Introduction

Welcome to the final year of your programme. One of the aims of the final year is to prepare you for the years ahead. The teaching will be structured differently, and you will be encouraged to work independently. We expect you to develop a breadth to your thinking and writing. This is the time to bring together knowledge gained during the past three years, looking for general principles which can be used productively. This mature approach should be expressed in your coursework, project report and examination answers. The key to success in final year is good time-management.

We recommend that you read this Course Information Document at the start of your final year.

In addition, there is important information about regulations, assessment and progression in the Life Sciences Handbook: Regulations & Advice; again, you should read this document at the start of the year and you must refer to it as necessary.

Please keep this Course Information Document for future reference after you graduate; you may need to provide course details for further study or other training.

While the information contained in the document is correct at the time of printing, it may be necessary to make changes. Check your online timetable, Moodle and your email messages regularly.

Final Year Structure

Component courses

The five component courses which make up the final year of your programme are:

1 x project or dissertation course (40 credits)

1 x the core course for your programme (20 credits)

3 x Honours options (3 x 20-credits)

Scheduling

Taught courses (core course and options)

Semester	Day	Course block	Suffix on Course Name
1	Monday	Core block	"…4X core"
1	Tuesday
1	Wednesday
1	Thursday
1	Friday	S1 option block	"…4Y option"
2	Monday	S2-A option block	"…4A option"
2	Tuesday	S2-B option block	"…4B option"
2	Wednesday	S2-E option block	"…4E option"
2	Thursday	S2-C option block	"…4C option"
2	Friday	S2-D option block	"…4D option"

Project

You should devote THREE days per week to the research phase of the project, normally all day Tuesday, Wednesday AM and all day Thursday during 10 weeks of Semester 1. The remaining half day can be undertaken Monday and/or Friday and/or Wednesday PM, depending on your own taught course timetable and the nature of your project.

Honours Options

You take three Honours options in total: one in Semester 1 and two in Semester 2.

The Semester 1 options are usually taught on Fridays, and you choose one option from the 4Y list.

Semester 2 options are arranged in five blocks, one for each day of the week (4A, 4B, 4C, 4D and 4E options). You choose two options from these five blocks, but no more than one for any block.

Once enrolment opens in August, you choose the options that you wish to study in final year. Please note that the list of offered Honours options changes slightly each year as options are introduced, withdrawn or moved to a different block; therefore, options you see in your MyCampus My Requirements report may not be available for you to choose when you reach final year.

Available option choices:

You do not have a free choice when choosing options. The following factors determine which options you can take.

1.     Each programme specifies which options are compulsory and recommended for that programme. You must choose options which satisfy the stated Requirements for your programme.

2.     In addition, each option specifies restrictions on admission (“Requirements of Entry” or “Enrolment Requirements”) to ensure that only students with the necessary academic background can enrol on that option. A few options allow any Life Sciences final-year student to enrol while other options only accept enrolment from students registered for a particular programme or set of programmes (for example Behavioural Ecology 4B option specifies the following: “Normally, only available to final-year Life Sciences students in the Animal Biology group programmes”).

3.     A few options require you to apply in advance during Year 3. You cannot take one of these options if you have not been approved in advance. Currently, these are:

·           Tropical Marine Biology (with Field Course) 4Y option

·           Marine Mammal Biology (with Field Course) 4Y option

·           Ecology & Conservation of African Ecosystems (with Field Course) 4Y option

·           Investigating Biological Function 4B option

4.    Most options limit the number of students that may enrol. For many options, the limit is around 30 students but some options have a lower or higher limit on class size. Enrolment is on a first-come, first-served basis.

5.    An option may be cancelled if too few students wish to do it or if there are other circumstances which mean an option cannot run.

Honours Project or Dissertation

You undertake a piece of independent work in final year, either a project or a dissertation. University regulations stipulate that you MUST obtain at least D3 in the “independent work” course for an Honours degree to be awarded.

You undertake a piece of independent work in final year, either a project or a dissertation. University regulations stipulate that you MUST obtain at least D3 in the “independent work” course for an Honours degree to be awarded.

During Year 3, you choose which type of final-year project you would like to do. There are four types of project within the Life Sciences portfolio:

·           Investigative (both laboratory-based “wet” projects and traditional “dry” projects)

·           Dissertation

·           Outreach (both School and Public Engagement)

·           Internship *

* Although the Internship type of project is available in theory to students on any programme, this will depend on internships being offered which are suitable to the programme. Until now, internships have only been available to students in Physiology & Sports Science.

The type of project you are allocated determines which project course you enrol on in MyCampus.

It may not be possible to allocate projects in line with your aspirations but staff seek to maximise each student’s preference. Your grades from Year 3 may be taken into account when project allocations are being made.

If you are a student in the Animal Biology Group (Marine & Freshwater Biology or Zoology), you are encouraged to think up possible projects yourself. However, you must find a member of staff willing to act as your supervisor.

Please refer to the current session’s Project Course Information Document for more information.

Course Contacts

2.1. Course Coordinators

2.2. Programme Coordinator for Final Year

2.3. Teaching Staff

2.4. External Examiner

2.5. Life Sciences Office

Course Summary

Course Code

BIOL4033

Course Title

Core Skills in Microbiology 4X core

Academic Session

2023-24

Short Description of the Course

The aim of this course is to provide Honours students in Microbiology with a firm grounding in the broader scientific skills they will need for the coming year and for their progression in science beyond graduation.

Requirements of Entry

Normally, only available to final-year Life Sciences students in a Microbiology programme. Visiting students may be allowed to enrol, at the discretion of the Life Sciences Chief Adviser and the Course Coordinator.

Associated Programmes

This course is offered by the Microbiology programme. It is a compulsory course for Honours programmes in Microbiology and Virology.

Available to visiting students

Yes

Available to Erasmus students

Yes

Typically offered

Semester 1

Timetable

There is normally 3 hours of teaching on Mondays.

Course Aims

This option aims to provide Honours students in Microbiology with knowledge of current research methods and skills in this discipline.

Intended Learning Outcomes of Course

By the end of this course, students will be able to:

Explain the key molecular techniques adapted for and utilised in microbiology diagnostics;

Conduct basic bioinformatics-based analysis based on amino acid sequence data;

Devise strategies for protein over-expression, purification and analysis;

Examine how genetics approaches can be used to genetically modify microbial pathogens;

Appraise assays that measure activation of the immune response and demonstrate the importance of antigen/antibody interactions in the study of the immune system in health and disease;

Discuss the main modes of research microscopy;

Discuss the legal requirements underpinning animal experimentation in the UK;

Give an account of the basic principles of transcriptome and proteome analysis of micro-organisms;

Discuss methods to generate molecular epidemiology data and key concepts in epidemiological investigations.

Minimum Requirements for Award of Credits

Students must submit at least 75% by weight of the components (including examinations) of the course’s summative assessment.

Description of Summative Assessment

The course will be assessed by a 2-hour examination (75%) and in-course assessment in which students write a short journal article based on data provided to them (25%).

Are reassessment opportunities normally available for all summative assessments in this course

Not applicable for Honours courses

Formative Assessment and Feedback

Formative assessment: students will be required to write a 1,500-word paper in their own time, for submission by a deadline. Tutors will mark the papers and complete online feedforward sheets which will be returned to the entire class prior to a formative feedback session in which generic feedback will additionally be given. This formative assessment will take the same form as the summative in-course assessment that follows on from it later in the course. Students will be provided with online feedback from the summative assessment and will be given verbal feedback by tutors in 10-minute one-to-one tutorials.

Examination Diet

April/May

Total Exam Duration

120 minutes

Session Summaries

 

Session 1: Option overview

Dr Richard Burchmore

Synopsis

The structure and philosophy of the Option will be described in some detail so that students can participate more effectively during the subsequent sessions.

Core skills in Microbiology is intended to give students a firm grounding in a range of research technologies that are broadly relevant in microbiology research. Aspects of data handling and ethical considerations will also be discussed. The technologies covered in the course will be illustrated with examples. Students are expected to engage with the literature to identify additional applications or innovations of these core skills.

The taught material delivered in sessions 2-10 will be complemented by two tutorials, one at the start, another mid-way through the option.

In tutorial 1, students will be given data relating to material delivered in sessions 2-5. They will also be presented with an overall investigative scenario and asked to write a 1,500-word paper that focusses on the data, for submission by 12:00 on the Thursday of option week 6 (Thu 27 Oct). The paper will follow a proscribed format, guided by a supplied template. Tutors will mark the papers and in tutorial 2 (Monday, week 8 (7 Nov)), formative feedback will be given one-to-one with tutees in 10-minute slots. Additional generic formative feedback will be posted on Moodle on Fri 11 Nov. This feedback can be utilised in preparing the final version for summative assessment with a deadline of Thursday week 10 (24 Nov). Tutors will double mark the papers and agree grades ready for handing back to students with online feedback by Thu 15 Dec.

In Semester 2, after option D, there will be 6 revision sessions for the Core Skills in Microbiology option. Students will be encouraged to table questions to lecturers in advance of these sessions.

 

Session 2: Next generation sequencing

Dr Taya Forde

Synopsis

Over the past decade, next-generation sequencing technology has enabled high-throughput sequencing of large numbers of microbes at a significantly reduced cost compared with traditional Sanger sequencing. This has resulted in an exponential increase in microbial sequence data, thereby rapidly expanding our understanding of microbial genetic and genomic diversity.

In this session, students will be introduced to the different types of sequencing platforms and how they work. They will gain familiarity with sequence data generated by these types of platforms, and how to assemble short read ‘shotgun’ sequence data into contigs or even whole genomes. They will also be introduced to different bioinformatics tools available for assessing sequence and assembly quality, and analysing the assembled sequences.

Aims

By the end of the class, students should be able to:

·        Describe how next generation sequencing works

·        Explain what distinguishes ‘next-generation’ from Sanger and ‘third-generation’ sequencing

·        Recognize the basic features of fasta and fastq files

·        Use publicly available tools to:

·        Access sequence data

·        Assess and improve sequence quality

·        Assemble next-generation sequence data

o   Search for closely related sequences in public databases

References

•        Heather and Chain, 2016 “The sequencing of sequencers: the history of sequencing DNA”. Genomics 107(1):1-8.

•        MacLean et al., 2009 “Application of ‘next-generation’ sequencing technologies to microbial genetics” Nature Reviews Microbiology 7:287.

Optional additional resources

•        Philipson et al., 2018 “Characterizing phage genomes for therapeutic applications” Viruses 10(4):188. (Used as the basis of the practical exercise)

•        Loman and Pallen, 2015 “Twenty years of bacterial genome sequencing”. Nat Rev Microbiol 13(12):787-94.

•        Edwards and Holt, 2013 “Beginner's guide to comparative bacterial genome analysis using next-generation sequence data” Microbial Informatics and Experimentation 3:2.

 

Session 3: Bioinformatics

Prof Olwyn Byron

Synopsis

Thousands of genomes have been sequenced. How can we identify and assign function to the genes encoded, based on these data? How can we make maximal use of existing data to predict the function and structure of proteins thus minimising experimental effort and expense while simultaneously accelerating research? Bioinformatics allows us to achieve these and other objectives using powerful, often web-based computer programs to interface with and interrogate databases of nucleic and amino acid sequences. In this session we will look at a number of commonly used bioinformatics databases and tools and complete an in silico analysis exercise.

Aims

At the end of this session, you should be able to:

·         Interrogate databases such as the NCBI to find and download genome, gene and protein sequences

·         Understand and describe the basis for the functioning of the Basic Local Alignment Search Tool (BLAST)

·         Conduct well-designed searches of nucleic acid and protein sequence databases for homologous sequences using the program BLAST

·         Align amino acid sequences using the program Clustal Omega

·         Appreciate the role of the global CASP competition in the objective assessment of state-of-the art capabilities in protein structure prediction and modeling

·         Predict and interpret the physico-chemical characteristics (including solubility) of a protein

·         Predict the protein secondary structure from the amino acid sequence using the Jpred4 server

·         Predict the tertiary structure of a protein from its amino acid sequence using homology-based modelling programs such as SWISS-MODEL, I-TASSER and Phyre2 and the novel machine learning based program AlphaFold

·         Visualise proteins, nucleic acids and carbohydrates using molecular graphics tools such as PyMol

·         Evaluate bioinformatically the several open reading frames (ORFs) of interest encoding proteins whose structures have not yet been solved

References

1.      Hosseingholi, E. Z., Rasooli, I. & Gargari, S. L. M. (2014). In silico analysis of Acinetobacter baumannii phospholipase D as a subunit vaccine candidate. Acta Biotheoretica 62, 455-478.

2.      Hussain, M., Gatherer, D. & Wilson, J. B. (2014). Modelling the structure of full-length Epstein‑Barr virus nuclear antigen 1. Virus Genes 49, 358-372.

3.      Kuhlman, B. & Bradley, P. (2019). Advances in protein structure prediction and design. Nature Reviews Molecular Cell Biology 20, 681-697.

4.      Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature 596, 583-589.

 

Session 4: Protein over-expression and analysis

Prof Olwyn Byron & Dr Ester Serrano

Synopsis

Understanding pathogenesis, virulence and function requires an understanding of the proteins produced by micro‑organisms and the host proteins with which they interact. Normally, native proteins are expressed by the parent organism at levels too low for effective characterisation and downstream use. In this session we will investigate selected methods for protein over-expression in E. coli and subsequent chromatographic and affinity purification. After proteins have been purified, they are often examined using a range of complementary biophysical and protein biochemical analytical methods. The principles of these techniques will be discussed.

Aims

At the end of this session, you should be able to

·        Describe the principles underlying the pET system for heterologous over-expression of proteins

·        Summarise the advantages and disadvantages of commonly used overexpression host systems

·        Recall the physicochemical principles underlying 1D and 2D gel electrophoresis

·        Explain how ion-exchange, size-exclusion, hydrophobic interaction and affinity chromatography can be used to purify proteins from cell lysate

·        Understand in particular the relationship between the pH of a protein solution, the ionisation state of the amino acid residue side-chains and the success, or otherwise, of purification by anion or cation exchange chromatography

·        Design a purification strategy for a protein based on its characteristics

·        Summarise the underlying principles of small angle X-ray scattering (SAXS) and X-ray crystallography (MX) and understand their role in protein characterisation

·        Successfully and efficiently purify proteins from cell lysate in silico using the Protein Purification tool

References

pET system	Novagen pET System Manual, 11th ed, especially pp 37-54 (downloadable from the L4 CSM Moodle site)
Protein over-expression in E. coli	Gopal, G. J. & Kumar, A. (2013). Strategies for the production of recombinant protein in Escherichia coli. Protein Journal 32, 419-425.
Protein purification	http://www.youtube.com/watch?v=OCi7T7o1Qmk
Protein Purification in silico tutorial	http://www.agbooth.com/pp_java/
SAXS movie	http://www.embl-hamburg.de/biosaxs/courses/
Application of SAXS & MX	Grinter, R., Josts, I., Zeth, K., Roszak A. W., McCaughey L., Cogdell, R. J., Milner, J. J., Kelly, S., Smith, B., Byron, O. and Walker D. (2014) Structure of the atypical bacteriocin pectocin M2 implies a novel mechanism of protein uptake. Molecular Microbiology, 93, 234-46 (doi: 10.1111/mmi.12655).
Application of SAXS & cryo-EM	Kim, G., Azmi, L., Jang, S., Jung, T., Hebert, H., Roe, A., Byron, O. and Song, J-J. (2019) Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity. Nature Communications 10: 4527 (doi: 10.1038/s41467-019-12427-8).
X-ray crystallography	http://www.youtube.com/watch?v=XUEw5CcN03E

 

Session 5: Post-genomic technologies

Dr Richard Burchmore

Synopsis

Since the first pathogen genomes were sequenced by relatively laborious approaches, it has become possible to rapidly sequence entire pathogen or host genomes. Understanding the information carried in these genomes remains a challenge. Technologies such as transcriptomics and proteomics have been enabled by the emergence of genome datasets, and hold the promise of linking genotype to phenotype by revealing which genes are expressed in response to specific developmental triggers or environmental stimuli.

Using transcriptomic approaches such as RNAseq, it is now possible to monitor the expression of thousands of genes simultaneously and build a global picture of the transcriptome, a dynamic pool of messenger RNA (mRNA) molecules that reveals gene expression activity at a point in time. Analysis of the proteome can reveal which mRNAs are translated into proteins. As genome sequences are generated for an increasing number of pathogens, transcriptomic and proteomic technologies become increasingly powerful tools to understand the molecular basis for important biological processes. Comparative transcriptomic and proteomic analysis of, for example, virulent and avirulent pathogens can highlight genes and proteins that are involved in virulence.

Transcriptomes and proteomes are complex mixtures or RNA and protein, respectively. The technologies that are employed to assess their compositions are quite different. Both are developing rapidly through a combination of academic innovation and commercial exploitation. This session will provide some background to the potential of, and challenges to, transcriptomic and proteomic analyses. It will include some examples of the application of these approaches to understand important pathogen phenotypes and host:pathogen interactions.

Aims

At the end of this session, you should be able to:

·         Understand the basics of microarray and RNAseq analysis

·         Understand the basics of proteome analysis

·         Develop an understanding of mass spectrometry as applied to biomolecules

·         Appraise the challenges to transcriptomics and proteomics, and the relative advantages of each

·         Become familiar with handling the data output from proteome analysis

·         Discuss recent developments in post-genomic technologies, such as spatial and single cell approaches

References

1.      Hegde, P., White I. & Debouck, C. The interplay of transcriptomics and proteomics. Curr. Op. Biotechnol. (2003) 14, 647-651.

2.      Tarun AS, Peng X, Dumpit RF, Ogata Y, Silva-Rivera H, Camargo N, Daly TM, Bergman LW, Kappe SH. A combined transcriptome and proteome survey of malaria parasite liver stages. (2008) Proc Natl Acad Sci U S A. 105(1):305-10.

3.      Plasmodium Parasites Viewed through Proteomics. Swearingen KE, Lindner SE.Trends Parasitol. 2018 Nov;34(11):945-960. doi: 10.1016/j.pt.2018.08.003.

4.      'Omic' Approaches to Study Uropathogenic Escherichia coli Virulence. Lo AW, Moriel DG, Phan MD, Schulz BL, Kidd TJ, Beatson SA, Schembri MA.Trends Microbiol. 2017 Sep;25(9):729-740. doi: 10.1016/j.tim.2017.04.006.

5.      Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Jean Beltran PM, Federspiel JD, Sheng X, Cristea IM.Mol Syst Biol. 2017 Mar 27;13(3):922. doi: 10.15252/msb.20167062.

 

Session 6: Genetic modification of pathogens

Dr Tansy Hammarton

Synopsis

The ability to genetically manipulate microbes and then to characterise their phenotypes is crucial for investigations into gene function. In this session, a variety of forward and reverse genetics approaches will be discussed, with examples of how these can be used to genetically modify bacterial, parasitic and viral pathogens in order to investigate pathogen biology and host-parasite interactions. The development of genetically modified microbes for commercial or therapeutic applications will also be discussed.

Aims

At the end of this session, you should be able to:

·        Explain the concepts of forward and reverse genetics and describe a range of molecular methods that can be used to modify microbes for each approach.

·        Demonstrate an understanding of “Molecular Koch’s postulates”.

·        Exhibit an understanding of reporter genes and how they are used.

·        Select appropriate molecular genetic approaches to functionally investigate genes involved in particular aspects of pathogen biology or host-parasite interactions

·        Discuss, with examples, therapeutic and commercial uses of genetically modified organisms, demonstrating an understanding of associated safety considerations.

References

https://www.jove.com/v/5542/genetic-screens

 

https://www.thermofisher.com/uk/en/home/life-science/antibodies/antibodies-learning-center/antibodies-resource-library/antibody-methods/epitope-tagging-overview.html

Jones et al., (2014) Regulators of Trypanosoma brucei cell cycle progression and differentiation identified using a kinome-wide RNAi screen. PLoS Pathog. 10:1003886. DOI: 10.1371/journal.ppat.1003886

Mojica, F. J. and L. Montoliu (2016). On the origin of CRISPR-Cas technology: from prokaryotes to mammals. Trends Microbiol. 24(10): 811-820. DOI: 10.1016/j.tim.2016.06.005

Baker et al., (2021) Systematic function analysis of Leishmania protein kinases identifies regulators of differentiation or survival. Nat. Commun. 12: 1244. DOI: 10.1038/s41467-021-21360-8

Misselwitz et al., (2011) RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and cdc42. Mol Sys. Biol. 7: 474 DOI: 10.1038/msb.2011.7

Baggen et al., (2021) Genome-wide CRISPR screening identifies TME106B as a proviral host factor for SARS-CoV-2. Nat Genet. 53: 435-444.  DOI: 10.1038/s41588-021-00805-2

 

Session 7: Diagnostics

Dr Duncan Clark

Synopsis

Pathology is the study of disease. It is composed of multiple specialities to provide diagnosis and treatment of millions of people every year. Within the NHS, over 70% of diagnoses involve pathology and over 700 million pathology tests are conducted in the NHS each year. Broad areas of pathology include: Histopathology, the study of disease in human tissue; Clinical Biochemistry/Chemical Pathology, the study of chemicals in blood and body fluids; Haematology, the study of blood and bone marrow plus transfusion; Genetics, the study of DNA and how diseases are inherited; Immunology, the study of disorders of the immune system; Microbiology, the study of infectious disease. Each of these specialities utilise a wide range of laboratory tests in their diagnostic investigations. However, these are often based on similar technologies and all are required to demonstrate the properties expected of a good diagnostic, irrespective of the speciality. For Microbiology (Infection), a range of phenotypic and genotypic approaches are generally used and this session will consider the importance of some of these newer key approaches and areas of innovation. It will reinforce the laboratory methods used, their advantages and disadvantages and highlight the parameters that need to be considered for a good diagnostic. The session will be interactive and students will consider appropriate diagnostic strategies for particular scenarios.

Aims

At the end of this session, you should be able to:

·         Understand the importance of test sensitivity and specificity, positive and negative predictive values

·         Describe the key molecular techniques specifically adapted and utilised in microbiology diagnostics

·         Know key developments in bacterial identification using MALDI-TOF as a recent example

·         Appreciate the importance and range of controls in any diagnostic test

·         Understand serological approaches to diagnostics and the importance of correct results interpretation

·         Understand approaches to investigate a new diagnostic

References

1.      PHE UK Standards for Microbiology Investigations. Evaluations, validations and verifications of diagnostic tests.
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/601969/Q_1i5.pdf
Pages 8-18 most relevant, particularly the definitions on pages 15-18

Gullett JC and Nolte FS. Quantitative Nucleic Acid Amplification Methods for Viral Infections. Clinical Chemistry 61:1 72–78 (2015)
Pages 72-74 useful for details on general methods

2.      Patel R. MALDI-TOF MS for the Diagnosis of Infectious Diseases. Clinical Chemistry 61:1 100–111 (2015)
Pages 100-103 useful for how MALDI-TOF works)

 

Session 8: Imaging techniques

Prof Andy Roe & Dr Swetha Vijayakrishnan

Synopsis

Microscopy is one of the most powerful tools to study the interactions between a pathogen and its host. Different approaches with different advantages and disadvantages can be applied in order to answer specific scientific questions. This lecture aims to give an overview of different techniques applied in imaging. We will discuss the different sizes of molecular samples and the best imaging approaches to study specific questions in host-pathogen biology including monitoring of infections in real-time.

Light microscopy methods will be discussed, with a special focus on the use of green fluorescent protein (GFP) and derivatives to study the function of microbial proteins. Recent developments, such as automated image analysis and super-resolution microscopy will be covered in this lecture.

Basic principles of scanning and transmission electron microscopy will be discussed with regards to the imaging of different biological specimens. This lecture will then go into the applications of electron imaging in structural biology and electron tomography for three-dimensional imaging. Soft X-ray imaging will be briefly presented. Correlated light/electron/X-ray methods for host-pathogen imaging will be discussed.

Finally, the importance of well-designed and unbiased experiments will be highlighted.

Aims

At the end of this session, you should be able to:

·         Compare and contrast different microscopy techniques and evaluate their strengths and weaknesses.

·         Describe different fluorescent probes and reporters and understand how and when to apply them.

·         Understand how correlated imaging may be used to bring together information from multiple imaging modalities.

·         Understand how to set up a well-controlled experiment and analyse the data in an unbiased manner.

References

1.     Sydor, A. M., Czymmek, K. J., Puchner, E. M. & Mennella, V. Super-resolution microscopy: from single molecules to supramolecular assemblies. Trends Cell Biol. 25, 730–748 (2015).

2.     Thorn, K. A quick guide to light microscopy in cell biology. Mol. Biol. Cell 27, 219–222 (2016).

3.     Chudakov, D., Matz, M., Lukyanov, S. & Lukyanov, K. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol. Rev. 90, 1103–1163 (2010). NOTE: this is a really extensive review and we don't expect anyone to read all of it. BUT, it does provide a great resource to dip into and covers the whole area very well.

4.     Lichtman, J. W. & Conchello, J. Fluorescence microscopy. 2, 1–60 (2009).

5.     J. Mahamid et al., Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science. 351, 969–972 (2016).

6.     R. Fernandez-Leiro, S. H. W. Scheres, Unravelling biological macromolecules with cryo-electron microscopy. Nature. 537, 339–346 (2016).

 

Session 9: Immunoassays

Dr Hannah Scales

Synopsis

Measuring the immune response generated by the host is fundamentally important, providing information about the role of a specific response in protection against infection. Furthermore, abnormalities can identify the onset and progression of both infectious and autoimmune diseases. This session aims to refresh your knowledge of the key cells of the innate and adaptive immune system that are activated in response to infection and discuss in detail one of the key methodologies used to examine cellular responses. The 1h lecture will include description one of the most commonly used techniques , flow cytometry and an introduction to some of the recent advances in this field such as spectral flow cytometry, CyTOF and imaging flow cytometry.

The 2h interactive session  will include hands on experience of the software frequently used to analyse the different cell populations. This teaching should provide students with the experience required for effective reading and critical evaluation of published data.

Aims

At the end of this session, you should be able to:

·         Explain the basic role of the different cells and cytokines associated with the activation of the innate and adaptive responses.

·         Interpret flow cytometry data and understand how it can be used to assess different aspects of the immune response.

·         Demonstrate the importance of antigen/antibody interactions in the study of the immune system in health and disease.

Session Requirements

·        10 days prior to the 2h afternoon interactive session, please download the following software resource to your laptops. This is a free copy of the software frequently used to analyse data from the FACS.  Free access for 30 days will be sufficient to provide experience of its use.

https://www.flowjo.com/solutions/flowjo/free-trial

The software can run on most machines, although recommended system requirements are as follows:

·        Minimum 8 GB RAM, recommended 16 GB RAM;

·        For MacOS 10.11 Sierra or newer, Core II Duo processor or better (recommended Intel i7 quad core processor).

·        For PC Minimum: Windows Vista (recommended Windows 10); x86 or x64 dual core processor (recommended Intel i7 quad core processor). 

If you are struggling to download the software, you might want to find a ‘buddy’ prior to the session. Any problems please let us know in advance

·        Flow cytometry data files will be posted on moodle prior to the session, please download these so you have them available to work with.

Resources

Video resource for FACS	https://www.jove.com/v/10494/flow-cytometry-fluorescence-activated-cell-sorting-facs-isolation
Introduction to Fluorescence	https://www.youtube.com/watch?v=ccR5snuCE80
Introduction to Flow Cytometry	https://www.youtube.com/watch?v=sfWWxFBltpQ&feature=youtu.be
Analysing Flow Cytometry Data	https://www.youtube.com/watch?v=SGFlr1jFNBM

Books/CDs/papers

Janeway’s Immunobiology. Ed 10 2018. Eds Kenneth Murphy and Casey Weaver. Available in paperback or ebook. Contains over 40 videos and student resources.

Nazila V. Jafari, Sarah A. Kuehne, Clare E. Bryant, Mamoun Elawad, Brendan W. Wren, Nigel P. Minton, Elaine Allan, Mona Bajaj-Elliott. Clostridium difficile Modulates Host Innate Immunity via Toxin-Independent and Dependent Mechanism(s) PLoS ONE. 2013; 8(7): e69846.

 

Session 10: Animal technology

Dr Gill Douce

Synopsis

The aims of this session are to:

·         Highlight the advantages and disadvantages of animal experimentation in the 21st century, including the impact of transgenic animal production and in vivo imaging on the understanding of host immunity to disease.

·         Gain an understanding of the ethical and legal considerations of animal experimentation and the continual need to refine, reduce and replace (3R’s) animal models of disease.

Aims

At the end of this session, you should be able to:

·         To discuss how transgenic animals are created and the impact these animals have on the study of human disease.

·         To appraise the licensing legislation that governs the use of animals in experimentation in the UK. This should include the role of the investigator, the supervisor, the designated certificate holder and the Home Office inspector in this process.

·         To demonstrate knowledge of the 3R’s concept (reduce, refine and replace) and their application.

Websites

ARRIVE 2.0 guidelines	https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000410
Fund for replacement of animals in medical experimentation	http://www.frame.org.uk
Understanding Animal Research	http://www.understandinganimalresearch.org.uk/
National Centre for the Replacement, Refinement and Reduction of Animals in Research	http://www.nc3rs.org.uk