Earth and Life Systems Alliance

The Earth and Life Systems Alliance (ELSA) is a strategic cornerstone of the Norwich Research Park (NRP). With its interdisciplinary approach to addressing the challenges of a changing climate, the Alliance not only carries out fundamental research but also applies the findings to real world scenarios.

elsa-logo

About the Earth and Life Systems Alliance

ELSA is built on the unique and world-class concentration of Earth and Life Scientists on the Norwich Research Park (NRP) which includes the University of East Anglia (UEA), John Innes Centre (JIC), The Sainsbury Laboratory (TSL) and The Earlham Institute (EI). Together, they have internationally renowned expertise in

  • Genetics and molecular biology of plants, animals and microbes
  • Biogeochemical cycles
  • Marine and atmospheric sciences
  • Population dynamics
  • Genomics and evolutionary genetics
  • Ecosystem services
  • Computer modelling

The aim of ELSA is to integrate and enhance internationally-excellent research in the Earth and Life Sciences across the NRP and to provide opportunities for ELSA researchers to exchange knowledge and develop new ideas for integrative, multidisciplinary research through scientific meetings, workshops, pump-priming projects and cross-NRP studentships. We also seek to attract world class researchers and fellows to the NRP, engage with funding agencies and stakeholders in promoting ELSA science and identify new funding opportunities to ensure development and sustainability of multidisciplinary research across the NRP.

Sea and sky

Some of ELSA’s scientists are studying fundamental processes at the level of individual genes and molecules in animals, plants and microbes. Together with other ELSA colleagues who are investigating species adaptation and evolution, the aim is understand how changes in biological processes can have larger scale impacts; for example, how single genetic mutations can trigger shifts in population numbers, species biodiversity and disrupt the balance of carbon and nitrogen in the oceans and atmosphere. Decisions around how land is used on the planet can alter entire landscapes and ecosystems, as well as affect societies and economies. These research outcomes are expected to directly inform policies around the use of resources and the environmental impact of various human activities.  ELSA microbiologists are brought together with other microbiologists on the Park through Microbes in Norwich.

The research agenda of the Alliance is focussed around three themes:

ELSA Research Fellowships

ELSA is seeking to attract the next generation of scientists to contribute to our world-class research.  ELSA supports outstanding individuals in their applications for Independent Research Fellowships (e.g. BBSRC, NERC, Marie Sklodowska-Curie, ERC, Leverhulme Trust) with the backing of our globally-renowned research institutions. Candidates who have research interests that fall broadly into the three key research themes of ELSA: Biodiversity and Adaptation, Elemental Cycles, and Food Security are invited to apply for our support. Key senior scientists at the NRP can help develop and enhance your Fellowship proposal, discuss your future research plans and provide expert advice on writing your Fellowship application whilst facilitating the potential to forge new collaborations.

If you are considering applying for a Fellowship in one of the ELSA themes then please contact us: j.c.murrell@uea.ac.uk or

Biodiversity and adaptation in the face of global environmental change

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Tracking Bustards. Robert J. Burnside, University of East Anglia. NRP Image Library 200

Pollution, crop monoculture, increased development activities, and changes in land use for food and fuel production are having dramatic consequences on ecosystems worldwide. Climate change is leading to novel weather patterns, including increasingly extreme weather events and dramatic variation in rainfall and temperatures. What exactly will be the impact of these changes on biodiversity as some species adapt successfully, or change their distribution, and others become extinct?

ELSA is providing the opportunity for researchers across the NRP to work synergistically to understand both the molecular basis of adaptation and its ecological impacts in a changing environment.

Central to the Biodiversity and Adaptation theme is a comprehensive understanding of existing populations adapted to contrasting habitats. Advanced genomic technologies and computer modelling approaches are being used to gain deeper understanding of how animals, plants and microbes adapt to their environment at the genomic and molecular levels. For example, research focuses on genetic adaptations that control the timing of reproduction of wild plants, the genetic and epigenetic evolution of plant pathogens such as the oomycetes Albugo candida and Phytophthora infestans, and plant resistance gene evolution. This knowledge will not only help inform rational breeding of crop varieties which are better adapted to changing climate around the world, but it will also further our understanding of the molecular basis of evolution.

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Vernalization in Arabidopsis. Caroline Dean and Andrew Davis, John Innes Centre. NRP Image Library 126

Linking the precise drivers of genetic and epigenetic adaptive variation with large scale consequences is a challenging goal that ELSA is uniquely placed to embrace. World-class research capacity in population genetics, genomics and population dynamics will feed directly into our understanding of the impacts of human intervention and climate change on biodiversity, as well as more targeted crop breeding programmes to develop crops better suited for changing environments.

Food security and global change

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Land and marine habitats are limiting resources in terms of food production, energy generation, conservation and urban development. Reconciling the increased demand for biofuels and renewable energy with the food security and conservation agendas is proving a major challenge. In addition, variation in land and water quality across the globe, coupled with local biotic and abiotic pressures, often limits the available options for plant cultivation. As weather patterns and temperatures across the globe are influenced by climate change, it is likely that new agricultural practices and crop varieties must be adopted in different regions of the world. In the marine environment, we already see fundamental changes in the productivity of many fished species and new threats and opportunities for aquaculture. As yet, it is unclear just what the conservation and socio-economic implications of this will be.

Researchers across the NRP are ideally placed to develop both practical solutions to these challenges as well as policy frameworks to shape decision-making about future use of the land and sea and ecosystem-based management. Traditionally these two approaches have not been aligned; however ELSA provides a forum through which communication and knowledge gaps between them are being addressed.

Within the University of East Anglia (UEA) there is extensive expertise in climate research, ecosystem management and terrestrial and marine biodiversity. These skills are uniquely complemented by the John Innes Centre’s (JIC) and The Sainsbury Laboratory’s (TSL) leading position in plant and microbial sciences relevant to the production of new and improved crops and the role of our strategic partner Cefas in aquatic food security and marine environmental management. Research into model plant systems, as well as commercially relevant crop species, is being leveraged to improve plant performance in the field.

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Specifically, ELSA is focussing on the role played by fundamental agricultural and aquatic sciences in shaping food production in the future, namely the potential to develop sustainable crop regimes, agricultural practices, aquaculture, and fisheries systems that complement the conservation agenda. A key goal is to ensure that high quality research is used to develop sustainable food production systems and underpin future policy decisions.

Within UEA there is significant expertise spanning the decision-support process, using qualitative and quantitative tools to develop participatory stakeholder approaches to policy changes. These skills are uniquely complemented by JIC’s and TSL’s leading position in plant and microbial sciences relevant to the production of new and improved crops. Experience with model crop systems is being translated to commercially relevant plant species to improve plant performance in the field.

Specifically, the Alliance is focussing on the role played by fundamental plant sciences in shaping agriculture in the future, namely the potential to develop sustainable crop regimes and agricultural practices that complement the conservation agenda. A key goal is to ensure that high quality plant research is utilised in agriculture systems and underpins future policy decisions within crop production.

Changes in agricultural practices and land-use, by definition, require accompanying policy decisions that influence global land-use. The aim of this pillar of the Alliance is to ensure these changes take place in tandem, by helping to model the implications of changes to land-use in the face of new approaches to land-use and climate change, and by ensuring suitable consultation and participation in the decision-making process.

Elemental cycles that sustain life and climate

Human activities are dramatically influencing the delicate balance of crucial elements in the Earth’s systems, leading to changes in the complex biogeochemical cycles of carbon, nitrogen and sulfur. These are the most important elements for biological systems and are often limiting factors to the survival of organisms. These elements exist in a variety of forms, for example, as gaseous compounds in the atmosphere, the cells of living organisms, or dissolved in seawater.

Understanding how elemental cycles interact is important at both the molecular and global levels. For example, some gaseous forms of nitrogen and carbon are powerful greenhouse gases, contributing to global climate change. Studied at the molecular and cellular levels, the production of these gases by soil microbes is crucial for efforts to combat climate change. An entire elemental cycle can respond to the levels of specific compounds and global biogeochemistry becomes altered. Maintaining the balance of terrestrial and aquatic ecosystems requires more sustainable practices. This equilibrium is now more under threat than ever before.

Within ELSA, an understanding of the individual biological processes at the cellular level in plants and microbes is being integrated with extensive knowledge of global biogeochemical cycles. There is long-standing research excellence centred around biological nitrogen fixation and carbon utilisation in plants. Other groups are focussing on the transport and metabolism of nitrogen and metals by plants and microbes. The University of East Anglia is internationally renowned for its expertise in climate system analysis, Earth System modelling and global biogeochemical cycling.

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Seaweeds and trace gases, Gill Malin, University of East Anglia. NRP Image Library 157

There is also a strong nucleus of environmental microbiologists who study cycling of carbon, nitrogen and sulfur in terrestrial, freshwater and marine environments, from the molecular and cellular level through to whole system analysis. Of particular interest is the microbial cycling of biogenic trace gases such as methane, nitrous oxide, dimethyl sulfide and isoprene, all of which affect our climate.

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Methane monooxygenase, Thomas Smith and Colin Murrell, University of East Anglia. NRP Image Library 131

ELSA expertise across the NRP facilitate an integrated study of natural biological processes involved in elemental cycling, as well as an understanding of their roles throughout evolution. A better understanding of the natural processes involved in elemental cycling will help ameliorate the effects of climate change, through changes to agricultural systems and ecosystem management. This includes for example, the potential role of biochar carbon sequestration in soils and sediments, or more efficient use of nitrogen by crops to reduce the levels of fertilisers needed. Expertise in climate system analysis and global biogeochemical cycles is enabling ELSA researchers to undertake integrated research into the biological systems involved in elemental cycling. This will provide a mechanistic understanding of the regulation of elemental cycles with the aim of developing more sustainable practices and mitigation strategies to counter the effects of human activities on these cycles.

Meet The Team


Colin Murrell
Prof Colin Murrell

Director
j.c.murrell@uea.ac.uk
01603 592959
Website

My research group studies the vital role that microbes play in consuming climate active gases and volatile organic compounds such as methane, methanol, isoprene and dimethylsulfide before they are released into the atmosphere. We investigate the metabolism and ecology of these microbes in terrestrial, marine and freshwater environments using cutting edge ecophysiology, molecular ecology, genomics and metagenomics techniques.

Cock van Oosterhout
Cock van Oosterhout

C.Van-Oosterhout@uea.ac.uk
01603 592921
Website

Given the wealth of Next Generation Sequence (NGS) data, it is an exciting time to be an evolutionary geneticist. My group uses NGS data to address big evolutionary questions that are relevant to conservation biology, host parasite co-evolution and adaptation to changing environments. We are working on various organisms, including fish (guppies, cichlids and salmon), birds (the pink pigeon and the Seychelles warbler), and numerous pathogens and parasites (e.g. gyrodactylids, the oomycete Albugo candida and aphids). We are also developing novel software applications to analyse genome data.

Levi Yant
Levi Yant

levi.yant@jic.ac.uk
01603 450799
Website

We study wild populations to determine how evolution finds solutions to difficult challenges, focusing on the repeatability of intracellular adaptation to whole genome duplication and as well as to severe environmental challenges. We can pinpoint the footprints of these selection events at the single gene level by leveraging population genome scanning approaches to detect selective sweeps and to understand patterns of gene flow across landscapes.

Kirsten Bomblies
Kirsten Bomblies

Kirsten.bomblies@jic.ac.uk
01603 450015
Website

My research group studies the evolution of meiosis in response to environmental and genomic challenges. It is clear that stresses such as temperature extremes and genome duplication can impair the core structural process of chromosome pairing, synapsis and recombination, yet many wild plants and animals have evolved solutions that allow them to remain fertile in conditions others cannot sustain. We employ genetic, genomic and molecular tools to understand the mechanistic basis underlying both the causes and consequences of the evolution of meiosis.

Jennifer Pratscher
Jennifer Pratscher

J.Pratscher@uea.ac.uk
Website

My research focuses on identifying and characterising atmospheric methane oxidizing bacteria in soils, combining single cell genomics with targeted isolation approaches and proteomics. In particular, we want to determine the impact of global warming and land use change on the activity of this group of bacteria and thus their contribution to the global sink strength of soils for atmospheric methane.

Theme Leaders


Biodiversity and adaptation in the face of global environmental change
Caroline Dean

Website

Research interests: Mechanisms and pathways of vernalization; regulators of plant reproductive strategies; FLC regulation on conserved chromatin silencing and non-coding RNAs in Arabidopsis adaptation.


Alistair Grant

Website

Research interests: Effects of climate change on Arabidopsis; rhizosphere microbial communities.


David Richardson

Website

Research interests: Evolutionary and behavioural ecology; molecular ecology; conservation of endangered island bird species.


Elemental cycles that sustain life and the planet
Tony Miller

Website

Research interests: Cell and molecular biology of nitrogen acquisition and signaling; membrane protein families that can transport nitrogen; plant/soil interface and rhizosphere processes.


Gill Malin

Website

Research interests: Biogenic production of trace gases; biological oceanography; biogeochemistry; the commercial exploitation potential of algae; effects of climate change on marine organisms.


Tom Clarke

Website

Research interests: Characterisation of enzymes that contain metal cofactors.


Food security and global change
Cristobal Uauy

Website

Research interests: Molecular genetic approaches in crop species.


Kevin Hiscock

Website

Research interests: Hydrology and hydrogeology; natural groundwater chemistry; stable isotope and dissolved gas applications in hydrogeology; contaminant hydrogeology; water resources management.


Shaun McGuire

Website

Research interests: Environment and development; technology and agrarian development; genetic resources management; farming systems ecology; biosafety.

ELSA Researchers


Faculty members and group leaders with ELSA focussed research interests located at one of the Norwich Research Park’s science partners are listed below.  For further information click on the name to link to the person’s homepage.

Name Affiliation Theme Research interests
Julian Andrews University of East Anglia Elemental Cycles Reconstruction of past environmental and climatic conditions using geochemistry and stable isotopes; historical carbon storage and nutrient cycling on coastal margins and their impact on society
Katy Appleton University of East Anglia Food Security Development of sustainable, multi-functional landscapes in rural areas; GIS analysis
Alex Baker University of East Anglia Elemental Cycles Atmospheric nutrient supply to the oceans; influences on iron solubility in aerosols; marine and atmospheric iodine cycling; trace metals and their impact on the marine carbon cycle
Dorothee Bakker University of East Anglia Elemental Cycles Oceanic carbon cycling; oceanic uptake of carbon dioxide; the role of biogeochemical cycles in climate change
Janneke Balk John Innes Centre Elemental Cycles Iron in plants and microbes
Brian Bandy University of East Anglia Elemental Cycles Atmospheric Trace Gases, particularly peroxides in the boundary layer and free troposphere
Mark Banfield John Innes Centre Biodiversity and Adaptation Structural biology of host-pathogen interactions; host-plant immunity and response of plant pathogens
Mike Bevan John Innes Centre Food Security  Genetics, biochemistry and physiology in the experimental plant Arabidopsis thaliana; structure and evolution of plant genomes; wheat genome sequencing and the influence of polyploidy on gene function and composition
Rosalind Boar University of East Anglia Biodiversity and Adaptation Limnology and ecology of East African lakes; nutrient and carbon cycling in shallow freshwater lakes; ecology and nitrogen dynamics in perennial swamp plants
Kirsten Bomblies John Innes Centre Biodiversity and Adaptation Adaptation to whole genome duplication; biogeography and habitat adaptation; evolutionary dynamics of interacting genes
Andrew Bourke University of East Anglia Biodiversity and Adaptation Evolutionary, ecological and genetic basis of social behaviour; conservation ecology and genetics of wild bees
James Brown John Innes Centre Food Security Breeding crops for disease resistance; trade-offs involving disease resistance; host-parasite coevolution
Erik Buitenhuis University of East Anglia Biodiversity and Adaptation Global ocean biogeochemical modelling; feedbacks between ocean ecosystems and climate change; eco-physiology
Simon Butler University of East Anglia Biodiversity and Adaptation Biodiversity conservation in agro-ecosystems; ecosystem services; frameworks for selecting indicator species
Julea Butt University of East Anglia Elemental Cycles Redox enzymes that Cycle N, Fe and S
Tracey Chapman University of East Anglia Biodiversity and Adaptation Evolution, sexual selection and sexual conflict for driving evolutionary change; improving control of pest insects by understanding mechanisms of reproductive success
Myles R. Cheesman University of East Anglia Elemental Cycles MCD and EPR spectroscopy to study proteins containing transition metal ions
Tom Clarke University of East Anglia Elemental Cycles Characterisation of enzymes that contain metal cofactors
Enrico Coen John Innes Centre Biodiversity and Adaptation Leaf development in Arabidopsis
Mark Coleman University of East Anglia Food Security Plant pathology and responses to stresses that damage DNA; biofuels and alternative crops
Richard Davies University of East Anglia Biodiversity and Adaptation Evolutionary and ecological determinants of biodiversity at different spatial scales; functional diversity and community assembly
Caroline Dean John Innes Centre Biodiversity and Adaptation Mechanisms and pathways of vernalization; regulators of plant reproductive strategies; FLC regulation on conserved chromatin silencing and non-coding RNAs in Arabidopsis adaptation
Paul Dennis University of East Anglia Elemental Cycles Stable isotope geochemistry; in-situ cosmogenic isotope chemistry; noble gas chemistry; terrestrial and marine palaeoclimate analysis; landscape evolution; hydrology and hydrogeology; isotopic oceanography; atmospheric chemistry; stable isotope instrumentation and techniques
Ray Dixon John Innes Centre Elemental Cycles Response of bacteria to environmental signals and their adaptive responses; signal transduction cascades regulating nitrogen fixation genes
Paul Dolman University of East Anglia Biodiversity and Adaptation Evidence based conservation; landscape scale population processes; conservation in anthropogenic landscapes
Stephen Dorling University of East Anglia Food Security Effects of weather and climate on food, water and energy security; effects of weather and climate on disease resistance in wheat and flowering in Brassica
Aldina Franco University of East Anglia Biodiversity and Adaptation Climate change; habitat fragmentation; dispersal and migration; selection of priority areas for conservation; agri-environmental policies; biodiversity conservation
Matt Gage University of East Anglia Biodiversity and Adaptation Reproduction; sexual selection and conflict; the evolution of sperm form and function
Andrew Gates University of East Anglia Elemental Cycles Use of molecular genetics, biochemical and biophysical methods in studying molecular enzymology and microbial physiology in nitrogen and iron cycles
Jenny Gill University of East Anglia Biodiversity and Adaptation Ecology and evolution of migratory systems; applied understanding and management of impacts of environmental changes on biodiversity
Phil Gilmartin University of East Anglia Biodiversity and Adaptation Gene regulation and flower development; genetic mechanisms of reproductive strategies
Alastair Grant University of East Anglia Biodiversity and Adaptation Effects of climate change on Arabidopsis; rhizosphere microbial communities
Simon Griffiths John Innes Centre Food Security Wheat genetics
Kevin Hiscock University of East Anglia Food Security Hydrology and hydrogeology; natural groundwater chemistry; stable isotope and dissolved gas applications in hydrogeology; contaminant hydrogeology; water resources management
Saskia Hogenhout John Innes Centre Food Security Molecular-plant-microbe-insect interactions; plant-insect-pathogen interactions
Matt Hutchings University of East Anglia Biodiversity and Adaptation Bioactive compounds in Streptomyces; formation and role of microbiomes on the fitness and reproduction of animal hosts
Judith Irwin John Innes Centre Food Security Vernalization response in Brassica oleracea and implications of climate change for crop scheduling
Simon Jennings University of East Anglia Biodiversity and Adaptation Population, community and ecosystem ecology; biodiversity; macroecology; food webs; life histories; stable isotope analysis; fisheries ecology and management; food security, environmental management systems and policy
Tim Jickells University of East Anglia Elemental Cycles Nutrient cycling in estuaries and coastal waters; impacts of atmospheric inputs on ocean biogeochemistry
Martin Johnson University of East Anglia Elemental Cycles Marine biogeochemistry and the nitrogen cycle
Andrew W B Johnston University of East Anglia Elemental Cycles Microbial cycling of organic sulfur compounds; biogeochemical cycles
Jonathan Jones Sainsbury Laboratory Food Security Molecular and genetic approaches to study disease resistance in plants; pathogen resistance
Tove H Jorgensen University of East Anglia Biodiversity and Adaptation Evolution of disease resistant genes in Brassicaceae; ecological and evolutionary forces in driving and maintaining biodiversity
Manoj Joshi University of East Anglia Elemental Cycles Climate change; palaeoclimates; radiative forcing and physical climate response, land-sea warming contrast; stratospheric processes and climate; biogeochemical processes and the physical climate
Jan Kaiser University of East Anglia Elemental Cycles Stable isotope measurements of atmospheric gases and aerosols and air-sea exchange; marine and terrestrial biogeochemistry
Sophien Kamoun Sainsbury Laboratory Food Security Evolution, genomics and genetics of oomycetes
Vinod Kumar John Innes Centre Food Security Environmental modulation of plant-pathogen interactions; gene regulation
Iain Lake University of East Anglia Food Security Environment, weather and health; climate change and health; water supply; GIS; transfer of organic pollutants into the food chain from river flooding
Bruce Lankford University of East Anglia Food Security Water resource planning and management; river basin management; irrigation systems analysis; community-based irrigation; design management interactions; conflict resolution and natural resource gaming
Nick Le Brun University of East Anglia Elemental Cycles Metal metabolism and toxicity in bacteria; O2 and stress sensing via metallo-regulators
Laura Lehtovirta-Morley University of East Anglia Elemental Cycles Ecology and physiology of microorganisms, terrestrial nitrogen cycle. ammonia oxidising archaea, global nitrogen cycle
Corinne Le Quere University of East Anglia Elemental Cycles Carbon dioxide emissions, climate and global change; response of the ocean carbon cycle to climate variability and change
Peter Liss University of East Anglia Elemental Cycles Environmental chemistry; biogeochemical interaction between the oceans and atmosphere; global change
Andrew Lovett University of East Anglia Food Security Applications of GIS and statistical methods in the environmental sciences; landscape planning and visualisation
Gill Malin University of East Anglia Elemental Cycles Biogenic production of trace gases; biological oceanography; biogeochemistry; the commercial exploitation potential of algae; effects of climate change on marine organisms
Jake Malone John Innes Centre & University of East Anglia Food Security Molecular mechanisms underlying bacterial signal transduction during responses to the environment
Shawn McGuire University of East Anglia Food Security Environment and Development; Technology and agrarian development; biology; ecology; ecology; genetic resources management; farming systems ecology; biosafety
Thomas Mock University of East Anglia Biodiversity and Adaptation Marine biogeochemical cycles; metagenomics ; transcriptomics ; physiological adaptation; diatom biology; photosynthesis; polar biology; biochemistry; biological oceanography
Richard Morris John Innes Centre Elemental Cycles Legume symbioses; plant biomechanics
Jeremy Murray John Innes Centre Food Security Arbuscular mycorrhization and nodulation
Colin Murrell University of East Anglia Elemental Cycles Microbiology of trace gases; biogeochemical cycles
Paul Nicholson John Innes Centre Biodiversity and Adaptation / Food Security Genetics and mechanisms of resistance to facultative pathogens of cereals
Giles Oldroyd John Innes Centre Elemental Cycles The legume-rhizobial symbiosis; signalling and engineering nitrogen fixation in cereals
Timothy Osborn University of East Anglia Elemental Cycles Climate variation causes; climate change projections; rainfall and atmospheric circulation changes
Lars Ostergaard John Innes Centre Food Security Genetic and hormonal regulation of fruit development in Brassica (oilseed rape)
Nikolai Pedentchouk University of East Anglia Elemental Cycles Development of compound-specific isotopic proxies for palaeohydrological and palaeoclimatic studies using modern terrestrial vegetation; climate change
Carlos Peres University of East Anglia Biodiversity and Adaptation Animal and plant biodiversity in Amazonian forests; reserve selection and design criteria in relation to regional gradients of biodiversity value
Jennifer Pratscher University of East Anglia Elemental Cycles Microbial molecular ecology; microbes involved in the uptake of atmospheric trace gases; effects of global warming and land-use change on microorganisms
Claire Reeves University of East Anglia Elemental Cycles Atmospheric chemistry and greenhouse gases
Brian Reid University of East Anglia Elemental Cycles Soil; biochar; agrochemicals; biogeochemistry; soil-contaminant-microbe interactions
David J  Richardson University of East Anglia Elemental Cycles Microbiology and biochemistry of nitrogen and iron cycling
David S Richardson University of East Anglia Biodiversity and Adaptation Evolutionary and behavioural ecology; molecular ecology; conservation of endangered island bird species
Christopher Ridout John Innes Centre Food Security Control of pests and diseases in crops
Carol Robinson University of East Anglia Biodiversity and Adaptation / Elemental Cycles Ecology and biogeochemistry of marine plankton ecosystems
Bill Sturges University of East Anglia Elemental Cycles Atmospheric trace gases and their importance for stratospheric ozone depletion, global warming, and as components of air pollution
Parv Suntharalingam University of East Anglia Elemental Cycles Biogeochemical cycles of carbon, nitrogen and sulfur; constraints from other chemical species on carbon cycling processes; numerical modelling; inverse analysis methods
Jon Todd University of East Anglia Elemental Cycles Bacterial metabolism of organic sulfur compounds; biogeochemical cycling
Trevor Tolhurst University of East Anglia Biodiversity and Adaptation Sedimentological dynamics; ecological structure and functioning of intertidal coastal environments; mediation of coastal dynamics by complex interactions
Cristobal Uauy John Innes Centre Food Security Molecular genetic approaches in crop species
Cock van Oosterhout University of East Anglia Biodiversity and Adaptation Evolution, population genetics and genomics of oomycete plant pathogens, Arabidopsis, diatoms, fish and birds
Naomi Vaughan University of East Anglia Food Security Mitigating carbon dioxide emissions; negative emissions and climate geo-engineering
Rachel Warren University of East Anglia Food Security Global climate policy; integrated assessment modelling; impacts of climate change on human systems and ecosystems; air pollution; stratospheric ozone depletion; economics of climate policy
Nicholas Watmough University of East Anglia Elemental Cycles Enzymes of the biological nitrogen cycle
Levi Yant John Innes Centre Biodiversity and Adaptation Repeatability of intracellular adaptation to whole genome duplication and severe environmental challenges; focused genome scans for selective sweeps
Sarah Yeates University of East Anglia Biodiversity and Adaptation Ecology and conservation; mutualisms and conservation
Ji Zhou Earlham Institute Food Security Using high-resolution and high-frequency in-field crop phenotypic measures to facilitate the assessment of genes controlling yield potential and environmental adaptation

Fish provide insight into the evolution of the immune system

New research from the University of East Anglia (UEA), UK, and Dalhousie University, Canada, reveals how immune systems can evolve resistance to parasites.
A study, published today in Nature Communications, solves the enigma of how species can adapt and change their immune system to cope with new parasitic threats – whilst at the same time [Continue reading»]

Anglers’ delight as algal blooms breakthrough highlights innovative science

Millions of fish-deaths caused by toxic Prymnesium algal blooms could be prevented with the application of a household chemical best known for bleaching hair, breakthrough research has revealed.
Trials carried out in the Norfolk and Suffolk Broads National Park have shown that at controlled concentrations hydrogen peroxide (H2O2) is deadly to Prymnesium parvum, the golden [Continue reading»]

Q and A with Sarah Worsley

Sarah is a PhD student working with Matt Hutchings (School of Biological Sciences, UEA and co-supervised by Colin Murrell, School of Environmental Sciences, UEA). Visit Matt’s website to find out more about this exciting work.
What is the background of your work?
Almost all eukaryotic organisms interact closely with a large number of microorganisms that [Continue reading»]

Interview with Colin Murrell – ELSA Director

Colin Murrell is a Professor in Environmental Microbiology, Director of the Earth and Life Systems Alliance (ELSA), Acting Chair for the 2017 Applied and Environmental Microbiology Gordon Research Conference and current President of ISME. As if that wasn’t enough, Colin is still heavily involved in many areas of research in his lab at UEA.
The [Continue reading»]

Save the Pink Pigeon!

The pink pigeon is an important conservation successes. Reduced to just 10 wild birds in 1990, this cousin of the Dodo now numbers in the 100s. However, the species maintains Endangered status, with over 60% of fledglings succumbing to a pathogen introduced by humans. This project will identify genes and gene variants that enable birds [Continue reading»]

Green peach aphid develops taste for diverse food sources

Host-parasite coevolution often results in specialisation of parasites via genetic adaptation to a small number of host species. However, the green peach aphid (Myzus persicae) colonises plant species across 40 families. Most remarkably, genetically identical individuals from the same clonal lineage can colonise distantly related plants, which makes M. persicae a highly destructive pest. Research [Continue reading»]

Genome sequence of a polar alga explains evolutionary adaptation to extreme and variable climates

An international team of researchers has identified the genetic mutations which allowed microalgae (phytoplankton) from the Southern Ocean to adapt to extreme and highly variable climates – a step towards understanding how polar organisms are impacted by climate change.  The team led by Prof Thomas Mock from the University of East Anglia (UEA) School of [Continue reading»]

As well as attracting funding from external sources such as research councils, charitable and philanthropic organisations and commercial partners, ELSA uses its own internal funding to support Norwich Research Park research projects. A selection of the funded projects can be seen below.

As well as attracting funding from external sources such as research councils, charitable and philanthropic organisations and commercial partners, ELSA uses its own internal funding to support Norwich Research Park research projects. A selection of the funded projects can be seen below.

Novel temperature sensing mechanisms that modulate disease

Investigators
Vinod Kumar (JIC), Alastair Grant (UEA)
Background
Climate change, most importantly increasing global temperatures associated with it poses a severe threat to global agriculture and biodiversity. The average growing season temperatures is expected to exceed historical extremes by the end of 21st century. Elevated temperatures cause increased susceptibility to pathogens resulting in increased [Continue reading»]

Investigation of long-term transpiration in wheat using stable hydrogen isotope composition of leaf waxes

Investigators
Nikolai Pedentchouk (UEA), Cristobal Uauy (JIC)
Background
Knowing various aspects of plant physiology is important for understanding the role of feedbacks between terrestrial vegetation and the global carbon and hydrological cycles. Recent global climate models incorporate evapotranspiration from land as one of the key components that influence water movement among the continents, ocean, and [Continue reading»]

Mining Biodiversity within Marine sponges for Bioactive compounds

Investigators
Lisa Crossman (UEA, SequenceAnalysis.co.uk), Matt Hutchings (UEA), Merv Bibb (JIC),  Jonathan Kennedy (UCC), Alan Dobson (UCC)
Background and Aims
The order Actinomycetales is a known source of novel bioactive compounds. An original belief that these organisms were restricted to terrestrial niches was recently discarded (Martinez et al., 2013).  Marine sponges harbour a wealth of [Continue reading»]

The Nannochloropsis oceanica (Yellow Sea, Qingdao) genome: gene mining by comparative genomics and RNA sequencing

Investigators
Thomas Mock (UEA), Vincent Moulton (UEA), Mario Caccamo (TGAC)
Background
Nannochloropsis belongs to the group of Heterokontophyta, a diverse algal group that includes brown algae and diatoms. The plastid of this alga is surrounded by four membranes derived from a secondary endosymbiotic event. Strains from this genus have been investigated for their lipid [Continue reading»]

How does sexual selection shape a genome?

Investigators
Matt Gage (UEA), Saskia Hogenhout (JIC)
Background
Sexual selection, Darwin’s second great idea, is an evolutionary force that acts on almost every species on earth involved in the struggle to sexually reproduce. In this ELSA project, we will aim to understand how sexual selection acts on the genome. The big question we ultimately plan [Continue reading»]

Connecting the Carbon Cycle to Iron Metabolism using Functional Genomics and Microbial Physiology

Investigators
Tom Clarke (UEA), Gary Rowley (UEA), Lisa Crossman (TGAC)
Background
Iron oxidising bacteria and iron reducing bacteria control the availability of soluble metal ions in a range of different environments, yet little is known about the microbial physiology of iron oxidising bacteria and whether the two types of bacteria exist independently or symbiotically.  The [Continue reading»]

Molecular mimicry and the hijacking of sex determination mechanisms in dioecious Silene dioica by the anther smut fungus Microbotryum violaceum.

Investigators
Phil Gilmartin (UEA), Sophien Kamoun (TSL)
Background
Silene dioica (red campion) and Silene latifolia (white campion) are two dioecious species with the Caryophyllaceaea that share a common XY sex determination mechanism that evolved prior to speciation.   Males are the heterogametic sex and possess a dominant Y chromosome.  Females are homogametic and possess two [Continue reading»]

Mechanisms driving changes in migratory behaviour on long lived birds in response to global environmental change

Investigators
Aldina Franco (UEA), David Richardson (UEA)
Background
The migratory patterns of animals are changing in response to global environmental change. Previously wholly migratory species wintering in Sub-Saharan Africa now have resident populations in Southern Europe. The causes of these changes are not fully established but both climate change and increased winter food availability have [Continue reading»]

Population genomics and evolution of Albugo candida plant pathogen

Investigators
Cock van Oosterhout (UEA), Jonathan Jones (TSL), Matt Clark (EI)
Background
Albugo candida is a fungus-like parasite which is an obligate biotroph, living off live plant tissue. Unlike other Albugo spp. which are species specific, A. candida consists of different races that can infect >200 host plant species. It causes “white blister” disease on [Continue reading»]

Established Projects

Should this be fed from posts?

Software

ELSA scientists have designed software to detect null alleles and other scoring errors in microsatellite analysis of population genetic data (Micro-Checker). In addition, they are currently developing software for the detection, visualisation and dating of recombination events and introgression in genome sequence data for evolutionary genetic analyses (HybRIDS vs. 1.0). Both software applications are made available through this site under the links below.

Microchecker

HybRIDS

Microchecker

Microsatellite Data Checking Software
Micro-Checker is a Windows application that checks for microsatellite null alleles and scoring errors. It also provides null allele estimates, and adjusts allele and genotypes frequencies.

By Cock van Oosterhout, Bill Hutchinson, Derek Wills and Peter Shipley

Abstract
Genetic studies that utilise archived, archaeological or extracorporeal samples (e.g. hairs, blood, feathers) are often hindered by low template DNA concentrations and/or the presence of polymerase chain reaction (PCR) inhibitors. Where microsatellite loci are specifically targeted, such factors may result in the incorrect assignment of microsatellite genotypes. Genotyping errors may also arise in studies using fresh DNA, where primer-site mutations result in non-amplified alleles (null alleles), and PCR artefacts cause large allele drop-out (i.e. short allele dominance) and stuttering. Such errors can cause deviations from Hardy-Weinberg equilibria, and may bias both spatial and temporal population genetic analyses.

MICRO-CHECKER is a Windows-based software package for Windows 98 SE, 2000 and XP (not yet tested on NT or ME), which can test the genotyping of microsatellite data from diploid populations. The program aids the identification of various genotyping errors, and can also detect typographic errors. MICRO-CHECKER estimates the frequency of null alleles at a locus using a series of algorithms. Importantly, MICRO-CHECKER can also adjust allele and genotype frequencies of the amplified alleles, which allows the data to be used in further population genetic analysis, for instance with GenePop, Arlequin or Fstat.

There are two versions of the Micro-Checker software. The first version is designed to be installed on the computer. If the user is unable to install the program (the user may not have the required administrator rights, for example), a second version is available that can be run directly from the folder where it has been unzipped.

Downloads

MicroChecker 2.2.3 (Installed Version) – (18.6mb) MicroChecker 2.2.3 (Stand-alone Version) – (19.7mb)

Related Downloads

Molecular Ecology Notes Paper – PDF (128.3kb)Inbreeding Corrected Null Allele Estimator – Excel (264.0kb)

This is an electronic version of an article published in Molecular Ecology Notes: complete citation information for the final version of the paper, as published in the print edition of Molecular Ecology Notes, is available on the Blackwell Synergy online delivery service, accessible via the journal’s website at http://www.blackwellpublishing.com/men or http://www.blackwell-synergy.com

HYBRIDCHECK

HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant blocks in genome sequence data

Benjamin Ward and Cock van Oosterhout

University of East Anglia, Norwich Research Park, Norwich, UK

email: Ben.Ward@sainsbury-laboratory.ac.uk and c.van-oosterhout@uea.ac.uk

HYBRIDCHECK (Hybridisation, Recombination, Introgression, Dating Software) is a bioinformatics tool designed to visualize the signal of recombination (and genetic introgression) in DNA sequence data present in large (multiple kb) contigs and whole genome sequence data of three or more individuals.It reports several summary statistics of these events, including breakpoint positions, number of SNPs, and it estimates the age of the recombination event. HYBRIDCHECK can also be applied to analyse smaller amplicons (1kb), as well as high density SNP data.Its primary use is to inform users about the prevalence of recombination, visualize the recombination blocks and the mosaic-like genome structure, calculate the divergence time of each block, and hence, date the age of each recombination event.

HYBRIDCHECK has a user-interface, and it is simple and relatively fast to run. The output of HYBRIDCHECK aims to direct the user to more computationally-intensive phylogenetic and population genetic analyses, e.g. to confirm the recombination events with multiple algorithms present in RDP3 (Martin et al. 2010), and/or date the divergence of the recombination blocks in a Bayesian framework, e.g. in BEAST (Drummond et al. 2012).

The analysis with HYBRIDCHECK consists of the following three-steps:

  1. Load nucleotide data in FASTA format into the R environment using the user interface.
  2. Analyse the sequence similarity of all possible sequence triplets with a sliding window approach.
  3. HYBRIDCHECK detects recombination blocks and calculates summary statistics for each recombination block (i.e. number of SNPs, breakpoint positions, length of recombination block, the probability that sequence similarity is caused by mutations rather than by recombination). HYBRIDCHECK also draws graphs of contigs illustrating the location of recombination blocks relative to base position, and it estimates the mean (5-95%CI) coalescence time of each recombination block, and it thereby dates each recombination event.Click here to visit the site and code repository that is curated by the team. It will be the most up to date with improvements and bugfixes in the future.

The three links below link directly to the most up to date versions of the software in the HYBRIDCHECK repository.

OSX: http://ward9250.github.io/HybridCheck/Installers/OSX/HybridCheck.app.zip

Windows: http://ward9250.github.io/HybridCheck/Installers/Windows/HybridCheckInstaller.EXE

Linux: http://ward9250.github.io/HybridCheck/Installers/Linux/HybridCheck_Linux_Installer.zip

It is recommended that new users follow the instructions on how to install from the R console, and also with Docker at this link:  http://ward9250.github.io/HybridCheck/use_HybridCheck.html

When using HYBRIDCHECK please cite:

Ward BJ, van Oosterhout C. 2016 HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data. Mol Ecol Resour. Mar;16(2):534-9.


Earlham institute
Quadram Institute Bioscience
John Innes Centre
The Sainsbury Laboratory
NHS NNUH
University of East Anglia

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