Claire Bonsergent, Marion Vittecoq, Carole Leray, Maggy Jouglin, Marie Buysse, Karen D. McCoy, Laurence Malandrin
Babesia sp. YLG has recently been described in Yellow-legged gull (Larus michahellis) chicks and belongs to the Peircei clade in the new classification of Piroplasms. Here, we studied Babesia sp. YLG vectorial transmission by ticks in the simplified environment of a single seabird breeding colony where the Yellow-legged gull is the sole vertebrate host, Ornithodoros maritimus (syn. Alectorobius maritimus) the sole tick species, and Babesia sp. YLG is the only blood parasite species detected in chicks of the colony. We collected ticks over four years, maintained certain individuals through moulting or oviposition, and dissected fresh ticks to isolate different organs and test for the presence of the parasite using molecular assays. We report the first strong evidence of a Piroplasmidae transmitted by a soft tick. Indeed, Babesia sp. YLG DNA was detected in the salivary glands of nymphs, females and males, a necessary organ to infect for transmission to a new vertebrate host. Parasite DNA was also found in tick ovaries, which could indicate possible transovarial transmission. Our detection of Babesia sp. YLG DNA in several male testes and in endospermatophores, and notably in a parasite-free female (uninfected ovaries and salivary glands), raise the interesting possibility of sexual transmission from infected males to uninfected females. Future work in this system will now need to focus on the degree to which the parasite can be maintained locally by ticks and the epidemiological consequences of infection for both O. maritimus and its avian host.
{"title":"A soft tick vector of Babesia sp. YLG in Yellow-legged gull (Larus michahellis) nests","authors":"Claire Bonsergent, Marion Vittecoq, Carole Leray, Maggy Jouglin, Marie Buysse, Karen D. McCoy, Laurence Malandrin","doi":"10.24072/pcjournal.316","DOIUrl":"https://doi.org/10.24072/pcjournal.316","url":null,"abstract":"Babesia sp. YLG has recently been described in Yellow-legged gull (Larus michahellis) chicks and belongs to the Peircei clade in the new classification of Piroplasms. Here, we studied Babesia sp. YLG vectorial transmission by ticks in the simplified environment of a single seabird breeding colony where the Yellow-legged gull is the sole vertebrate host, Ornithodoros maritimus (syn. Alectorobius maritimus) the sole tick species, and Babesia sp. YLG is the only blood parasite species detected in chicks of the colony. We collected ticks over four years, maintained certain individuals through moulting or oviposition, and dissected fresh ticks to isolate different organs and test for the presence of the parasite using molecular assays. We report the first strong evidence of a Piroplasmidae transmitted by a soft tick. Indeed, Babesia sp. YLG DNA was detected in the salivary glands of nymphs, females and males, a necessary organ to infect for transmission to a new vertebrate host. Parasite DNA was also found in tick ovaries, which could indicate possible transovarial transmission. Our detection of Babesia sp. YLG DNA in several male testes and in endospermatophores, and notably in a parasite-free female (uninfected ovaries and salivary glands), raise the interesting possibility of sexual transmission from infected males to uninfected females. Future work in this system will now need to focus on the degree to which the parasite can be maintained locally by ticks and the epidemiological consequences of infection for both O. maritimus and its avian host.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135814494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marie Laure Delignette-Muller, Aurélie Siberchicot, Floriane Larras, Elise Billoir
Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications.
{"title":"DRomics, a workflow to exploit dose-response omics data in ecotoxicology","authors":"Marie Laure Delignette-Muller, Aurélie Siberchicot, Floriane Larras, Elise Billoir","doi":"10.24072/pcjournal.325","DOIUrl":"https://doi.org/10.24072/pcjournal.325","url":null,"abstract":"Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135814352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
C.E. Morris, C. Lacroix, C. Chandeysson, C. Guilbaud, C. Monteil, S. Piry, E. Rochelle Newall, S. Fiorini, F. Van Gijsegem, M.A. Barny, O. Berge
Rivers, creeks, streams are integrators of biological, chemical and physical processes occurring in a catchment linking land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present – nor about their dynamics - along the full course of a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 105 bacteria L-1. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 ´ 104 bacteria L-1. Among the biological and chemical parameters that were characterized at each sampling site, temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. Our observations suggest that surveillance of river water for SRP could be leveraged to signal diagnostic and management reactions to avoid disease outbreaks. In contrast, the constant presence of Psy throughout the catchment in absence of regular and widespread disease outbreaks due to this group of bacteria suggests that surveillance should focus on future changes in land use, river water conditions and agronomic practices that could destabilize the mechanisms currently holding Psy outbreaks in check.
{"title":"Comparative abundance and diversity of populations of the Pseudomonas syringae and Soft Rot Pectobacteriaceae species complexes throughout the Durance River catchment from its French Alps sources to its delta","authors":"C.E. Morris, C. Lacroix, C. Chandeysson, C. Guilbaud, C. Monteil, S. Piry, E. Rochelle Newall, S. Fiorini, F. Van Gijsegem, M.A. Barny, O. Berge","doi":"10.24072/pcjournal.317","DOIUrl":"https://doi.org/10.24072/pcjournal.317","url":null,"abstract":"Rivers, creeks, streams are integrators of biological, chemical and physical processes occurring in a catchment linking land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present – nor about their dynamics - along the full course of a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 105 bacteria L-1. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 ´ 104 bacteria L-1. Among the biological and chemical parameters that were characterized at each sampling site, temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. Our observations suggest that surveillance of river water for SRP could be leveraged to signal diagnostic and management reactions to avoid disease outbreaks. In contrast, the constant presence of Psy throughout the catchment in absence of regular and widespread disease outbreaks due to this group of bacteria suggests that surveillance should focus on future changes in land use, river water conditions and agronomic practices that could destabilize the mechanisms currently holding Psy outbreaks in check.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"339 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136154061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
It is generally thought that behavioral flexibility, the ability to change behavior when circumstances change, plays an important role in the ability of species to rapidly expand their geographic range. Great-tailed grackles (Quiscalus mexicanus) are a social, polygamous species that is rapidly expanding its geographic range by settling in new areas and habitats. They are behaviorally flexible and highly associated with human-modified environments, eating a variety of human foods in addition to foraging on insects and on the ground for other natural food items. They offer an opportunity to assess the role of behavior change over the course of their expansion. We compared behavior in wild-caught grackles from two populations across their range (an older population in the middle of the northern expansion front: Tempe, Arizona, and a more recent population on the northern edge of the expansion front: Woodland, California) to investigate whether certain behaviors (flexibility, innovativeness, exploration, and persistence) have higher averages and variances in the newer or older population. We found that grackles in the edge population had a higher flexibility variance (measured by reversal learning) and a higher persistence average (they participated in a larger proportion of trials), and that there were no population differences in average levels of flexibility, innovativeness (number of loci solved on a multiaccess box), or exploration (latency to approach a novel environment). Our results elucidated that individuals differentially expressing a particular behavior in an edge population could facilitate the rapid geographic range expansion of great-tailed grackles, and we found no support for the importance of several traits that were hypothesized to be involved in such an expansion. Our findings highlight the value of population studies and of breaking down cognitive concepts into direct measures of individual abilities to better understand how species might adapt to novel circumstances.
{"title":"Implementing a rapid geographic range expansion - the role of behavior changes","authors":"Corina Logan, Kelsey McCune, Christa LeGrande-Rolls, Zara Marfori, Josephine Hubbard, Dieter Lukas","doi":"10.24072/pcjournal.320","DOIUrl":"https://doi.org/10.24072/pcjournal.320","url":null,"abstract":"It is generally thought that behavioral flexibility, the ability to change behavior when circumstances change, plays an important role in the ability of species to rapidly expand their geographic range. Great-tailed grackles (Quiscalus mexicanus) are a social, polygamous species that is rapidly expanding its geographic range by settling in new areas and habitats. They are behaviorally flexible and highly associated with human-modified environments, eating a variety of human foods in addition to foraging on insects and on the ground for other natural food items. They offer an opportunity to assess the role of behavior change over the course of their expansion. We compared behavior in wild-caught grackles from two populations across their range (an older population in the middle of the northern expansion front: Tempe, Arizona, and a more recent population on the northern edge of the expansion front: Woodland, California) to investigate whether certain behaviors (flexibility, innovativeness, exploration, and persistence) have higher averages and variances in the newer or older population. We found that grackles in the edge population had a higher flexibility variance (measured by reversal learning) and a higher persistence average (they participated in a larger proportion of trials), and that there were no population differences in average levels of flexibility, innovativeness (number of loci solved on a multiaccess box), or exploration (latency to approach a novel environment). Our results elucidated that individuals differentially expressing a particular behavior in an edge population could facilitate the rapid geographic range expansion of great-tailed grackles, and we found no support for the importance of several traits that were hypothesized to be involved in such an expansion. Our findings highlight the value of population studies and of breaking down cognitive concepts into direct measures of individual abilities to better understand how species might adapt to novel circumstances.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136310938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nikolaos Minadakis, Hefin Williams, Robert Horvath, Danka Caković, Christoph Stritt, Michael Thieme, Yann Bourgeois, Anne C. Roulin
Closely related to economically important crops, the grass Brachypodium distachyon has been originally established as a pivotal species for grass genomics but more recently flourished as a model for developmental biology. Grasses encompass more than 10,000 species and cover more than 40% of the world land area from tropical to temperate regions. Given that grasses also supply about a fifth of the world's dietary protein as cereal grains, unlocking the sources of phenotypic variation in B. distachyon is hence of prime interest in fundamental and applied research in agronomy, ecology and evolution. We present here the B. distachyon diversity panel, which encompasses 332 fully sequenced accessions covering the whole species distribution from Spain to Iraq. By combining population genetics, niche modeling and landscape genomics, we suggest that B. distachyon recolonized Europe and the Middle East following the last glacial maximum. Consequently, the species faced new environmental conditions which led to clear associations between bioclimatic variables and genetic factors as well as footprints of positive selection in the genome. Altogether, this genomic resource offers a powerful alternative to Arabidopsis thaliana to investigate the genetic bases of adaptation and phenotypic plasticity in plants and more specifically in monocots.
{"title":"The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches","authors":"Nikolaos Minadakis, Hefin Williams, Robert Horvath, Danka Caković, Christoph Stritt, Michael Thieme, Yann Bourgeois, Anne C. Roulin","doi":"10.24072/pcjournal.319","DOIUrl":"https://doi.org/10.24072/pcjournal.319","url":null,"abstract":"Closely related to economically important crops, the grass Brachypodium distachyon has been originally established as a pivotal species for grass genomics but more recently flourished as a model for developmental biology. Grasses encompass more than 10,000 species and cover more than 40% of the world land area from tropical to temperate regions. Given that grasses also supply about a fifth of the world's dietary protein as cereal grains, unlocking the sources of phenotypic variation in B. distachyon is hence of prime interest in fundamental and applied research in agronomy, ecology and evolution. We present here the B. distachyon diversity panel, which encompasses 332 fully sequenced accessions covering the whole species distribution from Spain to Iraq. By combining population genetics, niche modeling and landscape genomics, we suggest that B. distachyon recolonized Europe and the Middle East following the last glacial maximum. Consequently, the species faced new environmental conditions which led to clear associations between bioclimatic variables and genetic factors as well as footprints of positive selection in the genome. Altogether, this genomic resource offers a powerful alternative to Arabidopsis thaliana to investigate the genetic bases of adaptation and phenotypic plasticity in plants and more specifically in monocots.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136308966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σk k-mers and the interval [0, σk −1], where σ is the alphabet size. In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous, canonical k-mers are considered, i.e., the lexicographically smaller of a given k-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonical k-mers are not evenly distributed within the interval [0, σk −1]. We present a minimal encoding of canonical k-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0, σk/2−1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.
{"title":"General encoding of canonical k-mers","authors":"Roland Wittler","doi":"10.24072/pcjournal.323","DOIUrl":"https://doi.org/10.24072/pcjournal.323","url":null,"abstract":"To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σk k-mers and the interval [0, σk −1], where σ is the alphabet size. In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous, canonical k-mers are considered, i.e., the lexicographically smaller of a given k-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonical k-mers are not evenly distributed within the interval [0, σk −1]. We present a minimal encoding of canonical k-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0, σk/2−1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136308887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pierre Levallois, Mily Leblanc-Maridor, Annalisa Scollo, Paolo Ferrari, Catherine Belloc, Christine Fourichon
A tailor-made health plan is a set of recommendations for a farmer to achieve and maintain a high health and welfare status. Tailored to each farm, it is intended to be an effective way of triggering change. This study aimed to assess the effectiveness of tailor-made health plans in pig farms, designed in various situations after a systematic biosecurity and herd health audit. An intervention study was carried out in 20 farrow-to-finish pig farms. An initial standardized audit and discussion between the farm veterinarian and the farmer resulted in a specific plan. Compliance with recommendations was monitored during 8 months. Changes in health, performances and antimicrobial use were monitored. We defined two categories of plans: i) 14 plans targeting a given health disorder present in a farm; ii) 17 plans to improve prevention, not targeting a specific health disorder (a farm could have both types of plans). A small number of priority recommendations were made per farm. In 18 farms, farmers implemented 1 to 4 recommendations (none in 2 farms). Of the 17 non-disorder-specific plans, 11 were considered effective ( > 50% recommendations implemented), 3 intermediate (at least one but less than half of the recommendations implemented) and 3 ineffective (no implementation). Of the 14 disorder-specific plans, 9 were followed with full or good compliance ( > 50% recommendations implemented), 2 with intermediate compliance (1 recommendation implemented out of 2) and 3 with no compliance (no recommendation implemented). When at least one recommendation was implemented, change in clinical, performance and antimicrobial use indicators was assessed if a biological association with the disorder was deemed plausible and if their initial value showed room for improvement. Improvement was evidenced 4/9, 1/6 and 1/6 times for these indicators, respectively. Independently, veterinarians concluded that 8/14 plans were effective. Overall, tailor-made health plans were effective in triggering changes in farm management. Three key points were identified for future assessments of the effectiveness of tailor-made health plans. Compliance should be the first indicator of assessment. Outcome indicators and their monitoring periods should be adapted to each farm and to the targeted health disorder. Indicators should be combined to have a holistic description of the evolution of a health disorder. Further research is needed to identify how to select indicators to combine and how to combine them, according to health disorders.
{"title":"Combining several indicators to assess the effectiveness of tailor-made health plans in pig farms","authors":"Pierre Levallois, Mily Leblanc-Maridor, Annalisa Scollo, Paolo Ferrari, Catherine Belloc, Christine Fourichon","doi":"10.24072/pcjournal.318","DOIUrl":"https://doi.org/10.24072/pcjournal.318","url":null,"abstract":"A tailor-made health plan is a set of recommendations for a farmer to achieve and maintain a high health and welfare status. Tailored to each farm, it is intended to be an effective way of triggering change. This study aimed to assess the effectiveness of tailor-made health plans in pig farms, designed in various situations after a systematic biosecurity and herd health audit. An intervention study was carried out in 20 farrow-to-finish pig farms. An initial standardized audit and discussion between the farm veterinarian and the farmer resulted in a specific plan. Compliance with recommendations was monitored during 8 months. Changes in health, performances and antimicrobial use were monitored. We defined two categories of plans: i) 14 plans targeting a given health disorder present in a farm; ii) 17 plans to improve prevention, not targeting a specific health disorder (a farm could have both types of plans). A small number of priority recommendations were made per farm. In 18 farms, farmers implemented 1 to 4 recommendations (none in 2 farms). Of the 17 non-disorder-specific plans, 11 were considered effective ( > 50% recommendations implemented), 3 intermediate (at least one but less than half of the recommendations implemented) and 3 ineffective (no implementation). Of the 14 disorder-specific plans, 9 were followed with full or good compliance ( > 50% recommendations implemented), 2 with intermediate compliance (1 recommendation implemented out of 2) and 3 with no compliance (no recommendation implemented). When at least one recommendation was implemented, change in clinical, performance and antimicrobial use indicators was assessed if a biological association with the disorder was deemed plausible and if their initial value showed room for improvement. Improvement was evidenced 4/9, 1/6 and 1/6 times for these indicators, respectively. Independently, veterinarians concluded that 8/14 plans were effective. Overall, tailor-made health plans were effective in triggering changes in farm management. Three key points were identified for future assessments of the effectiveness of tailor-made health plans. Compliance should be the first indicator of assessment. Outcome indicators and their monitoring periods should be adapted to each farm and to the targeted health disorder. Indicators should be combined to have a holistic description of the evolution of a health disorder. Further research is needed to identify how to select indicators to combine and how to combine them, according to health disorders.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136312831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pairwise interactions in food webs, including those between predator and prey are often modulated by a third species. Such higher-order interactions are important structural components of natural food webs that can increase the stability of communities against perturbations and ensure continued ecosystem functioning. Particularly the flux of rare organic and inorganic compounds that are essential to species in the community can create higher-order interactions. Even though many such compounds exist, their effect on structuring communities is little understood. In this study, I perform invasion analyses on a general food web model that depicts apparent and exploitative competition. Introducing the provision of essential resources by a prey species to either its competitor or its predator as a higher-order interaction, I find that this mechanism can ensure the focal prey’s persistence. Larger dietary essentiality, i.e. a stronger dependence of the predator or the competitor on the essential resource can increase the invasion growth rate of the focal prey to positive values, thus promoting its persistence when it would go extinct for low essentiality. This research shows that essential resources and the higher-order interactions created by them should be considered in community ecology.
{"title":"Provision of essential resources as a persistence strategy in food webs","authors":"Michael Raatz","doi":"10.24072/pcjournal.315","DOIUrl":"https://doi.org/10.24072/pcjournal.315","url":null,"abstract":"Pairwise interactions in food webs, including those between predator and prey are often modulated by a third species. Such higher-order interactions are important structural components of natural food webs that can increase the stability of communities against perturbations and ensure continued ecosystem functioning. Particularly the flux of rare organic and inorganic compounds that are essential to species in the community can create higher-order interactions. Even though many such compounds exist, their effect on structuring communities is little understood. In this study, I perform invasion analyses on a general food web model that depicts apparent and exploitative competition. Introducing the provision of essential resources by a prey species to either its competitor or its predator as a higher-order interaction, I find that this mechanism can ensure the focal prey’s persistence. Larger dietary essentiality, i.e. a stronger dependence of the predator or the competitor on the essential resource can increase the invasion growth rate of the focal prey to positive values, thus promoting its persistence when it would go extinct for low essentiality. This research shows that essential resources and the higher-order interactions created by them should be considered in community ecology.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135827574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Veli-Matti Karhulahti, Miia Siutila, Jukka Vahlo, Raine Koskimaa
The academic debates regarding the psychiatric relevance of gaming disorder continue largely because the lived experiences of treatment-seekers remain mostly unstudied. This registered report addresses the above research gap with a longitudinal design that pursues a comparative descriptive understanding of how intensive gaming experiences evolve in both clinical and non-clinical life situations. Accompanied by a rich health survey, interpretative phenomenological analysis was adapted to understand in-depth interview data from treatment-seeking (n=5) and esports-playing (n=4) participants, the latter of which did not experience any gaming-related health problems. The interviews were carried out as a 1-year follow-up. The study finds intensive relationships with gaming to be experienced through
{"title":"Life Thinning and Gaming Disorder: A Longitudinal Qualitative Registered Report","authors":"Veli-Matti Karhulahti, Miia Siutila, Jukka Vahlo, Raine Koskimaa","doi":"10.24072/pcjournal.313","DOIUrl":"https://doi.org/10.24072/pcjournal.313","url":null,"abstract":"The academic debates regarding the psychiatric relevance of gaming disorder continue largely because the lived experiences of treatment-seekers remain mostly unstudied. This registered report addresses the above research gap with a longitudinal design that pursues a comparative descriptive understanding of how intensive gaming experiences evolve in both clinical and non-clinical life situations. Accompanied by a rich health survey, interpretative phenomenological analysis was adapted to understand in-depth interview data from treatment-seeking (n=5) and esports-playing (n=4) participants, the latter of which did not experience any gaming-related health problems. The interviews were carried out as a 1-year follow-up. The study finds intensive relationships with gaming to be experienced through","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135884194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Grégoire Perez, Laure Bournez, Nathalie Boulanger, Johanna Fite, Barbara Livoreil, Karen D. McCoy, Elsa Quillery, Magalie René-Martellet, Sarah I. Bonnet
The tick Ixodes ricinus is the most important vector species of infectious diseases in European France. Understanding its distribution, phenology, and host species use, along with the distribution and prevalence of associated pathogens at a national scale is essential for developing prevention strategies. The aim of this paper is to provide a systematic map and narrative review of the existing knowledge on the eco-epidemiology of I. ricinus in France. Using literature published up to 2020, the present paper provides a distribution map for the species and a summary of environmental factors explaining observed geographical differences in phenology and temporal differences in abundance. The diversity of vertebrate host species used by this tick, along with their degree of infestation when available, are presented and discussed with respect to their potential contribution to the population dynamics of I. ricinus and the circulation of tick-borne zoonotic pathogens. Prevalence data of detected pathogens are summarised in different maps. Results from 187 identified references show that the species is present in most departments, but scarce under Mediterranean climates and in coastal habitats. Its phenology is generally bimodal with climate-associated variations. Abundance seems positively influenced by forest cover and host abundance. Rodents and ruminants are the most studied species groups, but the diversity of sampling protocols (e.g., location, season, exhaustivity of inspection) precluded direct comparisons between groups. Data on pathogens are patchy, with most studies conducted near research laboratories. Among pathogens, Borrelia burgdorferi sensu lato is the most examined and seems most prevalent in north-eastern and central France. The review highlights the gaps in our knowledge of tick-host-pathogen interactions, their ecologies and their distributions, and demonstrates the need to address these gaps in order to optimize tick and tick-borne diseases prevention and control.
蓖麻蜱是欧洲法国最重要的传染病媒介物种。了解其分布、物候和寄主物种利用，以及相关病原体在全国范围内的分布和流行情况，对于制定预防策略至关重要。本文的目的是提供一个系统的地图和叙述综述现有知识的蓖麻毒素在法国的生态流行病学。本文利用截至2020年发表的文献，绘制了该物种的分布图，并总结了解释观测到的物候地理差异和丰度时间差异的环境因素。本文介绍并讨论了该蜱所使用的脊椎动物宿主物种的多样性，以及它们在可用时的侵袭程度，以及它们对蓖麻蜱种群动态和蜱传人畜共患病病原体传播的潜在贡献。在不同的地图中汇总了检测到的病原体的流行率数据。来自187个已确定参考文献的结果表明，该物种存在于大多数省，但在地中海气候和沿海生境中很少。它的物候通常是与气候相关的双峰变化。丰度似乎受到森林覆盖和寄主丰度的积极影响。啮齿类动物和反刍动物是研究最多的物种组，但采样方案的多样性(例如，地点、季节、检查的穷尽性)妨碍了组间的直接比较。关于病原体的数据不完整，大多数研究都是在研究实验室附近进行的。在病原体中，伯氏疏螺旋体(Borrelia burgdorferi sensu lato)是检测最多的，似乎在法国东北部和中部最流行。这篇综述强调了我们在蜱-宿主-病原体相互作用、它们的生态学和分布方面的知识差距，并表明有必要解决这些差距，以优化蜱和蜱传疾病的预防和控制。
{"title":"The distribution, phenology, host range and pathogen prevalence of Ixodes ricinus in France: a systematic map and narrative review","authors":"Grégoire Perez, Laure Bournez, Nathalie Boulanger, Johanna Fite, Barbara Livoreil, Karen D. McCoy, Elsa Quillery, Magalie René-Martellet, Sarah I. Bonnet","doi":"10.24072/pcjournal.291","DOIUrl":"https://doi.org/10.24072/pcjournal.291","url":null,"abstract":"The tick Ixodes ricinus is the most important vector species of infectious diseases in European France. Understanding its distribution, phenology, and host species use, along with the distribution and prevalence of associated pathogens at a national scale is essential for developing prevention strategies. The aim of this paper is to provide a systematic map and narrative review of the existing knowledge on the eco-epidemiology of I. ricinus in France. Using literature published up to 2020, the present paper provides a distribution map for the species and a summary of environmental factors explaining observed geographical differences in phenology and temporal differences in abundance. The diversity of vertebrate host species used by this tick, along with their degree of infestation when available, are presented and discussed with respect to their potential contribution to the population dynamics of I. ricinus and the circulation of tick-borne zoonotic pathogens. Prevalence data of detected pathogens are summarised in different maps. Results from 187 identified references show that the species is present in most departments, but scarce under Mediterranean climates and in coastal habitats. Its phenology is generally bimodal with climate-associated variations. Abundance seems positively influenced by forest cover and host abundance. Rodents and ruminants are the most studied species groups, but the diversity of sampling protocols (e.g., location, season, exhaustivity of inspection) precluded direct comparisons between groups. Data on pathogens are patchy, with most studies conducted near research laboratories. Among pathogens, Borrelia burgdorferi sensu lato is the most examined and seems most prevalent in north-eastern and central France. The review highlights the gaps in our knowledge of tick-host-pathogen interactions, their ecologies and their distributions, and demonstrates the need to address these gaps in order to optimize tick and tick-borne diseases prevention and control.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136362808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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