PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Shedding light on the bacterial resistance to toxic UV filters: a comparative genomic study
items: Degradation of lignocelluloses in straw using AC-1, a thermophilic composite microbial system
items: Changes in the urinary proteome in rats with regular swimming exercise
items: Co-culturing Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 allows sustainable denitrifying activities under marine conditions
items: Modeling the current distribution suitability and future dynamics of Culicoides imicola under climate change scenarios
items: Cryptic diversity in the subgenus Oxyphortica (Diptera, Drosophilidae, Stegana)
items: A new specimen of Sinopterus dongi (Pterosauria, Tapejaridae) from the Jiufotang Formation (Early Cretaceous, China)
items: Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus
items: Improved isolation and detection of toxigenic Vibrio parahaemolyticus from coastal water in Saudi Arabia using immunomagnetic enrichment
items: Multiple virulence factors regulated by AlgU contribute to the pathogenicity of Pseudomonas savastanoi pv. glycinea in soybean

Shedding light on the bacterial resistance to toxic UV filters: a comparative genomic study
type: item
type: AcademicArticle
description: UV filters are toxic to marine bacteria that dominate the marine biomass. Ecotoxicology often studies the organism response but rarely integrates the toxicity mechanisms at the molecular level. In this study, in silico comparative genomics between UV filters sensitive and resistant bacteria were conducted in order to unravel the genes responsible for a resistance phenotype. The genomes of two environmentally relevant Bacteroidetes and three Firmicutes species were compared through pairwise comparison. Larger genomes were carried by bacteria exhibiting a resistant phenotype, favoring their ability to adapt to environmental stresses. While the antitoxin and CRISPR systems were the only distinctive features in resistant Bacteroidetes, Firmicutes displayed multiple unique genes that could support the difference between sensitive and resistant phenotypes. Several genes involved in ROS response, vitamin biosynthesis, xenobiotic degradation, multidrug resistance, and lipophilic compound permeability were shown to be exclusive to resistant species. Our investigation contributes to a better understanding of UV filters resistance phenotypes, by identifying pivotal genes involved in key pathways.
format: application/pdf
format: text/html
creator: Clément Lozano
creator: Philippe Lebaron
creator: Sabine Matallana-Surget
subject: Bioinformatics
subject: Genetics
subject: Microbiology
subject: Ecotoxicology
subject: Environmental Impacts
description: doi:10.7717/peerj.12278
publisher: PeerJ Inc.
rights: © 2021 Lozano et al.
abstract: UV filters are toxic to marine bacteria that dominate the marine biomass. Ecotoxicology often studies the organism response but rarely integrates the toxicity mechanisms at the molecular level. In this study, in silico comparative genomics between UV filters sensitive and resistant bacteria were conducted in order to unravel the genes responsible for a resistance phenotype. The genomes of two environmentally relevant Bacteroidetes and three Firmicutes species were compared through pairwise comparison. Larger genomes were carried by bacteria exhibiting a resistant phenotype, favoring their ability to adapt to environmental stresses. While the antitoxin and CRISPR systems were the only distinctive features in resistant Bacteroidetes, Firmicutes displayed multiple unique genes that could support the difference between sensitive and resistant phenotypes. Several genes involved in ROS response, vitamin biosynthesis, xenobiotic degradation, multidrug resistance, and lipophilic compound permeability were shown to be exclusive to resistant species. Our investigation contributes to a better understanding of UV filters resistance phenotypes, by identifying pivotal genes involved in key pathways.
bibliographic citation: Lozano et al. (2021) Shedding light on the bacterial resistance to toxic UV filters: a comparative genomic study. PeerJ 9:e12278 https://doi.org/10.7717/peerj.12278
date submitted: 2021-06-18
date accepted: 2021-09-20
issued: 2021-11-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lozano
  given name: Clément
author list: Agent
  family name: Lebaron
  given name: Philippe
author list: Agent
  family name: Matallana-Surget
  given name: Sabine
doi: 10.7717/peerj.12278
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-01
copyright: © 2021 Lozano et al.
attribution name: Lozano et al.

Degradation of lignocelluloses in straw using AC-1, a thermophilic composite microbial system
type: item
type: AcademicArticle
description: In composting, the degradation of lignocellulose in straw is problematic due to its complex structures such as lignin. A common solution to this problem is the addition of exogenous inoculants. AC-1, a stable thermophilic microbial composite, was isolated from high temperature compost samples that can decompose lignocellulose at 50–70 °C. AC-1 had a best degradation efficiency of rice straw at 60 °C (78.92%), of hemicellulose, cellulose and lignin were 82.49%, 97.20% and 20.12%, respectively. It showed degrad-ability on both simple (filter paper, absorbent cotton) and complex (rice straw) cellulose materials. It produced acetic and formic acid during decomposition process and the pH had a trend of first downward then upward. High throughput sequencing revealed the main bacterial components of AC-1 were Tepidimicrobium, Haloplasma, norank-f-Limnochordaceae, Ruminiclostridium and Rhodothermus which provides major theoretical basis for further application of AC-1.
format: application/pdf
format: text/html
creator: Hongdou Liu
creator: Liqiang Zhang
creator: Yu Sun
creator: Guangbo Xu
creator: Weidong Wang
creator: Renzhe Piao
creator: Zongjun Cui
creator: Hongyan Zhao
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12364
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: In composting, the degradation of lignocellulose in straw is problematic due to its complex structures such as lignin. A common solution to this problem is the addition of exogenous inoculants. AC-1, a stable thermophilic microbial composite, was isolated from high temperature compost samples that can decompose lignocellulose at 50–70 °C. AC-1 had a best degradation efficiency of rice straw at 60 °C (78.92%), of hemicellulose, cellulose and lignin were 82.49%, 97.20% and 20.12%, respectively. It showed degrad-ability on both simple (filter paper, absorbent cotton) and complex (rice straw) cellulose materials. It produced acetic and formic acid during decomposition process and the pH had a trend of first downward then upward. High throughput sequencing revealed the main bacterial components of AC-1 were Tepidimicrobium, Haloplasma, norank-f-Limnochordaceae, Ruminiclostridium and Rhodothermus which provides major theoretical basis for further application of AC-1.
bibliographic citation: Liu et al. (2021) Degradation of lignocelluloses in straw using AC-1, a thermophilic composite microbial system. PeerJ 9:e12364 https://doi.org/10.7717/peerj.12364
date submitted: 2021-08-10
date accepted: 2021-10-01
issued: 2021-11-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hongdou
author list: Agent
  family name: Zhang
  given name: Liqiang
author list: Agent
  family name: Sun
  given name: Yu
author list: Agent
  family name: Xu
  given name: Guangbo
author list: Agent
  family name: Wang
  given name: Weidong
author list: Agent
  family name: Piao
  given name: Renzhe
author list: Agent
  family name: Cui
  given name: Zongjun
author list: Agent
  family name: Zhao
  given name: Hongyan
doi: 10.7717/peerj.12364
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-01
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Changes in the urinary proteome in rats with regular swimming exercise
type: item
type: AcademicArticle
description: Purpose Urine can sensitively reflect early pathophysiological changes in the body. The purpose of this study was to explore the changes of urine proteome in rats with regular swimming exercise. Methods In this study, experimental rats were subjected to daily moderate-intensity swimming exercise for 7 weeks. Urine samples were collected at weeks 2, 5, and 7 and were analyzed by using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Results Unsupervised clustering analysis of all urinary proteins identified at week 2 showed that the swimming group was distinctively different from the control group. Compared to the control group, a total of 112, 61 and 44 differential proteins were identified in the swimming group at weeks 2, 5 and 7, respectively. Randomized grouping statistical analysis showed that more than 85% of the differential proteins identified in this study were caused by swimming exercise rather than random allocation. According to the Human Protein Atlas, the differential proteins that have human orthologs were strongly expressed in the liver, kidney and intestine. Functional annotation analysis revealed that these differential proteins were involved in glucose metabolism and immunity-related pathways. Conclusion Our results revealed that the urinary proteome could reflect significant changes after regular swimming exercise. These findings may provide an approach to monitor the effects of exercise of the body.
format: application/pdf
format: text/html
creator: Wenshu Meng
creator: Dan Xu
creator: Yunchen Meng
creator: Weinan Zhang
creator: Yaqi Xue
creator: Zhiping Zhen
creator: Youhe Gao
subject: Animal Behavior
subject: Biochemistry
subject: Molecular Biology
subject: Kinesiology
subject: Urology
description: doi:10.7717/peerj.12406
publisher: PeerJ Inc.
rights: © 2021 Meng et al.
abstract: Purpose Urine can sensitively reflect early pathophysiological changes in the body. The purpose of this study was to explore the changes of urine proteome in rats with regular swimming exercise. Methods In this study, experimental rats were subjected to daily moderate-intensity swimming exercise for 7 weeks. Urine samples were collected at weeks 2, 5, and 7 and were analyzed by using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Results Unsupervised clustering analysis of all urinary proteins identified at week 2 showed that the swimming group was distinctively different from the control group. Compared to the control group, a total of 112, 61 and 44 differential proteins were identified in the swimming group at weeks 2, 5 and 7, respectively. Randomized grouping statistical analysis showed that more than 85% of the differential proteins identified in this study were caused by swimming exercise rather than random allocation. According to the Human Protein Atlas, the differential proteins that have human orthologs were strongly expressed in the liver, kidney and intestine. Functional annotation analysis revealed that these differential proteins were involved in glucose metabolism and immunity-related pathways. Conclusion Our results revealed that the urinary proteome could reflect significant changes after regular swimming exercise. These findings may provide an approach to monitor the effects of exercise of the body.
bibliographic citation: Meng et al. (2021) Changes in the urinary proteome in rats with regular swimming exercise. PeerJ 9:e12406 https://doi.org/10.7717/peerj.12406
date submitted: 2021-06-22
date accepted: 2021-10-08
issued: 2021-11-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Wenshu
author list: Agent
  family name: Xu
  given name: Dan
author list: Agent
  family name: Meng
  given name: Yunchen
author list: Agent
  family name: Zhang
  given name: Weinan
author list: Agent
  family name: Xue
  given name: Yaqi
author list: Agent
  family name: Zhen
  given name: Zhiping
author list: Agent
  family name: Gao
  given name: Youhe
doi: 10.7717/peerj.12406
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-01
copyright: ©2021 Meng et al.
attribution name: Meng et al.

Co-culturing Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 allows sustainable denitrifying activities under marine conditions
type: item
type: AcademicArticle
description: Background Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 are the principal bacteria involved in the denitrifying activities of a methanol-fed, fluidized-bed marine denitrification system. Strain NL23 possesses the complete denitrification pathway, but cannot grow under marine conditions in pure cultures. Strain JAM1 is a marine bacterium that lacks genes encoding a dissimilatory nitrite (NO2−) reductase and therefore cannot reduce NO2−. Here, we report the characterization of some of their physiological traits that could influence their co-habitation. We also perform co-cultures to assess the potential synergy between the two strains under marine and denitrifying conditions. Methodology Anoxic planktonic pure cultures of both strains were grown with different concentrations of nitrate (NO3−). Anoxic planktonic co-cultures could only be cultured on low NaCl concentrations for strain NL23 to grow. Biofilm co-cultures were achieved in a 500-mL bioreactor, and operated under denitrifying conditions with increasing concentrations of NaCl. NO3− and NO2− concentrations and the protein content were measured to derive the denitrification rates. The concentrations of both strains in co-cultures were determined by quantitative PCR (qPCR). Ectoine concentration was measured by mass spectrometry in the biofilm co-culture. The biofilm was visualized by fluorescence in situ hybridization. Reverse-transcription-qPCR and RNA-seq approaches were used to assess changes in the expression profiles of genes involved in the nitrogen pathways in the biofilm cultures. Results Planktonic pure cultures of strain JAM1 had a readiness to reduce NO3− with no lag phase for growth in contrast to pure cultures of strain NL23, which had a 2-3 days lag phase before NO3− starts to be consumed and growth to occur. Compared to strain NL23, strain JAM1 has a higher µmax for growth and higher specific NO3− reduction rates. Denitrification rates were twice h…
format: application/pdf
format: text/html
creator: Alexandra Cucaita
creator: Marianne Piochon
creator: Richard Villemur
subject: Biotechnology
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12424
publisher: PeerJ Inc.
rights: © 2021 Cucaita et al.
abstract: Background Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 are the principal bacteria involved in the denitrifying activities of a methanol-fed, fluidized-bed marine denitrification system. Strain NL23 possesses the complete denitrification pathway, but cannot grow under marine conditions in pure cultures. Strain JAM1 is a marine bacterium that lacks genes encoding a dissimilatory nitrite (NO2−) reductase and therefore cannot reduce NO2−. Here, we report the characterization of some of their physiological traits that could influence their co-habitation. We also perform co-cultures to assess the potential synergy between the two strains under marine and denitrifying conditions. Methodology Anoxic planktonic pure cultures of both strains were grown with different concentrations of nitrate (NO3−). Anoxic planktonic co-cultures could only be cultured on low NaCl concentrations for strain NL23 to grow. Biofilm co-cultures were achieved in a 500-mL bioreactor, and operated under denitrifying conditions with increasing concentrations of NaCl. NO3− and NO2− concentrations and the protein content were measured to derive the denitrification rates. The concentrations of both strains in co-cultures were determined by quantitative PCR (qPCR). Ectoine concentration was measured by mass spectrometry in the biofilm co-culture. The biofilm was visualized by fluorescence in situ hybridization. Reverse-transcription-qPCR and RNA-seq approaches were used to assess changes in the expression profiles of genes involved in the nitrogen pathways in the biofilm cultures. Results Planktonic pure cultures of strain JAM1 had a readiness to reduce NO3− with no lag phase for growth in contrast to pure cultures of strain NL23, which had a 2-3 days lag phase before NO3− starts to be consumed and growth to occur. Compared to strain NL23, strain JAM1 has a higher µmax for growth and higher specific NO3− reduction rates. Denitrification rates were twice h…
bibliographic citation: Cucaita et al. (2021) Co-culturing Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 allows sustainable denitrifying activities under marine conditions. PeerJ 9:e12424 https://doi.org/10.7717/peerj.12424
date submitted: 2021-07-16
date accepted: 2021-10-11
issued: 2021-11-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cucaita
  given name: Alexandra
author list: Agent
  family name: Piochon
  given name: Marianne
author list: Agent
  family name: Villemur
  given name: Richard
doi: 10.7717/peerj.12424
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-01
copyright: ©2021 Cucaita et al.
attribution name: Cucaita et al.

Modeling the current distribution suitability and future dynamics of Culicoides imicola under climate change scenarios
type: item
type: AcademicArticle
description: Background African horse sickness, a transboundary and non-contagious arboviral infectious disease of equids, has spread without any warning from sub-Saharan Africa towards the Southeast Asian countries in 2020. It is imperative to predict the global distribution of Culicoides imicola (C. imicola), which was the main vector of African horse sickness virus. Methods The occurrence records of C. imicola were mainly obtained from the published literature and the Global Biodiversity Information Facility database. The maximum entropy algorithm was used to model the current distribution suitability and future dynamics of C. imicola under climate change scenarios. Results The modeling results showed that the currently suitable habitats for C. imicola were distributed in most of the southern part areas of America, southwestern Europe, most of Africa, the coastal areas of the Middle East, almost all regions of South Asia, southern China, a few countries in Southeast Asia, and the whole Australia. Our model also revealed the important environmental variables on the distribution of C. imicola were temperature seasonality, precipitation of coldest quarter, and mean temperature of wettest quarter. Representative Concentration Pathways (RCPs) is an assumption of possible greenhouse gases emissions in the future. Under future climate change scenarios, the area of habitat suitability increased and decreased with time, and RCP 8.5 in the 2070s gave the worst prediction. Moreover, the habitat suitability of C. imicola will likely expand to higher latitudes. The prediction of this study is of strategic significance for vector surveillance and the prevention of vector-borne diseases.
format: application/pdf
format: text/html
creator: Hongyan Gao
creator: Long Wang
creator: Jun Ma
creator: Xiang Gao
creator: Jianhua Xiao
creator: Hongbin Wang
subject: Ecology
subject: Entomology
subject: Veterinary Medicine
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.12308
publisher: PeerJ Inc.
rights: © 2021 Gao et al.
abstract: Background African horse sickness, a transboundary and non-contagious arboviral infectious disease of equids, has spread without any warning from sub-Saharan Africa towards the Southeast Asian countries in 2020. It is imperative to predict the global distribution of Culicoides imicola (C. imicola), which was the main vector of African horse sickness virus. Methods The occurrence records of C. imicola were mainly obtained from the published literature and the Global Biodiversity Information Facility database. The maximum entropy algorithm was used to model the current distribution suitability and future dynamics of C. imicola under climate change scenarios. Results The modeling results showed that the currently suitable habitats for C. imicola were distributed in most of the southern part areas of America, southwestern Europe, most of Africa, the coastal areas of the Middle East, almost all regions of South Asia, southern China, a few countries in Southeast Asia, and the whole Australia. Our model also revealed the important environmental variables on the distribution of C. imicola were temperature seasonality, precipitation of coldest quarter, and mean temperature of wettest quarter. Representative Concentration Pathways (RCPs) is an assumption of possible greenhouse gases emissions in the future. Under future climate change scenarios, the area of habitat suitability increased and decreased with time, and RCP 8.5 in the 2070s gave the worst prediction. Moreover, the habitat suitability of C. imicola will likely expand to higher latitudes. The prediction of this study is of strategic significance for vector surveillance and the prevention of vector-borne diseases.
bibliographic citation: Gao et al. (2021) Modeling the current distribution suitability and future dynamics of Culicoides imicola under climate change scenarios. PeerJ 9:e12308 https://doi.org/10.7717/peerj.12308
date submitted: 2021-06-01
date accepted: 2021-09-22
issued: 2021-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Hongyan
author list: Agent
  family name: Wang
  given name: Long
author list: Agent
  family name: Ma
  given name: Jun
author list: Agent
  family name: Gao
  given name: Xiang
author list: Agent
  family name: Xiao
  given name: Jianhua
author list: Agent
  family name: Wang
  given name: Hongbin
doi: 10.7717/peerj.12308
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-29
copyright: © 2021 Gao et al.
attribution name: Gao et al.

Cryptic diversity in the subgenus Oxyphortica (Diptera, Drosophilidae, Stegana)
type: item
type: AcademicArticle
description: Phylogenetic relationships of the subgenus Oxyphortica were reconstructed based on two mitochondrial genes (COI and ND2). The results revealed the paraphyly of Oxyphortica and supported high levels of cryptic diversity within this subgenus. By integrating morphological characteristics and molecular evidence, we identified 17 new species as members of Oxyphortica: S. (O.) amphigya sp. nov., S. (O.) armillata sp. nov., S. (O.) ashima sp. nov., S. (O.) bawo sp. nov., S. (O.) crypta sp. nov., S. (O.) gelea sp. nov., S. (O.) hengduanmontana sp. nov., S. (O.) jinmingi sp. nov., S. (O.) mengbalanaxi sp. nov., S. (O.) mouig sp. nov., S. (O.) setipes sp. nov., S. (O.) shangrila sp. nov., S. (O.) tsauri sp. nov., S. (O.) valleculata sp. nov., S. (O.) wanhei sp. nov., S. (O.) yangjin sp. nov. and S. (O.) hypophaia sp. nov. To test the early morphological identifications and confirm the species boundaries, different species delimitation methods, including Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics and Phylogeography (BP&P), were used, together with traditional distance. All species boundaries were clearly defined. As Oxyphortica species are mainly distributed across Southwest China (e.g., 20 spp. from the Hengduan Mountains), the complex climate and topographic landforms of the area may be responsible for the high levels of species diversity and endemism.
format: application/pdf
format: text/html
creator: Ya-Lian Wang
creator: Nan-Nan Wang
creator: Yuan Zhang
creator: Shun-Chern Tsaur
creator: Hong-Wei Chen
subject: Biodiversity
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12347
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Phylogenetic relationships of the subgenus Oxyphortica were reconstructed based on two mitochondrial genes (COI and ND2). The results revealed the paraphyly of Oxyphortica and supported high levels of cryptic diversity within this subgenus. By integrating morphological characteristics and molecular evidence, we identified 17 new species as members of Oxyphortica: S. (O.) amphigya sp. nov., S. (O.) armillata sp. nov., S. (O.) ashima sp. nov., S. (O.) bawo sp. nov., S. (O.) crypta sp. nov., S. (O.) gelea sp. nov., S. (O.) hengduanmontana sp. nov., S. (O.) jinmingi sp. nov., S. (O.) mengbalanaxi sp. nov., S. (O.) mouig sp. nov., S. (O.) setipes sp. nov., S. (O.) shangrila sp. nov., S. (O.) tsauri sp. nov., S. (O.) valleculata sp. nov., S. (O.) wanhei sp. nov., S. (O.) yangjin sp. nov. and S. (O.) hypophaia sp. nov. To test the early morphological identifications and confirm the species boundaries, different species delimitation methods, including Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics and Phylogeography (BP&P), were used, together with traditional distance. All species boundaries were clearly defined. As Oxyphortica species are mainly distributed across Southwest China (e.g., 20 spp. from the Hengduan Mountains), the complex climate and topographic landforms of the area may be responsible for the high levels of species diversity and endemism.
bibliographic citation: Wang et al. (2021) Cryptic diversity in the subgenus Oxyphortica (Diptera, Drosophilidae, Stegana). PeerJ 9:e12347 https://doi.org/10.7717/peerj.12347
date submitted: 2021-02-26
date accepted: 2021-09-29
issued: 2021-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ya-Lian
author list: Agent
  family name: Wang
  given name: Nan-Nan
author list: Agent
  family name: Zhang
  given name: Yuan
author list: Agent
  family name: Tsaur
  given name: Shun-Chern
author list: Agent
  family name: Chen
  given name: Hong-Wei
doi: 10.7717/peerj.12347
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-29
copyright: © 2021 Wang et al.
attribution name: Wang et al.

A new specimen of Sinopterus dongi (Pterosauria, Tapejaridae) from the Jiufotang Formation (Early Cretaceous, China)
type: item
type: AcademicArticle
description: The Tapejarinae are edentulous pterosaurs that are relatively common in Cretaceous continental deposits in South America, North Africa, Europe, and China (mostly Early Cretaceous). The Chinese Jiufotang Formation is particularly rich in tapejarine specimens, having yielded over 10 described specimens and dozens of undescribed ones. For the Jiufotang Formation, a total of seven nominal tapejarid species and two genera have been proposed. Some debate exists over how many of those are valid or, alternatively, sexual or ontogenetic morphs of fewer (or even a single) species. Despite the abundance of specimens and the relevant taxonomic problems involved, detailed revisions of the matter are still lacking. This is partly due to the relatively scarce knowledge on the comparative osteology of the Sinopterus complex, which is hampered by the fact that most specimens have been only preliminarily described. In this contribution, we present a new postcranial specimen, D3072, which we attribute to the type-species of the genus, Sinopterus dongi. This new specimen helps shed some new light in the osteology of Sinopterus dongi, hopefully serving as a basis for future comparative studies involving further specimens and other proposed species and, subsequently, taxonomic revisions.
format: application/pdf
format: text/html
creator: Caizhi Shen
creator: Rodrigo V. Pêgas
creator: Chunling Gao
creator: Martin Kundrát
creator: Lijun Zhang
creator: Xuefang Wei
creator: Xuanyu Zhou
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12360
publisher: PeerJ Inc.
rights: © 2021 Shen et al.
abstract: The Tapejarinae are edentulous pterosaurs that are relatively common in Cretaceous continental deposits in South America, North Africa, Europe, and China (mostly Early Cretaceous). The Chinese Jiufotang Formation is particularly rich in tapejarine specimens, having yielded over 10 described specimens and dozens of undescribed ones. For the Jiufotang Formation, a total of seven nominal tapejarid species and two genera have been proposed. Some debate exists over how many of those are valid or, alternatively, sexual or ontogenetic morphs of fewer (or even a single) species. Despite the abundance of specimens and the relevant taxonomic problems involved, detailed revisions of the matter are still lacking. This is partly due to the relatively scarce knowledge on the comparative osteology of the Sinopterus complex, which is hampered by the fact that most specimens have been only preliminarily described. In this contribution, we present a new postcranial specimen, D3072, which we attribute to the type-species of the genus, Sinopterus dongi. This new specimen helps shed some new light in the osteology of Sinopterus dongi, hopefully serving as a basis for future comparative studies involving further specimens and other proposed species and, subsequently, taxonomic revisions.
bibliographic citation: Shen et al. (2021) A new specimen of Sinopterus dongi (Pterosauria, Tapejaridae) from the Jiufotang Formation (Early Cretaceous, China). PeerJ 9:e12360 https://doi.org/10.7717/peerj.12360
date submitted: 2021-08-04
date accepted: 2021-09-30
issued: 2021-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Caizhi
author list: Agent
  family name: Pêgas
  given name: Rodrigo V.
author list: Agent
  family name: Gao
  given name: Chunling
author list: Agent
  family name: Kundrát
  given name: Martin
author list: Agent
  family name: Zhang
  given name: Lijun
author list: Agent
  family name: Wei
  given name: Xuefang
author list: Agent
  family name: Zhou
  given name: Xuanyu
doi: 10.7717/peerj.12360
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-29
copyright: ©2021 Shen et al.
attribution name: Shen et al.

Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus
type: item
type: AcademicArticle
description: Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.
format: application/pdf
format: text/html
creator: Yaqun Zhang
creator: Chuantao Zhang
creator: Na Yao
creator: Jingxian Huang
creator: Xiangshan Sun
creator: Bingran Zhao
creator: Hengde Li
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12390
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.
bibliographic citation: Zhang et al. (2021) Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus. PeerJ 9:e12390 https://doi.org/10.7717/peerj.12390
date submitted: 2021-06-30
date accepted: 2021-10-05
issued: 2021-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yaqun
author list: Agent
  family name: Zhang
  given name: Chuantao
author list: Agent
  family name: Yao
  given name: Na
author list: Agent
  family name: Huang
  given name: Jingxian
author list: Agent
  family name: Sun
  given name: Xiangshan
author list: Agent
  family name: Zhao
  given name: Bingran
author list: Agent
  family name: Li
  given name: Hengde
doi: 10.7717/peerj.12390
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-29
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

Improved isolation and detection of toxigenic Vibrio parahaemolyticus from coastal water in Saudi Arabia using immunomagnetic enrichment
type: item
type: AcademicArticle
description: Background Vibrio parahaemolyticus is recognized globally as a cause of foodborne gastroenteritis and its widely disseminated in marine and coastal environment throughout the world. The main aim of this study was conducted to investigate the presence of toxigenic V. parahaemolyticus in costal water in the Eastern Province of Saudi Arabia by using immunomagnetic separation (IMS) in combination with chromogenic Vibrio agar medium and PCR targeting toxR gene of species level and virulence genes. Methods A total of 192 seawater samples were collected from five locations and enriched in alkaline peptone water (APW) broth. One-milliliter portion from enriched samples in APW were mixed with an immunomagnetic beads (IMB) coated with specific antibodies against V. parahaemolyticus polyvalent K antisera and separated beads with captured bacteria streaked on thiosulfate citrate bile salts sucrose (TCBS) agar and CHROMagar Vibrio (CaV) medium. Results Of the 192 examined seawater samples, 38 (19.8%) and 44 (22.9%) were positive for V. parahaemolyticus, producing green and mauve colonies on TCBS agar and CaV medium, respectively. Among 120 isolates of V. parahaemolyticus isolated in this study, 3 (2.5%) and 26 (21.7%) isolates of V. parahaemolyticus isolated without and with IMB treatment tested positive for the toxin regulatory (toxR) gene, respectively. Screening of the confirmed toxR gene-positive isolates revealed that 21 (17.5%) and 3 (2.5%) were positive for the thermostable direct hemolysin (tdh) encoding gene in strains isolated with IMB and without IMB treatment, respectively. None of the V. parahaemolyticus strains tested positive for the thermostable related hemolysin (trh) gene. In this study, we found that the CaV medium has no advantage over TCBS agar if IMB concentration treatment is used during secondary enrichment steps of environmental samples. The enterobacterial repetitive intergenic consensus (ERIC)-PCR DNA fingerprinting analysis revealed high genomic diver…
format: application/pdf
format: text/html
creator: Mariam Almejhim
creator: Mohammed Aljeldah
creator: Nasreldin Elhadi
subject: Genetics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12402
publisher: PeerJ Inc.
rights: © 2021 Almejhim et al.
abstract: Background Vibrio parahaemolyticus is recognized globally as a cause of foodborne gastroenteritis and its widely disseminated in marine and coastal environment throughout the world. The main aim of this study was conducted to investigate the presence of toxigenic V. parahaemolyticus in costal water in the Eastern Province of Saudi Arabia by using immunomagnetic separation (IMS) in combination with chromogenic Vibrio agar medium and PCR targeting toxR gene of species level and virulence genes. Methods A total of 192 seawater samples were collected from five locations and enriched in alkaline peptone water (APW) broth. One-milliliter portion from enriched samples in APW were mixed with an immunomagnetic beads (IMB) coated with specific antibodies against V. parahaemolyticus polyvalent K antisera and separated beads with captured bacteria streaked on thiosulfate citrate bile salts sucrose (TCBS) agar and CHROMagar Vibrio (CaV) medium. Results Of the 192 examined seawater samples, 38 (19.8%) and 44 (22.9%) were positive for V. parahaemolyticus, producing green and mauve colonies on TCBS agar and CaV medium, respectively. Among 120 isolates of V. parahaemolyticus isolated in this study, 3 (2.5%) and 26 (21.7%) isolates of V. parahaemolyticus isolated without and with IMB treatment tested positive for the toxin regulatory (toxR) gene, respectively. Screening of the confirmed toxR gene-positive isolates revealed that 21 (17.5%) and 3 (2.5%) were positive for the thermostable direct hemolysin (tdh) encoding gene in strains isolated with IMB and without IMB treatment, respectively. None of the V. parahaemolyticus strains tested positive for the thermostable related hemolysin (trh) gene. In this study, we found that the CaV medium has no advantage over TCBS agar if IMB concentration treatment is used during secondary enrichment steps of environmental samples. The enterobacterial repetitive intergenic consensus (ERIC)-PCR DNA fingerprinting analysis revealed high genomic diver…
bibliographic citation: Almejhim et al. (2021) Improved isolation and detection of toxigenic Vibrio parahaemolyticus from coastal water in Saudi Arabia using immunomagnetic enrichment. PeerJ 9:e12402 https://doi.org/10.7717/peerj.12402
date submitted: 2021-05-19
date accepted: 2021-10-07
issued: 2021-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almejhim
  given name: Mariam
author list: Agent
  family name: Aljeldah
  given name: Mohammed
author list: Agent
  family name: Elhadi
  given name: Nasreldin
doi: 10.7717/peerj.12402
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-29
copyright: © 2021 Almejhim et al.
attribution name: Almejhim et al.

Multiple virulence factors regulated by AlgU contribute to the pathogenicity of Pseudomonas savastanoi pv. glycinea in soybean
type: item
type: AcademicArticle
description: Pseudomonas savastanoi pv. glycinea (Psg) causes bacterial blight of soybean. To identify candidate virulence factors, transposon-mediated mutational analysis of Psg was carried out. We syringe-inoculated soybean leaves with Psg transposon mutants and identified 28 mutants which showed reduced virulence from 1,000 mutants screened. Next, we spray-inoculated soybean leaves with these mutants and demonstrated that the algU mutant showed significantly reduced virulence together with reduced bacterial populations in planta. Expression profiles comparison between the Psg wild-type (WT) and algU mutant in HSC broth revealed that expression of coronatine (COR)-related genes (including cmaA and corR) were down-regulated in the algU mutant compared with Psg WT. Moreover, we also showed that COR production were reduced in the algU mutant compared with WT. We also demonstrated that algD, which is related to alginate biosynthesis, showed reduced expression and biofilm formation was significantly suppressed in the algU mutant. Furthermore, hrpL also showed less expression in the algU mutant. These results indicate that AlgU plays a critical role in promoting Psg pathogenesis by regulating multiple virulence factors.
format: application/pdf
format: text/html
creator: Viet Tru Nguyen
creator: Nanami Sakata
creator: Giyu Usuki
creator: Takako Ishiga
creator: Yoshiteru Hashimoto
creator: Yasuhiro Ishiga
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12405
publisher: PeerJ Inc.
rights: © 2021 Nguyen et al.
abstract: Pseudomonas savastanoi pv. glycinea (Psg) causes bacterial blight of soybean. To identify candidate virulence factors, transposon-mediated mutational analysis of Psg was carried out. We syringe-inoculated soybean leaves with Psg transposon mutants and identified 28 mutants which showed reduced virulence from 1,000 mutants screened. Next, we spray-inoculated soybean leaves with these mutants and demonstrated that the algU mutant showed significantly reduced virulence together with reduced bacterial populations in planta. Expression profiles comparison between the Psg wild-type (WT) and algU mutant in HSC broth revealed that expression of coronatine (COR)-related genes (including cmaA and corR) were down-regulated in the algU mutant compared with Psg WT. Moreover, we also showed that COR production were reduced in the algU mutant compared with WT. We also demonstrated that algD, which is related to alginate biosynthesis, showed reduced expression and biofilm formation was significantly suppressed in the algU mutant. Furthermore, hrpL also showed less expression in the algU mutant. These results indicate that AlgU plays a critical role in promoting Psg pathogenesis by regulating multiple virulence factors.
bibliographic citation: Nguyen et al. (2021) Multiple virulence factors regulated by AlgU contribute to the pathogenicity of Pseudomonas savastanoi pv. glycinea in soybean. PeerJ 9:e12405 https://doi.org/10.7717/peerj.12405
date submitted: 2021-06-21
date accepted: 2021-10-08
issued: 2021-10-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nguyen
  given name: Viet Tru
author list: Agent
  family name: Sakata
  given name: Nanami
author list: Agent
  family name: Usuki
  given name: Giyu
author list: Agent
  family name: Ishiga
  given name: Takako
author list: Agent
  family name: Hashimoto
  given name: Yoshiteru
author list: Agent
  family name: Ishiga
  given name: Yasuhiro
doi: 10.7717/peerj.12405
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-29
copyright: © 2021 Nguyen et al.
attribution name: Nguyen et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359