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Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland
Get PDFPublication history: Accepted - 29 March 2023; Published - 25 May 2023.Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.This work was funded by the Department of Agriculture, Environment and Rural Affairs for Northern Ireland (DAERA-NI) through its Evidence and Innovation programme – project no. 15/3/07. Additional funding was provided by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC) – grant numbers BB/P0105598 and BB/M01262X.
A. A. is supported by a Bolashak International Scholarship
A concept for application of integrated digital technologies to enhance future smart agricultural systems
Get PDFPublication history: Accepted - 16 may 2023; Published - 17 May 2023.Future agricultural systems should increase productivity and sustainability of food production and supply. For this, integrated and efficient capture, management, sharing, and use of agricultural and environmental data from multiple sources is essential. However, there are challenges to understand and efficiently use different types of agricultural and environmental data from multiple sources, which differ in format and time interval. In this regard, the role of emerging technologies is considered to be significant for integrated data gathering, analyses and efficient use. In this study, a concept was developed to facilitate the full integration of digital technologies to enhance future smart and sustainable agricultural systems. The concept has been developed based on the results of a literature review and diverse experiences and expertise which enabled the identification of stat-of-the-art smart technologies, challenges and knowledge gaps. The features of the proposed solution include: data collection methodologies using smart digital tools; platforms for data handling and sharing; application of Artificial Intelligent for data integration and analysis; edge and cloud computing; application of Blockchain, decision support system; and a governance and data security system. The study identified the potential positive implications i.e. the implementation of the concept could increase data value, farm productivity, effectiveness in monitoring of farm operations and decision making, and provide innovative farm business models. The concept could contribute to an overall increase in the competitiveness, sustainability, and resilience of the agricultural sector as well as digital transformation in agriculture and rural areas. This study also provided future research direction in relation to the proposed concept. The results will benefit researchers, practitioners, developers of smart tools, and policy makers supporting the transition to smarter and more sustainable agriculture systems
At what scale should we assess the health of pelagic habitats? Trade-offs between small-scale manageable pressures and the need for regional upscaling
Get PDFPublication history: Accepted - 26 June 2023; Published online - 13 July 2023.Major planktonic lifeforms such as diatoms, dinoflagellates, meroplankton and holoplankton have recently shown significant and alarming changes in abundance - mainly downwards trends - around the northwest European shelf. This has major implications for food web connections and for ecosystem services including seafood provision and carbon storage. We have quantified these changes in abundance for 2006–2019/20 using a Plankton Index (PI) and show that the scale of spatial aggregation is critical to the ability of the PI to detect change, understand causal mechanisms, and provide advice to policymakers. We derived PI statistics in the Celtic and North Seas from data from the Continuous Plankton Recorder survey offshore and England’s Environment Agency inshore using three sets of spatial units: (i) Ecohydrodynamic (EHD) units based on hydro-biogeochemical modelling, (ii) ‘COMP4′ areas based on cluster analysis of satellite data for chlorophyll a and primary productivity, and (iii) English coastal and estuarine Water Framework Directive (WFD) waterbodies. For the largest scale areas, the EHD units (median size 87,000 km2), we find greater change in plankton communities than previously reported, suggesting that these shifts have continued and possibly intensified in recent years. The smaller-scale COMP4 areas (median size 6,700 km2) appear to encompass more spatially coherent changes in plankton community structure than EHD units; at this scale PI values indicate community shifts of greater magnitude. These COMP4 areas provide a reasonable compromise scale for linking offshore plankton communities to large-scale drivers of change such as climate warming. For inshore plankton communities, larger changes are detected at the smaller WFD waterbody scale (median size 11 km2). This scale allows direct links to coastal management measures and is more suitable for linking to land-sourced pressures. Recent integration of the UK’s OSPAR and WFD plankton monitoring data management enables the exploration of changes across spatial scales to develop a holistic understanding of ecosystem health. Regional-sea scale derivation of the PI for coastal waters provides a clear indication that changes are occurring, at least in phytoplankton communities, while localised PI statistics offer an additional layer of information which can be an important tool for linking to localised drivers of change including coastal anthropogenic pressures. Broadscale inshore zooplankton monitoring is needed to evaluate the coastal plankton community holistically; zooplankton communities offshore are also changing but these changes cannot currently be linked to coastal processes. Layering information across spatial scales provides a breadth of system-level understanding beyond what any one typology can provide.This work was supported by the Defra/HBDSEG project ME414135 ‘DDIPA: Next-level pelagic habitat analysis: Making use of improved data flows to Delve Deeper into Integrated UK Plankton Assessment’, and Cefas’ Environment and People science theme. AA’s contribution was also funded by the UK Natural Environment Research Council (NERC) through its National Capability Long-term Single Centre Science Programme, Climate Linked Atlantic Sector Science, grant number NE/R015953/1, contributing to Theme 3.1—Biological dynamics in a changing Atlantic. EB and MM were additionally supported by the Scottish Government’s Schedule of Service ST02GH
Human land use is comparable to climate as a driver of global plant occurrence and abundance across life forms
Get PDFPublication history: Accepted - 23 May 2023; Published online - 9 June 2023.Aim
Historically, climate has been a dominant driver of global vegetation patterns. Recently, ecological understanding has been updated to acknowledge the influence of human land use (the dominant driver of biodiversity change) in shaping global vegetation patterns. We test whether Raunkiær's life form, a plant classification system designed to reflect climatic drivers, affects how plants respond to both land use and climate.
Location
Forty-one countries across six continents.
Time period
1990 to 2013.
Major taxa studied
Terrestrial plants.
Methods
Combining data from the biodiversity and land use database PREDICTS, and plant trait databases TRY and BIEN, we use generalized linear mixed models with weighted effects coding to test whether Raunkiær's life form affects plant response to land use and climate in over 4800 species at over 300 sites globally.
Results
We provide evidence that human land use is comparable to climate in influencing life form occurrence and that land use produces divergent outcomes across life forms.
Main conclusions
Combined with climatic suitability, land use acts as a filter contracting the realized niche of trees and expanding the realized niche of disturbance-tolerant species. Our results highlight the fundamental role of human activity in shaping species' distribution.Irish Research Council, Grant/Award Number: GOIPD/2016/324, GOIPG/2018/475 and IRCLA/2017/60; Prince Albert II of Monaco Foundation (though Plants Under Pressure II), Grant/Award Number: E/M014533/
Disease Occurrence in- and the Transferal of Zoonotic Agents by North American Feedlot Cattle
Get PDFPublication history: Accepted - 15 February 2023; Published online - 20 February 2023North America is a large producer of beef and contains approximately 12% of the world’s cattle inventory. Feedlots are an integral part of modern cattle production in North America, producing a high-quality, wholesome protein food for humans. Cattle, during their final stage, are fed readily digestible high-energy density rations in feedlots. Cattle in feedlots are susceptible to certain zoonotic diseases that impact cattle health, growth performance, and carcass characteristics, as well as human health. Diseases are often transferred amongst pen-mates, but they can also originate from the environment and be spread by vectors or fomites. Pathogen carriage in the gastrointestinal tract of cattle often leads to direct or indirect contamination of foods and the feedlot environment. This leads to the recirculation of these pathogens that have fecal–oral transmission within a feedlot cattle population for an extended time. Salmonella, Shiga toxin-producing Escherichia coli, and Campylobacter are commonly associated with animal-derived foods and can be transferred to humans through several routes such as contact with infected cattle and the consumption of contaminated meat. Brucellosis, anthrax, and leptospirosis, significant but neglected zoonotic diseases with debilitating impacts on human and animal health, are also discussed.This research was funded by University of Georgia Foundation (UGA 20-400)
Simulating Phosphorus Load Reductions in a Nested Catchment Using a Flow Pathway-Based Modeling Approach
No full textPublication history: Accepted - 11 September 2023; Published - 14 September 2023.Catchment models are essential tools to identify and predict water quality problems linked to excessive nutrient applications (in this case phosphorus (P)). The Catchment Runoff Attenuation Flux Tool (CRAFT) has been successfully used to model nutrient fluxes and concentrations in north-western European catchments. The model is extremely parsimonious due to the relatively small number of parameters. However, an improvement to the representation of soluble P and particulate P fluxes in the fast-subsurface and surface runoff flow pathways was required. A case study in the north of Ireland applied the original and the new, enhanced (Dynamic) version of the CRAFT to the trans-border Blackwater catchment (UK and Republic of Ireland) covering nearly 1500 km2, with the land use predominantly livestock grazing. The larger size of the Blackwater also required a nested modeling approach to be implemented using a multiple sub-catchment variant (MultiCRAFT). P load reductions in the different sub-catchments were first identified using a simple approach based on the gap between the Water Framework Directive (WFD) limits for “Good” ecological status for soluble reactive P (SRP) concentrations and the recently observed concentrations. Modeling of different mitigation scenarios was then conducted using the MultiCRAFT framework with the best-performing variant of the CRAFT model embedded. The catchment was found to have flashy, episodic delivery of high concentrations of SRP and PP during runoff events which will require different sources (i.e., diffuse and point) of P to be targeted to achieve the WFD targets by the end of the decade. The modeling results thus showed that the required SRP load reductions could be best achieved using a combined scenario of mitigation measures that targeted diffuse sources contributing to both the surface runoff and fast-subsurface flow pathways, with point sources also identified as needing reduction in some sub-catchments.This research was funded by the NI Department of Agriculture, Environment and Rural Affairs (DAERA), Evidence and Innovation grant number 19-4-03, and by CatchmentCARE (INTERREG VA funded project, managed through the Special EU Programs Body (SEUPB), with match funding from DAERA in NI and DHPLG in ROI)
Campylobacter jejuni Modulates Reactive Oxygen Species Production and NADPH Oxidase 1 Expression in Human Intestinal Epithelial Cells
Get PDFPublcation history: Accepted - 14 December 2022; Published online - 30 January 2023Campylobacter jejuni is the major bacterial cause of foodborne gastroenteritis worldwide. Mechanistically, how this pathogen interacts with intrinsic defence machinery of human intestinal epithelial cells (IECs) remains elusive. To address this, we investigated how C. jejuni counteracts the intracellular and extracellular reactive oxygen species (ROS) in IECs. Our work shows that C. jejuni differentially regulates intracellular and extracellular ROS production in human T84 and Caco-2 cells. C. jejuni downregulates the transcription and translation of nicotinamide adenine dinucleotide phosphate (NAPDH) oxidase (NOX1), a key ROS-generating enzyme in IECs and antioxidant defence genes CAT and SOD1. Furthermore, inhibition of NOX1 by diphenylene iodonium (DPI) and siRNA reduced C. jejuni ability to interact, invade, and intracellularly survive within T84 and Caco-2 cells. Collectively, these findings provide mechanistic insight into how C. jejuni modulates the IEC defence machineryThis research was performed as part of the employment of the authors at the London School of Hygiene & Tropical Medicine
100 essential questions for the future of agriculture
Get PDFPublication history: Accepted - 8 March 2023; Published online - 11 April 2023.The world is at a crossroad when it comes to agriculture. The global population is growing, and the demand for food is increasing, putting a strain on our agricultural resources and practices. To address this challenge, innovative, sustainable, and inclusive approaches to agriculture are urgently required. In this paper, we launched a call for Essential Questions for the Future of Agriculture and identified a priority list of 100 questions. We focus on 10 primary themes: transforming agri-food systems, enhancing resilience of agriculture to climate change, mitigating climate change through agriculture, exploring resources and technologies for breeding, advancing cultivation methods, sustaining healthy agroecosystems, enabling smart and controlled-environment agriculture for food security, promoting health and nutrition-driven agriculture, exploring economic opportunities and addressing social challenges, and integrating one health and modern agriculture. We emphasise the critical importance of interdisciplinary and multidisciplinary research that integrates both basic and applied sciences and bridges the gaps among various stakeholders for achieving sustainable agriculture.
Key points
Growing demand and resource limitations pose a critical challenge for agriculture, necessitating innovative and sustainable approaches.
The paper identifies 100 priority questions for the future of agriculture, indicating current and future research directions.
Sustainable agriculture depends on interdisciplinary and multidisciplinary research that harmonises basic and applied sciences and fosters collaboration among different stakeholders
A framework for assessing the potential for a double dividend from a policy-induced reduction in alcohol consumption on the economy
Get PDFPublication history: Accepted - 10 March 2023; Published online - 13 April 2023.Objectives: Tax policies targeted at reducing alcohol consumption are typically understood to be associated
with economic losses, including in alcohol production and trade sectors. This study sought to
determine whether the overall effect of reduced alcohol consumption might be positive once improvements
in productivity associated with reduced alcohol-related consumption are considered.
Study design: This study used Computable General Equilibrium economic modelling.
Methods: An economic modelling framework was developed for Scotland, which considered the fiscal
and economic impacts of alcohol taxation and the economy-wide impacts. Simulation of hypothetical
alcohol taxes and improvements in labour productivity calibrated on losses due to absenteeism and
presenteeism in Scotland in 2017.
Results: The long-run impacts of a five pence increase in taxation alone produce negative economic
impacts on jobs and Gross Domestic Product in Scotland (1189 jobs and £71.12 million). These effects are
reduced by half e but remain negative e when the revenues from such policy are recycled to the
economy through government spending. A small improvement in labour productivity e equivalent to
4.95% of the total productivity gap from absenteeism and presenteeism estimated for Scotland e would
be sufficient to turn the economic consequence non-negative.
Conclusions: The overall macroeconomic impact of policies targeted at alcohol consumption should
include consideration of the potential productivity effect and that impact studies that do not include
such mechanisms are likely to overstate the negative economic impacts of alcohol policies.None declared
Fishing impacts on age structure may conceal environmental drivers of body size in exploited fish populations
Get PDFPublication history: Accepted - 8 January 2023; Published - 11 February 2023.Using analysis of field survey size-at-age data, we examine responses of European plaice (Pleuronectes platessa) to spatial differences in environmental variables in the North Sea.
Using available samples of plaice aged 1–7, northern and southern migrating groups of males and females grew differently. However, length-at-age growth patterns were not corroborated by complementary otolith-based estimates. Southern females and males were smaller than their northern counterparts until age 3. Southern males remained smaller up to age 7; by contrast southern and northern females reached similar size-at-age by year 4.
Due to covariation, the influence of spatially variable environmental conditions was equivocal. However, temperature, depth, fishing pressure, phosphate levels, distance from shore, and conspecific density were all significant predictors of size for plaice aged 1–7.
Our results suggest that fishing impacts on age structure limit the potential to examine the role of environmental variation on body size. For fish that rarely reach their full potential age and size, expected metabolic responses to warming may remain unexpressed, challenging predictions in a changing climate.This work was supported by a Natural Environment Research Council (NERC) NERC-Cefas CASE PhD Studentship (L.A.R.; NE/L501669/1), NERC KE Fellowship (S.D.S.; NE/J500616/2), and Cefas Seedcorn (E.H.)