The Go!Digital 3.0 project IUENNA—an acronym for “open I ng the so U th E rn jau N tal as a micro-regio N for future A rchaeology”—adopts a comprehensive open science methodology and concentrates on the archaeological micro-region of the Jauntal/Podjuna Valley in Carinthia, Austria. Key case studies include the Hemmaberg/gora svete Heme site and its associated locations: Globasnitz/Globasnica/Iuenna, Jaunstein/Podjuna, and St. Ste-fan/Šteben. The Hemmaberg site is among the most extensively researched Late Antique hilltop settlements—dating from the 4 th to the 6 th century AD—and serves as a primary research focus. This site moreover functions as a crucial reference point for early Christianity in the Southeast Alpine region and boasts a rich array of features
Go! Digital 3.0 项目 IUENNA--"open I ng the so U th E rn jau N tal as a micro-regio N for future A rchaeology "的首字母缩写--采用了一种全面的开放科学方法，集中研究奥地利克恩顿州 Jauntal/Podjuna 山谷的考古微型区域。主要案例研究包括 Hemmaberg/gora svete Heme 遗址及其相关地点：Globasnitz/Globasnica/Iuenna, Jaunstein/Podjuna 和 St.海马伯格遗址是研究最为广泛的晚期古代山顶定居点之一，其历史可追溯到公元 4 世纪至 6 世纪，也是主要的研究重点。此外，该遗址还是东南阿尔卑斯山地区早期基督教的重要参照点，并拥有丰富的特征
{"title":"IUENNA – openIng the soUthErn jauNtal as a micro-regioN for future Archaeology: A «para-description»","authors":"Dominik Hagmann, Franziska Reiner","doi":"10.24072/pcjournal.338","DOIUrl":"https://doi.org/10.24072/pcjournal.338","url":null,"abstract":"The Go!Digital 3.0 project IUENNA—an acronym for “open I ng the so U th E rn jau N tal as a micro-regio N for future A rchaeology”—adopts a comprehensive open science methodology and concentrates on the archaeological micro-region of the Jauntal/Podjuna Valley in Carinthia, Austria. Key case studies include the Hemmaberg/gora svete Heme site and its associated locations: Globasnitz/Globasnica/Iuenna, Jaunstein/Podjuna, and St. Ste-fan/Šteben. The Hemmaberg site is among the most extensively researched Late Antique hilltop settlements—dating from the 4 th to the 6 th century AD—and serves as a primary research focus. This site moreover functions as a crucial reference point for early Christianity in the Southeast Alpine region and boasts a rich array of features","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139002646","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}
Alison B. Duncan, Cassandra Marinosci, Céline Devaux, Sophie Lefèvre, Sara Magalhães, Joanne Griffin, Adeline Valente, Ophélie Ronce, Isabelle Olivieri
In structured populations, competition for mates between closely related males, termed Local Mate Competition (LMC), is expected to select for female-biased offspring sex ratios. However, the cues underlying sex allocation decisions remain poorly studied. Here, we test for several cues in the spider mite Tetranychus urticae, a species that was previously found to adjust the sex ratio of its offspring in response to the number of females within the local population, i.e. a patch. We here investigate whether the offspring sex ratio of T. urticae females changes in response to 1) the current number of females in the same patch, 2) the number of females in the patches of their mothers and 3) their relatedness to their mate. Single females on patches produced similar sex ratios to those of groups of 15 females; their mothers had been in identical conditions of panmixia. The offspring sex ratios of females mated with their brother did not differ from those of females mated with an unrelated male. Females however produced a more female-biased offspring sex ratio if their mothers were alone on a patch compared to 15 other females. Thus, maternal environment is used as a cue for the sex allocation of daughters. We discuss the conditions under which the maternal environment may be a reliable predictor of LMC experienced by grand-sons.
{"title":"Transgenerational cues about local mate competition affect offspring sex ratios in the spider mite Tetranychus urticae","authors":"Alison B. Duncan, Cassandra Marinosci, Céline Devaux, Sophie Lefèvre, Sara Magalhães, Joanne Griffin, Adeline Valente, Ophélie Ronce, Isabelle Olivieri","doi":"10.24072/pcjournal.343","DOIUrl":"https://doi.org/10.24072/pcjournal.343","url":null,"abstract":"In structured populations, competition for mates between closely related males, termed Local Mate Competition (LMC), is expected to select for female-biased offspring sex ratios. However, the cues underlying sex allocation decisions remain poorly studied. Here, we test for several cues in the spider mite Tetranychus urticae, a species that was previously found to adjust the sex ratio of its offspring in response to the number of females within the local population, i.e. a patch. We here investigate whether the offspring sex ratio of T. urticae females changes in response to 1) the current number of females in the same patch, 2) the number of females in the patches of their mothers and 3) their relatedness to their mate. Single females on patches produced similar sex ratios to those of groups of 15 females; their mothers had been in identical conditions of panmixia. The offspring sex ratios of females mated with their brother did not differ from those of females mated with an unrelated male. Females however produced a more female-biased offspring sex ratio if their mothers were alone on a patch compared to 15 other females. Thus, maternal environment is used as a cue for the sex allocation of daughters. We discuss the conditions under which the maternal environment may be a reliable predictor of LMC experienced by grand-sons.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"11 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136347412","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}
Vimbiso Chidoti, Hélène De Nys, Malika Abdi, Getrude Mashura, Valérie Pinarello, Ngoni Chiweshe, Gift Matope, Laure Guerrini, Davies Pfukenyi, Julien Cappelle, Ellen Mwandiringana, Dorothée Missé, Elizabeth Gori, Mathieu Bourgarel, Florian Liégeois
Astroviruses (AstVs) have been discovered in over 80 animal species including diverse bat species and avian species. A study on Astrovirus circulation and diversity in different insectivorous and frugivorous chiropteran species roosting in trees, caves and building basements was carried out at 11 different sites across Zimbabwe. Pooled and individual faecal sampling methods were used for this study, with collection dates ranging from June 2016 to July 2021. In two sites, Magweto and Chirundu, sampling was carried out at monthly intervals from August 2020 to July 2021. Astroviruses and bat mitochondrial genes were amplified using pan-AstVs and CytB /12S RNA PCR systems respectively. Phylogenetic analysis of the RdRp Astrovirus sequences revealed a high genetic diversity of astroviruses. All the bat astroviruses tested in this study clustered with the Mamastrovirus genus. Two distinct groups of amplified sequences were identified. One group was comprised of sequences isolated from Hipposideros, Rhinolophus and Eidolon helvum spp. clustered with Human Astrovirus strains: HuAstV types1-6, HuAstV-MLB1-3 and HuAstV-VA-1. The second group comprising the majority of the sequences clustered with different strains of Bat AstVs. Results from the longitudinal study at Magweto and Chirundu showed an overall AstV prevalence of 13.7% and 10.4% respectively. Peaks of AstV infection at Chirundu coincided with the period when juveniles are 4-6 months old. By combining data from our previous work on Coronaviruses, we also anaylzed co-infection of bats with Coronaviruses and Astroviruses at Magweto and Chirundu sites for which the prevalence of co-infection was 2.6% and 3.5% respectively.
星状病毒(AstVs)已在包括多种蝙蝠和鸟类在内的80多种动物中被发现。在津巴布韦11个不同地点对栖息在树木、洞穴和建筑物地下室的不同食虫和食果翼目动物的星状病毒传播和多样性进行了研究。本研究采用了混合和个体粪便采样方法，收集日期为2016年6月至2021年7月。在Magweto和Chirundu两个地点，从2020年8月至2021年7月每月进行一次抽样。采用pan- astv和CytB /12S RNA PCR系统分别扩增星状病毒和蝙蝠线粒体基因。对RdRp星状病毒序列的系统发育分析表明，星状病毒具有较高的遗传多样性。本研究中测试的所有蝙蝠星状病毒都属于星状病毒属。鉴定出两组不同的扩增序列。其中一组由从希波sideros、Rhinolophus和Eidolon helvum spp中分离的序列组成，与人类星状病毒株HuAstV type 1-6、HuAstV- mlb1 -3和HuAstV- va -1聚集。第二组包含大多数序列聚集在不同的蝙蝠astv株上。Magweto和Chirundu的纵向研究结果显示，asv的总体患病率分别为13.7%和10.4%。奇伦都的亚洲猪瘟病毒感染高峰恰好发生在雏鸡4-6个月大的时期。结合之前冠状病毒研究的数据，我们还分析了Magweto和Chirundu站点蝙蝠与冠状病毒和astrovirus的共同感染情况，其中共同感染的患病率分别为2.6%和3.5%。
{"title":"Longitudinal Survey of Astrovirus infection in different bat species in Zimbabwe: Evidence of high genetic Astrovirus diversity","authors":"Vimbiso Chidoti, Hélène De Nys, Malika Abdi, Getrude Mashura, Valérie Pinarello, Ngoni Chiweshe, Gift Matope, Laure Guerrini, Davies Pfukenyi, Julien Cappelle, Ellen Mwandiringana, Dorothée Missé, Elizabeth Gori, Mathieu Bourgarel, Florian Liégeois","doi":"10.24072/pcjournal.340","DOIUrl":"https://doi.org/10.24072/pcjournal.340","url":null,"abstract":"Astroviruses (AstVs) have been discovered in over 80 animal species including diverse bat species and avian species. A study on Astrovirus circulation and diversity in different insectivorous and frugivorous chiropteran species roosting in trees, caves and building basements was carried out at 11 different sites across Zimbabwe. Pooled and individual faecal sampling methods were used for this study, with collection dates ranging from June 2016 to July 2021. In two sites, Magweto and Chirundu, sampling was carried out at monthly intervals from August 2020 to July 2021. Astroviruses and bat mitochondrial genes were amplified using pan-AstVs and CytB /12S RNA PCR systems respectively. Phylogenetic analysis of the RdRp Astrovirus sequences revealed a high genetic diversity of astroviruses. All the bat astroviruses tested in this study clustered with the Mamastrovirus genus. Two distinct groups of amplified sequences were identified. One group was comprised of sequences isolated from Hipposideros, Rhinolophus and Eidolon helvum spp. clustered with Human Astrovirus strains: HuAstV types1-6, HuAstV-MLB1-3 and HuAstV-VA-1. The second group comprising the majority of the sequences clustered with different strains of Bat AstVs. Results from the longitudinal study at Magweto and Chirundu showed an overall AstV prevalence of 13.7% and 10.4% respectively. Peaks of AstV infection at Chirundu coincided with the period when juveniles are 4-6 months old. By combining data from our previous work on Coronaviruses, we also anaylzed co-infection of bats with Coronaviruses and Astroviruses at Magweto and Chirundu sites for which the prevalence of co-infection was 2.6% and 3.5% respectively.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"21 16","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135390329","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}
Inferring the strength of species interactions from demographic data is a challenging task. The Integrated Population Modelling (IPM) approach, bringing together population counts, capture-recapture, and individual-level fecundity data into a unified model framework, has been extended from single species to the community level. This allows to specify IPMs for multiple species with interactions specified as links between vital rates and stage-specific densities. However, there is no evaluation of such models when interactions are actually absent---while any interaction inference method runs the risk of producing false positives. We investigate here whether multispecies IPMs could output interactions where there are in fact none, building on an existing predator-prey IPM. We show that interspecific density-dependence estimates are centered on zero when simulated to be zero, and therefore their estimation is unbiased. Their coverage probability, quantifying how many times credible intervals include zero, is also satisfactory. We further confirm that adding random temporal variation to multispecies density-dependent link functions does not alter these results. This study therefore reaffirms the potential of multispecies IPMs to infer correctly how biotic interactions influence demography, although future studies should investigate model misspecifications.
{"title":"Assessing species interactions using integrated predator-prey models","authors":"Matthieu Paquet, Frédéric Barraquand","doi":"10.24072/pcjournal.337","DOIUrl":"https://doi.org/10.24072/pcjournal.337","url":null,"abstract":"Inferring the strength of species interactions from demographic data is a challenging task. The Integrated Population Modelling (IPM) approach, bringing together population counts, capture-recapture, and individual-level fecundity data into a unified model framework, has been extended from single species to the community level. This allows to specify IPMs for multiple species with interactions specified as links between vital rates and stage-specific densities. However, there is no evaluation of such models when interactions are actually absent---while any interaction inference method runs the risk of producing false positives. We investigate here whether multispecies IPMs could output interactions where there are in fact none, building on an existing predator-prey IPM. We show that interspecific density-dependence estimates are centered on zero when simulated to be zero, and therefore their estimation is unbiased. Their coverage probability, quantifying how many times credible intervals include zero, is also satisfactory. We further confirm that adding random temporal variation to multispecies density-dependent link functions does not alter these results. This study therefore reaffirms the potential of multispecies IPMs to infer correctly how biotic interactions influence demography, although future studies should investigate model misspecifications.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"79 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135341570","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}
François Criscuolo, Inès Fache, Bertrand Scaar, Sandrine Zahn, Josefa Bleu
Telomeres are non-coding DNA sequences located at the end of linear chromosomes, protecting genome integrity. In numerous taxa, telomeres shorten with age and telomere length (TL) is positively correlated with longevity. Moreover, TL is also affected by environmental stressors and/or resource-demanding situations particularly during early-life. Thus, TL has been used as a physiological marker of individual quality and also as an indicator of population trend in conservation physiology. In this study, we investigated the effects of hatching rank, year of birth (2014 to 2017), sex and nest environment on TL of 137 Little Owls nestlings (Athene noctua). Little Owls’ populations in Europe showed a marked declined in the end of the 20th century. Nowadays, in the studied Alsatian population, the population is increasing. In this study, our results indicated that telomeres are longer in females and, independently of sex, in nestlings with the highest body condition. There was also a negative effect of hatching rank but only for last-hatched nestlings in large clutches of 5 nestlings. We did not find any effect of the environmental covariates on nestlings’ TL. Finally, we found that nestlings’ TL were shorter the last year of the study, while nestlings’ body condition stayed unchanged over the same period. This result is intriguing given the local positive population dynamics and is further discussed in the context of physiological conservation. Future studies should investigate the link between reduced TL and survival prospects in this species.
{"title":"Telomere length varies with sex, hatching rank and year of birth in the Little Owl, Athene noctua","authors":"François Criscuolo, Inès Fache, Bertrand Scaar, Sandrine Zahn, Josefa Bleu","doi":"10.24072/pcjournal.341","DOIUrl":"https://doi.org/10.24072/pcjournal.341","url":null,"abstract":"Telomeres are non-coding DNA sequences located at the end of linear chromosomes, protecting genome integrity. In numerous taxa, telomeres shorten with age and telomere length (TL) is positively correlated with longevity. Moreover, TL is also affected by environmental stressors and/or resource-demanding situations particularly during early-life. Thus, TL has been used as a physiological marker of individual quality and also as an indicator of population trend in conservation physiology. In this study, we investigated the effects of hatching rank, year of birth (2014 to 2017), sex and nest environment on TL of 137 Little Owls nestlings (Athene noctua). Little Owls’ populations in Europe showed a marked declined in the end of the 20th century. Nowadays, in the studied Alsatian population, the population is increasing. In this study, our results indicated that telomeres are longer in females and, independently of sex, in nestlings with the highest body condition. There was also a negative effect of hatching rank but only for last-hatched nestlings in large clutches of 5 nestlings. We did not find any effect of the environmental covariates on nestlings’ TL. Finally, we found that nestlings’ TL were shorter the last year of the study, while nestlings’ body condition stayed unchanged over the same period. This result is intriguing given the local positive population dynamics and is further discussed in the context of physiological conservation. Future studies should investigate the link between reduced TL and survival prospects in this species.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135391306","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}
Cédric Hubas, Julie Gaubert-Boussarie, An-Sofie D’Hondt, Bruno Jesus, Dominique Lamy, Vona Meleder, Antoine Prins, Philippe Rosa, Willem Stock, Koen Sabbe
{"title":"Identification of microbial exopolymer producers in sandy and muddy intertidal sediments by compound-specific isotope analysis","authors":"Cédric Hubas, Julie Gaubert-Boussarie, An-Sofie D’Hondt, Bruno Jesus, Dominique Lamy, Vona Meleder, Antoine Prins, Philippe Rosa, Willem Stock, Koen Sabbe","doi":"10.24072/pcjournal.336","DOIUrl":"https://doi.org/10.24072/pcjournal.336","url":null,"abstract":"","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135871977","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}
Network structure is often considered one of the most important features of a network, and various models exist to generate graphs having one of the most studied types of structures, such as blocks/communities or spatial structures. In this article, we introduce a framework for the generation of random graphs with a controlled size —number of nodes, edges— and a customizable structure, beyond blocks and spatial ones, based on node-pair rank and a tunable probability function allowing to control the amount of randomness. We introduce a structure zoo —a collection of original network structures— and conduct experiments on the small-world properties of networks generated by those structures. Finally, we introduce an implementation as a Python library named Structify-net.
{"title":"Structify-Net: Random Graph generation with controlled size and customized structure","authors":"Remy Cazabet, Salvatore Citraro, Giulio Rossetti","doi":"10.24072/pcjournal.335","DOIUrl":"https://doi.org/10.24072/pcjournal.335","url":null,"abstract":"Network structure is often considered one of the most important features of a network, and various models exist to generate graphs having one of the most studied types of structures, such as blocks/communities or spatial structures. In this article, we introduce a framework for the generation of random graphs with a controlled size —number of nodes, edges— and a customizable structure, beyond blocks and spatial ones, based on node-pair rank and a tunable probability function allowing to control the amount of randomness. We introduce a structure zoo —a collection of original network structures— and conduct experiments on the small-world properties of networks generated by those structures. Finally, we introduce an implementation as a Python library named Structify-net.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135778376","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}
Florian Taraveau, Thomas Pollet, Maxime Duhayon, Laëtitia Gardès, Hélène Jourdan-Pineau
Over the past decade, many studies have demonstrated the crucial role of the tick microbiome in tick biology. The soft tick Ornithodoros moubata is a hematophagous ectoparasite of Suidae, best known for transmitting the African swine fever virus. Its bacterial microbiota is characterized by a high prevalence of Francisella-like and Rickettsia endosymbionts. The present study aims to better understand the potential influence of these two major members of the tick microbiota on the reproductive fitness of O. moubata. A total of 132 adult female ticks were treated with antibiotics using gentamycin or rifampicin added to the blood meal. Half of the ticks were also supplemented with B vitamins to address the nutritional role of endosymbionts. Over two periods of 50 days, several traits related to the reproductive fitness were monitored to investigate the importance of Francisella and Rickettsia for these traits. It appeared that most of the reproductive parameters considered were not affected. However, antibiotic treatments induced an increase in the tick survival, indicating a potential fitness cost of harboring endosymbionts during the tick reproductive cycle. Similarly, 366 first stage nymphs of O. moubata were exposed to the same treatments for molecular quantification of both endosymbionts. Results from qPCR suggested that the treatments had a bacteriostatic effect on endosymbionts without completely eliminating neither Francisella-like endosymbiont nor Rickettsia.
{"title":"Influence of endosymbionts on the reproductive fitness of the tick Ornithodoros moubata","authors":"Florian Taraveau, Thomas Pollet, Maxime Duhayon, Laëtitia Gardès, Hélène Jourdan-Pineau","doi":"10.24072/pcjournal.334","DOIUrl":"https://doi.org/10.24072/pcjournal.334","url":null,"abstract":"Over the past decade, many studies have demonstrated the crucial role of the tick microbiome in tick biology. The soft tick Ornithodoros moubata is a hematophagous ectoparasite of Suidae, best known for transmitting the African swine fever virus. Its bacterial microbiota is characterized by a high prevalence of Francisella-like and Rickettsia endosymbionts. The present study aims to better understand the potential influence of these two major members of the tick microbiota on the reproductive fitness of O. moubata. A total of 132 adult female ticks were treated with antibiotics using gentamycin or rifampicin added to the blood meal. Half of the ticks were also supplemented with B vitamins to address the nutritional role of endosymbionts. Over two periods of 50 days, several traits related to the reproductive fitness were monitored to investigate the importance of Francisella and Rickettsia for these traits. It appeared that most of the reproductive parameters considered were not affected. However, antibiotic treatments induced an increase in the tick survival, indicating a potential fitness cost of harboring endosymbionts during the tick reproductive cycle. Similarly, 366 first stage nymphs of O. moubata were exposed to the same treatments for molecular quantification of both endosymbionts. Results from qPCR suggested that the treatments had a bacteriostatic effect on endosymbionts without completely eliminating neither Francisella-like endosymbiont nor Rickettsia.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135883688","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}
Gonché Danesh, Corentin Boennec, Laura Verdurme, Mathilde Roussel, Sabine Trombert-Paolantoni, Benoit Visseaux, Stéphanie Haim-Boukobza, Samuel Alizon
Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.
{"title":"COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences","authors":"Gonché Danesh, Corentin Boennec, Laura Verdurme, Mathilde Roussel, Sabine Trombert-Paolantoni, Benoit Visseaux, Stéphanie Haim-Boukobza, Samuel Alizon","doi":"10.24072/pcjournal.333","DOIUrl":"https://doi.org/10.24072/pcjournal.333","url":null,"abstract":"Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136114333","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：