Fundamental Topics in Molecular Immunology 4Y Course Information 2023-2024
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.
Professor Robert Nibbs, Robert.Nibbs@glasgow.ac.uk
Deputy: Professor Simon Milling, Simon.Milling@glasgow.ac.uk
Professor Simon Milling, Simon.Milling@glasgow.ac.uk
Teaching staff names can be found on your online timetable and contact details can be found on the University website Staff A-Z
Dr Janine Coombes, Robert Gordon University
The Life Sciences Office is located in Room 354 of the Sir James Black Building. Opening hours for enquiries are: Monday to Friday: 9:30am to 4:30pm.
BIOL4185
Course Title
Fundamental Topics in Molecular Immunology 4Y option
Academic Session
2023-24
Short Description of the Course
This course focuses on enabling students to develop a detailed understanding of the fundamental molecular pathways involved in controlling immune responses, and an awareness of recent developments in molecular immunology.
Requirements of Entry
Normally, only available to final-year School of Life Sciences students in an Immunology programme. Visiting students may be allowed to enrol, at the discretion of the School of Life Sciences Chief Adviser and the Course Coordinator.
Associated Programmes
This course is offered by the Immunology programme. It is a compulsory course for Honours programmes in Immunology.
Available to visiting students
Yes
Available to Erasmus students
Yes
Typically offered
Semester 1
Timetable
Normally, there are 3 hours of teaching on Fridays, which
may be split over more than one session.
Course Aims
The aims of this course are to develop:
a thorough understanding of fundamental concepts involved in regulation and function of the adaptive immune system;
an awareness and knowledge of current controversies and emerging questions in the biology of lymphocytes.
Intended Learning Outcomes of Course
By the end of this course, students will be able to:
Discuss and critically appraise the current state of understanding of molecular immunology;
Interpret and present information from relevant research literature;
Analyse data and relate results to the relevant literature;
Evaluate how knowledge in molecular immunology is created by experimentation and observation.
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 consisting of a data analysis exercise (25%).
Are reassessment opportunities normally available for all summative assessments in this course
Not applicable for Honours courses
Formative Assessment and Feedback
Feedback will be given to the class, during the teaching sessions, in a session dedicated to practicing writing answers to exam essay questions.
Students will be given the opportunity to undertake a formative data handling and presentation task using data provided by teaching staff and drawing on advice provided in one of the taught sessions. The work will be assessed by a member of staff and/or the student’s peer group. Students will receive verbal feedback as a class or individual written feedback — areas for improvement will be identified and ways to improve described. Students will then be given the opportunity to change their work, which will be assessed by the staff member, and final written or verbal formative feedback provided.
Drawing on this practice and associated feedback, the students will then undertake another data handling and presentation task using a different set of data and then submit this for summative assessment.
Examination Diet
April/May
Total Exam Duration
120 minutes
Submission deadline: 4pm Wednesday 1st November 2023
Scientists need to be able to analyse and present data. They need to be able to examine datasets; extract key information; analyse data using appropriate statistical tests; and present it in attractive, accurate, understandable, and informative ways. This is also a key transferable skill useful in any profession in which data and information needs to be analysed and presented effectively. For the in-course assessment in this course you will need to examine, select, analyse and present data from a complex dataset that will be made available to you on Moodle. This task will also help with the analysis and presentation of data associated with your Honours Project.
The following will help you with your DAPT:
Level-3 experience. In Level-3 you undertook a DAPT using data provided by your lecturers. You should remind yourself of the teaching and feedback that you received related to this activity, and the challenges and problems you encountered when doing this work. The associated lecture ‘Getting to Grips with Scientific Data’ can be found on the Level-4 Fundamental Topics in Molecular Immunology Moodle page in the folder relating to Session 1 of the course. You will probably have analysed and presented data in other courses or during work placements so it might be helpful to look back at these too.
DAPT Preparation session (session 1 of the course). In this session, Prof Nibbs and Dr Pingen will present lectures on data presentation and statistics, respectively, and there will be an opportunity for you to discuss the DAPT with each other and with Prof Nibbs and Dr Pingen. Further details can be found in the Session Summaries section of this CID.
Optional Formative DAPT. You will be given the opportunity to undertake a formative DAPT using the information in the ‘Practice DAPT Dataset’ folder on Moodle. You should draw on points 1 and 2 above to help you complete the practice DAPT. Using the practice DAPT dataset and the associated methods document you should: write a brief Abstract; prepare a Figure and Figure Legend; and apply an appropriate statistical test to the data, which should be represented in the Figure and Figure Legend. Use the ‘DAPT Report Format’ information below to guide you. You can discuss your practice DAPT with your classmates and ask them to provide feedback on what you have prepared but ensure that what you submit is all your own work. Once complete, you can submit your work AS A PDF FILE via the ‘Submission of Practice DAPT’ portal on Moodle by Monday 2nd October 2023 at the latest. The Course Coordinator will provide verbal or written feedback (to the whole class or individually). Where appropriate, areas for improvement will be identified and ways to improve described. You can then change your work in response to the feedback and send it to the Course Coordinator for final written or verbal formative feedback.
Note: To save you time, the ‘Practice DAPT Dataset’ is simpler than the dataset you will use for your assessed DAPT. This means that it will not be possible to provide feedback on data selection, but you will receive feedback on the content and format of your Abstract, Figure, and Legend, and on your use of statistics.
The DAPT that you need to complete for summative assessment should be based on the data and the associated Methods document that can be found in the ‘DAPT Dataset for Summative Assessment’ folder. You should scrutinise this dataset carefully to allow you to identify those parts that you think are interesting and potentially important. To inform this decision-making process, it would be sensible to prepare graphs, and perform appropriate statistical tests, on many, or all, parts of the dataset. You should include some of the cytokine data and some of the cell data. Once you have decided on what parts of the dataset you are going to use in your final submission, you should prepare a document (the DAPT report) that contains the components described in the ‘DAPT Report Format’ section below. To analyse the data and prepare your Figures, you can use any software packages you wish.
Title: Write a brief title that summarises what is shown in the data that you have selected.
ID: Provide your matriculation number.
Abstract: The Abstract should be less than 200 words and should summarise what was done in the study and what is shown by the data that you selected for inclusion in the Figures. This should resemble an Abstract that would be present in a research article. Typically, they start with a statement about the area of study; then outline what was done in the study; then describe what was discovered; and finally state why this is (or might be) important, scientifically or clinically. References should not be included.
Justification of data selection: You should provide a short statement of less than 100 words that explains why you chose the data that you have included in your Figure(s).
Figures: You should present the data you have selected in a maximum of THREE attractive, accurate, understandable and informative Figures. The data in each Figure should be analysed using an appropriate statistical test. All the information required to fully understand the data should be present in the Figures or in the associated Figure Legends. To help you do this, look at Figures in research articles and draw on your experience of doing the practice DAPT and other data analysis and presentation in previous years. Session 1 of the course will also be helpful when constructing Figures and will include advice such as: ensure that variation within groups is represented (SDs, SEMs); check that your graph axes are clearly labelled; make sure all text is large enough and readable; include colour for emphasis and to make your figures more visually-appealing; include a Key if you think it helps the reader to quickly access the information; and represent statistically significant differences on the Figure (using p<0.05 as the cut-off).
Figure Legend(s): Each Figure should be accompanied by a Figure Legend that provides all the information the reader needs to understand the Figure. The format and construction of Figure Legends will be explored and discussed in detail in Session 1 of the course, but here are some general guiding principles. First, the Figure Legend should have a title in bold text that summarises the conclusion(s) that stem(s) from the data shown in the Figure. Second, it should be possible to understand ALL the contents of a Figure by reading the Figure Legend without looking elsewhere. Third, a Figure Legend should not contain any discussion of the data, or its importance, limitations etc.. Fourth, legends should be succinct and unambiguous - make it as easy as possible for the reader to understand what the Figure is about. Fifth, there should be a clear statement of how the data are presented in the Figure (e.g. Mean+/-SD) and of which statistical tests have been applied – if significant differences have been indicated by symbols on the Figure, then these must be defined in the Legend. Sixth, any abbreviations in the Figure should be defined in the Legend, and seventh, you should try to have Legend and Figure on the same page – it makes it easier for the reader! Discussions in Session 1 will emphasise these key principles.
For all components of the DAPT, remember that Immunology teaching staff will assess your work, so it would be wise to ensure that it is well written and carefully formatted; that the Figures are attractive, accurate, understandable and informative; and that the Figure Legends are clear and complete.
The grade for the DAPT constitutes 25% of your overall grade for this course.
Your final DAPT report must be submitted for assessment no later than 4pm on Wednesday 1st November 2023. You will be informed if there is any change to this deadline. You must submit an electronic version AS A PDF FILE via the ‘DAPT: Submission for Summative Assessment’ portal on Moodle. It is essential that what you submit is ALL YOUR OWN WORK. There will be a Turnitin check of your work when you submit through Moodle, and those marking your work will be advised to check it for signs of plagiarism and for evidence that students have copied the work of other students. Any significant concerns identified by Turnitin, or by the markers, might be referred to the University Senate and could result in punitive measures, including grade reduction or the award of H. If you have any doubts or concerns about any of this, please contact Prof Nibbs.
Two members of staff will assess your submitted work and then agree grades and feedback. They will then complete a Markers Grade and Feedback form. You can view a copy of this form on Moodle. It shows the five components of the DAPT that will be assessed by the markers, and the percentage of the overall grade that is assigned to each component. Once all student work has been assessed, the completed Markers Grade and Feedback form relating to your work will be made available to you.
Session 1: Data Analysis and Presentation Task (Preparation for In-Course Assessment)
Prof Robert Nibbs & Dr Marieke Pingen
Synopsis
After a brief Introduction to the content of the Fundamental Topics in Molecular Immunology course, this session will act as preparation for the Data Analysis and Presentation Task (DAPT), the in-course assessment component of this course worth 25% of the overall course grade. Details of the DAPT are included in the ‘In-Course Assessment’ section of this Course Information Document. This session also aims to help you with the analysis and presentation of data in your Project, and to encourage you to think critically about data you see in papers, seminars, group meetings etc..
In the session, Prof Nibbs will give a lecture focussing on Data Presentation and Dr Pingen will give an overview of Statistics. In addition, building on the information in this Course Information Document, you will be given details about what you are expected to do in the DAPT and will have the opportunity to ask any questions you may have about it and its assessment. This could include a group discussion to identify likely problems/challenges and discuss how these might be avoided or overcome.
OPTIONAL: Following the session, you can use the ‘Practice DAPT Dataset’ on Moodle to prepare a Figure (with statistics), Figure Legend and short Abstract. If you submit your work by Moodle, Prof Nibbs will provide verbal or written feedback (individually, or as a group to all those that submitted work). Where appropriate, areas for improvement will be identified and ways to improve described. You could also ask your classmates to provide feedback on what you have prepared. In response to all this feedback, you can then modify your work and send it to Prof Nibbs by email for final formative feedback.
Aims
At the end of the session you should be able to describe:
Effective ways of analysing data and presenting it in a Figure
The typical contents of a Figure Legend
Appropriate statistical tests that could be applied to specific types of data
What you need to do to complete a DAPT report for formative and summative assessment
Session 2: Chemokines & Inflammation
Prof Robert Nibbs
Synopsis
Chemokines are the key regulators of the migration of leukocytes during both normal and pathological inflammatory responses. Understanding the nature of the chemokine-driven leukocyte migration and inflammatory responses is essential for our understanding of the pathogenesis of all inflammatory pathologies. This session will review chemokines and their receptors and focus specifically on inflammatory chemokines. It will highlight the biochemical and biological complexity of this family, explore different types of leukocyte migration induced by chemokines, and examine the ways that chemokines and other chemoattractants drive inflammatory responses. The mechanisms regulating interstitial migration, such as neutrophil ‘swarming’, will be examined in detail with reference to primary research articles. We will also explore the potential therapeutic benefits of targeting of the chemokine network and the challenges that face the development of effective chemokine receptor antagonists for the treatment of human disease.
Aims
By the end of this session, you should have an understanding of:
Chemokines and the distinction between homeostatic and inflammatory chemokines
The complex nature of inflammatory chemokine/receptor interactions
Key cell types responding to individual inflammatory chemokines and their role in inflammation
The importance of inflammatory chemokines in orchestrating pathological inflammatory responses
The different types of cell migration that are activated by chemokines
Mechanisms regulating interstitial neutrophil ‘swarming’
The challenges facing the therapeutic targeting of the inflammatory chemokine system
Session 3: Cell Migration & Adaptive Immunity
Prof Robert Nibbs
Synopsis
Leukocyte migration is essential for effective immunosurveillance and a central component of all immune and inflammatory responses. In the absence of appropriate migratory responses, leukocytes fail to get to the correct location to perform their function. This session aims to reveal how cell migration and a diverse repertoire of chemoattractants and their receptors is critical for immune surveillance and execution of effective adaptive immune responses.
Aims
At the end of this session, you should be able to:
Describe the critical functions of specific chemokine receptors in primary and secondary lymphoid tissues
Discuss the importance of migratory receptors and the regulation of their activity in B cell biology
Discuss the function of atypical chemokine receptors in secondary lymphoid tissues
Summarise the importance of chemokine receptor switching in T cell function
Describe the role of non-chemokine chemoattractants (e.g. S1P and oxysterols) in regulating leukocyte migration
Session 4: Transcriptional Control of Inflammation
Dr Ruaidhrí Carmody
Synopsis
The signal transduction pathways activated by many immunoreceptors (TLR, TCR, BCR, TNFR, cytokine receptors etc) lead to the activation of the NF-ĸB family of transcription factors. NF-ĸB is the master regulator of inflammatory responses and is a key factor controlling immune development and homeostasis. The fundamentals of NF-κB activation and its regulation will be a focus of this session. Although this session will focus on the control of Toll-like receptor-induced transcription it will also highlight principles and concepts applicable to other immunoreceptors. This session will also cover Toll-like receptor tolerance, a key mechanism controlling innate transcriptional responses in the context of infection.
Aims
By the end of this session, you should be able to:
Describe the NF-ĸB family of transcription factors and the mechanisms controlling its activity
Describe the key mechanisms that negatively regulate TLR induced transcription
Describe and discuss the concept of toll-like receptor tolerance and innate immune memory
Session 5: Transcriptional Regulation of Lineage Commitment
Dr Ruaidhrí Carmody
Synopsis
What makes a T cell a T cell, a macrophage a macrophage or a granulocyte a granulocyte? The morphological and functional differences between cells of the immune system are easily recognised but how do these differences arise and how are they regulated? This session will lay the basis for understanding the role of transcription factors in determining cell lineage. The general principles will be elaborated and illustrated by specific examples of transcriptional factors which determine cell lineage fates.
Aims
At the end of this session, you should be able to describe:
The general principles of transcription factor determination of cell lineage fate
The techniques used to study transcription factors and chromatin
The role of Pu.1 in determining macrophage differentiation
Session 6: Osteoimmunology: The cross-regulation between bone and the immune system
Dr Carmen Huesa
Synopsis
Osteoimmunology describes the research field that deals with the cross-regulation between bone cells and the immune system. Today it is evident that both systems influence each other and this impacts human physiology and pathology. In this lecture we will explore bone as a tissue and the cells that make it as well as the cross-over with the immune system.
Aims
At the end of the session you should have an understanding of:
Bone and bone remodelling;
Cells in bone, how they emerge, and what their functions are;
Bone-immune system crosstalk and its importance in health and disease.
Session 7: Innate Immune Features of Inflammatory Lung Disease
Prof Robert Gray
Synopsis
Currently unavailable.
Session 8: Future Proposal Advice (MSci students only)
Prof Robert Nibbs
Synopsis
As part of their Final Year Honours Project, students on the MSci programme need to prepare a ‘Future Proposal’. It is worth 20% of the overall grade awarded to the Project. In this session, Prof Nibbs will discuss what’s expected in a Future Proposal and provide some advice about writing one. He will also try to answer any questions that students may have and encourage class discussion of ideas and challenges associated with this part of the assessment. Students should also look at other key resources, such as the exemplars and the help video on the Final Year Honours Project Moodle page. They should also discuss the Future Proposal with their Project supervisor.
Aims
At the end of the session, you should have an understanding of:
The structure and content of a Future Proposal
How to approach writing a Future Proposal, and the key challenges that will need to overcome during this exercise
Session 9: Essay Writing and AI
Prof Simon Milling
Synopsis
Currently unavailable.
Session 10: Host/Microbiota Interactions
Prof Simon Milling
Synopsis
There has been a surge of interest in the way we interact with the large numbers of micro-organisms that populate our intestines. We have co-evolved with these organisms, and the interactions between them and the cells of our immune system have important effects on our health and can contribute to disease. In this session we will revise the important background information about the development and structure of the microbiota. We will then discuss specific cellular and molecular interactions that that contribute to the proper functioning of the immune response. Finally, we will discuss how perturbation in the microbiota may (or may not) contribute to the pathogenesis of conditions such as arthritis and obesity. Finally, we will consider recent efforts to improve human health by manipulating the microbiota, and the prospects for future therapeutic interventions.
Aims
At the end of this session, you should have an understanding of:
Recent advances in the understanding of the commensal microbiota
The characteristics of the microbiota, its development, and diversity
Cellular and molecular interactions between the intestinal immune system and the microbiota
The contributions of the microbiota to controlling intestinal immune responses
The potential for manipulating the microbiota for therapeutic purposes
Session 11: Epigenetic Mechanisms and Innate Memory
Dr Mariola Kurowska-Stolarska & Dr Orhan Rasid
Dr Mariola Kurowska-Stolarska
Synopsis
This session will discuss different mechanisms of the regulation of gene expression in the context of immune responses and how the deregulation in these mechanisms leads to diseases. In the last part, examples of therapies that target epigenetic mechanisms will be provided.
Aims
At the end of this session, you should have an understanding of:
The terms epigenetic and genetic
Transcription and post-transcriptional processes
Biogenesis of microRNAs and their role in the regulation of immune gene expression
Epigenetic modifications of DNA and histones
Contribution of epigenetics (including microRNA) to human pathologies
Dr Orhan Rasid
Synopsis
In addition to adaptive memory, there is increasing evidence of immunological memory mediated by innate immune cells. This session will present the various examples of innate memory, discussing concepts like trained immunity and NK cell memory. The various models in which innate immune memory has been described will be explored together with the currently known mechanisms behind these and the possible implications for disease, vaccination, and immunotherapy.
Aims
At the end of this session, you should be able to:
Describe the various models of innate immune memory;
Explain the properties and mechanisms behind innate immune memory in different cell types;
Understand the roles of innate immune memory in disease and therapies.
Session 12: Exam Practice
Prof Robert Nibbs
This session aims to hone your skills of writing under examination-like conditions. Several weeks before the session, you will be given a research article via Moodle that you should read carefully and understand as fully as possible. In the mock exam, you will be expected to answer short-answer questions (SAQs) based on the research article. This will be done under examination-like conditions such as might be encountered during an online exam (or in an exam hall in the unlikely event that exams move onto campus). Subsequently, you will be provided with some model answers or written feedback. Alternatively, we might discuss the SAQs as a group, considering planning, content, figures, time management etc. - Prof Nibbs will contribute to such discussions, but it is envisaged that they will principally be a ‘student-led’ process.
Aims
At the end of the session you should be able to:
Demonstrate a deeper understanding of a research article
Describe what is expected in answers to SAQs written under exam conditions
Session 13: Memory
Prof James Brewer
Synopsis
Memory T and B cells are generated during a primary adaptive immune response. These cells have a number of features that differentiate them from naïve T and B cells and furnish the immune system with the capacity to ‘remember’ previous (infectious) challenges. Ultimately, memory cells respond to re-exposure to infection more rapidly and more effectively providing host immunity. An excellent example of immunological memory is the ability of childhood immunisation programmes to provide long-term protection against infection. This session will focus on how memory T and B cells are generated, current theories of how these cells are maintained and the important features of these cells that prevent infection on re-exposure to pathogens.
Aims
At the end of the session you should be able to:
Describe the features of memory T and B cells and explain how these contribute to immunity to infection
Critically review current theories of differentiation of memory T and B cells
Summarise current theories regarding the maintenance of memory T and B cells