PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives
items: Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes
items: AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis
items: Biomarkers of non-communicable chronic disease: an update on contemporary methods
items: Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard
items: Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy
items: Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species
items: Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits
items: Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis
items: Disentangling bias for non-destructive insect metabarcoding

Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives
type: item
type: AcademicArticle
description: The need for comprehensive and effective coral restoration projects, as part of a broader conservation management strategy, is accelerating in the face of coral reef ecosystem decline. This study aims to expand the currently limited knowledge base for restoration techniques in the Maldives by testing the performance of mid-water rope nurseries in a lagoon and a reef habitat. We examined whether different coral farming habitats impacted fragment survival, health and growth of two coral genera and how the occurrence of mutualistic fauna, predation and disease influenced coral rearing success. Two nurseries were stocked with a total of 448 Pocillopora verrucosa and 96 Acropora spp. fragments, divided into different groups (four Pocillopora groups: lagoon nursery at 5 m; reef nursery at 5, 10 and 15 m; two Acropora groups: lagoon nursery at 5 m and reef nursery at 5 m). Eight fragment replicates from the same donor colony (Pocillopora genets: N = 14, Acropora genets N = 6) were used in each group and monitored for one year. Our results show that fragment survival was high in both farming habitats (>90%), with P. verrucosa surviving significantly better in the lagoon and Acropora spp. surviving and growing significantly faster in the reef nursery. P. verrucosa growth rates were similar between reef and lagoon habitat. Different rearing depths in the reef nursery had no impact on the survival of P. verrucosa but coral growth decreased considerably with depth, reducing fragments’ ecological volume augmentation and growth rates by almost half from 5 to 15 m depth. Further, higher fish predation rates on fragments were recorded on the reef, which did not impact overall nursery performance. Mutualistic fauna, which correlated positively with fragment survival, was more frequently observed in the lagoon nursery. The occurrence of disease was noted in both habitats, even though implications for fragment health were more severe in the lagoon. Overall, our study demonstrates that…
format: application/pdf
format: text/html
creator: Inga Dehnert
creator: Luca Saponari
creator: Paolo Galli
creator: Simone Montano
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.12874
publisher: PeerJ Inc.
rights: © 2022 Dehnert et al.
abstract: The need for comprehensive and effective coral restoration projects, as part of a broader conservation management strategy, is accelerating in the face of coral reef ecosystem decline. This study aims to expand the currently limited knowledge base for restoration techniques in the Maldives by testing the performance of mid-water rope nurseries in a lagoon and a reef habitat. We examined whether different coral farming habitats impacted fragment survival, health and growth of two coral genera and how the occurrence of mutualistic fauna, predation and disease influenced coral rearing success. Two nurseries were stocked with a total of 448 Pocillopora verrucosa and 96 Acropora spp. fragments, divided into different groups (four Pocillopora groups: lagoon nursery at 5 m; reef nursery at 5, 10 and 15 m; two Acropora groups: lagoon nursery at 5 m and reef nursery at 5 m). Eight fragment replicates from the same donor colony (Pocillopora genets: N = 14, Acropora genets N = 6) were used in each group and monitored for one year. Our results show that fragment survival was high in both farming habitats (>90%), with P. verrucosa surviving significantly better in the lagoon and Acropora spp. surviving and growing significantly faster in the reef nursery. P. verrucosa growth rates were similar between reef and lagoon habitat. Different rearing depths in the reef nursery had no impact on the survival of P. verrucosa but coral growth decreased considerably with depth, reducing fragments’ ecological volume augmentation and growth rates by almost half from 5 to 15 m depth. Further, higher fish predation rates on fragments were recorded on the reef, which did not impact overall nursery performance. Mutualistic fauna, which correlated positively with fragment survival, was more frequently observed in the lagoon nursery. The occurrence of disease was noted in both habitats, even though implications for fragment health were more severe in the lagoon. Overall, our study demonstrates that…
bibliographic citation: Dehnert et al. (2022) Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives. PeerJ 10:e12874 https://doi.org/10.7717/peerj.12874
date submitted: 2021-09-01
date accepted: 2022-01-11
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dehnert
  given name: Inga
author list: Agent
  family name: Saponari
  given name: Luca
author list: Agent
  family name: Galli
  given name: Paolo
author list: Agent
  family name: Montano
  given name: Simone
doi: 10.7717/peerj.12874
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: ©2022 Dehnert et al.
attribution name: Dehnert et al.

Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes
type: item
type: AcademicArticle
description: Background Wind, an important abiotic stress factor, affects forests in coastal areas, causes tree damage and timber loss. Methods Two genotypes of Eucalyptus camaldulensis-strong wind-resistant CA5 and weak wind-resistant C037 were used for RNA-seq analysis to screen for candidate wind-resistance genes and transcription factors (TFs) by comparing the transcriptome analysis of the two varieties in response to wind stress. Results It showed that 7061 differentially expressed unigenes could be annotated including 4,110 up-regulated unigenes and 2,951 down-regulated unigenes. Gene Ontology (GO) analysis revealed that six cellulose pathways were involved in response to wind stress. The unigenes in phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways were found to be differentially expressed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, 37 differentially expressed genes were functionally annotated to be involved in the secondary metabolism of phenylalanine (ko00940). Seventy-eight TFs related to the regulating cellulose and lignin synthesis were expressed differently from the various treatments. The expressions of C3H, POX, MYB, NAC, Gene008307, and Gene011799 were significantly upregulated in CA5. Overall, the main response of Eucalyptus to wind stress was associated with cell wall biosynthesis; key genes of cellulose and lignin biosynthesis pathways and related TFs were involved in the tree response to wind stress.
format: application/pdf
format: text/html
creator: Xiuhua Shang
creator: Peijian Zhang
creator: Guo Liu
creator: Ni Zhan
creator: Zhihua Wu
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12954
publisher: PeerJ Inc.
rights: © 2022 Shang et al.
abstract: Background Wind, an important abiotic stress factor, affects forests in coastal areas, causes tree damage and timber loss. Methods Two genotypes of Eucalyptus camaldulensis-strong wind-resistant CA5 and weak wind-resistant C037 were used for RNA-seq analysis to screen for candidate wind-resistance genes and transcription factors (TFs) by comparing the transcriptome analysis of the two varieties in response to wind stress. Results It showed that 7061 differentially expressed unigenes could be annotated including 4,110 up-regulated unigenes and 2,951 down-regulated unigenes. Gene Ontology (GO) analysis revealed that six cellulose pathways were involved in response to wind stress. The unigenes in phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways were found to be differentially expressed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, 37 differentially expressed genes were functionally annotated to be involved in the secondary metabolism of phenylalanine (ko00940). Seventy-eight TFs related to the regulating cellulose and lignin synthesis were expressed differently from the various treatments. The expressions of C3H, POX, MYB, NAC, Gene008307, and Gene011799 were significantly upregulated in CA5. Overall, the main response of Eucalyptus to wind stress was associated with cell wall biosynthesis; key genes of cellulose and lignin biosynthesis pathways and related TFs were involved in the tree response to wind stress.
bibliographic citation: Shang et al. (2022) Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes. PeerJ 10:e12954 https://doi.org/10.7717/peerj.12954
date submitted: 2021-08-04
date accepted: 2022-01-27
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shang
  given name: Xiuhua
author list: Agent
  family name: Zhang
  given name: Peijian
author list: Agent
  family name: Liu
  given name: Guo
author list: Agent
  family name: Zhan
  given name: Ni
author list: Agent
  family name: Wu
  given name: Zhihua
doi: 10.7717/peerj.12954
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: ©2022 Shang et al.
attribution name: Shang et al.

AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis
type: item
type: AcademicArticle
description: Ascorbic acid (AsA) is an important nutrient in celery, the conversion of D-mannose-1-P to GDP-D-mannose catalyzed by GDP-D-mannose pyrophosphorylase (GMPase) represents the first committed step in the biosynthesis of AsA. To clarify the function of the AgGMP gene of celery, the AgGMP gene was cloned from celery cv. ‘Jinnan Shiqin’ . It contains an open reading frame (ORF) with the length of 1,086 bp, encoding 361 amino acids. AgGMP protein was highly conserved among different plant species. Phylogenetic analysis demonstrated that the GMP proteins from celery and carrot belonged to the same branch. AgGMP protein was mainly composed of three α-helixes and certain random coils. No signal peptide was found in the AgGMP protein. The subcellular localization indicated that the AgGMP protein was located in the cytoplasm. The relative expression levels of AgGMP in ‘Jinnan Shiqin’ were significantly up-regulated at 2 h and 4 h under drought stress treatments. AsA contents in transgenic Arabidopsis lines hosting AgGMP gene were higher than that in wild type plants, and the root lengths were also longer in the MS medium containing 300 mM mannitol. The present study provides useful evidence for the functional involvement of AgGMP in regulating AsA accumulation and response to drought stress in celery.
format: application/pdf
format: text/html
creator: Yan-Hua Liu
creator: Hao Wang
creator: Jie-Xia Liu
creator: Sheng Shu
creator: Guo-Fei Tan
creator: Meng-Yao Li
creator: Ao-Qi Duan
creator: Hui Liu
creator: Ai-Sheng Xiong
subject: Genetics
subject: Molecular Biology
subject: Plant Science
subject: Infectious Diseases
description: doi:10.7717/peerj.12976
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Ascorbic acid (AsA) is an important nutrient in celery, the conversion of D-mannose-1-P to GDP-D-mannose catalyzed by GDP-D-mannose pyrophosphorylase (GMPase) represents the first committed step in the biosynthesis of AsA. To clarify the function of the AgGMP gene of celery, the AgGMP gene was cloned from celery cv. ‘Jinnan Shiqin’ . It contains an open reading frame (ORF) with the length of 1,086 bp, encoding 361 amino acids. AgGMP protein was highly conserved among different plant species. Phylogenetic analysis demonstrated that the GMP proteins from celery and carrot belonged to the same branch. AgGMP protein was mainly composed of three α-helixes and certain random coils. No signal peptide was found in the AgGMP protein. The subcellular localization indicated that the AgGMP protein was located in the cytoplasm. The relative expression levels of AgGMP in ‘Jinnan Shiqin’ were significantly up-regulated at 2 h and 4 h under drought stress treatments. AsA contents in transgenic Arabidopsis lines hosting AgGMP gene were higher than that in wild type plants, and the root lengths were also longer in the MS medium containing 300 mM mannitol. The present study provides useful evidence for the functional involvement of AgGMP in regulating AsA accumulation and response to drought stress in celery.
bibliographic citation: Liu et al. (2022) AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis. PeerJ 10:e12976 https://doi.org/10.7717/peerj.12976
date submitted: 2021-10-01
date accepted: 2022-01-31
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yan-Hua
author list: Agent
  family name: Wang
  given name: Hao
author list: Agent
  family name: Liu
  given name: Jie-Xia
author list: Agent
  family name: Shu
  given name: Sheng
author list: Agent
  family name: Tan
  given name: Guo-Fei
author list: Agent
  family name: Li
  given name: Meng-Yao
author list: Agent
  family name: Duan
  given name: Ao-Qi
author list: Agent
  family name: Liu
  given name: Hui
author list: Agent
  family name: Xiong
  given name: Ai-Sheng
doi: 10.7717/peerj.12976
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: © 2022 Liu et al.
attribution name: Liu et al.

Biomarkers of non-communicable chronic disease: an update on contemporary methods
type: item
type: AcademicArticle
description: Chronic diseases constitute a major global burden with significant impact on health systems, economies, and quality of life. Chronic diseases include a broad range of diseases that can be communicable or non-communicable. Chronic diseases are often associated with modifications of normal physiological levels of various analytes that are routinely measured in serum and other body fluids, as well as pathological findings, such as chronic inflammation, oxidative stress, and mitochondrial dysfunction. Identification of at-risk populations, early diagnosis, and prediction of prognosis play a major role in preventing or reducing the burden of chronic diseases. Biomarkers are tools that are used by health professionals to aid in the identification and management of chronic diseases. Biomarkers can be diagnostic, predictive, or prognostic. Several individual or grouped biomarkers have been used successfully in the diagnosis and prediction of certain chronic diseases, however, it is generally accepted that a more sophisticated approach to link and interpret various biomarkers involved in chronic disease is necessary to improve our current procedures. In order to ensure a comprehensive and unbiased coverage of the literature, first a primary frame of the manuscript (title, headings and subheadings) was drafted by the authors working on this paper. Second, based on the components drafted in the preliminary skeleton a comprehensive search of the literature was performed using the PubMed and Google Scholar search engines. Multiple keywords related to the topic were used. Out of screened papers, only 190 papers, which are the most relevant, and recent articles were selected to cover the topic in relation to etiological mechanisms of different chronic diseases, the most recently used biomarkers of chronic diseases and finally the advances in the applications of multivariate biomarkers of chronic diseases as statistical and clinically applied tool for the early diagnosis of chronic…
format: application/pdf
format: text/html
creator: Solaiman M. Al-hadlaq
creator: Hanan A. Balto
creator: Wail M. Hassan
creator: Najat A. Marraiki
creator: Afaf K. El-Ansary
subject: Cardiology
subject: Diabetes and Endocrinology
subject: Evidence Based Medicine
subject: Statistics
description: doi:10.7717/peerj.12977
publisher: PeerJ Inc.
rights: © 2022 Al-hadlaq et al.
abstract: Chronic diseases constitute a major global burden with significant impact on health systems, economies, and quality of life. Chronic diseases include a broad range of diseases that can be communicable or non-communicable. Chronic diseases are often associated with modifications of normal physiological levels of various analytes that are routinely measured in serum and other body fluids, as well as pathological findings, such as chronic inflammation, oxidative stress, and mitochondrial dysfunction. Identification of at-risk populations, early diagnosis, and prediction of prognosis play a major role in preventing or reducing the burden of chronic diseases. Biomarkers are tools that are used by health professionals to aid in the identification and management of chronic diseases. Biomarkers can be diagnostic, predictive, or prognostic. Several individual or grouped biomarkers have been used successfully in the diagnosis and prediction of certain chronic diseases, however, it is generally accepted that a more sophisticated approach to link and interpret various biomarkers involved in chronic disease is necessary to improve our current procedures. In order to ensure a comprehensive and unbiased coverage of the literature, first a primary frame of the manuscript (title, headings and subheadings) was drafted by the authors working on this paper. Second, based on the components drafted in the preliminary skeleton a comprehensive search of the literature was performed using the PubMed and Google Scholar search engines. Multiple keywords related to the topic were used. Out of screened papers, only 190 papers, which are the most relevant, and recent articles were selected to cover the topic in relation to etiological mechanisms of different chronic diseases, the most recently used biomarkers of chronic diseases and finally the advances in the applications of multivariate biomarkers of chronic diseases as statistical and clinically applied tool for the early diagnosis of chronic…
bibliographic citation: Al-hadlaq et al. (2022) Biomarkers of non-communicable chronic disease: an update on contemporary methods. PeerJ 10:e12977 https://doi.org/10.7717/peerj.12977
date submitted: 2021-07-15
date accepted: 2022-01-31
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-hadlaq
  given name: Solaiman M.
author list: Agent
  family name: Balto
  given name: Hanan A.
author list: Agent
  family name: Hassan
  given name: Wail M.
author list: Agent
  family name: Marraiki
  given name: Najat A.
author list: Agent
  family name: El-Ansary
  given name: Afaf K.
doi: 10.7717/peerj.12977
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: ©2022 Al-hadlaq et al.
attribution name: Al-hadlaq et al.

Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard
type: item
type: AcademicArticle
description: High levels of within-individual variation (WIV) in reiterative components in plants such as leaves, flowers, and fruits have been shown to increase individual fitness by multiple mechanisms including mediating interactions with natural enemies. This relationship between WIV and fitness has been studied almost exclusively in plant systems. While animals do not exhibit conspicuous reiterative components, they have traits that can vary at the individual level such as erythrocyte size. It is currently unknown if WIV in animals can influence individual fitness by mediating the outcome of interactions with natural enemies as it has been shown in plants. To address this issue, we tested for a relationship between WIV in erythrocyte size, hemoparasite infection status, and body condition (a proxy for fitness) in a Caribbean anole lizard. We quantified the coefficient of variation of adult erythrocytes size in $n = 95$ infected and $n = 107$ non-infected lizards. We found higher degrees of erythrocyte size variation in infected lizards than in non-infected individuals. However, we found no significant relationship between infection status or erythrocyte size variation, and lizard body condition. These results suggest that higher WIV in erythrocyte size in infected lizards is not necessarily adaptive but likely a consequence of the host response to infection. Many hemoparasites destroy their host cells as part of their life cycle. To compensate, the host lizard may respond by increasing production of erythrocytes resulting in higher WIV. Our results emphasize the need to better understand the role of within-animal variation as a neglected driver or consequence of ecological and evolutionary interactions.
format: application/pdf
format: text/html
creator: Virnaliz Cruz
creator: Omar Cruz-Pantoja
creator: Raymond Tremblay
creator: Miguel Acevedo
subject: Ecology
subject: Parasitology
subject: Zoology
subject: Hematology
description: doi:10.7717/peerj.12761
publisher: PeerJ Inc.
rights: © 2022 Cruz et al.
abstract: High levels of within-individual variation (WIV) in reiterative components in plants such as leaves, flowers, and fruits have been shown to increase individual fitness by multiple mechanisms including mediating interactions with natural enemies. This relationship between WIV and fitness has been studied almost exclusively in plant systems. While animals do not exhibit conspicuous reiterative components, they have traits that can vary at the individual level such as erythrocyte size. It is currently unknown if WIV in animals can influence individual fitness by mediating the outcome of interactions with natural enemies as it has been shown in plants. To address this issue, we tested for a relationship between WIV in erythrocyte size, hemoparasite infection status, and body condition (a proxy for fitness) in a Caribbean anole lizard. We quantified the coefficient of variation of adult erythrocytes size in $n = 95$ infected and $n = 107$ non-infected lizards. We found higher degrees of erythrocyte size variation in infected lizards than in non-infected individuals. However, we found no significant relationship between infection status or erythrocyte size variation, and lizard body condition. These results suggest that higher WIV in erythrocyte size in infected lizards is not necessarily adaptive but likely a consequence of the host response to infection. Many hemoparasites destroy their host cells as part of their life cycle. To compensate, the host lizard may respond by increasing production of erythrocytes resulting in higher WIV. Our results emphasize the need to better understand the role of within-animal variation as a neglected driver or consequence of ecological and evolutionary interactions.
bibliographic citation: Cruz et al. (2022) Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard. PeerJ 10:e12761 https://doi.org/10.7717/peerj.12761
date submitted: 2019-07-15
date accepted: 2021-12-16
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cruz
  given name: Virnaliz
author list: Agent
  family name: Cruz-Pantoja
  given name: Omar
author list: Agent
  family name: Tremblay
  given name: Raymond
author list: Agent
  family name: Acevedo
  given name: Miguel
doi: 10.7717/peerj.12761
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Cruz et al.
attribution name: Cruz et al.

Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy
type: item
type: AcademicArticle
description: Background Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species. Methods We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs. Results This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trape…
format: application/pdf
format: text/html
creator: Fernando Cortés-Carrasco
creator: Manuel Elías-Gutiérrez
creator: María del Socorro García-Madrigal
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12774
publisher: PeerJ Inc.
rights: © 2022 Cortés-Carrasco et al.
abstract: Background Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species. Methods We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs. Results This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trape…
bibliographic citation: Cortés-Carrasco et al. (2022) Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy. PeerJ 10:e12774 https://doi.org/10.7717/peerj.12774
date submitted: 2021-02-19
date accepted: 2021-12-20
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cortés-Carrasco
  given name: Fernando
author list: Agent
  family name: Elías-Gutiérrez
  given name: Manuel
author list: Agent
  family name: García-Madrigal
  given name: María del Socorro
doi: 10.7717/peerj.12774
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: © 2022 Cortés-Carrasco et al.
attribution name: Cortés-Carrasco et al.

Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species
type: item
type: AcademicArticle
description: Background Population dynamics are driven by a number of biotic (e.g., density-dependence) and abiotic (e.g., climate) factors whose contribution can greatly vary across study systems (i.e., populations). Yet, the extent to which the contribution of these factors varies across populations and between species and whether spatial patterns can be identified has received little attention. Methods Here, we used a long-term (1982–2011), broad scale (182 sites distributed across metropolitan France) dataset to study spatial patterns in the population’s dynamics of three freshwater fish species presenting contrasted life-histories and patterns of elevation range shifts in recent decades. We used a hierarchical Bayesian approach together with an elasticity analysis to estimate the relative contribution of a set of biotic (e.g., strength of density dependence, recruitment rate) and abiotic (mean and variability of water temperature) factors affecting the site-specific dynamic of two different size classes (0+ and >0+ individuals) for the three species. We then tested whether the local contribution of each factor presented evidence for biogeographical patterns by confronting two non-mutually exclusive hypotheses: the “range-shift” hypothesis that predicts a gradient along elevation or latitude and the “abundant-center” hypothesis that predicts a gradient from the center to the edge of the species’ distributional range. Results Despite contrasted life-histories, the three species displayed similar large-scale patterns in population dynamics with a much stronger contribution of biotic factors over abiotic ones. Yet, the contribution of the different factors strongly varied within distributional ranges and followed distinct spatial patterns. Indeed, while abiotic factors mostly varied along elevation, biotic factors—which disproportionately contributed to population dynamics—varied along both elevation and latitude. Conclusions Overall while our results provide stronger support f…
format: application/pdf
format: text/html
creator: Mathieu Chevalier
creator: Pablo Tedesco
creator: Gael Grenouillet
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Ecology
subject: Freshwater Biology
subject: Population Biology
description: doi:10.7717/peerj.12857
publisher: PeerJ Inc.
rights: © 2022 Chevalier et al.
abstract: Background Population dynamics are driven by a number of biotic (e.g., density-dependence) and abiotic (e.g., climate) factors whose contribution can greatly vary across study systems (i.e., populations). Yet, the extent to which the contribution of these factors varies across populations and between species and whether spatial patterns can be identified has received little attention. Methods Here, we used a long-term (1982–2011), broad scale (182 sites distributed across metropolitan France) dataset to study spatial patterns in the population’s dynamics of three freshwater fish species presenting contrasted life-histories and patterns of elevation range shifts in recent decades. We used a hierarchical Bayesian approach together with an elasticity analysis to estimate the relative contribution of a set of biotic (e.g., strength of density dependence, recruitment rate) and abiotic (mean and variability of water temperature) factors affecting the site-specific dynamic of two different size classes (0+ and >0+ individuals) for the three species. We then tested whether the local contribution of each factor presented evidence for biogeographical patterns by confronting two non-mutually exclusive hypotheses: the “range-shift” hypothesis that predicts a gradient along elevation or latitude and the “abundant-center” hypothesis that predicts a gradient from the center to the edge of the species’ distributional range. Results Despite contrasted life-histories, the three species displayed similar large-scale patterns in population dynamics with a much stronger contribution of biotic factors over abiotic ones. Yet, the contribution of the different factors strongly varied within distributional ranges and followed distinct spatial patterns. Indeed, while abiotic factors mostly varied along elevation, biotic factors—which disproportionately contributed to population dynamics—varied along both elevation and latitude. Conclusions Overall while our results provide stronger support f…
bibliographic citation: Chevalier et al. (2022) Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species. PeerJ 10:e12857 https://doi.org/10.7717/peerj.12857
date submitted: 2021-07-15
date accepted: 2022-01-09
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chevalier
  given name: Mathieu
author list: Agent
  family name: Tedesco
  given name: Pablo
author list: Agent
  family name: Grenouillet
  given name: Gael
doi: 10.7717/peerj.12857
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Chevalier et al.
attribution name: Chevalier et al.

Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits
type: item
type: AcademicArticle
description: Background Animal models are significant for understanding human osteoarthritis (OA). This study compared the synovial fluid proteomics changes in surgical and chemical induced OA models. Methods Thirty rabbits either had anterior cruciate ligament transection (ACLT) procedure or injected intra-articularly with monosodium iodoacetate (MIA, 8 mg) into the right knee. The joints were anatomically assessed, and the synovial fluid proteins analyzed using two-dimensional polyacrylamide gel electrophoresis (2DGE) and MALDI TOF/TOF mass spectrometry analysis at 4, 8 and 12 weeks. The proteins’ upregulation and downregulation were compared with control healthy knees. Results Seven proteins (histidine-rich glycoprotein, beta-actin-like protein 2 isoform X1, retinol-binding protein-4, alpha-1-antiproteinase, gelsolin isoform, serotransferrin, immunoglobulin kappa-b4 chain-C-region) were significantly expressed by the surgical induction. They characterized cellular process (27%), organization of cellular components or biogenesis (27%), localization (27%) and biological regulation (18%), which related to synovitis, increased cellularity, and subsequently cartilage damage. Three proteins (apolipoprotein I-IV precursor, serpin peptidase inhibitor and haptoglobin precursor) were significantly modified by the chemical induction. They characterized stimulus responses (23%), immune responses (15%), biological regulations (15%), metabolism (15%), organization of cellular components or biogenesis (8%), cellular process (8%), biological adhesions (8%) and localization (8%), which related to chondrocytes glycolysis/death, neovascularization, subchondral bone necrosis/collapse and inflammation. Conclusions The surgical induced OA model showed a wider range of protein changes, which were most upregulated at week 12. The biological process proteins expressions showed the chemical induced joints had slower OA progression compared to surgical induced joints. The chemical induced OA joints sho…
format: application/pdf
format: text/html
creator: Sharifah Zakiah Syed Sulaiman
creator: Wei Miao Tan
creator: Rozanaliza Radzi
creator: Intan Nur Fatiha Shafie
creator: Mokrish Ajat
creator: Rozaihan Mansor
creator: Suhaila Mohamed
creator: Norasfaliza Rahmad
creator: Angela Min Hwei Ng
creator: Seng Fong Lau
subject: Biochemistry
subject: Molecular Biology
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.12897
publisher: PeerJ Inc.
rights: © 2022 Syed Sulaiman et al.
abstract: Background Animal models are significant for understanding human osteoarthritis (OA). This study compared the synovial fluid proteomics changes in surgical and chemical induced OA models. Methods Thirty rabbits either had anterior cruciate ligament transection (ACLT) procedure or injected intra-articularly with monosodium iodoacetate (MIA, 8 mg) into the right knee. The joints were anatomically assessed, and the synovial fluid proteins analyzed using two-dimensional polyacrylamide gel electrophoresis (2DGE) and MALDI TOF/TOF mass spectrometry analysis at 4, 8 and 12 weeks. The proteins’ upregulation and downregulation were compared with control healthy knees. Results Seven proteins (histidine-rich glycoprotein, beta-actin-like protein 2 isoform X1, retinol-binding protein-4, alpha-1-antiproteinase, gelsolin isoform, serotransferrin, immunoglobulin kappa-b4 chain-C-region) were significantly expressed by the surgical induction. They characterized cellular process (27%), organization of cellular components or biogenesis (27%), localization (27%) and biological regulation (18%), which related to synovitis, increased cellularity, and subsequently cartilage damage. Three proteins (apolipoprotein I-IV precursor, serpin peptidase inhibitor and haptoglobin precursor) were significantly modified by the chemical induction. They characterized stimulus responses (23%), immune responses (15%), biological regulations (15%), metabolism (15%), organization of cellular components or biogenesis (8%), cellular process (8%), biological adhesions (8%) and localization (8%), which related to chondrocytes glycolysis/death, neovascularization, subchondral bone necrosis/collapse and inflammation. Conclusions The surgical induced OA model showed a wider range of protein changes, which were most upregulated at week 12. The biological process proteins expressions showed the chemical induced joints had slower OA progression compared to surgical induced joints. The chemical induced OA joints sho…
bibliographic citation: Syed Sulaiman et al. (2022) Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits. PeerJ 10:e12897 https://doi.org/10.7717/peerj.12897
date submitted: 2021-06-04
date accepted: 2022-01-16
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Syed Sulaiman
  given name: Sharifah Zakiah
author list: Agent
  family name: Tan
  given name: Wei Miao
author list: Agent
  family name: Radzi
  given name: Rozanaliza
author list: Agent
  family name: Shafie
  given name: Intan Nur Fatiha
author list: Agent
  family name: Ajat
  given name: Mokrish
author list: Agent
  family name: Mansor
  given name: Rozaihan
author list: Agent
  family name: Mohamed
  given name: Suhaila
author list: Agent
  family name: Rahmad
  given name: Norasfaliza
author list: Agent
  family name: Ng
  given name: Angela Min Hwei
author list: Agent
  family name: Lau
  given name: Seng Fong
doi: 10.7717/peerj.12897
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Syed Sulaiman et al.
attribution name: Syed Sulaiman et al.

Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis
type: item
type: AcademicArticle
description: This study aimed to conduct a network meta-analysis (NMA) to compare the efficacy of brain natriuretic peptide (BNP) vs nicorandil for preventing contrast-induced nephropathy (CIN). Databases of Pubmed, Cochrane, Embase, Web of Science were searched by keywords for eligible studies of randomized controlled trials investigating different agents (BNP, nicorandil, nitroglycerin, intravenous saline) for preventing CIN. The outcomes included a change in serum creatinine level at 48 h and the incidence of CIN after percutaneous coronary intervention (PCI) or coronary angiography (CAG). A total of 13 studies with 3,462 patients were included. Compared with intravenous saline alone, except for nitroglycerin (odds ratio [OR]: 1.02, 95% CI [0.36–2.88]), the other drugs significantly reduced the CIN incidence with OR of 0.35 (95% CI [0.24–0.51]) for BNP, 0.52 (0.29, 0.94) for usual-dose nicorandil, 0.28 (0.19, 0.43) for double-dose nicorandil. BNP and double-dose nicorandil significantly decreased the change of serum creatinine (SCr) levels with mean difference (MD) of −6.98, (−10.01, −3.95) for BNP, −8.78, (−11.63, −5.93) for double-dose nicorandil. No significant differences were observed in the change of SCr levels for nitroglycerin (−4.97, [−11.46, 1.52]) and usual-dose nicorandil (−2.32, [−5.52, 0.89]) compared with intravenous saline alone. For double-dose nicorandil, the CIN incidence and the change of SCr level in group of 4–5 days treatment course were more than group of less than or equal to 24 h treatment course (OR of 1.48, [0.63–3.46] and MD of 2.48, [−1.96, 6.91]). In conclusion, BNP and double-dose nicorandil can have effects on preventing the incidence of CIN and double-dose nicorandil performed better than BNP. In double-dose nicorandil groups, a course of less than or equal to 24 h before and after procedure performed with better efficacy than a course of 4–5 days.
format: application/pdf
format: text/html
creator: Ziwei Mei
creator: Songmei Luo
creator: Peipei Chen
creator: Qiankun Zhang
creator: Limei Zhou
creator: Chaoyong Zhu
creator: Hong Zhu
creator: Lie Jin
subject: Biochemistry
subject: Diabetes and Endocrinology
subject: Nephrology
subject: Pharmacology
description: doi:10.7717/peerj.12975
publisher: PeerJ Inc.
rights: © 2022 Mei et al.
abstract: This study aimed to conduct a network meta-analysis (NMA) to compare the efficacy of brain natriuretic peptide (BNP) vs nicorandil for preventing contrast-induced nephropathy (CIN). Databases of Pubmed, Cochrane, Embase, Web of Science were searched by keywords for eligible studies of randomized controlled trials investigating different agents (BNP, nicorandil, nitroglycerin, intravenous saline) for preventing CIN. The outcomes included a change in serum creatinine level at 48 h and the incidence of CIN after percutaneous coronary intervention (PCI) or coronary angiography (CAG). A total of 13 studies with 3,462 patients were included. Compared with intravenous saline alone, except for nitroglycerin (odds ratio [OR]: 1.02, 95% CI [0.36–2.88]), the other drugs significantly reduced the CIN incidence with OR of 0.35 (95% CI [0.24–0.51]) for BNP, 0.52 (0.29, 0.94) for usual-dose nicorandil, 0.28 (0.19, 0.43) for double-dose nicorandil. BNP and double-dose nicorandil significantly decreased the change of serum creatinine (SCr) levels with mean difference (MD) of −6.98, (−10.01, −3.95) for BNP, −8.78, (−11.63, −5.93) for double-dose nicorandil. No significant differences were observed in the change of SCr levels for nitroglycerin (−4.97, [−11.46, 1.52]) and usual-dose nicorandil (−2.32, [−5.52, 0.89]) compared with intravenous saline alone. For double-dose nicorandil, the CIN incidence and the change of SCr level in group of 4–5 days treatment course were more than group of less than or equal to 24 h treatment course (OR of 1.48, [0.63–3.46] and MD of 2.48, [−1.96, 6.91]). In conclusion, BNP and double-dose nicorandil can have effects on preventing the incidence of CIN and double-dose nicorandil performed better than BNP. In double-dose nicorandil groups, a course of less than or equal to 24 h before and after procedure performed with better efficacy than a course of 4–5 days.
bibliographic citation: Mei et al. (2022) Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis. PeerJ 10:e12975 https://doi.org/10.7717/peerj.12975
date submitted: 2021-11-23
date accepted: 2022-01-31
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mei
  given name: Ziwei
author list: Agent
  family name: Luo
  given name: Songmei
author list: Agent
  family name: Chen
  given name: Peipei
author list: Agent
  family name: Zhang
  given name: Qiankun
author list: Agent
  family name: Zhou
  given name: Limei
author list: Agent
  family name: Zhu
  given name: Chaoyong
author list: Agent
  family name: Zhu
  given name: Hong
author list: Agent
  family name: Jin
  given name: Lie
doi: 10.7717/peerj.12975
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Mei et al.
attribution name: Mei et al.

Disentangling bias for non-destructive insect metabarcoding
type: item
type: AcademicArticle
description: A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
format: application/pdf
format: text/html
creator: Francesco Martoni
creator: Alexander M. Piper
creator: Brendan C. Rodoni
creator: Mark J. Blacket
subject: Bioinformatics
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.12981
publisher: PeerJ Inc.
rights: © 2022 Martoni et al.
abstract: A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
bibliographic citation: Martoni et al. (2022) Disentangling bias for non-destructive insect metabarcoding. PeerJ 10:e12981 https://doi.org/10.7717/peerj.12981
date submitted: 2021-10-01
date accepted: 2022-02-01
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martoni
  given name: Francesco
author list: Agent
  family name: Piper
  given name: Alexander M.
author list: Agent
  family name: Rodoni
  given name: Brendan C.
author list: Agent
  family name: Blacket
  given name: Mark J.
doi: 10.7717/peerj.12981
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: © 2022 Martoni et al.
attribution name: Martoni et al.

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