A Decision Support tool for Potato Blackleg Disease (DeS-BL)
Lead Research Organisation:
THE JAMES HUTTON INSTITUTE
Department Name: Cell & Molecular Sciences
Abstract
Blackleg disease of potato caused by P. atrosepticum (Pba) is the most damaging bacterial plant pathogen in the UK, costing £50M p.a. in losses for the potato industry. Current knowledge assumes that disease is caused through Pba-infected seed tubers. However, our recent unpublished data have shown that under high soil moisture following irrigation, disease appears in plants grown from pathogen free seed (minitubers). The most likely explanation is that bacteria enter the plant and cause disease directly from the soil; something not previously considered. We have also shown that Pba is able to colonise roots of other plant species (including crops), possibly as natural rhizosphere-dwelling saprophytes in the soil. In pot trials with Pba alone, we showed there was no movement of Pba from soil into the plant. However, when free-living nematodes (FLN) were added to soil, a 100-fold increase in Pba in stems occurred.
Through these and other findings we now have the potential to make a step change in how we manage blackleg. We will address knowledge gaps firstly by using Light Sheet and Confocal Laser Scanning microscopy, transparent soils and mesocosm studies to assess the role of FLN as vectors of Pba and how infection occurs. We will also examine how changes in standard irrigation regimes can help to reduce levels of blackleg in ware crops (where irrigation is often over-applied to avoid common scab disease that occurs in dry conditions), and how it might change FLN communities around potato root systems. Similarly, we will identify cover crops that limit natural Pba colonisation on their roots as a possible way to reduce Pba numbers in soil prior to planting potato. Little is known about the microbiome on potato roots and how these might be influenced to favour or reduce colonisation by Pba. We will therefore characterise the potato microbiome prior to and following irrigation using shotgun metagenomics sequencing and the latest bioinformatics tools, with a focus on the Pectobacteriaceae and wider Gamma-proteobacteria. We will also use GC-MS to examine how changes in root architecture and the constituents of root exudates influence the composition of these bacterial groups, to assess whether the use irrigation and cover crops alter the balance between beneficial and harmful bacteria associated with potato. Finally, we will determine whether novel antimicrobials (bacteriocins) in closely related non-pathogenic bacteria in the microbiome could act as a management option against Pba.
Our recent modelling research using the Scottish Government's in-house potato inspections database (SPUDS), shows that blackleg incidence on a national scale does not occur randomly but in clusters. Reason(s) for this remain unclear but could be due to several things that, when identified, may assist growers in managing their crops, e.g. potato crop distribution, weather, soil type, soil moisture, leaf wetness, FLN distribution, crop type and rotation prior to planting. Using data generated from this project, an extensive array of data from other recent and historical investigations and the latest data from government and industry we will model, using innovative machine learning methods, at national scale these data to identify trends and drivers of Pba incidence in both space and time and, through this, produce predictive models to support development of a set of decision support tools for evaluation by stakeholders during the project and early adoption thereafter. Further, through scenario testing, we will quantify the predicted effects of climate change on future blackleg incidence in association with FLN presence thus providing the industry with robust and novel data to underpin sector resilience planning.
Through these and other findings we now have the potential to make a step change in how we manage blackleg. We will address knowledge gaps firstly by using Light Sheet and Confocal Laser Scanning microscopy, transparent soils and mesocosm studies to assess the role of FLN as vectors of Pba and how infection occurs. We will also examine how changes in standard irrigation regimes can help to reduce levels of blackleg in ware crops (where irrigation is often over-applied to avoid common scab disease that occurs in dry conditions), and how it might change FLN communities around potato root systems. Similarly, we will identify cover crops that limit natural Pba colonisation on their roots as a possible way to reduce Pba numbers in soil prior to planting potato. Little is known about the microbiome on potato roots and how these might be influenced to favour or reduce colonisation by Pba. We will therefore characterise the potato microbiome prior to and following irrigation using shotgun metagenomics sequencing and the latest bioinformatics tools, with a focus on the Pectobacteriaceae and wider Gamma-proteobacteria. We will also use GC-MS to examine how changes in root architecture and the constituents of root exudates influence the composition of these bacterial groups, to assess whether the use irrigation and cover crops alter the balance between beneficial and harmful bacteria associated with potato. Finally, we will determine whether novel antimicrobials (bacteriocins) in closely related non-pathogenic bacteria in the microbiome could act as a management option against Pba.
Our recent modelling research using the Scottish Government's in-house potato inspections database (SPUDS), shows that blackleg incidence on a national scale does not occur randomly but in clusters. Reason(s) for this remain unclear but could be due to several things that, when identified, may assist growers in managing their crops, e.g. potato crop distribution, weather, soil type, soil moisture, leaf wetness, FLN distribution, crop type and rotation prior to planting. Using data generated from this project, an extensive array of data from other recent and historical investigations and the latest data from government and industry we will model, using innovative machine learning methods, at national scale these data to identify trends and drivers of Pba incidence in both space and time and, through this, produce predictive models to support development of a set of decision support tools for evaluation by stakeholders during the project and early adoption thereafter. Further, through scenario testing, we will quantify the predicted effects of climate change on future blackleg incidence in association with FLN presence thus providing the industry with robust and novel data to underpin sector resilience planning.
Technical Summary
We have used soil microcosms to show that the causal agent of blackleg disease (Pba) can infect potato plants and cause disease directly from the soil, not only tubers. This is exacerbated by the presence of free-living nematodes (FLN) and excess water, providing new possibilities for research and disease control. Our multidisciplinary team of science and stakeholder experts will investigate the role of vectors, irrigation and crop rotation on Pba infection working from field and mesocosm scales to rhizosphere microbial communities. We wish to see how large-scale changes in the field impact on root architecture and exudate production and what influence this has on rhizosphere microbial communities and competition. The latest bacterial genomics, bioinformatics, imaging and GC-MS tools will be used, with potentially far reaching consequences beyond the present study.
Our key questions are: Do FLN act as vectors of Pba, how does infection occur and can blackleg be reduced by managing FLN in the soil though irrigation and /or nematicide? Do Pba-carrying insects transmit the pathogen between plants? Does irrigation and the use of cover crops change the microbiome in favour of or away from Pba and relatives, and what role do changes in root architecture and exudates play? Can we identify bacteriocins and their producing strains amongst these microbial communities and patent them for use in disease control?
We have unprecedented access to national datasets that have not previously been linked with blackleg disease research. These include over 10,000 national soil samples with FLN data, synthetic aperture radar (SAR) soil moisture data, the National Soil Archive and several other data sets. With these, and data from the project, we will use machine learning, game theory and other modelling approaches to find relationships between these data and blackleg and bring the information together in a decision support tool for the potato industry.
Our key questions are: Do FLN act as vectors of Pba, how does infection occur and can blackleg be reduced by managing FLN in the soil though irrigation and /or nematicide? Do Pba-carrying insects transmit the pathogen between plants? Does irrigation and the use of cover crops change the microbiome in favour of or away from Pba and relatives, and what role do changes in root architecture and exudates play? Can we identify bacteriocins and their producing strains amongst these microbial communities and patent them for use in disease control?
We have unprecedented access to national datasets that have not previously been linked with blackleg disease research. These include over 10,000 national soil samples with FLN data, synthetic aperture radar (SAR) soil moisture data, the National Soil Archive and several other data sets. With these, and data from the project, we will use machine learning, game theory and other modelling approaches to find relationships between these data and blackleg and bring the information together in a decision support tool for the potato industry.
Planned Impact
Research outlined in this proposal is focused on strategic science aimed at improving control of the bacterial pathogen Pectobacterium atrosepticum (Pba); the causal agent of blackleg disease, which costs the UK potato industry £50M annually. Blackleg can occur at any time and in any stock across the whole supply chain.
Who might benefit from this research? Blackleg affects both seed and ware producers across all sectors of the potato industry, e.g. fresh, processed, and salad in an industry of c. 3000 growers producing > 6 M tonnes of potatoes from 120,000 ha of land p.a. The UK's seed potato industry is world renowned and the basis of a highly respected global export market. For the seed industry, blackleg, and therefore the outcomes of this project, affect the whole supply chain from those producing high grade seed, mainly in the north of Scotland, to distributors across the UK and exporters worldwide. Most ware growers in the UK, based mainly in England and Wales, have a direct interest in seed being free from Pba to limit blackleg and its associated economic and reputational loss. All parts of the industry will therefore benefit from this research. Defra and Scottish Government, agriculture industries (including agrochemical, cover crop and precision agriculture), and the public will also benefit. Many of the issues with blackleg seen in the UK also occur across Europe and in many other regions of the world. Globally, a third of potatoes are grown in China and India, and increasingly in sub-Saharan Africa. This project therefore also offers potential improvements in potato production in developing nations. The academic community in the UK and internationally will also benefit by research advances across a range of scientific areas and their multidisciplinary nature brought together to benefit plant health.
How might they benefit from this research? Blackleg continues to be the main cause of seed downgrading and failure by a factor of 10 in most years, with knock-on effects on ware growers, who mostly identify seed as being the cause of blackleg in their ware crops. Blackleg has become more common in the UK over the last 8-10 years, with no clear reason why. Control options have remained relatively unchanged for over 50 years. A new approach to control is therefore desperately needed by the industry. This project achieves this on many levels, offering not one but multiple possible improvements in control by moving away from traditional research (often on seed contamination) to focus more on soil and the wider environment. Potential improvements for the control of blackleg from the project include changes to irrigation regimes, monitoring and management of free-living nematode (putative Pba vectors), changes in crop rotations and the use of cover crops, and the use of physical protection to reduce aerial transmission, all brought together and supported by environmental data subjected to novel machine learning methods to develop a series of integrated decision support tools for industry use. To ensure that the industry benefits from our findings, an economic and social appraisal of the project outcomes will be undertaken to ensure no barriers to adoption exist for industry uptake. In addition, we have our industry collaborators available throughout the project to discuss practical aspects of our findings, and to co-construct a wide range of stakeholder engagement activities during the life of the project and beyond. Defra and Scottish Government will benefit through a resilient potato industry and its economic output and export potential. There will be benefits to industry through a potential new application of an existing product (nematicide to treat blackleg), marketing and sale of cover crops and new uses for precision agriculture and associated decision tools. The public will benefit through cheaper retail potato prices.
Who might benefit from this research? Blackleg affects both seed and ware producers across all sectors of the potato industry, e.g. fresh, processed, and salad in an industry of c. 3000 growers producing > 6 M tonnes of potatoes from 120,000 ha of land p.a. The UK's seed potato industry is world renowned and the basis of a highly respected global export market. For the seed industry, blackleg, and therefore the outcomes of this project, affect the whole supply chain from those producing high grade seed, mainly in the north of Scotland, to distributors across the UK and exporters worldwide. Most ware growers in the UK, based mainly in England and Wales, have a direct interest in seed being free from Pba to limit blackleg and its associated economic and reputational loss. All parts of the industry will therefore benefit from this research. Defra and Scottish Government, agriculture industries (including agrochemical, cover crop and precision agriculture), and the public will also benefit. Many of the issues with blackleg seen in the UK also occur across Europe and in many other regions of the world. Globally, a third of potatoes are grown in China and India, and increasingly in sub-Saharan Africa. This project therefore also offers potential improvements in potato production in developing nations. The academic community in the UK and internationally will also benefit by research advances across a range of scientific areas and their multidisciplinary nature brought together to benefit plant health.
How might they benefit from this research? Blackleg continues to be the main cause of seed downgrading and failure by a factor of 10 in most years, with knock-on effects on ware growers, who mostly identify seed as being the cause of blackleg in their ware crops. Blackleg has become more common in the UK over the last 8-10 years, with no clear reason why. Control options have remained relatively unchanged for over 50 years. A new approach to control is therefore desperately needed by the industry. This project achieves this on many levels, offering not one but multiple possible improvements in control by moving away from traditional research (often on seed contamination) to focus more on soil and the wider environment. Potential improvements for the control of blackleg from the project include changes to irrigation regimes, monitoring and management of free-living nematode (putative Pba vectors), changes in crop rotations and the use of cover crops, and the use of physical protection to reduce aerial transmission, all brought together and supported by environmental data subjected to novel machine learning methods to develop a series of integrated decision support tools for industry use. To ensure that the industry benefits from our findings, an economic and social appraisal of the project outcomes will be undertaken to ensure no barriers to adoption exist for industry uptake. In addition, we have our industry collaborators available throughout the project to discuss practical aspects of our findings, and to co-construct a wide range of stakeholder engagement activities during the life of the project and beyond. Defra and Scottish Government will benefit through a resilient potato industry and its economic output and export potential. There will be benefits to industry through a potential new application of an existing product (nematicide to treat blackleg), marketing and sale of cover crops and new uses for precision agriculture and associated decision tools. The public will benefit through cheaper retail potato prices.
Organisations
- THE JAMES HUTTON INSTITUTE (Lead Research Organisation)
- DEFRA Westminster (Co-funder)
- SCOTTISH GOVERNMENT (Co-funder)
- Bayer (Collaboration)
- Newcastle University (Collaboration)
- University of Warwick (Collaboration)
- National Institute of Agronomy and Botany (NIAB) (Collaboration)
- AHDB (Agri & Horticulture Dev Board) (Project Partner)
- Bayer CropScience Limited (UK) (Project Partner)
- Sci & Adv for Scottish Agriculture SASA (Project Partner)
Publications

Aqueel R
(2024)
Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective
in Frontiers in Microbiology

Ge S
(2023)
In situ control of root-bacteria interactions using optical trapping in transparent soil.
in Journal of experimental botany

Ge S
(2021)
In situ laser manipulation of root tissues in transparent soil.
in Plant and soil

Koci O
(2024)
CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.
in Microbiome

Orlando V
(2020)
Comparing the efficiency of six common methods for DNA extraction from root-lesion nematodes (Pratylenchus spp.)
in Nematology

Skelsey P
(2023)
Landscape Epidemiology of Potato Blackleg.
in Phytopathology

Toth I
(2022)
Microbe Profile: Pectobacterium atrosepticum: an enemy at the door
in Microbiology

Van Der Wolf J
(2021)
Plant Diseases Caused by Dickeya and Pectobacterium Species

Van Gijsegem F
(2021)
Plant Diseases Caused by Dickeya and Pectobacterium Species

Van Gijsegem F
(2021)
Plant Diseases Caused by Dickeya and Pectobacterium Species
Title | How the Potato Shaped our World |
Description | Discussions with a writer illustrator (Laura Darling) to engage the James Hutton Institute through funding from the Scottish Society of Crop Research to publish an illustrated book o0n the history of the potato as a tool for outreach to the general public about the importance of potato. |
Type Of Art | Creative Writing |
Year Produced | 2022 |
Impact | Not yet created |
URL | https://www.darlingbyname.com/ |
Title | Jewellery from bacteria |
Description | Arts student Chloe Fitzpatrick from the University of Dundee has been working with members of the project team to use Pectobacterium and other bacteria to develop jewellery. |
Type Of Art | Artwork |
Year Produced | 2022 |
Impact | Chloe won the Sir James Black award, which recognises outstanding contributions to research and scholarship, for her work with bacteria, has 106,000 followers on TikTok and over 10 million views. She currently has an exhibition of BioArt at Kulanshi Art Centre in Nur-Sultan, Kazakhstan and appeared on the BBC news on 4th October 2022. https://www.bbc.co.uk/news/uk-scotland-tayside-central-62251818 |
URL | https://www.bbc.co.uk/news/uk-scotland-tayside-central-62251818 |
Description | We have several key findings from this work. Our work on bacteriocins to develop a biocontrol method for blackleg disease is going through commercialisation and a business case has been developed together with additional funding to support the commercialisation. We also have a potential new method of screening for resistance to blackleg disease in potato through examining root exudate products, which will make this work significantly easier for the potato breeding industries. New discoveries using microscopy are providing new insights into how Pectobacterium infects potato, offering new routes for disease control. Changes in microbiome associated with blackleg disease may offer new diagnostics for disease-inducing conditions or for the use of suppressive microbes as biocontrol agents. A number of datasets and methodologies have also been made available to others within the Bacterial Plant Diseases Programme and beyond to help build on modelling and bioinformatics research. Evidence of insect transmission of Pectobacterium suggests that the covering of high grade potato seed stocks will allow a reduction in contamination and so reduce blackleg disease throughout the supply chain. |
Exploitation Route | See above. There are a number of potential end user benefits to the work. Repeated here: We have several key findings from this work. Our work on bacteriocins to develop a biocontrol method for blackleg disease is going through commercialisation and a business case has been developed together with additional funding to support the commercialisation. We also have a potential new method of screening for resistance to blackleg disease in potato through examining root exudate products, which will make this work significantly easier for the potato breeding industries. New discoveries using microscopy are providing new insights into how Pectobacterium infects potato, offering new routes for disease control. Changes in microbiome associated with blackleg disease may offer new diagnostics for disease-inducing conditions or for the use of suppressive microbes as biocontrol agents. A number of datasets and methodologies have also been made available to others within the Bacterial Plant Diseases Programme and beyond to help build on modelling and bioinformatics research. Evidence of insect transmission of Pectobacterium suggests that the covering of high grade potato seed stocks will allow a reduction in contamination and so reduce blackleg disease throughout the supply chain. |
Sectors | Agriculture Food and Drink Government Democracy and Justice |
Description | Part of our work is going through commercialisation and a business case has been developed. We also have a potential new method of screening for resistance to blackleg disease in potato, which will make the development of new blackleg resistant varieties significantly easier for the potato breeding industries. New discoveries using microscopy are providing new insights into how Pectobacterium infects potato, offering new routes for disease control and showing, categorically, that infection can take place in potato directly from the environment. Changes in microbiome associated with blackleg disease may offer new diagnostics for disease-inducing conditions or for the use of suppressive microbes as biocontrol agents. A number of datasets and methodologies have also been made available to other groups to help build on modelling and bioinformatics research. Also over 50 Engagement Activities have taken place along with nine publications; publications being directly relevant to the private sector as well as academia. For example, book chapters have been written for a general audience that includes the private sector to increase their understanding of the bacterial disease (potato blackleg). Another publication on DNA extraction methods for free living nematodes (FLN) is written to allow the private sector and possibly government as well as academics to develop improved diagnostics for FLN to enable uptake into their integrated pest management activities. Knowledge exchange amongst stakeholders is key to the uptake of new methodologies and already we have engaged with the private sector and stakeholders on over 50 occasions to explain our aims, objectives and the outcomes of our work. This is especially important as the aim is to develop a decision support tool, which the industry must fully understand and be geared up to implement prior to the tool becoming available. |
First Year Of Impact | 2020 |
Sector | Agriculture, Food and Drink |
Impact Types | Societal Economic Policy & public services |
Description | Healthy Soils contribution to Scottish Government consultation on a proposed new Agricultural Bill |
Geographic Reach | National |
Policy Influence Type | Contribution to a national consultation/review |
Description | Pathways to collaborative networking series for Project Investigators: Understanding microbial communities through in situ omics data synthesis - New developments |
Geographic Reach | Asia |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | Seminar on Blackleg |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | Bacteriocin Commercial Scoping |
Amount | £14,400 (GBP) |
Funding ID | 302389 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2022 |
End | 03/2022 |
Description | British Society for Plant Pathology Studentship 2021 |
Amount | £4,000 (GBP) |
Organisation | British Society of Plant Pathoogy |
Sector | Learned Society |
Country | United Kingdom |
Start | 04/2021 |
End | 09/2021 |
Description | British Society for Plant Pathology Studentship 2022 |
Amount | £4,000 (GBP) |
Organisation | British Society of Plant Pathoogy |
Sector | Learned Society |
Country | United Kingdom |
Start | 04/2022 |
End | 08/2022 |
Description | CASDU CROP SOLUTIONS: Developing a commercial bacteriocin-based treatment for protecting seed and ware potatoes against Blackleg disease and soft rot. |
Amount | £8,000 (GBP) |
Organisation | IBioIC |
Sector | Academic/University |
Country | United Kingdom |
Start | 02/2023 |
End | 07/2023 |
Description | Institutional Strategic Support Fund Early Career Catalyst Grant: "How do free-living nematodes (FLN) interact with the microbial populations in soil. " |
Amount | £22,346 (GBP) |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2022 |
End | 09/2022 |
Description | Society of Applied Microbiology studentship 2021 |
Amount | £2,500 (GBP) |
Organisation | Society for Applied Microbiology |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 04/2021 |
End | 09/2021 |
Description | Understanding the impact of sustainable agricultural practices on crop development by focusing on microbial ecology and the exposome |
Amount | £65,177 (GBP) |
Organisation | University of Glasgow |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2023 |
Description | University of Glasgow Impact Accelerator Account |
Amount | £24,059 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 02/2023 |
End | 07/2023 |
Description | Wellcome Trust Institutional Strategic Support Fund (ISSF) - Feasibility Scheme Application [204820/Z/16/Z](2022) - PI: Dr Ciara Keating |
Amount | £8,848 (GBP) |
Organisation | University of Glasgow |
Sector | Academic/University |
Country | United Kingdom |
Start | 08/2022 |
End | 02/2023 |
Description | • Harry Smith Vacation Studentship |
Amount | £2,720 (GBP) |
Organisation | Microbiology Society |
Sector | Learned Society |
Country | United Kingdom |
Start | 05/2022 |
End | 09/2022 |
Title | Lightsheet microscope |
Description | Set up and programming of a bespoke lightsheet microscope for use by the James Hutton Institute and University of Dundee both for this project and for future activity, both joint and independent. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This microscope will make a major impact on our ability across the Dundee teams to investigate a wide range of biological functions. It's primary role will be to investigate the pathogen - plant root interface but has the potential for other macroscopic biological and physical analyses. |
Title | Orion Cluster |
Description | The grant help in extending Orion Cluster https://userweb.eng.gla.ac.uk/umer.ijaz/#orion a £200K+ microbial high perfomance computing facility managed by Dr Umer Zeeshan Ijaz |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | The cluster serves as the backbone to process genomics data generate from the grant |
Title | Update/improvement of Orion Computer Cluster |
Description | The grant helped in extending Orion Cluster https://userweb.eng.gla.ac.uk/umer.ijaz/#orion a £200K+ microbial high perfomance computing facility managed by Dr Umer Zeeshan Ijaz |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | The cluster serves as the backbone to process genomics data generate from the grant |
Title | A machine learning algorithm for predicting hot-spots of disease incidence |
Description | An adaptive Boosted Decision Tree algorithm was trained, tuned, and tested for it's ability to predict statistically significant hot- and cold-spots of blackleg incidence. The algorithm was able to predict these patterns of disease with an accuracy of 97.3%. |
Type Of Material | Computer model/algorithm |
Year Produced | 2021 |
Provided To Others? | No |
Impact | The algorithm is being used to identify the principal soil / weather / crop / landscape risk factors that are driving patterns of blackleg infestation. |
Title | Amplicon sequencing data from experimental field trial |
Description | Bacterial amplicon sequencing data of DNA from soil from experimental field trials at NIAB, Cambridge testing the impact of irrigation and pathogen burden on crop yields, disease prevalence, and microbial communities. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | No |
Impact | We are currently drafting a publication on this work highlighting that pathogen burden impacts soil microbial communities. |
Title | Amplicon sequencing data of DNA from soil from experimental field trials at NIAB, Cambridge |
Description | Bacterial amplicon sequencing data of DNA from soil from experimental field trials at NIAB, Cambridge testing the impact of irrigation and nematicide on crop yields, disease prevalence, and microbial communities. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | No |
Impact | Currently under analysis |
Title | Amplicon sequencing data of DNA from soil from field trials at the James Hutton Institute |
Description | Amplicon sequencing data of DNA from soil from field trials at the James Hutton Institute testing the impact of cover crops on soil microbial communities. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | No |
Impact | Currently under analysis |
Title | CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets |
Description | The past few years have seen an increased utility of shotgun metagenomics for microbial community surveys over traditional amplicon sequencing. This is made possible by the technological advancement in methods development that enables us now to assemble short sequence reads into longer contiguous regions that can be binned together to identify species they are part of, e.g., through our previous published software, CONCOCT (Nature Methods, 11(11), pp. 1144-1146). The advantage of shotgun metagenomics is that coding regions of these contigs can further be annotated against public databases to give an assessment of the functional diversity. With integrated solutions gaining importance by complementing metagenomics with other meta'omics technologies (e.g., metabolomics), there is a need to have a single platform to consolidate all these realisations on the same sample space. Thus, continuing the work on CONCOCT, we have developed CViewer, a Java-based statistical framework to integrate all levels of gene products, mRNA, protein, metabolites for microbial communities and allows exploration of their response to environmental factors through multivariate statistical analysis. |
Type Of Material | Computer model/algorithm |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | The associated publication is currently in review O. Koci, R. K. Russell, M. G. Sheikh, C. Edwards, K. Gerasimidis, and U. Z. Ijaz#. CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets. bioRxiv 2023.06.07.544017, 2023. DOI: 10.1101/2023.06.07.544017 |
URL | https://github.com/KociOrges/cviewer |
Title | Optimized Hot Spot Analysis of Blackleg Incidence |
Description | ArcGIS was used to perform an Optimized Hot Spot Analysis on a database containing information on blackleg incidence across Scotland (2012-2019). The resulting patterns of statistically significant hot- and cold-spots of disease provide an unprecedented overview of blackleg outbreaks across Scotland. |
Type Of Material | Data analysis technique |
Year Produced | 2021 |
Provided To Others? | No |
Impact | The output of this analysis is being used to investigate the driving factors of blackleg spread, and to develop a predictive machine learning algorithm. |
Description | Exploiting Bacteriocins as treatments for Diseases in Cherry |
Organisation | National Institute of Agronomy and Botany (NIAB) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have tested 24 strains of Pseudomonas syringae isolated from infected cherry trees in the UK for sensitivity to two bacteriocins, Puticacin L1 and Syringacin M1. We have identified several bacteriocin-sensitive strains. We are now collaborating on studies to test the efficacy of bacteriocin treatment on bacterial titres in infected plants |
Collaborator Contribution | Partners have sent us isolates for testing. Partners have assisted in genome sequencing of resistant and sensitive strains of Pseuomonas syringae. |
Impact | No outcomes yet |
Start Year | 2020 |
Description | Exploiting Bacteriocins as treatments for plant diseases caused by Xanthomonas species. |
Organisation | University of Warwick |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have identified 5 new bacteriocins from Xanthomonas species. Partners have sent us 20 strains of different Xanthomonas spp from UK and worldwide. We have tested these for sensitivity. We are now initiating experiments to test the efficacy in suppressing infections in UK brassica crops |
Collaborator Contribution | Strains sent for analysis. |
Impact | None yet |
Start Year | 2020 |
Description | industrial collaboration with a Bayer Crop Science |
Organisation | Bayer |
Department | Bayer CropScience Ltd |
Country | United Kingdom |
Sector | Private |
PI Contribution | We developed a peptide based chemical application to boost crop productivity under stress |
Collaborator Contribution | Bayer Crop Science tested this technology in crops species such as a wheat |
Impact | This is multidisciplinary (Chemical Biology) collaboration where Bayer have funded a technician for 2 years to provide proof of concept for the technology. |
Start Year | 2016 |
Description | nutrient effect on Septoria resistance in wheat |
Organisation | Newcastle University |
Department | School of Biology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Generated new molecular tools for the development of control strategies against septoria tritici blotch disease in wheat |
Collaborator Contribution | Knowledge of nutrient use efficiency in wheat |
Impact | Publications; Lee et al., 2015 New Phytologist BBSRC grant BB/M022048/1 Industrial funding form KWS breeding company Patents filed on the discoveris from the work |
Start Year | 2012 |
Description | 2022 Ontario Potato Conference |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Potato grower event looking for solutions to blackleg disease following major losses over the last 8-10 years. Involving experts from abroad and new solutions to this devastating disease. Organiser responded: 'I have got lots of excellent comments from growers, they say your talk was very practical and will help them to better manage blackleg.' |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.potatoesincanada.com/webinars/ontario-potato-conference/ |
Description | A technical report for potato industry stakeholders |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Contribution of a detailed technical article to the Cambridge University Potato Growers Research Association (CUPGRA) Annual Report for 2020. This article described the field work done in 2020 and provided some context and interpretation. The report is sent to c. 150 members who are stakeholders in the UK/International potato supply chain and includes growers, agronomists, researchers, ag-chem industry and potato processors and packers. |
Year(s) Of Engagement Activity | 2021 |
Description | AHDB Agronomy Week 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Roy Neilson presented the project with a focus on nematodes to 75-80 crop agronomists, who will then ensure the latest scientific ideas and practices are disseminated to growers across the UK through ongoing dialogue in order to improve crop production and food security. |
Year(s) Of Engagement Activity | 2020 |
URL | https://ahdb.org.uk/events/agronomy-week-2020 |
Description | AHDB Potato Showcase Week 6th - 9th July 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Ian Toth presented the project to members of the potato potato industry during a webinar entitled 'The future of potato rotations, blackleg management and aphids. Mainly national audience but some international industry and scientists present. |
Year(s) Of Engagement Activity | 2020 |
URL | https://ahdb.org.uk/news/the-ahdb-potato-showcase-week-6th-9th-july-2020 |
Description | AHDB Webinar 'Impact of research on blackleg management' |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | AHDB jointly organised webinar between the scientist and AHBD to present previous and new research (the current project) on blackleg to ensure a flow of information and to let people know what will be taking place in the new project. |
Year(s) Of Engagement Activity | 2020 |
URL | https://register.gotowebinar.com/recording/3217709094922133776 |
Description | An update to the latest research on blackleg disease |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | A workshop with scientists and industry to update on the latest research on potato blackleg disease. |
Year(s) Of Engagement Activity | 2022 |
Description | BPD Plant Health Week Webinar - Blackleg presentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Series of short presentations as part of a webinar to promote the Bacterial Plant Diseases Programme projects to a general audience and to emphasise the importance of the work to global food security and the economy. |
Year(s) Of Engagement Activity | 2023 |
URL | https://bacterialplantdiseases.uk/event/the-impact-of-bacterial-diseases-on-crops-and-food-supply/ |
Description | BSPP2021 - Our Plants, Our Future (OPOF) - Joint conference from BSPP and the EFPP |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | A poster presented in BSPP2021 conference as follows: Title: The influence of Pectobacterium (blackleg) loads and Irrigation practices on soil microbial community dynamics. Authors: Keating, C., Kilbride, E., Laird, J., Stalham, M., Smart, S., Humphries, S., Milner, J., Toth, I., Ijaz, U. Z. Mable, B, K. Submission Theme: COMBATTING PLANT HEALTH PROBLEMS |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.bspp.org.uk/conferences/bspp2021/ |
Description | BSPP2021 - Undergraduate Student Bursary Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Alexandru Popescu, an undergraduate student at University of Glasgow, received funding from British Society for Plant Pathology Undergraduate Vacation Bursary (2021) to work on development of a curated database and workflow for searching for existing and novel bacteriocins produced by bacterial genera associated with plant pathogens. On the conclusion of his placement, he presented his findings in BSPP2021 conference for Undergraduate Student Bursary Holders. This conference was instrumental in Alexandru Popescu winning 2022 Sandwich Student Recruitment at The Francis Crick Institute. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.youtube.com/watch?v=p2UQkelO4PQ |
Description | Blackleg: Current understanding of epidemiology and control |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Association of Independent Potato Consultants meeting and debrief on latest findings from research on potato blackleg disease |
Year(s) Of Engagement Activity | 2022 |
Description | Blog in association with Scotland's Plant Health Centre |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Third sector organisations |
Results and Impact | As part of the International Year of Plant Health and Nation Plant Health Week (19th-25th September 2020) a blog was written entitled 'Protecting our Humble Spud' to show the importance of plant health in protecting potato production and the importance of this industry to the public. It describes one of the other pathogens (Liberibacter) in the Bacterial Diseases Initiative. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.planthealthcentre.scot/blog/protecting-our-humble-spud |
Description | CUPGRA (Cambridge University Potato Growers Research Association) Open day |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | We were invited to explain the motivation and main findings of our research on our DesBL project to an open day involving a diverse membership of stakeholders in the potato supply chain who value independent, high-quality research. The meeting was held at NIAB in Cambridge and involved a series of research talks and talks by practioners. Ian Toth presented an overview of the DeSBL project during this session. We then visited the potato fields and Barbara Mable explained the experiments that we are conducting to understand the impacts of irrigation treatments, potato stocks and pathogen loads on microbial communities associated with the soil. It was highly beneficial for the researchers to see the experimental plots and there were useful interactions with practitioners. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.cupgra.com/ |
Description | CUPGRA Virtual Open Day |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | Presentation on the potato irrigation aspects of the project while stood in a field trial for the project (but presented virtually). Presented to the potato industry by Mark Stalham to advise growers how they might use irrigation to control blackleg and other diseases of potato and about other aspects of the project. This will have a direct influence on how growers in the region apply irrigation to control these diseases. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.youtube.com/watch?v=eaGKwne0MyI&feature=emb_title |
Description | Crop Protection in Northern Britain conference |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | 70+ members of the arable / potato industry, scientists and some policy met to discuss the latest findings with regard to sustainable production of arable / potato growing in northern regions of Britain. Interest from industry about new approaches to disease control and a face to face meeting promised later in the year. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.cpnb.org/ |
Description | Dr Umer Zeeshan Ijaz - BBSRC's EBNet Webinar: Using Big Data Approaches to Understand Microbial Communities, UK |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | An invited lecture on the topic "Understanding microbial communities through in situ omics data synthesis" a talk organized on February 10th, under EBNet Working Group "Bioinformatics Training for Microbial Environmental Biotechnologies" with details given at https://ebnet.ac.uk/ebnet-rc22-bigdata/ The intended purpose of the talk was to discuss the recent advancements in microbial informatics driven by machine learning and numerical ecology and covering concepts such as integrated omics, community assembly mechanisms in microbial communities, network inference, hardware devices exploiting and harnessing the microbes, as well as major software and hardware systems originating from University of Glasgow |
Year(s) Of Engagement Activity | 2022 |
URL | https://ebnet.ac.uk/ebnet-rc22-bigdata/ |
Description | Early findings of the BBSRC Blackleg Project CUPGRA Dec 2022 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Series of four workshops to update industry on the latest findings from the BBSRC DeS BL blackleg project |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.cupgra.com/_files/ugd/f77b24_45d9dda4f2f145caadd67faa963f0730.pdf?index=true |
Description | Fighting Bac: Making microbes our allies (Stakeholder Workshop Nov 22) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | In this workshop we shared our research findings so far, as well as ideas for the next steps to turn this research into pioneering products or processes. Stakeholders were be invited to contribute to this future-focussed conversation, identifying potential areas of collaboration and knowledge exchange. The workshop particularly focused on the next steps for translating these findings into real world innovations and how stakeholders could get involved. The event was attended by 100+ online and the presentation received many questions and discussion. |
Year(s) Of Engagement Activity | 2022 |
URL | https://bacterialplantdiseases.uk/event/making-microbes-our-allies/ |
Description | Grower magazine article entitled 'Managed irrigation key to preventing blackleg' in the Farming section of the Courier and Advertiser |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | This is an article in a regional newspaper Farming section read by the local public and farming communities |
Year(s) Of Engagement Activity | 2023 |
Description | Invited Speaker (Umer Zeeshan Ijaz), Glasgow Geroscience Group Sandpit 2, Meikleour, Scotland |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Other audiences |
Results and Impact | Dr Umer Zeeshan Ijaz was invited speaker at Glasgow Geroscience Group Sandpit 2, Meikleour, Scotland (09-11/11/2023) where he presented his work on in situ tools (arising from his lab) to facilitate bioinformatics and statistical analyses of microbial communities. The intended activity was to explore further funding opportunities of mutual interest. |
Year(s) Of Engagement Activity | 2023 |
Description | Invited Speaker (Umer Zeeshan Ijaz), Nutrition Sensing and Ageing, A joint workshop of the AGEing and Nutrient Sensing (AGENTs) Network and the Scottish Alliance for Food (SCAF), Advanced Research Centre (ARC), University of Glasgow |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | Dr Umer Zeeshan Ijaz gave an invited talk to Nutrition Sensing and Ageing, A joint workshop of the AGEing and Nutrient Sensing (AGENTs) Network and the Scottish Alliance for Food (SCAF), Advanced Research Centre (ARC), University of Glasgow (07-08/03/2024) |
Year(s) Of Engagement Activity | 2024 |
URL | https://www.linkedin.com/posts/scaf-arc_nutrition-ageing-sensing-activity-7171531985549533184-p63O?u... |
Description | Invited Speaker (Umer Zeeshan Ijaz), School of Interdisciplinary Engineering & Science (SINES), NUST Islamabad, Pakistan |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Dr Umer Zeeshan Ijaz gave an invited talk to School of Interdisciplinary Engineering & Science (SINES), NUST Islamabad, Pakistan Topic of Research Seminar: i-Talk: Understanding Microbial Ecology through in situ Data Synthesis Subject Field of Topic: Bioinformatics Date and Venue: 20th February, 2024 at 1100 Hrs, Seminar Hall, School of Interdisciplinary Engineering & Science (SINES), NUST Islamabad |
Year(s) Of Engagement Activity | 2024 |
URL | https://research.nust.edu.pk/seminar-and-workshop/i-talk-understanding-microbial-ecology-through-in-... |
Description | Invited Talk and Official Visit (Umer Zeeshan Ijaz), Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan (c/o Professor Kauser Abdulla Malik (HEC Distinguished Professor, Dean of Postgraduate Studies, and Minister for Food Security, Government of Pakistan), and Professor Samina Mehnaz (Chairperson/Head of School) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Dr Umer Zeeshan Ijaz visited (01/08/2023) Forman Christian College (A Chartered University) https://www.fccollege.edu.pk/ to meet Professor Dr Kauser Abdulla Malik (https://en.wikipedia.org/wiki/Kauser_Abdulla_Malik), and faculty members/graduate students at Kauser Abdulla Malik School of Life Sciences including Professor Samina Mehnaz, Chairperson/Head of School (https://www.fccollege.edu.pk/member/dr-samina-mehnaz/). After giving an invited talk, he was shown different labs, and the departments, and were briefed about the degree programmes that were being run. Also were discussed opportunities of mutual interest, and further collaborative opportunities on OMICs technologies with our lab at University of Glasgow. Additionally, meeting with ex vice chancellor of GC University, Lahore also took place whilst talking with Professor Malik in his office. |
Year(s) Of Engagement Activity | 2023 |
Description | Invited conference presentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The activity was an invited conference presentation entitled "Healthy Soils for Crop Production" at the winter meeting of the Scottish Society for Crop Research. At the peak of the presentation, 79 delegates were online from UK, Europe, Asia and Oceania. There was the standard Q&A session which generated several questions. In terms of impact, I have had a follow-up from a commercial company who would like to collaborate on a particular topic. |
Year(s) Of Engagement Activity | 2021 |
Description | Invited keynote conference presentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | As part of an invited keynote presentation to the annual AAB nematology conference, the DeS-BL project was used as an exemplar of bringing together several ecology-based methodologies to deliver DeS-BL outcomes. Project structure was communicated to the audience highlighting how the methods previously discussed in the presentation were being deployed. Some social media activity (primarily Twitter) was generated in real time and direct engagement ensued with delegates through the chat function of the presentation platform. As a direct consequence of the conference being online, participants included those located in the UK, Europe, India, Australia and North America. A post-event email exchange occurred with a delegate located in Portugal who wished to discuss a nematode related problem in amenity turf. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.cvent.com/events/advances-in-nematology-2020/event-summary-c404b6de6b474f24b9a91b7dbe0b8... |
Description | Keynote presentation at International Conference on Plant Pathogenic Bacteria (ICPPB) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | International conference on plant pathogenic bacteria where the Bacterial Plant Diseases Programme and the DES BL project were presented and discussed with a main theme of the importance of collaboration. The presentation stimulated interest, especially from younger scientists about how collaboration can lead to better research outputs. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.icppb2020.it |
Description | Knowledge Exchange with Cambridge University Potato Growers Association (CUPGRA) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | Over 50 potato industry people attended the event to learn more about the blackleg project and they participated in discussions on how the different aspects of the project might help them in their business. Engagement with one agronomist, was followed up by email to engage more in future activates. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.niab.com/cupgra |
Description | Masterclass: Making the most of Knowledge Exchange and Impact Generation |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Study participants or study members |
Results and Impact | A Bacterial Plant Diseases Programme Initiative to help improve the impact of the science being undertaken. |
Year(s) Of Engagement Activity | 2020 |
Description | Media / news output entitled 'CUPGRA focus on addressing challenges in the potato sector' in Vegetable Farmer magazine |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Article on major grower magazine on progress of the research and the outcomes associated with it. |
Year(s) Of Engagement Activity | 2023 |
Description | Molecular Microbial Ecology Group (MMEG), "Impact of pathogen burden and management practices on potato blackleg disease prevalence and soil microbial community dynamics" (Glasgow, December 2022) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Third sector organisations |
Results and Impact | Molecular Microbial Ecology Group (MMEG), "Impact of pathogen burden and management practices on potato blackleg disease prevalence and soil microbial community dynamics" (Glasgow, December 2022). Presented our findings of the project to peers. |
Year(s) Of Engagement Activity | 2022 |
URL | https://mmeg2022.weebly.com/program.html |
Description | New Twitter profile '@Blackleg_Hub' |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | New Twitter profile to let people know what is happening on the project and related activities. |
Year(s) Of Engagement Activity | 2020 |
URL | https://twitter.com/Blackleg_Hub |
Description | New website developed for the project called the 'Blackleg Hub' |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Website built for the project as a one stop shop for all things related to the project including a description of the work packages and team involved but also news, events, blogs and publications. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.blackleghub.ac.uk/ |
Description | Official Visit (Umer Zeeshan Ijaz) and Round Table Discussion with Faculty and Graduate Students, Department of Biosciences, COMSATS University Islamabad, Pakistan (c/o Professor Qaiser Fatmi, Head of Department of Bioscience) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Dr Umer Zeeshan Ijaz visited different lab (20/07/2023), where the PIs and students showed the lab facilities, and the current projects being conducted in different research groups in the Bioscience and Computer Science department, and also held a round table talk with the faculty members. Additionally, we met Professor Majid Iqbal Khan (Head of Department, Computer Science) to discuss collaborative opportunities. He also visited International Office, and met with the Head, Ali Tawab Baloch, and colleagues, to discuss MoUs and other opportunities of mutual interests. |
Year(s) Of Engagement Activity | 2023 |
Description | Official Visit (Umer Zeeshan Ijaz), Alltech Pakistan (c/o Dr Shahzad Naveed Jadoon, Director & CEO) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Dr Umer Zeeshan Ijaz was hosted (24/07/2023) by Dr Shahzad Naveed Jadoon, Director and CEO of Alltech Pakistan, a regional company of Alltech (https://www.alltech.com/) whose mission is to improve the health and performance of people, animals and plants through nutrition and scientific innovation. Dr Ijaz gave an introduction to the work he is doing in Glasgow, and amongst other things were also discussed the SalmoSim project where he had his previous association with Alltech through a BBSRC project. He also discussed opportunities to collaborate together particularly on problems that are indigenous to Pakistan, and that require expertise that exists in his lab at Glasgow. |
Year(s) Of Engagement Activity | 2023 |
Description | Official Visit (Umer Zeeshan Ijaz), Animal Sciences Institute (ASI), Pakistan Agricultural Research Council, Ministry of National Food Security & Research, Government of Pakistan (c/o Dr Hamid Irshad, Principal Scientific Officer) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Umer Zeeshan Ijaz visited (21/07/2023) National Agricultural Research Centre, Pakistan Agricultural Research Council (PARC), Ministry of National Food Security & Research (http://www.parc.gov.pk/). PARC-National Agricultural Research Centre (NARC), Islamabad was established in 1984, and is the premier research establishment of the Pakistan Agricultural Research Council (PARC) at the federal level. NARC, with a total land area of approximately 1396 acres, is located near Rawal Lake, six kilometers south-east of Islamabad. The physical facilities include experimental fields, laboratories, green houses, gene bank, and national insect museum. The component divisions of crop, animal, natural resources and social sciences are playing a pivotal role in the national agricultural research system. He met with Dr Hamid Irshad (Principle Scientific Officer; Animal Sciences Research Institute) and colleagues, who briefed him about the use of next generation sequencing facility in their regular day to day work. Particularly, they are constructing a huge sample collection of bacterial/other isolates where their interest lies in strain level, phylogenetic, core, and ancillary gene analyses. Dr Ijaz discussed opportunities to collaborate together. |
Year(s) Of Engagement Activity | 2023 |
Description | Official Visit (Umer Zeeshan Ijaz), Ecotoxicology Research Institute, Pakistan Agricultural Research Council, Ministry of National Food Security & Research, Government of Pakistan (c/o Dr Farrakh Mehboob, Program Leader and Principal Scientific Officer) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Umer Zeeshan Ijaz was hosted (21/07/2023 ) by Dr Farrukh Mahboob (Program Leader, Ecotoxicology Research Program at National Agricultural Research Centre (NARC), Islamabad (http://www.parc.gov.pk/Detail/MWEwZjAwZGYtZmMyNS00NzZiLWI4ODktYTY4OGEwODA0YTdm). Ecotoxicology Research Institute was established in 1993 with the technical and financial assistance of Danish International Development Agency (DANIDA) through United Nations industrial Development Organization (UNIDO) and has now been merged with Institute of Plant & Environmental Protection (IPEP) and re-named as Ecotoxicology Research Program during re-organization of NARC. They are: developing and validating analytical methodologies for monitoring of xenobiotics in food chain and ecosystem, evaluating the impact of xenobiotics on non-target organisms, and on studying the microbial degradation of xenobiotics. Dr Mahboob briefed him about the work on detecting the pesticide residues and showed equipment housed in his lab (attached videos). These include UHPLC-MS/MS, GS-MS/MS, GC-MS (Pesticide Analyzer), GC(ECD, FID, NPD), HPLC (DAD, FLD), GPC, TLC, Spectrophotometer, Soxhlet/ Solvent extraction apparatus, Rotary evaporator, SPE, Nitrogen generator, Sonicator, Water purification system, pH meter, Incubators, Shakers, Ovens, Centrifuges. |
Year(s) Of Engagement Activity | 2023 |
Description | Official Visit (Umer Zeeshan Ijaz), Health Services Academy, Ministry of National Health Services, Government of Pakistan (c/o Professor Ramesh Kumar, and Dr Tariq Mahmoud Ali (Registrar)) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Third sector organisations |
Results and Impact | Dr Umer Zeeshan Ijaz visited (21/07/2023) Health Services Academy (HSA), Ministry of National Health Services, Government of Pakistan (https://www.hsa.edu.pk/). Although (HSA) was established as an in-service training institution in 1988, since 2002, it was granted status of an autonomous institution, and now comes under Ministry of National Health Services Regulation and Coordination. With Professor Ramesh Kumar, and Dr Tariq Mahmoud Ali (Registrar), he discussed the possibility of running joint training workshops, incubating local talent, and exposing them to guest lectures to be given by Dr Ijaz/colleagues at Glasgow. |
Year(s) Of Engagement Activity | 2023 |
Description | Official Visit (Umer Zeeshan Ijaz), National Institute for Genomics & Advanced Biotechnology (NIGAB), Government of Pakistan (c/o Dr Ghulam Muhammad Ali, Chairman, Pakistan Agricultural Research Council) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Umer Zeeshan Ijaz was hosted (03/08/2023) by Dr. Ghulam Muhammad Ali, Chairman, Pakistan Agricultural Research Council (https://pk.linkedin.com/in/dr-ghulam-muhammad-ali-10280651) and gave a seminar on his research activities at University of Glasgow, which was followed by a round table discussion, and lab visit of National Institute for Genomics and Advanced Biotechnology (NIGAB) http://nigab.parc.gov.pk/ which is a state of the art complex of biotechnology in Islamabad, Pakistan and houses 28 labs including bioinformatics lab, animal house, biosecurity level-III facilities, glass houses and containment facilities. His talk was attended by PIs of these 28 labs, and afterwards, as a round table discussion, collaborative ventures of mutual interest were explored. |
Year(s) Of Engagement Activity | 2023 |
Description | Official Visit (Umer Zeeshan Ijaz), National Institute of Health, Islamabad, Pakistan (c/o Dr Massab Umair, Head of Virology and Senior Scientific Officer) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Massab Umair [Head of Department, Virology, National Institute of Health (NIH), Islamabad, Pakistan] hosted (21/07/2023) Dr Umer Zeeshan Ijaz at National Institute of Health (https://www.nih.org.pk). NIH is one of the most prestigious institutions of the Pakistan involved in diagnostic services, research and production of various vaccines, and was very active during COVID-19 pandemic. Dr Ijaz was shown numerous labs for communicable diseases including Dengue, Avian Influenza, Congo, SARS, Hepatitis, HIV/AIDS, Polio, Measles. Of these ,Polio reference laboratory is considered one of the best in Asia. Additionally, the facility houses a next generation sequencing lab, where he was briefed about sequencing facilities. Also discussed were the possibility of joint ventures utilising these resources. |
Year(s) Of Engagement Activity | 2023 |
Description | Official Visit (Umer Zeeshan Ijaz), National Veterinary Laboratory, Ministry of National Food Security and Research, Government of Pakistan (c/o Dr Khurshid Ahmad, Principal Scientific Officer and Director General) |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Umer Zeeshan Ijaz visited National Veterinary Laboratories (NVL) https://mnfsr.trancemedia.pk/national-veterinary-laboratory/. NVL serves as a national reference laboratory for animal diseases that are of economic and trade significances, and routinely tests residues of livestock and livestock products to meet EU and WTO sanitary conditions. They also evaluate veterinary drugs for quality, safety, and potency. Dr Ijaz met with Director General, Dr Khursheed Ahmed along with other colleagues who briefed him about current activities at NVL, particularly those that involve NGS as well as monitoring of antimicrobial resistance in Pakistan. Some of the work directly aligns with the work being done in the Environmental'Omics lab (led by Dr Ijaz) which he briefed about. |
Year(s) Of Engagement Activity | 2023 |
Description | Online Invited Webinar (Umer Zeeshan Ijaz), National University of Science and Technology (NUST), Pakistan (c/o Dr Aneela Javed, Head of the Research Department, NUST Atta ur Rahman School of Biosciences (ASAB) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Dr Umer Zeeshan Ijaz presented his work to PhD students/faculty members of Atta ur Rahman School of Biosciences (ASAB), National University of Science and Technology (NUST), Pakistan, on in situ tools (arising from his lab) to facilitate bioinformatics and statistical analyses of microbial communities (24/08/2023). |
Year(s) Of Engagement Activity | 2023 |
Description | Oral Presentation at the International Erwinia Workshop - New approaches to blackleg disease control |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | The 4th International Erwinia Workshop was held in Assisi, Italy from 2-3 July 2022. This is a scientific conference which attracts attendees from all those working on any aspect of the biology and control of Erwinia, Pectobacterium, Dickeya, Pantoea and related plant pathogens. The workshop consisted of a series of oral and poster presentations with the aim of exchanging ideas and building collaborations. Title of oral presentation: New approaches to blackleg disease control. Humphris S., Dong X., Liu Y., Neilson R., Skelsey P., Toth I., et al. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.icppb2020.it/international-erwinia-conference/ |
Description | Organiser of the International Erwinia Workshop (IEW) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Over 60 scientists working on Pectobacterium and related species attended the workshop in Assisi, Italy, which stimulated new areas of activity for research in this area internationally |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.icppb2020.it/international-erwinia-conference/ |
Description | Pakistan-UK education gateway |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Under Pakistan-UK education gateway, a high profile delegate of 20+ Vice Chancellors (VCs) of numerous universities from Pakistan, British Council and Higher Education Commission, Pakistan visited University of Glasgow (February 13th-14th, 2023): https://twitter.com/UofGGovRel/status/1625193454358740992 Three of the VCs: Lt Gen Wasim Alamgir, National University of Medical Sciences (https://en.wikipedia.org/wiki/National_University_of_Medical_Sciences); Professor Habib Bokhari, Kohsar University Murree (https://en.wikipedia.org/wiki/Kohsar_University_Murree); and Professor Qaisar Abbas, University of Sargodha (https://en.wikipedia.org/wiki/University_of_Sargodha) further visited Dr Ijaz's lab in Mazumdar-Shaw Advanced Research Centre (ARC), and were briefed about the ongoing research activities including DES-BL project in a talk entitled "Understanding microbial communities through in situ omics data synthesis - New developments". Amongst other things, student projects of visiting PGRs from Pakistan in Dr Ijaz's lab, and further collaborative opportunities were discussed. The event was covered by local news media in Pakistan |
Year(s) Of Engagement Activity | 2023 |
Description | Physics Colloquium at the University of Dundee: "Laser Nematodes and other Adventures in the Rhizosphere: Plant Root Environment Microscopy" |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | Talk to a physics audience comprised of honours undergraduate and postgraduate students plus academics from physics and more widely in the School of Science and Engineering at the University of Dundee. The presentation covered the imaging and manipulation tools being developed for studying bacteria-nematode-plant root interactions and their role in the Blackleg bacterial plant disease. |
Year(s) Of Engagement Activity | 2022 |
Description | Potatoes in Practice |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Exhibit describing the latest research on Blackleg disease across Scottish Government and external projects |
Year(s) Of Engagement Activity | 2022 |
URL | http://pip.hutton.ac.uk |
Description | Potatoes in Practice |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Over 700 people associated with the potato industry attended a potato field event where we had a stall and field plots to describe our research project and the anticipated outcomes |
Year(s) Of Engagement Activity | 2021 |
URL | https://pip.hutton.ac.uk/ |
Description | Potatoes in Practice |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Potatoes in Practice is the UK's largest field event for potatoes and was attended by over 600 people. We had a field plot and also a poster display as part of a marquee stand to describe the aims and objectives of the blackleg research and anticipated outcomes. |
Year(s) Of Engagement Activity | 2022 |
URL | https://pip.hutton.ac.uk/ |
Description | Presentation at CUPGRA Annual Research Review |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | The findings from the 2020 field experiments were discussed in an online webinar with members of the Cambridge University Potato Growers Research Association |
Year(s) Of Engagement Activity | 2021 |
Description | Presentation at Scotland's Plant Health Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | Presentation to update the conference abut activities from the Plant Health Centre but including information on the Bacterial Plant Diseases Programme and DeS BL project |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.planthealthcentre.scot/events/scotlands-plant-health-conference-2022 |
Description | Presentation at grower event for the Scottish Society for Crop Research (SSCR) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Industry/Business |
Results and Impact | Invited presentation to discuss funding successors from SSCR, which included the DeS BL project |
Year(s) Of Engagement Activity | 2022 |
Description | Scottish Farmer news article |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Article entitled: 'PCN and blackleg challenges highlighted at potato event 'in the following journals /magazines / newspapers Vegetable Farmer The Scottish Farmer Potato Pro Potato News Today |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.thescottishfarmer.co.uk/news/23253348.pcn-blackleg-main-topics-cambridge-potato-conferen... |
Description | Seminar at Uppsala University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Included a description of the DeSBl project in an invited departmental seminar. I was invited to act as external examiner for a PhD defense and gave a talk while I was there. |
Year(s) Of Engagement Activity | 2022 |
Description | Seminar at Uppsala University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Invited to act as external examiner for a PhD viva and gave a departmental seminar while I was there that included description of parts of the DES-BL project. |
Year(s) Of Engagement Activity | 2022 |
Description | Understanding dynamics aids control |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Media interview by Lucy de la Pasture, a journalist for Crop Protection Magazine (http://www.cpm-magazine.co.uk/) which was a follow up to the presentation I gave at AHDB Agronomy Week (see entry for that engagement). The interview was the basis for an article summarising the Des-BL project. An immediate outcome has been an approach by an industry player who wishes some small-scale collaboration to test a proof-of-concept. In the long-term, the article will be behind a pay wall. However, a copy of the article can be provided on request. |
Year(s) Of Engagement Activity | 2021 |
URL | http://www.cpm-magazine.co.uk/2021/02/08/potatoes-understanding-dynamics-aids-control/ |
Description | Visit from Chief Scientific Advisor and deputy |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | Visit to James Hutton Institute by Mat Williams, CSA, ENRA and Sallie Bailey, Deputy CSA to discuss all aspects of crop science at the institute. |
Year(s) Of Engagement Activity | 2022 |
Description | Workshop alongside project meeting |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | As part of an end of year project meeting industry representatives were invited to discuss the findings of the project to date and discuss next steps and, in some cases, how they might get invovled |
Year(s) Of Engagement Activity | 2021 |