PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Investigation of lipolytic activity of the red king crab hepatopancreas homogenate by NMR spectroscopy
items: Molecular genetic diversity of seaweeds morphologically related to Ulva rigida at three sites along the French Atlantic coast
items: Small-scale drivers on plant and ant diversity in a grassland habitat through a multifaceted approach
items: Linking individual and population patterns of rocky-shore mussels
items: Macrophage immunomodulatory activity of Acanthopanax senticousus polysaccharide nanoemulsion via activation of P65/JNK/ikkαsignaling pathway and regulation of Th1/Th2 Cytokines
items: Three new species of Byrsopteryx Flint microcaddisflies from Peru (Insecta: Trichoptera) including DNA-based larval associations
items: Living on the edge: genetic structure and geographic distribution in the threatened Markham’s Storm-Petrel (Hydrobates markhami)
items: Integrated analysis and the identification of a circRNA-miRNA-mRNA network in the progression of abdominal aortic aneurysm
items: Spatiotemporal patterns of the COVID-19 epidemic in Mexico at the municipality level
items: Bacterial diversity and potential risk factors associated with Salmonella contamination of seafood products sold in retail markets in Bangkok, Thailand

Investigation of lipolytic activity of the red king crab hepatopancreas homogenate by NMR spectroscopy
type: item
type: AcademicArticle
description: The digestive gland of craboids (hepatopancreas) is rich in a huge number of various enzymes (collagenases, nucleases, hyaluronidases, proteases), which are well studied at the moment. However, little is known about crustacean lipases. In this work, using 1H NMR spectroscopy, it was found that the hepatopancreas homogenate of the red king crab Paralithodes camtschaticus demonstrates high lipolytic activity against triacetin in a wide pH range and shows moderate activity against the caprylic/capric triglyceride emulsion. Under the action of the hepatopancreas homogenate, triacylglycerols are converted into 1,2-diacylglycerol, and then into 2-monoacylglycerol and 1-monoacylglycerol. The 1-monoacylglycerol predominates in the reaction products. The use of NMR spectroscopy makes it possible to quickly detect hydrolysis products and evaluate the reaction direction.
format: application/pdf
format: text/html
creator: Maria Timchenko
creator: Vladislav Molchanov
creator: Maxim Molchanov
creator: Alexander Timchenko
creator: Evgeny Sogorin
subject: Biochemistry
subject: Biophysics
subject: Biotechnology
description: doi:10.7717/peerj.12742
publisher: PeerJ Inc.
rights: © 2022 Timchenko et al.
abstract: The digestive gland of craboids (hepatopancreas) is rich in a huge number of various enzymes (collagenases, nucleases, hyaluronidases, proteases), which are well studied at the moment. However, little is known about crustacean lipases. In this work, using 1H NMR spectroscopy, it was found that the hepatopancreas homogenate of the red king crab Paralithodes camtschaticus demonstrates high lipolytic activity against triacetin in a wide pH range and shows moderate activity against the caprylic/capric triglyceride emulsion. Under the action of the hepatopancreas homogenate, triacylglycerols are converted into 1,2-diacylglycerol, and then into 2-monoacylglycerol and 1-monoacylglycerol. The 1-monoacylglycerol predominates in the reaction products. The use of NMR spectroscopy makes it possible to quickly detect hydrolysis products and evaluate the reaction direction.
bibliographic citation: Timchenko et al. (2022) Investigation of lipolytic activity of the red king crab hepatopancreas homogenate by NMR spectroscopy. PeerJ 10:e12742 https://doi.org/10.7717/peerj.12742
date submitted: 2021-09-10
date accepted: 2021-12-13
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Timchenko
  given name: Maria
author list: Agent
  family name: Molchanov
  given name: Vladislav
author list: Agent
  family name: Molchanov
  given name: Maxim
author list: Agent
  family name: Timchenko
  given name: Alexander
author list: Agent
  family name: Sogorin
  given name: Evgeny
doi: 10.7717/peerj.12742
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: ©2022 Timchenko et al.
attribution name: Timchenko et al.

Molecular genetic diversity of seaweeds morphologically related to Ulva rigida at three sites along the French Atlantic coast
type: item
type: AcademicArticle
description: Foliose species of the genus Ulva are notoriously difficult to identify due to their variable morphological characteristics and high phenotypic plasticity. We reassessed the taxonomic status of several distromatic foliose Ulva spp., morphologically related to Ulva rigida, using DNA barcoding with the chloroplastic tufA and rbcL (for a subset of taxa) genes for 339 selected attached Ulva specimens collected from three intertidal rocky sites. Two of the collection sites were in Brittany and one site was in Vendée, along the Atlantic coast of France. Molecular analyses included several museum specimens and the holotype of Ulva armoricana Dion, Reviers & Coat. We identified five different tufA haplotypes using a combination of phylogenetic analysis, with the support of several recently sequenced holotypes and lectotypes, and a species delimitation method based on hierarchical clustering. Four haplotypes were supported by validly named species: Ulva australis Areschoug, Ulva fenestrata Postels & Ruprecht, Ulva lacinulata (Kützing) Wittrock and U. rigida C. Agardh. The later was additionally investigated using rbcL. The fifth haplotype represented exact sequence matches to an unnamed species from European Atlantic coasts. Our results support: (1) the synonymy of both U. rigida sensu Bliding non C. Agardh and U. armoricana with U. lacinulata. This finding is based on current genetic analysis of tufA from the U. armoricana holotype and recent molecular characterization of the lectotype of U. laetevirens, which is synonymous to U. australis, (2) the presence of U. australis as a misidentified introduced species in Brittany, and (3) the presence of U. fenestrata and U. rigida in southern Brittany. The taxonomic history of each species is discussed, highlighting issues within distromatic foliose taxa of the genus Ulva and the need to genetically characterize all its available type specimens.
format: application/pdf
format: text/html
creator: Manon Dartois
creator: Eric Pante
creator: Amélia Viricel
creator: Vanessa Becquet
creator: Pierre-Guy Sauriau
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.11966
publisher: PeerJ Inc.
rights: © 2021 Dartois et al.
abstract: Foliose species of the genus Ulva are notoriously difficult to identify due to their variable morphological characteristics and high phenotypic plasticity. We reassessed the taxonomic status of several distromatic foliose Ulva spp., morphologically related to Ulva rigida, using DNA barcoding with the chloroplastic tufA and rbcL (for a subset of taxa) genes for 339 selected attached Ulva specimens collected from three intertidal rocky sites. Two of the collection sites were in Brittany and one site was in Vendée, along the Atlantic coast of France. Molecular analyses included several museum specimens and the holotype of Ulva armoricana Dion, Reviers & Coat. We identified five different tufA haplotypes using a combination of phylogenetic analysis, with the support of several recently sequenced holotypes and lectotypes, and a species delimitation method based on hierarchical clustering. Four haplotypes were supported by validly named species: Ulva australis Areschoug, Ulva fenestrata Postels & Ruprecht, Ulva lacinulata (Kützing) Wittrock and U. rigida C. Agardh. The later was additionally investigated using rbcL. The fifth haplotype represented exact sequence matches to an unnamed species from European Atlantic coasts. Our results support: (1) the synonymy of both U. rigida sensu Bliding non C. Agardh and U. armoricana with U. lacinulata. This finding is based on current genetic analysis of tufA from the U. armoricana holotype and recent molecular characterization of the lectotype of U. laetevirens, which is synonymous to U. australis, (2) the presence of U. australis as a misidentified introduced species in Brittany, and (3) the presence of U. fenestrata and U. rigida in southern Brittany. The taxonomic history of each species is discussed, highlighting issues within distromatic foliose taxa of the genus Ulva and the need to genetically characterize all its available type specimens.
bibliographic citation: Dartois et al. (2021) Molecular genetic diversity of seaweeds morphologically related to Ulva rigida at three sites along the French Atlantic coast. PeerJ 9:e11966 https://doi.org/10.7717/peerj.11966
date submitted: 2020-09-30
date accepted: 2021-10-04
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dartois
  given name: Manon
author list: Agent
  family name: Pante
  given name: Eric
author list: Agent
  family name: Viricel
  given name: Amélia
author list: Agent
  family name: Becquet
  given name: Vanessa
author list: Agent
  family name: Sauriau
  given name: Pierre-Guy
doi: 10.7717/peerj.11966
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: ©2021 Dartois et al.
attribution name: Dartois et al.

Small-scale drivers on plant and ant diversity in a grassland habitat through a multifaceted approach
type: item
type: AcademicArticle
description: Semi-natural grasslands are characterized by high biodiversity and require multifaceted approaches to monitor their biodiversity. Moreover, grasslands comprise a multitude of microhabitats, making the scale of investigation of fundamental importance. Despite their wide distribution, grasslands are highly threatened and are considered of high conservation priority by Directive no. 92/43/EEC. Here, we investigate the effects of small-scale ecological differences between two ecosites present within the EU habitat of Community Interest of semi-natural dry grasslands on calcareous substrates (6210 according to Dir. 92/43/EEC) occurring on a Mediterranean mountain. We measured taxonomic and functional diversity of plant and ant communities, evaluating the differences among the two ecosites, how these differences are influenced by the environment and whether vegetation affects composition of the ant community. Our results show that taxonomic and functional diversity of plant and ant communities are influenced by the environment. While vegetation has no effect on ant communities, we found plant and ant community composition differed across the two ecosites, filtering ant and plant species according to their functional traits, even at a small spatial scale. Our findings imply that small-scale monitoring is needed to effectively conserve priority habitats, especially for those that comprise multiple microhabitats.
format: application/pdf
format: text/html
creator: Michele Mugnai
creator: Clara Frasconi Wendt
creator: Paride Balzani
creator: Giulio Ferretti
creator: Matteo Dal Cin
creator: Alberto Masoni
creator: Filippo Frizzi
creator: Giacomo Santini
creator: Daniele Viciani
creator: Bruno Foggi
creator: Lorenzo Lazzaro
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.12517
publisher: PeerJ Inc.
rights: © 2021 Mugnai et al.
abstract: Semi-natural grasslands are characterized by high biodiversity and require multifaceted approaches to monitor their biodiversity. Moreover, grasslands comprise a multitude of microhabitats, making the scale of investigation of fundamental importance. Despite their wide distribution, grasslands are highly threatened and are considered of high conservation priority by Directive no. 92/43/EEC. Here, we investigate the effects of small-scale ecological differences between two ecosites present within the EU habitat of Community Interest of semi-natural dry grasslands on calcareous substrates (6210 according to Dir. 92/43/EEC) occurring on a Mediterranean mountain. We measured taxonomic and functional diversity of plant and ant communities, evaluating the differences among the two ecosites, how these differences are influenced by the environment and whether vegetation affects composition of the ant community. Our results show that taxonomic and functional diversity of plant and ant communities are influenced by the environment. While vegetation has no effect on ant communities, we found plant and ant community composition differed across the two ecosites, filtering ant and plant species according to their functional traits, even at a small spatial scale. Our findings imply that small-scale monitoring is needed to effectively conserve priority habitats, especially for those that comprise multiple microhabitats.
bibliographic citation: Mugnai et al. (2021) Small-scale drivers on plant and ant diversity in a grassland habitat through a multifaceted approach. PeerJ 9:e12517 https://doi.org/10.7717/peerj.12517
date submitted: 2021-07-23
date accepted: 2021-10-27
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mugnai
  given name: Michele
author list: Agent
  family name: Frasconi Wendt
  given name: Clara
author list: Agent
  family name: Balzani
  given name: Paride
author list: Agent
  family name: Ferretti
  given name: Giulio
author list: Agent
  family name: Dal Cin
  given name: Matteo
author list: Agent
  family name: Masoni
  given name: Alberto
author list: Agent
  family name: Frizzi
  given name: Filippo
author list: Agent
  family name: Santini
  given name: Giacomo
author list: Agent
  family name: Viciani
  given name: Daniele
author list: Agent
  family name: Foggi
  given name: Bruno
author list: Agent
  family name: Lazzaro
  given name: Lorenzo
doi: 10.7717/peerj.12517
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: © 2021 Mugnai et al.
attribution name: Mugnai et al.

Linking individual and population patterns of rocky-shore mussels
type: item
type: AcademicArticle
description: Individual traits and population parameters can be used as proxies of processes taking place within a range of scales, thus improving the way we can evaluate species response to environmental variability. In intertidal rocky shores, patterns at the within-site scale, i.e., between centimeters to hundreds of meters, are important for understanding the population response into these highly variable environments. Here, we studied a rocky-shore mussel population at the within-site spatial scale (1) to test how intertidal height and orientation of the shore affect individual traits and population parameters, (2) to infer the link between individual and population level features, and (3) to explore the upscaling mechanisms driving population structure and processes. We analyzed the patterns of six population parameters: density, biomass, crowding, median individual size, recruitment and mortality rate, and four individual traits: growth rate, spawning phenology, size and condition index. Crowding was defined as the degree of overlapping of individuals within a given area, for which we created a “crowding index”. Mussels were studied along the intertidal height gradient in two rocky shores with contrasted orientation at one site over a full year. Our results showed a significant effect of intertidal height and shore orientation on most of individual traits and population parameters studied. In contrast, biomass contained in a full covered surface did not vary in space nor in time. This pattern likely results from relatively constant crowding and a trade-off between median individuals’ size and density. We hypothesize that growth, mortality and recruitment rates may all play roles in the stability of the crowding structure of mussel aggregations. Variation in spawning phenology between the two shores in the study site was also observed, suggesting different temporal dynamics of microclimate conditions. Interestingly, despite the different population size distribution betwee…
format: application/pdf
format: text/html
creator: Romina Vanessa Barbosa
creator: Cédric Bacher
creator: Fred Jean
creator: Yoann Thomas
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.12550
publisher: PeerJ Inc.
rights: © 2021 Barbosa et al.
abstract: Individual traits and population parameters can be used as proxies of processes taking place within a range of scales, thus improving the way we can evaluate species response to environmental variability. In intertidal rocky shores, patterns at the within-site scale, i.e., between centimeters to hundreds of meters, are important for understanding the population response into these highly variable environments. Here, we studied a rocky-shore mussel population at the within-site spatial scale (1) to test how intertidal height and orientation of the shore affect individual traits and population parameters, (2) to infer the link between individual and population level features, and (3) to explore the upscaling mechanisms driving population structure and processes. We analyzed the patterns of six population parameters: density, biomass, crowding, median individual size, recruitment and mortality rate, and four individual traits: growth rate, spawning phenology, size and condition index. Crowding was defined as the degree of overlapping of individuals within a given area, for which we created a “crowding index”. Mussels were studied along the intertidal height gradient in two rocky shores with contrasted orientation at one site over a full year. Our results showed a significant effect of intertidal height and shore orientation on most of individual traits and population parameters studied. In contrast, biomass contained in a full covered surface did not vary in space nor in time. This pattern likely results from relatively constant crowding and a trade-off between median individuals’ size and density. We hypothesize that growth, mortality and recruitment rates may all play roles in the stability of the crowding structure of mussel aggregations. Variation in spawning phenology between the two shores in the study site was also observed, suggesting different temporal dynamics of microclimate conditions. Interestingly, despite the different population size distribution betwee…
bibliographic citation: Barbosa et al. (2021) Linking individual and population patterns of rocky-shore mussels. PeerJ 9:e12550 https://doi.org/10.7717/peerj.12550
date submitted: 2021-05-17
date accepted: 2021-11-04
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barbosa
  given name: Romina Vanessa
author list: Agent
  family name: Bacher
  given name: Cédric
author list: Agent
  family name: Jean
  given name: Fred
author list: Agent
  family name: Thomas
  given name: Yoann
doi: 10.7717/peerj.12550
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: ©2021 Barbosa et al.
attribution name: Barbosa et al.

Macrophage immunomodulatory activity of Acanthopanax senticousus polysaccharide nanoemulsion via activation of P65/JNK/ikkαsignaling pathway and regulation of Th1/Th2 Cytokines
type: item
type: AcademicArticle
description: Nanoemulsions (NE) are used widely in pharmaceutical drug formulations and vaccine preparation, and Acanthopanax senticousus polysaccharide (ASPS) is a natural bioactive compound with immunostimulatory activity. Therefore, NE-loaded ASPS is expected to provide immunological enhancement for effective treatment. In the present study, Acanthopanax senticousus polysaccharide (ASPS was encapsulated into nanoemulsions, the resultant ASPS–NE were coated with a negative charge, and the immune enhancement mechanism of these ASPS-NE formulations was analyzed. The immunosuppressive animal models (70 ICR mice, male) for the study were established using cyclophosphamide. In addition, the activation of splenocyte proliferation, phagocytosis of the macrophages, the ratio of CD4+ to CD8+, the concentrations of the cytokines in serum, Western blot analysis was used for the analysis of the P65/JNK/ikk α signaling pathway in the peritoneal macrophage s. The results revealed that the ASPS-NE could stimulated the proliferation of splenocytes and enhance immunity. The ASPS-NE induced the expression of different cytokines (TNF-α, IFN-γ, IL-2, and IL-6), could activate the expressions of P65, JNK, and ikkα, and regulated the Th1/Th2 cytokines. These findings demonstrated the potential of ASPS-NE formulations for drug delivery and to induce potent and sustained immune responses.
format: application/pdf
format: text/html
creator: Xianghui Li
creator: Zhiqiang Zhang
creator: Zhenhuan Guo
creator: Li Zhao
creator: Yonglu Liu
creator: Xia Ma
creator: Qigai He
subject: Molecular Biology
subject: Veterinary Medicine
subject: Immunology
description: doi:10.7717/peerj.12575
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Nanoemulsions (NE) are used widely in pharmaceutical drug formulations and vaccine preparation, and Acanthopanax senticousus polysaccharide (ASPS) is a natural bioactive compound with immunostimulatory activity. Therefore, NE-loaded ASPS is expected to provide immunological enhancement for effective treatment. In the present study, Acanthopanax senticousus polysaccharide (ASPS was encapsulated into nanoemulsions, the resultant ASPS–NE were coated with a negative charge, and the immune enhancement mechanism of these ASPS-NE formulations was analyzed. The immunosuppressive animal models (70 ICR mice, male) for the study were established using cyclophosphamide. In addition, the activation of splenocyte proliferation, phagocytosis of the macrophages, the ratio of CD4+ to CD8+, the concentrations of the cytokines in serum, Western blot analysis was used for the analysis of the P65/JNK/ikk α signaling pathway in the peritoneal macrophage s. The results revealed that the ASPS-NE could stimulated the proliferation of splenocytes and enhance immunity. The ASPS-NE induced the expression of different cytokines (TNF-α, IFN-γ, IL-2, and IL-6), could activate the expressions of P65, JNK, and ikkα, and regulated the Th1/Th2 cytokines. These findings demonstrated the potential of ASPS-NE formulations for drug delivery and to induce potent and sustained immune responses.
bibliographic citation: Li et al. (2021) Macrophage immunomodulatory activity of Acanthopanax senticousus polysaccharide nanoemulsion via activation of P65/JNK/ikkαsignaling pathway and regulation of Th1/Th2 Cytokines. PeerJ 9:e12575 https://doi.org/10.7717/peerj.12575
date submitted: 2021-05-14
date accepted: 2021-11-09
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xianghui
author list: Agent
  family name: Zhang
  given name: Zhiqiang
author list: Agent
  family name: Guo
  given name: Zhenhuan
author list: Agent
  family name: Zhao
  given name: Li
author list: Agent
  family name: Liu
  given name: Yonglu
author list: Agent
  family name: Ma
  given name: Xia
author list: Agent
  family name: He
  given name: Qigai
doi: 10.7717/peerj.12575
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: ©2021 Li et al.
attribution name: Li et al.

Three new species of Byrsopteryx Flint microcaddisflies from Peru (Insecta: Trichoptera) including DNA-based larval associations
type: item
type: AcademicArticle
description: In this paper, we have described and illustrated three new species of Byrsopteryx from Peru: Byrsopteryx inti, sp. nov. Byrsopteryx mamaocllo sp. nov., and Byrsopteryx mancocapac sp. nov. Larvae of the latter two were also associated to male specimens based on comparison of a fragment of COI gene and pharate male identification. Byrsopteryx inti sp. nov. and Byrsopteryx mamaocllo sp. nov. share a unique feature: a semi-dome process formed by a thickened area on male forewings. The three species can be easily identified by wing coloration and male genitalia. Furthermore, Byrsopteryx inti sp. nov. can be recognized by its sternum VIII with a median digitate process on posterior margin, slightly capitate; and by long dorsolateral processes from segment VIII, which cross each other apically in dorsal view. Byrsopteryx mamaocllo sp. nov. can be distinguished by sternum VIII bearing a pair of short, posterior, spinelike processes, which are curved inwards and bordered by a rounded, membranous structure, and by a pair of short, heavily sclerotized, dorsolateral processes. Byrsopteryx mancocapac sp. nov. can be distinguished by strong spine-like processes arising dorsally from subgenital plate and by sternum VIII with posterior margin divided into two plate-like lobes. Larvae of B. mamaocllo sp. nov. and B. mancocapac sp. nov. are similar to other Byrsopteryx larvae known. They can be distinguished from each other by the shape of the operculum formed by terga VIII and IX, and number of setae on the second abdominal pleurite. Maximum likelihood analyses of 20 COI sequences, including nine Byrsopteryx species, placed B. inti sp. nov. and B. mamaocllo sp. nov. as sister species and related to a clade including B. gomezi, B. tapanti, and B. esparta, while B. mancocapac sp. nov. was found as sister to B. abrelata. Despite the close phylogenetic relationship found between B. inti sp. nov. and B. mamaocllo sp. nov., they are separated by 14.9% minimum K2P divergence of COI. The hi…
format: application/pdf
format: text/html
creator: Allan P.M. Santos
creator: Daniela Maeda Takiya
subject: Biodiversity
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12645
publisher: PeerJ Inc.
rights: © 2021 Santos and Takiya
abstract: In this paper, we have described and illustrated three new species of Byrsopteryx from Peru: Byrsopteryx inti, sp. nov. Byrsopteryx mamaocllo sp. nov., and Byrsopteryx mancocapac sp. nov. Larvae of the latter two were also associated to male specimens based on comparison of a fragment of COI gene and pharate male identification. Byrsopteryx inti sp. nov. and Byrsopteryx mamaocllo sp. nov. share a unique feature: a semi-dome process formed by a thickened area on male forewings. The three species can be easily identified by wing coloration and male genitalia. Furthermore, Byrsopteryx inti sp. nov. can be recognized by its sternum VIII with a median digitate process on posterior margin, slightly capitate; and by long dorsolateral processes from segment VIII, which cross each other apically in dorsal view. Byrsopteryx mamaocllo sp. nov. can be distinguished by sternum VIII bearing a pair of short, posterior, spinelike processes, which are curved inwards and bordered by a rounded, membranous structure, and by a pair of short, heavily sclerotized, dorsolateral processes. Byrsopteryx mancocapac sp. nov. can be distinguished by strong spine-like processes arising dorsally from subgenital plate and by sternum VIII with posterior margin divided into two plate-like lobes. Larvae of B. mamaocllo sp. nov. and B. mancocapac sp. nov. are similar to other Byrsopteryx larvae known. They can be distinguished from each other by the shape of the operculum formed by terga VIII and IX, and number of setae on the second abdominal pleurite. Maximum likelihood analyses of 20 COI sequences, including nine Byrsopteryx species, placed B. inti sp. nov. and B. mamaocllo sp. nov. as sister species and related to a clade including B. gomezi, B. tapanti, and B. esparta, while B. mancocapac sp. nov. was found as sister to B. abrelata. Despite the close phylogenetic relationship found between B. inti sp. nov. and B. mamaocllo sp. nov., they are separated by 14.9% minimum K2P divergence of COI. The hi…
bibliographic citation: Santos et al. (2021) Three new species of Byrsopteryx Flint microcaddisflies from Peru (Insecta: Trichoptera) including DNA-based larval associations. PeerJ 9:e12645 https://doi.org/10.7717/peerj.12645
date submitted: 2021-10-01
date accepted: 2021-11-26
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Allan P.M.
author list: Agent
  family name: Takiya
  given name: Daniela Maeda
doi: 10.7717/peerj.12645
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: ©2021 Santos and Takiya
attribution name: Santos and Takiya

Living on the edge: genetic structure and geographic distribution in the threatened Markham’s Storm-Petrel (Hydrobates markhami)
type: item
type: AcademicArticle
description: Migratory birds are threatened by habitat loss and degradation, illegal killings, ineffective conservation policies, knowledge gaps and climate change. These threats are particularly troubling in the Procellariiformes (Aves), one of the most endangered bird groups. For “storm-petrels”, their cryptic breeding behavior, asynchrony between populations, and light pollution pose additional threats that contribute to increased mortality.Markham’s Storm-Petrel (Hydrobates markhami), a poorly known migratory species, is a pelagic bird that breeds in dispersed colonies in the Sechura and Atacama Deserts, with asynchronous reproduction between colonies, and is highly affected by artificial lights. Considering its complex conservation scenario and singular breeding, we expected to find narrow habitat distribution conditions, strong geographic genetic structure, and spatially differentiation related to human population activities (e.g., light pollution) and the climate global change. To evaluate these predictions, we analyzed the phylogeography, current and future potential distribution based on mitochondrial gene ND1 and geographic records.The phylogeographic analyses revealed three well-supported clades (i.e., Paracas, Arica, and Salar Grande), and the geographical distribution modeled using an intrinsic conditional model (iCAR) suggests a positive relationship with the mean temperature of the wettest quarter and of the driest quarter, solar radiation, and anthropogenic disturbance. The future predictions under moderate and severe scenarios of global change indicated a drastic distribution area reduction, especially in the southern zone around Tarapacá and Antofagasta in Chile. These suggest a potential loss of unique genetic diversity and the need for conservation actions particularly focused at the edges of the H. markhami distribution.
format: application/pdf
format: text/html
creator: Heraldo V. Norambuena
creator: Reinaldo Rivera
creator: Rodrigo Barros
creator: Rodrigo Silva
creator: Ronny Peredo
creator: Cristián E. Hernández
subject: Biogeography
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12669
publisher: PeerJ Inc.
rights: © 2021 Norambuena et al.
abstract: Migratory birds are threatened by habitat loss and degradation, illegal killings, ineffective conservation policies, knowledge gaps and climate change. These threats are particularly troubling in the Procellariiformes (Aves), one of the most endangered bird groups. For “storm-petrels”, their cryptic breeding behavior, asynchrony between populations, and light pollution pose additional threats that contribute to increased mortality.Markham’s Storm-Petrel (Hydrobates markhami), a poorly known migratory species, is a pelagic bird that breeds in dispersed colonies in the Sechura and Atacama Deserts, with asynchronous reproduction between colonies, and is highly affected by artificial lights. Considering its complex conservation scenario and singular breeding, we expected to find narrow habitat distribution conditions, strong geographic genetic structure, and spatially differentiation related to human population activities (e.g., light pollution) and the climate global change. To evaluate these predictions, we analyzed the phylogeography, current and future potential distribution based on mitochondrial gene ND1 and geographic records.The phylogeographic analyses revealed three well-supported clades (i.e., Paracas, Arica, and Salar Grande), and the geographical distribution modeled using an intrinsic conditional model (iCAR) suggests a positive relationship with the mean temperature of the wettest quarter and of the driest quarter, solar radiation, and anthropogenic disturbance. The future predictions under moderate and severe scenarios of global change indicated a drastic distribution area reduction, especially in the southern zone around Tarapacá and Antofagasta in Chile. These suggest a potential loss of unique genetic diversity and the need for conservation actions particularly focused at the edges of the H. markhami distribution.
bibliographic citation: Norambuena et al. (2021) Living on the edge: genetic structure and geographic distribution in the threatened Markham’s Storm-Petrel (Hydrobates markhami). PeerJ 9:e12669 https://doi.org/10.7717/peerj.12669
date submitted: 2021-05-11
date accepted: 2021-12-01
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Norambuena
  given name: Heraldo V.
author list: Agent
  family name: Rivera
  given name: Reinaldo
author list: Agent
  family name: Barros
  given name: Rodrigo
author list: Agent
  family name: Silva
  given name: Rodrigo
author list: Agent
  family name: Peredo
  given name: Ronny
author list: Agent
  family name: Hernández
  given name: Cristián E.
doi: 10.7717/peerj.12669
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: ©2021 Norambuena et al.
attribution name: Norambuena et al.

Integrated analysis and the identification of a circRNA-miRNA-mRNA network in the progression of abdominal aortic aneurysm
type: item
type: AcademicArticle
description: Background Abdominal aortic aneurysm (AAA) is a disease commonly seen in the elderly. The aneurysm diameter increases yearly, and the larger the AAA the higher the risk of rupture, increasing the risk of death. However, there are no current effective interventions in the early stages of AAA. Methods Four gene expression profiling datasets, including 23 normal artery (NOR) tissue samples and 97 AAA tissue samples, were integrated in order to explore potential molecular biological targets for early intervention. After preprocessing, differentially expressed genes (DEGs) between AAA and NOR were identified using LIMMA package. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were conducted using the DAVID database. The protein-protein interaction network was constructed and hub genes were identified using the STRING database and plugins in Cytoscape. A circular RNA (circRNA) profile of four NOR tissues versus four AAA tissues was then reanalyzed. A circRNA-miRNA-mRNA interaction network was constructed after predictions were made using the Targetscan and Circinteractome databases. Results A total of 440 DEGs (263 up-regulated and 177 down-regulated) were identified in the AAA group, compared with the NOR group. The majority were associated with the extracellular matrix, tumor necrosis factor-α, and transforming growth factor-β. Ten hub gene-encoded proteins (namely IL6, RPS27A, JUN, UBC, UBA52, FOS, IL1B, MMP9, SPP1 and CCL2) coupled with a higher degree of connectivity hub were identified after protein‐protein interaction network analysis. Our results, in combination with the results of previous studies revealed that miR-635, miR-527, miR-520h, miR-938 and miR-518a-5p may be affected by circ_0005073 and impact the expression of hub genes such as CCL2, SPP1 and UBA52. The miR-1206 may also be affected by circ_0090069 and impact RPS27A expression. Conclusions This circRNA-miRNA-mRNA network may perform critical roles in AAA and may be a novel target fo…
format: application/pdf
format: text/html
creator: Ke Si
creator: Da Lu
creator: Jianbo Tian
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.12682
publisher: PeerJ Inc.
rights: © 2021 Si et al.
abstract: Background Abdominal aortic aneurysm (AAA) is a disease commonly seen in the elderly. The aneurysm diameter increases yearly, and the larger the AAA the higher the risk of rupture, increasing the risk of death. However, there are no current effective interventions in the early stages of AAA. Methods Four gene expression profiling datasets, including 23 normal artery (NOR) tissue samples and 97 AAA tissue samples, were integrated in order to explore potential molecular biological targets for early intervention. After preprocessing, differentially expressed genes (DEGs) between AAA and NOR were identified using LIMMA package. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were conducted using the DAVID database. The protein-protein interaction network was constructed and hub genes were identified using the STRING database and plugins in Cytoscape. A circular RNA (circRNA) profile of four NOR tissues versus four AAA tissues was then reanalyzed. A circRNA-miRNA-mRNA interaction network was constructed after predictions were made using the Targetscan and Circinteractome databases. Results A total of 440 DEGs (263 up-regulated and 177 down-regulated) were identified in the AAA group, compared with the NOR group. The majority were associated with the extracellular matrix, tumor necrosis factor-α, and transforming growth factor-β. Ten hub gene-encoded proteins (namely IL6, RPS27A, JUN, UBC, UBA52, FOS, IL1B, MMP9, SPP1 and CCL2) coupled with a higher degree of connectivity hub were identified after protein‐protein interaction network analysis. Our results, in combination with the results of previous studies revealed that miR-635, miR-527, miR-520h, miR-938 and miR-518a-5p may be affected by circ_0005073 and impact the expression of hub genes such as CCL2, SPP1 and UBA52. The miR-1206 may also be affected by circ_0090069 and impact RPS27A expression. Conclusions This circRNA-miRNA-mRNA network may perform critical roles in AAA and may be a novel target fo…
bibliographic citation: Si et al. (2021) Integrated analysis and the identification of a circRNA-miRNA-mRNA network in the progression of abdominal aortic aneurysm. PeerJ 9:e12682 https://doi.org/10.7717/peerj.12682
date submitted: 2021-06-29
date accepted: 2021-12-02
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Si
  given name: Ke
author list: Agent
  family name: Lu
  given name: Da
author list: Agent
  family name: Tian
  given name: Jianbo
doi: 10.7717/peerj.12682
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: © 2021 Si et al.
attribution name: Si et al.

Spatiotemporal patterns of the COVID-19 epidemic in Mexico at the municipality level
type: item
type: AcademicArticle
description: In recent history, Coronavirus Disease 2019 (COVID-19) is one of the worst infectious disease outbreaks affecting humanity. The World Health Organization has defined the outbreak of COVID-19 as a pandemic, and the massive growth of the number of infected cases in a short time has caused enormous pressure on medical systems. Mexico surpassed 3.7 million confirmed infections and 285,000 deaths on October 23, 2021. We analysed the spatio-temporal patterns of the COVID-19 epidemic in Mexico using the georeferenced confirmed cases aggregated at the municipality level. We computed weekly Moran’s I index to assess spatial autocorrelation over time and identify clusters of the disease using the “flexibly shaped spatial scan” approach. Finally, we compared Euclidean, cost, resistance distances and gravitational model to select the best-suited approach to predict inter-municipality contagion. We found that COVID-19 pandemic in Mexico is characterised by clusters evolving in space and time as parallel epidemics. The gravitational distance was the best model to predict newly infected municipalities though the predictive power was relatively low and varied over time. This study helps us understand the spread of the epidemic over the Mexican territory and gives insights to model and predict the epidemic behaviour.
format: application/pdf
format: text/html
creator: Jean-François Mas
creator: Azucena Pérez-Vega
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
subject: Respiratory Medicine
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12685
publisher: PeerJ Inc.
rights: © 2021 Mas and Pérez-Vega
abstract: In recent history, Coronavirus Disease 2019 (COVID-19) is one of the worst infectious disease outbreaks affecting humanity. The World Health Organization has defined the outbreak of COVID-19 as a pandemic, and the massive growth of the number of infected cases in a short time has caused enormous pressure on medical systems. Mexico surpassed 3.7 million confirmed infections and 285,000 deaths on October 23, 2021. We analysed the spatio-temporal patterns of the COVID-19 epidemic in Mexico using the georeferenced confirmed cases aggregated at the municipality level. We computed weekly Moran’s I index to assess spatial autocorrelation over time and identify clusters of the disease using the “flexibly shaped spatial scan” approach. Finally, we compared Euclidean, cost, resistance distances and gravitational model to select the best-suited approach to predict inter-municipality contagion. We found that COVID-19 pandemic in Mexico is characterised by clusters evolving in space and time as parallel epidemics. The gravitational distance was the best model to predict newly infected municipalities though the predictive power was relatively low and varied over time. This study helps us understand the spread of the epidemic over the Mexican territory and gives insights to model and predict the epidemic behaviour.
bibliographic citation: Mas et al. (2021) Spatiotemporal patterns of the COVID-19 epidemic in Mexico at the municipality level. PeerJ 9:e12685 https://doi.org/10.7717/peerj.12685
date submitted: 2021-01-25
date accepted: 2021-12-03
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mas
  given name: Jean-François
author list: Agent
  family name: Pérez-Vega
  given name: Azucena
doi: 10.7717/peerj.12685
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: © 2021 Mas and Pérez-Vega
attribution name: Mas and Pérez-Vega

Bacterial diversity and potential risk factors associated with Salmonella contamination of seafood products sold in retail markets in Bangkok, Thailand
type: item
type: AcademicArticle
description: Consumption of contaminated food causes 600 million cases, including 420,000 of fatal infections every year. Estimated cost from food-borne illnesses is USD 110 billion per year, which is an economic burden to low- and middle-income countries. Thailand is a leading producer and consumer of seafood, but little is known about bacterial contamination in seafood. In particular, public health agencies need to know the relationship between Salmonella contamination in seafood and risk factors, as assessed with readily available culture-dependent and bacterial phenotyping methods. To address this, levels of indicator bacteria, Salmonella and Vibrio in various seafood products were determined to identify risk factors associated with Salmonella contamination. A total of 335 samples were collected from October 2018 to July 2019 at seafood markets throughout Bangkok, Thailand; overall sample composition was Pacific white shrimp (n = 85), oysters (n = 82), blood cockles (n = 84), and Asian seabass (n = 84). Prevalence was 100% for fecal coliforms and 85% for E. coli. In contrast, prevalence was 59% for V. parahaemolyticus, 49% for V. cholerae, 19% for V. alginolyticus, 18% for V. vulnificus, and 36% for Salmonella. Highest concentrations of fecal coliforms and E. coli were in oysters. Highest concentrations of Salmonella with Matopeni (31%) being the predominant serotype were in shrimp. Salmonella contamination was significantly associated with type of seafood, sampling location, retail conditions, and the presence of E. coli, V. alginolyticus and V. vulnificus. A cutoff value for E. coli concentration of 1.3 × 104 MPN/g predicted contamination of Salmonella, with a sensitivity of 84% and specificity of 61%. Displaying seafood products on ice, presence of E. coli and Vibrio, and seafood derived from Eastern Thailand were associated with an increased risk of Salmonella contamination.
format: application/pdf
format: text/html
creator: Edward R. Atwill
creator: Saharuetai Jeamsripong
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.12694
publisher: PeerJ Inc.
rights: © 2021 Atwill and Jeamsripong
abstract: Consumption of contaminated food causes 600 million cases, including 420,000 of fatal infections every year. Estimated cost from food-borne illnesses is USD 110 billion per year, which is an economic burden to low- and middle-income countries. Thailand is a leading producer and consumer of seafood, but little is known about bacterial contamination in seafood. In particular, public health agencies need to know the relationship between Salmonella contamination in seafood and risk factors, as assessed with readily available culture-dependent and bacterial phenotyping methods. To address this, levels of indicator bacteria, Salmonella and Vibrio in various seafood products were determined to identify risk factors associated with Salmonella contamination. A total of 335 samples were collected from October 2018 to July 2019 at seafood markets throughout Bangkok, Thailand; overall sample composition was Pacific white shrimp (n = 85), oysters (n = 82), blood cockles (n = 84), and Asian seabass (n = 84). Prevalence was 100% for fecal coliforms and 85% for E. coli. In contrast, prevalence was 59% for V. parahaemolyticus, 49% for V. cholerae, 19% for V. alginolyticus, 18% for V. vulnificus, and 36% for Salmonella. Highest concentrations of fecal coliforms and E. coli were in oysters. Highest concentrations of Salmonella with Matopeni (31%) being the predominant serotype were in shrimp. Salmonella contamination was significantly associated with type of seafood, sampling location, retail conditions, and the presence of E. coli, V. alginolyticus and V. vulnificus. A cutoff value for E. coli concentration of 1.3 × 104 MPN/g predicted contamination of Salmonella, with a sensitivity of 84% and specificity of 61%. Displaying seafood products on ice, presence of E. coli and Vibrio, and seafood derived from Eastern Thailand were associated with an increased risk of Salmonella contamination.
bibliographic citation: Atwill et al. (2021) Bacterial diversity and potential risk factors associated with Salmonella contamination of seafood products sold in retail markets in Bangkok, Thailand. PeerJ 9:e12694 https://doi.org/10.7717/peerj.12694
date submitted: 2021-05-14
date accepted: 2021-12-06
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Atwill
  given name: Edward R.
author list: Agent
  family name: Jeamsripong
  given name: Saharuetai
doi: 10.7717/peerj.12694
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: © 2021 Atwill and Jeamsripong
attribution name: Atwill and Jeamsripong

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