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HAPE Core researchers


Dr Lisa M. Avery

Lead -  Centre for Human and Animal Pathogens in the Environment

Lisa is a senior environmental microbiologist in the Environmental and Biochemical Sciences group. She is interested in pathogen transport and survival (in particular E. coli O157: H7 and Mycobacterium paratuberculosis and Clostridium species) in environmental matrices including water, soil and organic wastes. Lisa is currently involved in understanding changes in pathogen transmission in Sub-Saharan Africa through the implementation of biogas digesters for treatment of organic wastes. She is involved in applying a novel microbial source apportionment approach to surface waters and is also responsible for research into pathogen and indicator prevalence in Scottish water bodies. Other recent work has focused on identifying factors affecting E. coli adsorption to clay colloids and stream biofilms; determining what drives E. coli transport and longevity within streams and identification of pathogens which could contaminate organic wastes applied to land. In addition, she has an active interest in wastewater treatment and reuse.

Professor Ian Toth

Ian Toth

Ian is a bacteriologist in the Cell and Molecular Sciences group working on bacterial plant and animal pathogens from the family Enterobacteriaceae. He has worked on the interaction between species of Pectobacterium / Dickeya / Erwinia / Pantoea and their plant hosts for over 25 years and has, for the last 10 years, undertaken genome sequencing and functional genomics of these pathogens to better understand the molecular bases of these interactions. In 2006, he published with Leighton Pritchard a genomic comparison between plant and human enteobacterial pathogens (Toth et al. 2006), where it was revealed that horizontally-acquired DNA in human/animal pathogens may play a role in the interaction with plants. These finding are currently being investigated through his collaboration with Nicola Holden and Leighton Pritchard. In addition, he has been involved with Nicola and Leighton in the development of genome-based methodologies for the production of realtime diagnostic primers and probes for both human and plant pathogens. This has led to the production of strain-specific diagnostic primer sets for E. coli O104:H4 involved in a foodborne outbreak in Germany in 2010 (Pritchard et al. 2012).

Dr Nicola Holden

Nicola Holden

Nicola is a molecular microbiologist in the Cell and Molecular Sciences group principally interested in the interactions between human pathogens and plants. Ready-to-eat and minimally-produced foods have been associated with food-borne outbreaks. Pathogenic bacteria can cycle from farm animals into the wider environment and plant crops, where they pose a threat to human and animal health. One of the first stages in the interactions between bacteria and any host is adherence of the bacterial cell to the host tissue. Often adherence is mediated by surface-expressed organelles protruding from the bacterial cells, which target specific receptors present on the host cell surface. Part of the work is to identify whether any bacterial organelles mediate binding to plant tissue, and if so, which plant molecules are they targeting. We are also interested in how the plant affects bacterial gene expression and whether there are any differences between plant species and bacterial pathogens. Finally, another aspect of the work aims to determine the likelihood of transmission of bacteria to crop plants, by fingerprinting bacteria isolated from the environment. The overall goal of work in the lab to gain a deeper understanding of the nature of bacteria-plant interactions, which will in turn identify the points in the transmission cycle that can be broken.

Dr Eulyn Pagaling

Eulyn is an environmental microbiologist in the Ecological Sciences group. She completed her PhD in environmental microbiology (working on extremophiles) in 2008 at the University of Leicester, and worked at the University of Edinburgh and the University of Hawaii at Manoa prior to her appointment at The James Hutton Institute in 2015. Currently, she works on the prevalence of human and animal pathogens, antimicrobial resistance and pharmaceuticals in the environment

Dr Rupert Hough

Rupert Hough

Rupert leads the Information and Computational Sciences group. His background is in risk and exposure modelling and environmental epidemiology. He has interests in both chemical and biological hazards, especially where they occur together. He has specific interests in modelling the flow of hazards, including pathogens, through food chains using various source-pathway-receptor approaches to estimate subsequent exposure of livestock and/or humans. He has applied these approaches to a number of contexts including health risks associated with application of different organic amendments (composts, sludges, digestates, and manures) to various primary production systems ranging from ready to eat salad production, through to brewing of beer from combinable crop systems. Current work includes the environmental factors affecting the prevalence and spread of Mycobacterium avium paratuberculosis, the cause of Johne’s disease in cattle.

Leighton Pritchard

Dr Leighton Pritchard

Leighton’s research centres around plant-pathogen interactions. Primarily, he aims to understand what it is about microbes that enables them to infect and colonise plants, and what it is is about plants that allows microbes to colonise and cause disease on them. As a computational biologist, most of his work involves the computational and mathematical analysis of biological data such as genome sequences, microarray gene expression profiles and networks of metabolic and regulatory processes. He is in the Information and Computational Sciences group.

Dr Dominic Duckett

Dominic Duckett

Dominic is a social scientist in the Social, Economic and Geographical Sciences Group. He currently applies social theories of risk to issues around livestock diseases for the Scottish Government’s Centre for Excellence in Epidemiology, Population Health and Disease Control (EPIC). His interests include zoonotic diseases and the particular societal risks that they pose, and socio-technical aspects of risk for example the adoption of disease control and surveillance technologies. Dominic’s current focus is on farmer and other land manager behaviour in relation to animal disease risk and the particular conditions of either policy change or outbreaks. Dominic has been working directly with farmers and other land managers, studying their behaviours through participatory and qualitative methods. A general sociological interest in expert/lay knowledge constructions and the sociology of scientific knowledge (SSK) underlies these different projects.

Ms. Claire Abel

Claire is a research assistant with over 20 years laboratory experience including nine years in microbiological laboratories and two years with Scottish Water, before joining the Institute in 2002 where she has worked in both the Soils and Catchment Management groups. She has expertise in culture-based microbiology, manages and undertakes environmental sampling regimes and carries out PCR, q-PCR and prepares samples for sequencing.

Dr Ashleigh Holmes

Ashleigh's research interests are in microbial pathogenicity, particularly in the regulation and expression of virulence factors. Her research includes type III secretion system effectors, particularly regulation and expression of non-LEE encoded effectors and how they contribute to  pathogenesis of E. coli O157:H7 in mammals. She is particularly interested in the pathogenesis of E. coli O157:H7 in planta and the factors required for the bacterium’s interaction with plant tissue.



Areas of Interest

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.