Autophagy - A review of techniques
The third edition of “Guidelines for the use and interpretation of assays for monitoring autophagy” was recently published in the leading journal Autophagy, featuring the Earlham Institute's (EI) Autophagy Regulatory Network resource and co-authored by Dr Tamas Korcsmaros, Computational Biology Fellow at EI and Institute of Food Research (IFR).
In this comprehensive review with over 2,450 authors, the topics covered reflect the range of specialist fields within autophagy, and the diversity of animal, plant and fungal cell types that must inevitably invoke autophagy. Even within a single species or organism, the complexity is such that autophagy can be divided into many types.
Autophagy, in general, means ‘biological self-destruction’; it exists in all eukaryotes, including unicellular parasites, plants, fungi and animals. Autophagy is usually considered as a stress response mechanism used under conditions of starvation, infection and diseases such as cancer and neurodegeneration. It is also important in normal development, gut function, wound healing, and (healthy) ageing.
In such cases, autophagy involves the degradation of material in double membrane ‘autophagosomes’ within cells. As the core autophagy process involves several dozen proteins, their precise and context-dependent regulation requires many further proteins and different mechanisms.
The third edition of this Guideline review provides recommendations for best practices, particularly with regard to monitoring and measuring autophagy, and diagnosing/describing the type of autophagy being investigated – multiple assays are currently required and the appropriate choice of these depends upon the question at hand.
A major addition to this new version is the presentation of computational tools and resources developed in the last few years to assist autophagy researchers in data analysis and data sharing. One such resource featured in the review is the Autophagy Regulatory Network database1, which provides an integrated and systems-level source for autophagy research in humans.
The Autophagy Regulatory Network can be used to analyse autophagy for both global or for gene-specific studies. Currently, it contains data on more than 14,000 proteins, including 38 core autophagy proteins and 113 predicted regulators. A flexible download functionality enables users to customize and filter the database.
Dr Korcsmaros, who contributed the last chapter of the study, said: “We published the Autophagy Regulatory Network exactly one year ago. Since then, the cell biology and autophagy community have started to use it, provided feedbacks and allowed the analysis of autophagy-related systems at a level that was not possible before. Featuring this resource in this key publication (receiving over 2,000 reads just in the first two days), and listing TGAC and IFR among the 2,135 key institutes studying autophagy is a great acknowledgement of our work. We hope that this third edition will serve the community with relevant protocols and tools to study autophagy."
The publication, titled: “Guidelines for the use and interpretation of assays for monitoring autophagy” is published in Autophagy.2
EI is strategically funded by BBSRC and operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
Notes to editors.
Notes to editors
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About Earlham Institute
The Earlham Institute (EI) is a world-leading research institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) - £6.45M in 2015/2016 - as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities.
The Biotechnology and Biological Sciences Research Council (BBSRC) invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by Government, BBSRC invested over £509M in world-class bioscience in 2014-15 and is the leading funder of wheat research in the UK (over £100M investment on UK wheat research in the last 10 years). We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.
About the Institute of Food Research
The mission of the Institute of Food Research is to be an international leader in research that addresses the fundamental relationships between food and health, food and the gut and the sustainability of the food chain in order to further the production of safe, healthy foods. It is a company limited by guarantee, with charitable status.
IFR is one of eight institutes that receive strategic funding from the Biotechnology and Biological Sciences Research Council. IFR received a total of £17.9M investment from BBSRC in 2013-14.
The institutes deliver innovative, world class bioscience research and training, leading to wealth and job creation, generating high returns for the UK economy. They have strong links with business, industry and the wider community, and support policy development.
The institutes' research underpins key sectors of the UK economy such as agriculture, bioenergy, biotechnology, food and drink and pharmaceuticals. In addition, the institutes maintain unique research facilities of national importance.