XDF Programme Tutorials

A selection of presentations delivered by researchers from the Institute of Genetics and Molecular Medicine in Edinburgh as part of the Cross-disciplinary Fellowships [XDF] Programme. These tutorials cover a broad range of biomedical science (and related) topics and are intended to provide general introduction to complex biomedical problems for people with little previous exposure to biomedical research.

Note that on the 1st April 2021 the Institute of Genetics and Molecular Medicine has been renamed to the Institute of Genetics and Cancer (IGC).

How to Write a Successful Grant Application?

Prof Chris Ponting, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (18 June 2019)

Ability to secure funding to advance research projects is essential for every active scientist but  writting a successful grant application is becoming increasingly difficult in today's very competitive science environment. This tutorial by Professor Chris Ponting provides an overview of funding oportunities for UK based investigators and multiple useful tips that can help you with preparation of your own applications for funding.  (The video is accessible to University of Edinburgh affiliates only). 

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Computing the Cancer Genome

Prof Colin Semple, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (30 September 2019).

Understanding the cancer genome is crucial for understanding cancer as a disease and development of better personalised treatments. This tutorial by Professor Colin Semple provides some insights into how computational approaches can help us understand tumour biology. (The video is accessible to University of Edinburgh affiliates only).

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How does RNA fold?

Dr Grzegorz Kudla, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (14 October 2019).

RNA folding is the process by which a linear ribonucleic acid (RNA) molecules acquire secondary structure through intra-molecular interactions. Although this process is essential for correct function of every living cell there is still a lot to be learned about it. In this tutorial Doctor Grzegorz Kudla talks about importance of- and mechanisms involved in RNA folding. He also discusses how computational approaches can help to advance this field of research. (The video is accesible without restrictions).

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Cracking the genetic code: what are proteins and how they are made

Dr Carolina Uggenti, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine (7 October 2019).

Proteins are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of the body’s tissues and organs. In this tutorial Doctor Carolina Uggenti describes how smaller units called amino acids can be combined to make proteins and how the sequence of amino acids determines each protein's unique 3-dimensional structure. (The video is accesible without restrictions).

Genetic causes of eye diseases

Dr Amy Findlay, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (18 November 2019).

Over 60% of cases of childhood blindness are caused by genetic factors (congenital glaucoma, ocular malformations, atrophy of the optic nerve and retinitis pigmentosa). In adults, genetic factors can also be associated with serious eye diseases, including glaucoma and macular degeneration. Learn more about genetic causes of eye diseases from this tutorial by Dr Amy Findlay (The video is accessible to University of Edinburgh affiliates only).

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What mass spectrometry can do for you?

Dr Jimi Wills, Mass Spectrometry Laboratory Manager, Institute of Genetics and Molecular Medicine (25 November 2019).

Mass spectrometry is a powerful analytical technique used to quantify known materials, to identify unknown compounds within a sample, and to elucidate the structure and chemical properties of different molecules. Its applications in biomedicine are numerous and continously expanding. Learn more about principles, instrumentation and utility of mass spectrometry in biomedical research from this tutorial by Dr Jimi Wills (The video is accessible to University of Edinburgh affiliates only).

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How to create a research cohort for health data science?

Prof David Porteous, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine (13 January 2020).

Building research cohorts for health data science is a very important but often difficult and time consuming task that requires careful planning and a lot of consideration. In this tutorial Professor David Porteous - one of the key figures behind the Generation Scotland project talks about  difficulties and benefits associated with establishing a well defined research cohorts for health data science. He also discusses how data secured through creation of  such cohorts can be accessed and used for the benefits of society. (The video is accesible without restrictions, appologies for some background noise).

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Super-resolution microscopy

Dr Ann Wheeler, Advanced Microscopy Resource, Institute of Genetics and Molecular Medicine (27 January 2020).

Recent developments in super-resolution fluorescence microscopy techniques allow the observation of many biological structures not resolvable in conventional fluorescence microscopy achieving a spatial resolution that is not limited by the diffraction of light. New advances in these techniques now give them the ability to image three-dimensional (3D) structures, measure interactions by multicolor colocalization, and record dynamic processes in living cells at the nanometer scale. Super-resolution fluorescence microscopy is becoming a widely used tool for cell and tissue imaging to provide previously unobserved details of biological structures and processes. The tutorial by Dr Ann Wheeler provides introduction to this technology and overwiews Edinburgh capabilities in this area. (The video is accessible to University of Edinburgh affiliates only).

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What is molecular pathology?

Prof Mark Arends & Prof Simon Herrington, Cancer Research UK Edinburgh Centre and Edinburgh Pathology, Institute of Genetics and Molecular Medicine (3 February 2020).

Pathology is the science of the causes and effects of diseases and as such constitutes an integral and very important part of disease-linked research activities. The tutorial by Professors Mark Arends and Simon Herrington provides an overview of molecular pathology - an area of pathology playing increasingly noticeable role in everyday hospital practice. (The video is accessible to University of Edinburgh affiliates only).

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What is drug discovery and how we do it?

Prof Neil Carragher, Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine (24 February 2020).

Drug discovery is a multi-million-pound business and one of the key-activities of the pharma -industry, but there is growing role for academia led drug discovery projects, particularly when it comes to novel approaches. In his tutorial Professor  Neil Carragher provides introduction to the drug discovery and overview of the changing drug discovery landscape with particular emphasis on multiparametric high-content phenotypic screening strategies. He also provides overview of drug discovery activities at the IGMM and the University of Edinburgh. (The video is accessible to University of Edinburgh affiliates only).

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How are genes regulated?

Prof Wendy Bickmore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (2 March 2020).

 Appropriate regulation of gene function is essential for the function of every living cell and abnormalities in this process are often linked to disease. Despite many years of intensive investigations we still know surprisingly little about mechanisms of gene regulation, particularly in complex multicellular organisms. In fact there is still a considerable debate on the definition of the "gene" itself. In her tutorial Professor Wendy Bickmore provides an overview of  our current knowledge of gene regulation with particular emphasis on gene regulation processes studied in IGMM. (The video is accessible to University of Edinburgh affiliates only).

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Clinical trials in breast cancer - the final frontier of lab research?

Prof David  Cameron, Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine (9 March 2020).

Clinical trials represent an essential step before new treatments can enter clinical practice. In his tutorial Professor David Cameron provides an overview of different types of clinical trials, design principles, methodologies used, difficulties encountered and many other "real life issues" that need to be considered.  Being both, a mathematician and a clinical trialist, he underlines the importance of proper stratification, data collection and data analysis approaches. (The video is accessible to University of Edinburgh affiliates only).

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How do genes evolve?

Prof Chris Ponting, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (21 September 2020).

Gene evolution is the process by which genes change in structure (sequence), size, number or location over time, it is part of the evolution of the genome. Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes, both prokaryotic and eukaryotic, available to the scientific community and the public at large. In this tutorial  Professor Chris Ponting provides  some insights into our current knowledge on how genes evolve. (The video is accessible to University of Edinburgh affiliates only).

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What is bioimage analysis?

Dr Peter Bankhead, Edinburgh Pathology, Centre for Genomic and Experimental Medicine & Cancer Research UK Edinburgh Centre,  Institute of Genetics and Molecular Medicine (5 October 2020).

Bioimage analysis is the process by which one extracts and processes data from scientific images. It focuses on the use of computational techniques to analyze bioimages, especially cellular and molecular images, at large scale and high throughput. The goal is to obtain useful knowledge out of complicated and heterogeneous images and related metadata. Dr Bankhead is expert bioimage informatician and the lead developer of QuPath - an open, powerful, flexible and extensible software platform for pathology image analysis.  In his tutorial he provides an easy to follow  introduction into the field of  bioimage analysis. (The video is accessible to University of Edinburgh affiliates only).

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Introduction to health economics

Alistair Bullen, Edinburgh Clinical Trials Unit (19 October 2020).

Health economics is a branch of economics concerned with issues related to efficiency, effectiveness, value and behavior in the production and consumption of health and healthcare. Although health economics often influence decisions made by health care providers and policy makers they are often slightly "esoteric" for many biomedical researchers. In his tutorial Alistair provides introduction to this field and methodology used by health economists. (The video is accessible to University of Edinburgh affiliates only).

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What is cellular senescence?

Dr Juan Carlos Acosta, Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine (2 November 2020).

Cellular senescence is often defined as irreversible cell cycle arrest that can be driven by a variety of mechanisms, but finer details of this process and its relevance to therapy of human diseases (in particular cancer) are more elusive and still subject of intensive investigation. In his tutorial  Dr Juan Carlos Acosta introduces this interesting topic to the lay audience. (The video is accessible to University of Edinburgh affiliates only).

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Genome editing and how it can be used for therapy

Dr Peter Tennant, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (16 November 2020).

Genome editing technologies enable scientists to make modifications to DNA, leading to changes in physical traits, like eye color, and disease risk. Scientists use different technologies to do this and in his tutorial Dr Peter Tennant provides overview of these technologies. He also discusses applications of genome editing in the targeted therapy of human diseases. (The video is accessible to University of Edinburgh affiliates only).

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Sort yourself out: introduction to innate immunity

Dr Carolina Uggenti, Centre for Genomic and Experimental Medicine,  Institute of Genetics and Molecular Medicine (18 January 2021).

Innate immunity (also called natural or native immunity) provides the early line of defence against microbes. It consists of cellular and biochemical defence mechanisms that are in place even before infection and are poised to respond rapidly to infections. In her tutorial Dr Carolina Uggenti provides an overview of this important topic. (The video is accessible to University of Edinburgh affiliates only).

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What is a complex trait?

Dr Pippa Thomson, Centre for Genomic and Experimental Medicine,  Institute of Genetics and Molecular Medicine (1 February 2021).

Complex traits, also known as quantitative traits, are traits that do not behave according to simple Mendelian inheritance laws and are often influenced by both environmental and genetic factors. In this tutorial Dr Pippa Thomson introduces this important topic to a lay audience discussing some of genetic, statistical and molecular approaches used to understand the genetic basis of complex human diseases like schizophrenia. (The video is accessible to University of Edinburgh affiliates only).

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What is RNA and how is it made?

Dr Christine Mordstein, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (8 February 2021).

In her tutorial Dr Christine Mordstein discusses the very basics of RNA biology with the aim of providing a broad overview of what RNA is and how it is made. She describes the key steps in RNA synthesis and processing (transcription, capping/splicing/polyadenylation etc) with the primary focus on protein-coding RNAs. Where applicable the importance of understanding RNA biology from a disease perspective is highlighted. (The video is accessible to University of Edinburgh affiliates only).

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The diverse world of non-coding RNA

Dr Catherine Heath, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (15 February 2021).

A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. ncRNAs are abundant and are very diverse as to their structure and functions, from transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), through small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and other ncRNAs with known/suspected functions, to some RNA transcripts of unknown functions. In her tutorial Dr Catherine Heath  introduces the diverse world of non-coding RNA to a lay audience. (The video is accessible to University of Edinburgh affiliates only).

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Biobanks, population cohorts and some ethical considerations

Dr Shona Kerr, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (1 March 2021).

Biobanks play increasingly important role in modern biomedical research providing breadth of valuable data that can be accessed and analysed by scientists for the benefit of the society. Shona plays a key role in the Viking Genes project (https://www.ed.ac.uk/viking) and in her tutorial she highlights challenges and opportunities associated with this project comparing it to some other biobanks. She also delves into the topic of return (or not) of actionable results from exome sequence data. The tutorial demystifies many aspects of modern biobanking projects. (The video is accessible to University of Edinburgh affiliates only).

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What can biology learn from soft matter (and vice-versa)?

Dr Davide Michieletto, School of Physics and Astronomy and Dr Mattia Marenda, Institute of Genetics and Molecular Medicine (15 March 2021).

Soft matter or soft condensed matter is a subfield of condensed matter comprising a variety of physical systems that are deformed or structurally altered by thermal or mechanical stress of the magnitude of thermal fluctuations. They include liquids, colloids, polymers, foams, gels, granular materials, liquid crystals, pillows, flesh, and a number of biological materials. In their talk Drs Michieletto and Marenda go through the following topics: (1) Macroscopic "soft matter” and cell behaviour (i.e. how cells and tissues interact with environment and among themselves); (2) Intracellular "soft matter”, organisation and function (i.e. viscoelastic properties of actin, DNA, proteins etc and why these matter for biological function); (3) Experimental methods and algorithms to quantify the above (rheology, microrheology, microscopy, particle tracking, tensiometry, relaxation modulus, etc). The tutorial is intended for a lay audience and should demystify many aspects of the soft matter research and its relevance to biological systems.(The video is accessible to University of Edinburgh affiliates only).

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An introduction to epigenetics and its role in cancer

Dr Donncha Dunican, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (29 March 2021).

In his tutorial Dr Donncha Dunican provides an introduction to epigenetics, defining this field of research and discussing DNA methylation and chromatin modifications. He describes some tools used in epigenetics research and gives examples of what can happen when epigenetics go wrong (particularly in the context of cancer and including examples of his own research). The tutorial helps to understand many aspects of modern epigenetics research. (The video is accessible to University of Edinburgh affiliates only).

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What can we do with genetically tractable model organisms?

Dr Cameron Wyatt, Zebrafish Facility Manager, Institute of Genetics and Cancer (12 April 2021).

Model organisms are non-human species that are used in the laboratory to help scientists understand biological processes. They have been widely utilised in biomedical research over the years, usually because they are relatively easy to maintain and breed in a laboratory setting and have particular experimental advantages. It is fair to say that many scientific breakthroughs would not be possible without proper use of model organisms. In his tutorial Dr Wyatt discusses different applications of animal models in biomedical sciences with particular emphasis on zebrafish. (The video is accessible to University of Edinburgh affiliates only).

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More tutorials coming soon...