current examples to illustrate this approach and we will explore how insights from these studies can inform drug development.

Cyril Sanders
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: c.m.sanders@sheffield.ac.uk

[10 credits]

This module will illustrate to you how modern methods are being used to improve diagnosis of cancer and how new therapies are being designed.

How have molecular insights into cancer helped research? How can molecular oncology be used to improve screening programmes? How does it currently help in cancer diagnosis, treatment and prognosis? Can it yet be used to select treatments? Examples will illustrate novel molecular insights and you will learn about their clinical context.

Penny Ottewell
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: p.d.ottewell@sheffield.ac.uk

[10 credits]

This module teaches you how to be involved in a scientific meeting, make a presentation and organise a description of your pathway-appropriate project.

This module is primarily designed to develop your skills on oral presentation and communication, both essential parts of your training as a research scientist. Another learning objective is that you will gain an appreciation of the enormous variety of research carried out here in the Medical School.

You will have 2 weeks to discuss your presentation with your research project supervisor and prepare a 20 minute presentation which includes:

• General background to the project and hypothesis being tested
• The hypothesis and aims of the project
• A description of the experimental techniques used
• A description and discussion of the results obtained so far
• Conclusions so far and clear details of future work

This module is placed 5 weeks after the start of the research projects, this is to ensure that you understand the nature of your research project and to prepare you with the necessary skills for giving a lab meeting presentation / seminar during your time with the research group. It is not expected that you will have lots of data to show at this point, and you will not be marked or assessed in any way on the number of results you have. However it is expected that you understand why you have done the work you are presenting and understand and explain the future direction of your project.

Lisa Parker
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: l.c.parker@sheffield.ac.uk

[60 credits]

This module introduces you to doing science; working on your own project, with supervision, in a research laboratory.

This module is central to the entire course. You will learn how to plan, execute and analyse the results of experiments and how to progress from one set of experiments to another.

Your achievement as well as your research skills, including your technical ability in the laboratory and your ability to interpret and critic your own results in this module is assessed by the quality of your thesis (up to 100 pages) which is submitted at the end of the module.

The assessment is based upon the scientific background, results, analysis and interpretation of the data in the discussion and the presentation of the thesis.

You will be supervised by a competent active laboratory scientist. You will also meet with assigned Personal Tutors who will check that your work is progressing satisfactorily.

Rachid Tazi-Ahnini
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Tel: +44 (0)114 215 9556 Email: r.taziahnini@sheffield.ac.uk

[15 credits]

This module teaches the analytical and practical skills to understand how proteins function through their interactions with other gene products and how drugs are designed to interfere specifically with certain interactions and not others.

How do gene products interact with one another?

How do coding mutations affect these interactions?

Why are drugs effective in some individuals and not others?

Answering these questions requires the ability to visualize and analyse interactions between proteins and other biological molecules at a molecular level.

This module will equip students with the analytical and practical skills to understand how proteins function through their interactions with other molecules. Students will learn to analyse molecular interactions using advanced molecular graphics and docking software and to apply this knowledge to the analysis of molecular interactions and the design of drug-like molecules.

The module will be delivered and assessed largely through computer laboratory-based sessions, private study and a small number of seminars. Topics will include the visualisation and manipulation of biological molecules in 3D, sequence and structure alignments, inference of function from sequence, structure prediction, analysis of molecular interactions, predicting the effect of mutation and computer assisted drug design.

Jon Sayers
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Tel: +44 (0)114 215 9552
Email: j.r.sayers@sheffield.ac.uk

[15 credits]

This module focuses on the theories and software tools for understanding the regulatory mechanisms that control the expression and function of genes, both individually and as component of co-ordinated gene networks.

Objectives

Students will be able (1) To suggest ways in which the biological relevance of genes can be tested.  (2) To apply a detailed understanding of the function of a sequence.  (3) To design in outline experiments that can be used to test for the interaction of molecules within biological systems.  (4) To analyse data to uncover putative gene interactions.  (5) To create and analyse simple meaningful computer models of gene interations.

The Assessment

This will be distributed on the final day of teaching.  The work on Section C will start in class on day 3.

Section A

30% of the assignment marks will come from a task set by Professor Nick Monk and Dr Alex Fletcher (Stats and Maths).  This will involve an exercise in using network modelling software to simulate a hypothetical drug treatment outcome.  It will test you ability to construct models similar to those that you will have been shown in class.

Section B

35% of the assignment marks will come from analysing an individual data set from a real RNA-seq study.  You will identify genes that appear to have been modulated by the treatment regime and you will use gene ontology and network tools to identify significant genes, processes and interactions.

Section C

35% of the mark will be for preparing a PowerPoint presentation on your investigation of the significance of an apparent anomaly in the "Central Dogma" of Molecular Biology.

Dr Martin Nicklin
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX

Tel: +44 (0)114 215 9541
Email: m.nicklin@sheffield.ac.uk

[10 credits]

This module teaches you how to be involved in a scientific meeting, make a presentation and organise a description of your pathway-appropriate project.

This module is primarily designed to develop your skills on oral presentation and communication, both essential parts of your training as a research scientist. Another learning objective is that you will gain an appreciation of the enormous variety of research carried out here in the Medical School.

You will have 2 weeks to discuss your presentation with your research project supervisor and prepare a 20 minute presentation which includes:

This module is placed 5 weeks after the start of the research projects, this is to ensure that you understand the nature of your research project and to prepare you with the necessary skills for giving a lab meeting presentation / seminar during your time with the research group. It is not expected that you will have lots of data to show at this point, and you will not be marked or assessed in any way on the number of results you have. However it is expected that you understand why you have done the work you are presenting and understand and explain the future direction of your project.

Lisa Parker
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: l.c.parker@sheffield.ac.uk

[60 credits]

This module introduces you to doing science; working on your own project, with supervision, in a research laboratory.

This module is central to the entire course. You will learn how to plan, execute and analyse the results of experiments and how to progress from one set of experiments to another.

Your achievement as well as your research skills, including your technical ability in the laboratory and your ability to interpret and critic your own results in this module is assessed by the quality of your thesis (up to 100 pages) which is submitted at the end of the module.

The assessment is based upon the scientific background, results, analysis and interpretation of the data in the discussion and the presentation of the thesis.

You will be supervised by a competent active laboratory scientist. You will also meet with assigned Personal Tutors who will check that your work is progressing satisfactorily.

Rachid Tazi-Ahnini
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Tel: +44 (0)114 215 9556
Email: r.taziahnini@sheffield.ac.uk

[10 credits]

This module illustrates with recent examples how you can now investigate important molecular changes that occur in disease states and investigate their significance in pathogenesis.

Molecular and cellular pathways that are modified by diseases

• Cell growth
• Apoptosis and necrosis
• Cell migration in inflammation and cancer
• Endocrine signalling

Methodology

• Identification of functional proteins
• Experimental modulation of genes
• Biological imaging systems

Helen Marriott
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: h.m.marriott@sheffield.ac.uk

[10 credits]

This module teaches you by example how disease processes are modelled in appropriate systems.

This is an example-led module that introduces you to some of the model systems that can be used to understand pathological processes and test potential therapeutic agents. Systems studied go from simple in vitro human cell systems, through invertebrate models to the use of complex mammals. The advantages, disadvantages, capabilities, costs and ethics of each system will be discussed.  This module will also allow you to gain hands on practical skills.

• Introduction to model systems for human disease processes.
• Cell/Tissue Culture
• Innovative imaging systems
• Flow cytometry
• Human in vitro cell systems
• Non-mammalian models - Fruitfly (Drosophila melanogaster); Zebrafish (Danio rerio)
• Mammalian models

Lynne Prince
Module Leader (Deputy Module Lead: Iwan Evans)
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: l.r.prince@sheffield.ac.uk

[10 credits]

This module introduces you to how novel therapeutic strategies are translated from experimental models into marketable treatments.

This is an example-led module demonstrating the route from a laboratory-tested concept for a therapeutic agent to the development of a drug by the pharmaceutical industry.

• delivery routes for therapeutic agents
• Developing new Biotech agents
• Patenting new therapeutic agents
• Spinning out a Biotech company
• Pharmacokinetics
• The ethics of clinical trials
• Design of clinical trials and their interpretation
• Drug development by the pharmaceutical industry
• A worked example in translational medicine/ therapy of motor neurone disease

Jon Sayers
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Tel: +44 (0)114 215 9552
Email: j.r.sayers@sheffield.ac.uk

[10 credits]

This module teaches you how to be involved in a scientific meeting, make a presentation and organise a description of your pathway-appropriate project.

This module is primarily designed to develop your skills on oral presentation and communication, both essential parts of your training as a research scientist. Another learning objective is that you will gain an appreciation of the enormous variety of research carried out here in the Medical School.

You will have 2 weeks to discuss your presentation with your research project supervisor and prepare a 20 minute presentation which includes:

• General background to the project and hypothesis being tested
• The hypothesis and aims of the project
• A description of the experimental techniques used
• A description and discussion of the results obtained so far
• Conclusions so far and clear details of future work

This module is placed 5 weeks after the start of the research projects, this is to ensure that you understand the nature of your research project and to prepare you with the necessary skills for giving a lab meeting presentation / seminar during your time with the research group. It is not expected that you will have lots of data to show at this point, and you will not be marked or assessed in any way on the number of results you have. However it is expected that you understand why you have done the work you are presenting and understand and explain the future direction of your project.

Lisa Parker
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: l.c.parker@sheffield.ac.uk

[60 credits]

This module introduces you to doing science; working on your own project, with supervision, in a research laboratory.

This module is central to the entire course. You will learn how to plan, execute and analyse the results of experiments and how to progress from one set of experiments to another.

Your achievement as well as your research skills, including your technical ability in the laboratory and your ability to interpret and critic your own results in this module is assessed by the quality of your thesis (up to 100 pages) which is submitted at the end of the module.

The assessment is based upon the scientific background, results, analysis and interpretation of the data in the discussion and the presentation of the thesis.

You will be supervised by a competent active laboratory scientist. You will also meet with assigned Personal Tutors who will check that your work is progressing satisfactorily.

Rachid Tazi-Ahnini
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Tel: +44 (0)114 215 9556
Email: r.taziahnini@sheffield.ac.uk

[10 credits]

This module will begin with a few lectures that aim to cover important ways in which the host immune system defends against pathogens. This will serve as an extension of the immunology material introduced in the core modules and is essential for a full understanding of the variety of mechanisms pathogens use to evade or subvert host defences. The module will then proceed to discuss the virulence mechanisms of some important pathogenic viruses, fungi and protozoans.

Dr Helen Marriott
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email:  Dr Helen Marriott

[10 credits]

The major aim of this module will be to provide a broad explanation of the multi-faceted nature and complexity of bacterial pathogenicity. It will explain that pathogenicity is not just down to the expression of a particular toxin, but bacteria have developed very elegant and complex processes through which they colonise a host and cause disease. The module will use a step by step approach using some of the main models and paradigms of how bacteria are able to colonise the host and cause disease at a mechanistic level.

Here are the quiz answers!

Dr Jon Shaw
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Tel:  44 (0) 114 215 9553
Email:  Dr J G Shaw

[10 credits]

The overall aim of this module will be to raise awareness of, and convey, the principles underlying the expanding arsenal of experimental approaches that are currently being employed to (i) identify virulence genes,
(ii) elucidate the molecular mechanisms underlying their genetic control, (iii) characterise their protein products both in terms of their structure and function at the molecular level, and (iv) unravel the molecular mechanisms by which virulence proteins are targeted to host cells or the extracellular milieu.

Dr Mark Thomas
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Tel:  44 (0) 114 226 1227
Email:  Dr Mark Thomas

[10 credits]

This module teaches you how to be involved in a scientific meeting, make a presentation and organise a description of your pathway-appropriate project.

This module is primarily designed to develop your skills on oral presentation and communication, both essential parts of your training as a research scientist. Another learning objective is that you will gain an appreciation of the enormous variety of research carried out here in the Medical School.

You will have 2 weeks to discuss your presentation with your research project supervisor and prepare a 20 minute presentation which includes:

• General background to the project and hypothesis being tested
• The hypothesis and aims of the project
• A description of the experimental techniques used
• A description and discussion of the results obtained so far
• Conclusions so far and clear details of future work

This module is placed 5 weeks after the start of the research projects, this is to ensure that you understand the nature of your research project and to prepare you with the necessary skills for giving a lab meeting presentation / seminar during your time with the research group. It is not expected that you will have lots of data to show at this point, and you will not be marked or assessed in any way on the number of results you have. However it is expected that you understand why you have done the work you are presenting and understand and explain the future direction of your project.

Lisa Parker
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Email: l.c.parker@sheffield.ac.uk

[60 credits]

This module introduces you to doing science; working on your own project, with supervision, in a research laboratory.

This module is central to the entire course. You will learn how to plan, execute and analyse the results of experiments and how to progress from one set of experiments to another.

Your achievement as well as your research skills, including your technical ability in the laboratory and your ability to interpret and critic your own results in this module is assessed by the quality of your thesis (up to 100 pages) which is submitted at the end of the module.

The assessment is based upon the scientific background, results, analysis and interpretation of the data in the discussion and the presentation of the thesis.

You will be supervised by a competent active laboratory scientist. You will also meet with assigned Personal Tutors who will check that your work is progressing satisfactorily.

Rachid Tazi-Ahnini
Module Leader
University of Sheffield Medical School
Beech Hill Road
Sheffield
S10 2RX
Tel: +44 (0)114 215 9556
Email: r.taziahnini@sheffield.ac.uk