Search

Copyright of Environnement, Risques & Santé is the property of John Libbey Eurotext Ltd. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Introduction: Predicting the performance (yield or other integrative traits) of cultivated plants is complex because it involves not only estimating the genetic value of the candidates to selection, the interactions between the genotype and the environment (GxE) but also the epistatic interactions between genomic regions for a given trait, and the interactions between the traits contributing to the integrative trait. Classical Genomic Prediction (GP) models mostly account for additive effects and are not suitable to estimate non-additive effects such as epistasis. Therefore, the use of machine learning and deep learning methods has been previously proposed to model those non-linear effects. Methods: In this study, we propose a type of Artificial Neural Network (ANN) called Convolutional Neural Network (CNN) and compare it to two classical GP regression methods for their ability to predict an integrative trait of sorghum: aboveground fresh weight accumulation. We also suggest that the use of a crop growth model (CGM) can enhance predictions of integrative traits by decomposing them into more heritable intermediate traits. Results: The results show that CNN outperformed both LASSO and Bayes C methods in accuracy, suggesting that CNN are better suited to predict integrative traits. Furthermore, the predictive ability of the combined CGM-GP approach surpassed that of GP without the CGM integration, irrespective of the regression method used. Discussion: These results are consistent with recent works aiming to develop Genome-to-Phenotype models and advocate for the use of non-linear prediction methods, and the use of combined CGM-GP to enhance the prediction of crop performances. [ABSTRACT FROM AUTHOR]

The need for strengthening national capacities for disease prevention, preparedness, and response is increasingly becoming urgent. Central to this is strengthening existing systems and workforce capacity for disease surveillance and disease outbreak response. This study aimed to evaluate the national capacity and needs of veterinary services in Vietnam in animal disease surveillance and outbreak investigation skills. A cross-sectional, convergent, mixed-methods study was conducted between November 2020 and April 2021. An online questionnaire was administered to government field veterinarians, followed by descriptive and multivariable analyses to understand field capacity, specifically levels of experience in outbreak investigation and animal health surveillance. Semi-structured interviews were conducted with various stakeholders in veterinary services and interview transcripts were coded and thematically analyzed. Qualitative results were used to contextualize quantitative findings from the survey. Overall, 178 field veterinary staff completed the online survey, and 25 stakeholders were interviewed. Eighty percent of respondents reported a high priority for further training in both animal disease surveillance and outbreak investigation. Training and competence were more limited at the district and commune levels, highlighting a gap in capacity at the subnational level. Reasons included a lack of in-depth training opportunities, limited access to resources and high staff turnover. Respondents who completed postgraduate qualifications in epidemiology or Field Epidemiology Training Programs were more likely to have higher levels of experience in animal health surveillance and outbreak investigation. This study identified gaps in knowledge and adoption of practices most often related to local-level or less experienced veterinary staff with limited training opportunities in epidemiology. Findings inform the prioritization of training and planning activities to further enhance the national capacity of veterinary services in Vietnam. Underlying explanations for existing gaps in capacity include inequities in skill development and training opportunities across levels of veterinary staff, gaps in the chain of command and unequal funding across provinces. [ABSTRACT FROM AUTHOR]

Innovation literature has identified innovation intermediaries as essential actors in the innovation process that intermediate knowledge between the sources and users of innovation. Our research investigates how intermediaries strengthen less mature innovation systems in emerging economies by integrating the supply and demand of knowledge in agriculture through building knowledge infrastructures. We argue that these organizations become essential sources of technological opportunities in natural resource industries by nurturing less mature innovation systems and creating knowledge infrastructure. Our analysis of a subset of innovation intermediaries, fifteen Research and Technology Organizations in the Colombian agricultural sector, help to explain how these organizations fulfil their role of generating and disseminating scientific and technological knowledge. We highlight the importance of private and public funding, focalized public policy, and national and international collaboration to foster intermediaries' research and development capabilities. [ABSTRACT FROM AUTHOR]

Between 2013 and 2017, we carried out nine field missions in the Lago Grande de Curuai floodplain, located in Pará state – North of Brazil – to collect samples for monitoring surface water quality. This site separated from the river by a narrow bank is composed of a network of channels and shallow lakes, a morphology shared by the floodplains of the lower Amazon. A multiparameter probe was used in situ to measure electrical conductivity, temperature, pH, dissolved oxygen, chlorophyll, turbidity, depth and a Secchi disk to estimate transparency. Water grab samples were analysed for suspended material, alkalinity, humic acid, phosphorus, nitrogen, carbon and chlorophyll. Sampling stations were distributed over the seven larger lakes in the floodplain and sampled at different periods of the hydrological cycle. The number of samples varied with the floodplain water level, with a minimum of 25 samples for each field visit. This data set is a collection of water quality data to assist in the limnological or biogeochemical studies of surface waters in Amazonian floodplain lakes, and the product of successive French‐Brazilian projects: (1) the Clim‐FABIAM 'Climate changes and Floodplain lake biodiversity in the Amazon Basin: how to cope and help the ecological and economic sustainability' funded by the French Foundation for biodiversity research (FRB), (2) the project Bloom‐ALERT –'Environmental sensitivity and population health vulnerability to cyanobacteria in the Amazon: towards shared indicators' funded by the French‐Brazilian research program GUYAMAZON 2014, and the project (3) 'Ecossistemas das várzeas e biodiversidade: Impactos das mudanças ambientais e climáticas considerando cenários de desenvolvimento sustentáveis' (Project number 490634/2013‐3) funded by the Brazilian National scientific Research Council CNPq. [ABSTRACT FROM AUTHOR]

Crimean–Congo hemorrhagic fever (CCHF) is a zoonotic tick-borne disease, caused by an arbovirus of the genus Orthonairovirus and the family Nairoviridae. Crimean–Congo hemorrhagic fever virus (CCHFV) is widespread in several regions of the world. While the virus is not pathogenic to all susceptible livestock and wild mammals, it can lead to severe hemorrhagic fever in humans. In this review, we compiled published data on CCHFV infections in humans, animals, and ticks in Tunisia. Based on that, we discussed the epidemiology and the distribution patterns of CCHFV infections highlighting the risk factors for this virus in the country. CCHF infection prevalence in humans was estimated to 2.76% (5/181) and 5% (2/38) in Tunisian febrile patients and Tunisian slaughterhouse workers, respectively. Concurrently, seroprevalence in domestic ungulates (sheep, goats, cattle, and dromedaries) ranged from zero to 89.7%, and only one Hyalomma impeltatum tick specimen collected from dromedaries in southern Tunisian was positive for CCHFV by reverse transcriptase–polymerase chain reaction (0.6%; 1/165). As Tunisian studies on CCHFV are geographically scattered and limited due to very small sample sizes, further studies are needed to improve the knowledge on the epidemiology of CCHF in Tunisia. [ABSTRACT FROM AUTHOR]

Bananas are a staple food that considerably contributes to both food security and income generation, especially in countries of Africa, Asia, and Central and South America. The banana plant (Musa spp.) is affected by various pathogens, of main concern being the plant-parasitic nematodes associated with the rhizosphere, the most important of which are Radopholus similis (burrowing nematode), Helicotylenchus sp. (spiral nematode), Pratylenchus sp. (root lesion nematode), and Meloidogyne sp. (gall nematode). Infected plants reduce their ability to absorb water and nutrients, which can lead to delayed flowering, fewer bunches, and lower fruit mass. Obtaining nematode-resistant banana cultivars through genetic improvement is an effective and sustainable option compared with chemical control with nematicides. Here, we provide the first systematic review of existing banana sources of resistance to nematodes to aid the management and control of nematodes in banana and plantain crops. Articles selected from different databases were evaluated, and searches were conducted using pre-established inclusion and exclusion criteria. We found 69 studies dealing with genetic improvement for nematode resistance in banana cultivation. Our findings revealed that sources of resistance are currently under investigation to combat the diseases caused by different nematode species in banana plants. [ABSTRACT FROM AUTHOR]

Similarly to other tropical, arid and semi-arid regions of the World, livestock production in the Sahel is based on extensive grazing in rangelands where managing herd mobility (transhumance and nomadism) is key to productivity and sustainability. However, in this region, government planning, impact assessments and climate change adaptation solutions face several methodological limitations and lack of data availability particularly about the feed and forage resources and how there are used by livestock. Existing feed balances at national or regional level in Sub-Saharan Africa are still largely perfectible. To address these limitations, FAO and CIRAD (French Agricultural Research Centre for International Development) have developed a tool called Feed Balance Sheet (FBS) adapted to the Sahelian livestock systems to help countries carry out improved feed balances. This new FBS tool provides the following improvements to existing feed balances in countries: (i) it considers the seasonality of feed availability and quality as well as the seasonality of animal requirements; (ii) it includes protein and energy in addition to dry matter; (iii) it takes into account a wide range of resources, including browsing of woody biomass. This article describes the methodological development and the assumptions underlying this tool, which has already been piloted in 6 countries in Western and Central Africa. It also presents the results from 2 countries (Mali and Chad) and draws conclusions on the tool's relevance and guidance for its application. It can be used to improve the resilience of pastoral communities in the Sahel and better plan responses to droughts and other types of crises. Its use requires dedicated training and partnerships between governments and science organizations for accessing the appropriate input data. Based on the tool's experience in six countries (including 2 for which results are presented in this paper), we have confirmed the key role that CIRAD, FAO and their partners must play during the first few years in coaching the different teams at the country level. [ABSTRACT FROM AUTHOR]

Côte d'Ivoire remains the world's leading producer of cocoa beans. However, cocoa farming is now recognized as a primary cause of deforestation in the country. To combat deforestation, the Ivorian government recently advocates for agroforestry, a farming technique involving the cultivation of cocoa trees with fruit or forest trees. Yet, the impact of these associated trees and their shade on the quality of produced cocoa beans remains relatively unknown. This study is aimed at evaluating the influence of tree shade in cocoa farms on the quality of cocoa beans produced in the Bonon area. Morphological, biochemical, and functional analyses were performed on cocoa beans from shaded, partially shaded, and sunny subplots. Overall, only beans from shaded subplots showed better commercial quality. Regarding nutritional potential, results demonstrated that acidity, protein content, and vitamin C levels were influenced by shade. Low protein levels were observed in beans from sunny areas. The presence of moderate shade significantly favored good foaming power and foam stability. These findings play a key role in the perceived quality and application of these beans in the food and cosmetic industry. Moreover, these discoveries open new research perspectives in the field of food biochemistry and sustainable agriculture. [ABSTRACT FROM AUTHOR]

Agriculture is the main driver of the rapid collapse of biodiversity, upon which all life on Earth, including agricultural production, depends. As we face the challenge of feeding a growing human population under a changing climate regime, the pressure on biodiversity is expected to further intensify. While the potential to expand and improve natural habitats for biodiversity conservation has been widely explored in large-scale scenarios of agricultural systems, the critical role of agricultural landscapes’ management on halting the loss of biodiversity remains unexplored at this scale. We argue that, to achieve an effective conservation of biodiversity (both natural and agricultural), the combined multivariate effects of agriculture on biodiversity must be accounted for, including its surface area as well as its management. Based on a literature review, we identified the main biodiversity pressures stemming from agriculture: land-use change, contribution to climate change, water withdrawal, pesticide pollution, nutrient (nitrogen and phosphorus) pollution, and landscape and farmscale simplification (of croplands and pastures). For each one, we proposed a critical boundary, based on reviews of studies covering a range of taxa, biodiversity metrics, and biomes, below or above which negative impacts on biodiversity are minimized or positive effects arise. Implemented simultaneously, the identified boundaries would integrate biodiversity conservation within and across farmlands and minimize agriculture’s far-reaching impacts on biodiversity. We present a framework called “agricultural boundaries for biodiversity” that will allow to explore the potential of developing agricultural systems that effectively reconcile food production and biodiversity conservation at large scales. [ABSTRACT FROM AUTHOR]

The rice blast fungus Magnaporthe oryzae differentiates specialized cells called appressoria that are required for fungal penetration into host leaves. In this study, we identified the novel basic leucine zipper (bZIP) transcription factor BIP1 (B-ZIP Involved in Pathogenesis-1) that is essential for pathogenicity. BIP1 is required for the infection of plant leaves, even if they are wounded, but not for appressorium-mediated penetration of artificial cellophane membranes. This phenotype suggests that BIP1 is not implicated in the differentiation of the penetration peg but is necessary for the initial establishment of the fungus within plant cells. BIP1 expression was restricted to the appressorium by both transcriptional and post-transcriptional control. Genome-wide transcriptome analysis showed that 40 genes were down regulated in a BIP1 deletion mutant. Most of these genes were specifically expressed in the appressorium. They encode proteins with pathogenesis-related functions such as enzymes involved in secondary metabolism including those encoded by the ACE1 gene cluster, small secreted proteins such as SLP2, BAS3, BAS4, and AVR-Pi9 effectors, as well as plant cuticle and cell wall degrading enzymes. Interestingly, this BIP1 network is different from other known infection-related regulatory networks, highlighting the complexity of gene expression control during plant-fungal interactions. Promoters of BIP1-regulated genes shared a GCN4/bZIP-binding DNA motif (TGACTC) binding in vitro to BIP1. Mutation of this motif in the promoter of MGG_08381.7 from the ACE1 gene cluster abolished its appressorium-specific expression, showing that BIP1 behaves as a transcriptional activator. In summary, our findings demonstrate that BIP1 is critical for the expression of early invasion-related genes in appressoria. These genes are likely needed for biotrophic invasion of the first infected host cell, but not for the penetration process itself. Through these mechanisms, the blast fungus strategically anticipates the host plant environment and responses during appressorium-mediated penetration. Author summary: The identification of gene regulatory networks controlling pathogenicity is a major research goal for understanding plant infection and for developing new strategies for disease control. Rice is the staple food for half the world's population, but its cultivation is threatened by the rice blast fungus Magnaporthe oryzae that causes severe yield losses. This fungus can breach intact plant leaves using specialized cells called appressoria. Here, we have identified in a pathogenicity mutant screen using random insertional mutagenesis, the novel M. oryzae bZIP transcription factor BIP1 that is essential for the infection. BIP1 is not implicated in the development of appressoria or the subsequent penetration of host leaves, but is necessary for the initial establishment of the fungus within plant cells. BIP1 orchestrates the expression of a unique set of early invasion-related genes within appressoria, encoding secreted effectors, enzymes, secondary metabolism-related enzymes, and signaling membrane receptors. Our experimental data suggest that BIP1 controls their expression by interacting directly with a TGACTC motif present in their promoters. Remarkably distinct from other known pathogenicity networks, the BIP1 regulatory network underscores the intricate control of fungal gene expression during infection. BIP1 seems to prepare M. oryzae for early biotrophic growth during appressorium-mediated penetration. [ABSTRACT FROM AUTHOR]

The Nagoya Protocol on Access and Benefit-sharing (ABS) of the Convention on Biological Diversity (CBD) is a fundamental international agreement that plays a crucial role in the protection and equitable utilization of plant genetic resources. While this agreement is essential for conservation and sustainable use, it presents specific challenges to coffee research and industry. One major issue is the requirement to obtain prior informed consent (PIC) from the source country or community, which can be a complex and time-consuming process, especially in regions with limited governance capacity. Additionally, the mandates of this agreement necessitate benefit-sharing with the source community, a requirement that poses implementation challenges, particularly for small businesses or individual researchers. Despite these challenges, the importance of the Nagoya Protocol in the coffee sector cannot be overstated. It contributes significantly to the conservation of coffee genetic resources and the sustainable utilization of these resources, ensuring fair distribution of benefits. To address the complexities presented by this international framework, coffee researchers and industry need to engage proactively with source countries and communities. This includes developing clear and equitable benefit-sharing and implementing strategies for compliance. This article explores the impact of the Nagoya Protocol on the coffee industry, particularly emphasizing the need for balancing scientific investigation with the ethical considerations of resource sharing. It also discusses practical strategies for navigating the complexities of this agreement, including research focused on authenticity control and the challenges in conducting large-scale coffee studies. The conclusion underscores the potential for international collaboration, particularly through platforms like the International Coffee Organization (ICO), to harmonize research activities with the ethical imperatives of the Nagoya Protocol. [ABSTRACT FROM AUTHOR]