PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Are incremental exercise relationships between rating of perceived exertion and oxygen uptake or heart rate reserve valid during steady-state exercises?
items: A new species of Languidipes Hubbard (Ephemeroptera, Polymitarcyidae) from Borneo
items: Significance of NKX2-1 as a biomarker for clinical prognosis, immune infiltration, and drug therapy in lung squamous cell carcinoma
items: The Chronic Time Pressure Inventory: further assessment of factorial structure and validity
items: The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny—a case study on dwarf chameleons
items: Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities
items: Pollen thermotolerance of a widespread plant, Lotus corniculatus, in response to climate warming: possible local adaptation of populations from different elevations
items: Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease
items: Interactions between chaperone and energy storage networks during the evolution of Legionella pneumophila under heat shock
items: The low survival rate of European hare leverets in arable farmland: evidence from the predation experiment

Are incremental exercise relationships between rating of perceived exertion and oxygen uptake or heart rate reserve valid during steady-state exercises?
type: item
type: AcademicArticle
description: Background Rating of perceived exertion (RPE) is considered a valid method for prescribing prolonged aerobic steady-state exercise (SSE) intensity due to its association with physiological indicators of exercise intensity, such as oxygen uptake (V̇O2) or heart rate (HR). However, these associations between psychological and physiological indicators of exercise intensity were found during graded exercise tests (GXT) but are currently used to prescribe SSE intensity even though the transferability and validity of the relationships found during GXT to SSE were not investigated. The present study aims to verify whether (a) RPE-HR or RPE-V̇O2 relations found during GXTs are valid during SSEs, and (b) the duration and intensity of SSE affect these relations. Methods Eight healthy and physically active males (age 22.6 ± 1.2 years) were enrolled. On the first visit, pre-exercise (during 20 min standing) and maximal (during a GXT) HR and V̇O2 values were measured. Then, on separate days, participants performed 4 SSEs on the treadmill by running at 60% and 80% of the HR reserve (HRR) for 15 and 45 min (random order). Individual linear regressions between GXTs’ RPE (dependent variable) and HRR and V̇O2 reserve (V̇O2R) values (computed as the difference between maximal and pre-exercise values) were used to predict the RPE associated with %HRR (RPEHRR) and %V̇O2R (RPEV̇O2R) during the SSEs. For each relation (RPE-%HRR and RPE-%V̇O2R), a three-way factorial repeated measures ANOVA (α = 0.05) was used to assess if RPE (dependent variable) was affected by exercise modality (i.e., RPE recorded during SSE [RPESSE] or GXT-predicted), duration (i.e., 15 or 45 min), and intensity (i.e., 60% or 80% of HRR). Results The differences between RPESSE and GXT-predicted RPE, which were assessed by evaluating the effect of modality and its interactions with SSE intensity and duration, showed no significant differences between RPESSE and RPEHRR. However, when RPESSE was compared with RPEV̇O2R, al…
format: application/pdf
format: text/html
creator: Carlo Ferri Marini
creator: Lorenzo Micheli
creator: Tommaso Grossi
creator: Ario Federici
creator: Giovanni Piccoli
creator: Luca Zoffoli
creator: Luca Correale
creator: Stefano Dell’Anna
creator: Carlo Alberto Naldini
creator: Francesco Lucertini
creator: Matteo Vandoni
subject: Anatomy and Physiology
subject: Cardiology
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.17158
publisher: PeerJ Inc.
rights: © 2024 Ferri Marini et al.
abstract: Background Rating of perceived exertion (RPE) is considered a valid method for prescribing prolonged aerobic steady-state exercise (SSE) intensity due to its association with physiological indicators of exercise intensity, such as oxygen uptake (V̇O2) or heart rate (HR). However, these associations between psychological and physiological indicators of exercise intensity were found during graded exercise tests (GXT) but are currently used to prescribe SSE intensity even though the transferability and validity of the relationships found during GXT to SSE were not investigated. The present study aims to verify whether (a) RPE-HR or RPE-V̇O2 relations found during GXTs are valid during SSEs, and (b) the duration and intensity of SSE affect these relations. Methods Eight healthy and physically active males (age 22.6 ± 1.2 years) were enrolled. On the first visit, pre-exercise (during 20 min standing) and maximal (during a GXT) HR and V̇O2 values were measured. Then, on separate days, participants performed 4 SSEs on the treadmill by running at 60% and 80% of the HR reserve (HRR) for 15 and 45 min (random order). Individual linear regressions between GXTs’ RPE (dependent variable) and HRR and V̇O2 reserve (V̇O2R) values (computed as the difference between maximal and pre-exercise values) were used to predict the RPE associated with %HRR (RPEHRR) and %V̇O2R (RPEV̇O2R) during the SSEs. For each relation (RPE-%HRR and RPE-%V̇O2R), a three-way factorial repeated measures ANOVA (α = 0.05) was used to assess if RPE (dependent variable) was affected by exercise modality (i.e., RPE recorded during SSE [RPESSE] or GXT-predicted), duration (i.e., 15 or 45 min), and intensity (i.e., 60% or 80% of HRR). Results The differences between RPESSE and GXT-predicted RPE, which were assessed by evaluating the effect of modality and its interactions with SSE intensity and duration, showed no significant differences between RPESSE and RPEHRR. However, when RPESSE was compared with RPEV̇O2R, al…
bibliographic citation: Ferri Marini et al. (2024) Are incremental exercise relationships between rating of perceived exertion and oxygen uptake or heart rate reserve valid during steady-state exercises?. PeerJ 12:e17158 https://doi.org/10.7717/peerj.17158
date submitted: 2023-09-21
date accepted: 2024-03-04
issued: 2024-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferri Marini
  given name: Carlo
author list: Agent
  family name: Micheli
  given name: Lorenzo
author list: Agent
  family name: Grossi
  given name: Tommaso
author list: Agent
  family name: Federici
  given name: Ario
author list: Agent
  family name: Piccoli
  given name: Giovanni
author list: Agent
  family name: Zoffoli
  given name: Luca
author list: Agent
  family name: Correale
  given name: Luca
author list: Agent
  family name: Dell’Anna
  given name: Stefano
author list: Agent
  family name: Naldini
  given name: Carlo Alberto
author list: Agent
  family name: Lucertini
  given name: Francesco
author list: Agent
  family name: Vandoni
  given name: Matteo
doi: 10.7717/peerj.17158
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-03
copyright: ©2024 Ferri Marini et al.
attribution name: Ferri Marini et al.

A new species of Languidipes Hubbard (Ephemeroptera, Polymitarcyidae) from Borneo
type: item
type: AcademicArticle
description: The genus Languidipes is currently represented by three species distributed in southeastern Asia, India, and Sri Lanka. Languidipes corporaali is the most widely distributed species, and both, male and female imagos, as well as nymphs, are known. In contrast, the other species, L. taprobanes and L. lithophagus, are only known from nymphs. Here, we describe a new species, Languidipes janae sp nov, based on male imagos collected from Borneo, Indonesia. This new species is characterized by the presence of ommation on mesonotum, and penis almost completely divided, with sub-quadrate base and a small outer projection basal to the long and slender distal arms. This constitutes the first record of the genus for Borneo. A cladistic analysis of the subfamily Asthenopodinae supports its taxonomic status.
format: application/pdf
format: text/html
creator: Guillermo Eduardo Hankel
creator: Carlos Molineri
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Freshwater Biology
description: doi:10.7717/peerj.17327
publisher: PeerJ Inc.
rights: © 2024 Hankel and Molineri
abstract: The genus Languidipes is currently represented by three species distributed in southeastern Asia, India, and Sri Lanka. Languidipes corporaali is the most widely distributed species, and both, male and female imagos, as well as nymphs, are known. In contrast, the other species, L. taprobanes and L. lithophagus, are only known from nymphs. Here, we describe a new species, Languidipes janae sp nov, based on male imagos collected from Borneo, Indonesia. This new species is characterized by the presence of ommation on mesonotum, and penis almost completely divided, with sub-quadrate base and a small outer projection basal to the long and slender distal arms. This constitutes the first record of the genus for Borneo. A cladistic analysis of the subfamily Asthenopodinae supports its taxonomic status.
bibliographic citation: Hankel et al. (2024) A new species of Languidipes Hubbard (Ephemeroptera, Polymitarcyidae) from Borneo. PeerJ 12:e17327 https://doi.org/10.7717/peerj.17327
date submitted: 2024-01-08
date accepted: 2024-04-11
issued: 2024-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hankel
  given name: Guillermo Eduardo
author list: Agent
  family name: Molineri
  given name: Carlos
doi: 10.7717/peerj.17327
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-03
copyright: ©2024 Hankel and Molineri
attribution name: Hankel and Molineri

Significance of NKX2-1 as a biomarker for clinical prognosis, immune infiltration, and drug therapy in lung squamous cell carcinoma
type: item
type: AcademicArticle
description: Background This study was performed to determine the biological processes in which NKX2-1 is involved and thus its role in the development of lung squamous cell carcinoma (LUSC) toward improving the prognosis and treatment of LUSC. Methods Raw RNA sequencing (RNA-seq) data of LUSC from The Cancer Genome Atlas (TCGA) were used in bioinformatics analysis to characterize NKX2-1 expression levels in tumor and normal tissues. Survival analysis of Kaplan–Meier curve, the time-dependent receiver operating characteristic (ROC) curve, and a nomogram were used to analyze the prognosis value of NKX2-1 for LUSC in terms of overall survival (OS) and progression-free survival (PFS). Then, differentially expressed genes (DEGs) were identified, and Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA) were used to clarify the biological mechanisms potentially involved in the development of LUSC. Moreover, the correlation between the NKX2-1 expression level and tumor mutation burden (TMB), tumor microenvironment (TME), and immune cell infiltration revealed that NKX2-1 participates in the development of LUSC. Finally, we studied the effects of NKX2-1 on drug therapy. To validate the protein and gene expression levels of NKX2-1 in LUSC, we employed immunohistochemistry(IHC) datasets, The Gene Expression Omnibus (GEO) database, and qRT-PCR analysis. Results NKX2-1 expression levels were significantly lower in LUSC than in normal lung tissue. It significantly differed in gender, stage and N classification. The survival analysis revealed that high expression of NKX2-1 had shorter OS and PFS in LUSC. The multivariate Cox regression hazard model showed the NKX2-1 expression as an independent prognostic factor. Then, the nomogram predicted LUSC prognosis. There are 51 upregulated DEGs and 49 downregulated DEGs in the NKX2-1 high-level groups. GO, KEGG and GSEA analysis revealed that DEGs were enriched in cell cycle and DNA replication.Th…
format: application/pdf
format: text/html
creator: Huiyue Lin
creator: Juyong Wang
creator: Qing Shi
creator: Minmin Wu
subject: Bioinformatics
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.17338
publisher: PeerJ Inc.
rights: © 2024 Lin et al.
abstract: Background This study was performed to determine the biological processes in which NKX2-1 is involved and thus its role in the development of lung squamous cell carcinoma (LUSC) toward improving the prognosis and treatment of LUSC. Methods Raw RNA sequencing (RNA-seq) data of LUSC from The Cancer Genome Atlas (TCGA) were used in bioinformatics analysis to characterize NKX2-1 expression levels in tumor and normal tissues. Survival analysis of Kaplan–Meier curve, the time-dependent receiver operating characteristic (ROC) curve, and a nomogram were used to analyze the prognosis value of NKX2-1 for LUSC in terms of overall survival (OS) and progression-free survival (PFS). Then, differentially expressed genes (DEGs) were identified, and Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA) were used to clarify the biological mechanisms potentially involved in the development of LUSC. Moreover, the correlation between the NKX2-1 expression level and tumor mutation burden (TMB), tumor microenvironment (TME), and immune cell infiltration revealed that NKX2-1 participates in the development of LUSC. Finally, we studied the effects of NKX2-1 on drug therapy. To validate the protein and gene expression levels of NKX2-1 in LUSC, we employed immunohistochemistry(IHC) datasets, The Gene Expression Omnibus (GEO) database, and qRT-PCR analysis. Results NKX2-1 expression levels were significantly lower in LUSC than in normal lung tissue. It significantly differed in gender, stage and N classification. The survival analysis revealed that high expression of NKX2-1 had shorter OS and PFS in LUSC. The multivariate Cox regression hazard model showed the NKX2-1 expression as an independent prognostic factor. Then, the nomogram predicted LUSC prognosis. There are 51 upregulated DEGs and 49 downregulated DEGs in the NKX2-1 high-level groups. GO, KEGG and GSEA analysis revealed that DEGs were enriched in cell cycle and DNA replication.Th…
bibliographic citation: Lin et al. (2024) Significance of NKX2-1 as a biomarker for clinical prognosis, immune infiltration, and drug therapy in lung squamous cell carcinoma. PeerJ 12:e17338 https://doi.org/10.7717/peerj.17338
date submitted: 2023-12-30
date accepted: 2024-04-15
issued: 2024-05-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Huiyue
author list: Agent
  family name: Wang
  given name: Juyong
author list: Agent
  family name: Shi
  given name: Qing
author list: Agent
  family name: Wu
  given name: Minmin
doi: 10.7717/peerj.17338
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-01
copyright: © 2024 Lin et al.
attribution name: Lin et al.

The Chronic Time Pressure Inventory: further assessment of factorial structure and validity
type: item
type: AcademicArticle
description: Background Chronic time pressure represents a prevalent concern within modern society, and effective measurement is crucial for research advancement. The Chronic Time Pressure Inventory (CTPI) has thus far demonstrated adequate psychometric properties. However, only two studies have examined the measure and evidence of its validity is limited. Accordingly, the current investigation, via two independent studies, assessed the factorial composition and validity (convergent/discriminant) of the CTPI. Methods Study 1 (N = 398) examined competing factorial models and validity in relation to the Big Five personality traits (Extraversion, Agreeableness, Conscientiousness, Neuroticism, Openness). Study 2 (N = 358) replicated the analysis of factor structure and assessed validity in comparison with five time perspectives (Past Negative, Present Fatalistic, Future, Past Positive, Present Hedonistic). Participants across both studies completed standardized self-report measures capturing the variables. Results Comparison of confirmatory factor analysis (CFA) and exploratory structural equation modelling (ESEM) factor solutions indicated that an ESEM bifactor model provided the strongest data-model fit. This included a general chronic time pressure component alongside specific subfactors of Feeling Harried and Cognitive Awareness of Time Shortage. All scale items reflected the general factor; however, some items loaded weakly on the intended specific factor. The CTPI is thus a robust indicator of chronic time pressure but needs refinement as a measure of the specific factors. Convergent/discriminant validity analyses inferred that the CTPI captured chronic time pressure as a related, but distinct, construct to perceived stress, and evidenced a relationship with theoretically associated constructs (Big Five personality traits and time perspective). Overall, the CTPI is a sound measure of chronic time pressure and has the potential to further cohesive research efforts on the contri…
format: application/pdf
format: text/html
creator: Andrew Denovan
creator: Neil Dagnall
creator: Ken Drinkwater
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.17373
publisher: PeerJ Inc.
rights: © 2024 Denovan et al.
abstract: Background Chronic time pressure represents a prevalent concern within modern society, and effective measurement is crucial for research advancement. The Chronic Time Pressure Inventory (CTPI) has thus far demonstrated adequate psychometric properties. However, only two studies have examined the measure and evidence of its validity is limited. Accordingly, the current investigation, via two independent studies, assessed the factorial composition and validity (convergent/discriminant) of the CTPI. Methods Study 1 (N = 398) examined competing factorial models and validity in relation to the Big Five personality traits (Extraversion, Agreeableness, Conscientiousness, Neuroticism, Openness). Study 2 (N = 358) replicated the analysis of factor structure and assessed validity in comparison with five time perspectives (Past Negative, Present Fatalistic, Future, Past Positive, Present Hedonistic). Participants across both studies completed standardized self-report measures capturing the variables. Results Comparison of confirmatory factor analysis (CFA) and exploratory structural equation modelling (ESEM) factor solutions indicated that an ESEM bifactor model provided the strongest data-model fit. This included a general chronic time pressure component alongside specific subfactors of Feeling Harried and Cognitive Awareness of Time Shortage. All scale items reflected the general factor; however, some items loaded weakly on the intended specific factor. The CTPI is thus a robust indicator of chronic time pressure but needs refinement as a measure of the specific factors. Convergent/discriminant validity analyses inferred that the CTPI captured chronic time pressure as a related, but distinct, construct to perceived stress, and evidenced a relationship with theoretically associated constructs (Big Five personality traits and time perspective). Overall, the CTPI is a sound measure of chronic time pressure and has the potential to further cohesive research efforts on the contri…
bibliographic citation: Denovan et al. (2024) The Chronic Time Pressure Inventory: further assessment of factorial structure and validity. PeerJ 12:e17373 https://doi.org/10.7717/peerj.17373
date submitted: 2023-05-17
date accepted: 2024-04-18
issued: 2024-05-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Denovan
  given name: Andrew
author list: Agent
  family name: Dagnall
  given name: Neil
author list: Agent
  family name: Drinkwater
  given name: Ken
doi: 10.7717/peerj.17373
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-01
copyright: © 2024 Denovan et al.
attribution name: Denovan et al.

The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny—a case study on dwarf chameleons
type: item
type: AcademicArticle
description: Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.
format: application/pdf
format: text/html
creator: Devon C. Main
creator: Jody M. Taft
creator: Anthony J. Geneva
creator: Bettine Jansenvan Vuuren
creator: Krystal A. Tolley
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.17076
publisher: PeerJ Inc.
rights: © 2024 Main et al.
abstract: Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.
bibliographic citation: Main et al. (2024) The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny—a case study on dwarf chameleons. PeerJ 12:e17076 https://doi.org/10.7717/peerj.17076
date submitted: 2023-11-09
date accepted: 2024-02-19
issued: 2024-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Main
  given name: Devon C.
author list: Agent
  family name: Taft
  given name: Jody M.
author list: Agent
  family name: Geneva
  given name: Anthony J.
author list: Agent
  family name: Jansenvan Vuuren
  given name: Bettine
author list: Agent
  family name: Tolley
  given name: Krystal A.
doi: 10.7717/peerj.17076
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-30
copyright: ©2024 Main et al.
attribution name: Main et al.

Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities
type: item
type: AcademicArticle
description: Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and cons…
format: application/pdf
format: text/html
creator: Alice J. Clark
creator: Sophie R. Atkinson
creator: Valentina Scarponi
creator: Tim Cane
creator: Nathan R. Geraldi
creator: Ian W. Hendy
creator: J. Reuben Shipway
creator: Mika Peck
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.17091
publisher: PeerJ Inc.
rights: © 2024 Clark et al.
abstract: Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and cons…
bibliographic citation: Clark et al. (2024) Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities. PeerJ 12:e17091 https://doi.org/10.7717/peerj.17091
date submitted: 2023-09-04
date accepted: 2024-02-20
issued: 2024-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clark
  given name: Alice J.
author list: Agent
  family name: Atkinson
  given name: Sophie R.
author list: Agent
  family name: Scarponi
  given name: Valentina
author list: Agent
  family name: Cane
  given name: Tim
author list: Agent
  family name: Geraldi
  given name: Nathan R.
author list: Agent
  family name: Hendy
  given name: Ian W.
author list: Agent
  family name: Shipway
  given name: J. Reuben
author list: Agent
  family name: Peck
  given name: Mika
doi: 10.7717/peerj.17091
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-30
copyright: ©2024 Clark et al.
attribution name: Clark et al.

Pollen thermotolerance of a widespread plant, Lotus corniculatus, in response to climate warming: possible local adaptation of populations from different elevations
type: item
type: AcademicArticle
description: One of the most vulnerable phases in the plant life cycle is sexual reproduction, which depends on effective pollen transfer, but also on the thermotolerance of pollen grains. Pollen thermotolerance is temperature-dependent and may be reduced by increasing temperature associated with global warming. A growing body of research has focused on the effect of increased temperature on pollen thermotolerance in crops to understand the possible impact of temperature extremes on yield. Yet, little is known about the effects of temperature on pollen thermotolerance of wild plant species. To fill this gap, we selected Lotus corniculatus s.l. (Fabaceae), a species common to many European habitats and conducted laboratory experiments to test its pollen thermotolerance in response to artificial increase in temperature. To test for possible local adaptation of pollen thermal tolerance, we compared data from six lowland (389–451 m a.s.l.) and six highland (841–1,030 m a.s.l.) populations. We observed pollen germination in vitro at 15 °C, 25 °C, 30 °C, and 40 °C. While lowland plants maintained a stable germination percentage across a broad temperature range (15–30 °C) and exhibited reduced germination only at extremely high temperatures (40 °C), highland plants experienced reduced germination even at 30 °C–temperatures commonly exceeded in lowlands during warm summers. This suggests that lowland populations of L. corniculatus may be locally adapted to higher temperature for pollen germination. On the other hand, pollen tube length decreased with increasing temperature in a similar way in lowland and highland plants. The overall average pollen germination percentage significantly differed between lowland and highland populations, with highland populations displaying higher germination percentage. On the other hand, the average pollen tube length was slightly smaller in highland populations. In conclusion, we found that pollen thermotolerance of L. corniculatus is reduced at high tem…
format: application/pdf
format: text/html
creator: Karolína Jackwerth
creator: Paolo Biella
creator: Jan Klečka
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.17148
publisher: PeerJ Inc.
rights: © 2024 Jackwerth et al.
abstract: One of the most vulnerable phases in the plant life cycle is sexual reproduction, which depends on effective pollen transfer, but also on the thermotolerance of pollen grains. Pollen thermotolerance is temperature-dependent and may be reduced by increasing temperature associated with global warming. A growing body of research has focused on the effect of increased temperature on pollen thermotolerance in crops to understand the possible impact of temperature extremes on yield. Yet, little is known about the effects of temperature on pollen thermotolerance of wild plant species. To fill this gap, we selected Lotus corniculatus s.l. (Fabaceae), a species common to many European habitats and conducted laboratory experiments to test its pollen thermotolerance in response to artificial increase in temperature. To test for possible local adaptation of pollen thermal tolerance, we compared data from six lowland (389–451 m a.s.l.) and six highland (841–1,030 m a.s.l.) populations. We observed pollen germination in vitro at 15 °C, 25 °C, 30 °C, and 40 °C. While lowland plants maintained a stable germination percentage across a broad temperature range (15–30 °C) and exhibited reduced germination only at extremely high temperatures (40 °C), highland plants experienced reduced germination even at 30 °C–temperatures commonly exceeded in lowlands during warm summers. This suggests that lowland populations of L. corniculatus may be locally adapted to higher temperature for pollen germination. On the other hand, pollen tube length decreased with increasing temperature in a similar way in lowland and highland plants. The overall average pollen germination percentage significantly differed between lowland and highland populations, with highland populations displaying higher germination percentage. On the other hand, the average pollen tube length was slightly smaller in highland populations. In conclusion, we found that pollen thermotolerance of L. corniculatus is reduced at high tem…
bibliographic citation: Jackwerth et al. (2024) Pollen thermotolerance of a widespread plant, Lotus corniculatus, in response to climate warming: possible local adaptation of populations from different elevations. PeerJ 12:e17148 https://doi.org/10.7717/peerj.17148
date submitted: 2023-07-04
date accepted: 2024-03-01
issued: 2024-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jackwerth
  given name: Karolína
author list: Agent
  family name: Biella
  given name: Paolo
author list: Agent
  family name: Klečka
  given name: Jan
doi: 10.7717/peerj.17148
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-30
copyright: © 2024 Jackwerth et al.
attribution name: Jackwerth et al.

Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease
type: item
type: AcademicArticle
description: Pulmonary hypertension (PH), a common complication in dogs affected by degenerative mitral valve disease (DMVD), is a progressive disorder characterized by increased pulmonary arterial pressure (PAP) and pulmonary vascular remodeling. Phosphorylation of proteins, impacting vascular function and cell proliferation, might play a role in the development and progression of PH. Unlike gene or protein studies, phosphoproteomic focuses on active proteins that function as end-target proteins within signaling cascades. Studying phosphorylated proteins can reveal active contributors to PH development. Early diagnosis of PH is crucial for effective management and improved clinical outcomes. This study aimed to identify potential serum biomarkers for diagnosing PH in dogs affected with DMVD using a phosphoproteomic approach. Serum samples were collected from healthy control dogs (n = 28), dogs with DMVD (n = 24), and dogs with DMVD and PH (n = 29). Phosphoproteins were enriched from the serum samples and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Data analysis was performed to identify uniquely expressed phosphoproteins in each group and differentially expressed phosphoproteins among groups. Phosphoproteomic analysis revealed nine uniquely expressed phosphoproteins in the serum of dogs in the DMVD+PH group and 15 differentially upregulated phosphoproteins in the DMVD+PH group compared to the DMVD group. The phosphoproteins previously implicated in PH and associated with pulmonary arterial remodeling, including small nuclear ribonucleoprotein G (SNRPG), alpha-2-macroglobulin (A2M), zinc finger and BTB domain containing 42 (ZBTB42), hemopexin (HPX), serotransferrin (TRF) and complement C3 (C3), were focused on. Their unique expression and differential upregulation in the serum of DMVD dogs with PH suggest their potential as biomarkers for PH diagnosis. In conclusion, this phosphoproteomic study identified uniquely expressed and differentially upregu…
format: application/pdf
format: text/html
creator: Siriwan Sakarin
creator: Anudep Rungsipipat
creator: Sittiruk Roytrakul
creator: Janthima Jaresitthikunchai
creator: Narumon Phaonakrop
creator: Sawanya Charoenlappanit
creator: Siriwan Thaisakun
creator: Sirilak Surachetpong
subject: Biochemistry
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.17186
publisher: PeerJ Inc.
rights: © 2024 Sakarin et al.
abstract: Pulmonary hypertension (PH), a common complication in dogs affected by degenerative mitral valve disease (DMVD), is a progressive disorder characterized by increased pulmonary arterial pressure (PAP) and pulmonary vascular remodeling. Phosphorylation of proteins, impacting vascular function and cell proliferation, might play a role in the development and progression of PH. Unlike gene or protein studies, phosphoproteomic focuses on active proteins that function as end-target proteins within signaling cascades. Studying phosphorylated proteins can reveal active contributors to PH development. Early diagnosis of PH is crucial for effective management and improved clinical outcomes. This study aimed to identify potential serum biomarkers for diagnosing PH in dogs affected with DMVD using a phosphoproteomic approach. Serum samples were collected from healthy control dogs (n = 28), dogs with DMVD (n = 24), and dogs with DMVD and PH (n = 29). Phosphoproteins were enriched from the serum samples and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Data analysis was performed to identify uniquely expressed phosphoproteins in each group and differentially expressed phosphoproteins among groups. Phosphoproteomic analysis revealed nine uniquely expressed phosphoproteins in the serum of dogs in the DMVD+PH group and 15 differentially upregulated phosphoproteins in the DMVD+PH group compared to the DMVD group. The phosphoproteins previously implicated in PH and associated with pulmonary arterial remodeling, including small nuclear ribonucleoprotein G (SNRPG), alpha-2-macroglobulin (A2M), zinc finger and BTB domain containing 42 (ZBTB42), hemopexin (HPX), serotransferrin (TRF) and complement C3 (C3), were focused on. Their unique expression and differential upregulation in the serum of DMVD dogs with PH suggest their potential as biomarkers for PH diagnosis. In conclusion, this phosphoproteomic study identified uniquely expressed and differentially upregu…
bibliographic citation: Sakarin et al. (2024) Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease. PeerJ 12:e17186 https://doi.org/10.7717/peerj.17186
date submitted: 2023-11-13
date accepted: 2024-03-11
issued: 2024-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sakarin
  given name: Siriwan
author list: Agent
  family name: Rungsipipat
  given name: Anudep
author list: Agent
  family name: Roytrakul
  given name: Sittiruk
author list: Agent
  family name: Jaresitthikunchai
  given name: Janthima
author list: Agent
  family name: Phaonakrop
  given name: Narumon
author list: Agent
  family name: Charoenlappanit
  given name: Sawanya
author list: Agent
  family name: Thaisakun
  given name: Siriwan
author list: Agent
  family name: Surachetpong
  given name: Sirilak
doi: 10.7717/peerj.17186
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-30
copyright: © 2024 Sakarin et al.
attribution name: Sakarin et al.

Interactions between chaperone and energy storage networks during the evolution of Legionella pneumophila under heat shock
type: item
type: AcademicArticle
description: Waterborne transmission of the bacterium Legionella pneumophila has emerged as a major cause of severe nosocomial infections of major public health impact. The major route of transmission involves the uptake of aerosolized bacteria, often from the contaminated hot water systems of large buildings. Public health regulations aimed at controlling the mesophilic pathogen are generally concerned with acute pasteurization and maintaining high temperatures at the heating systems and throughout the plumbing of hot water systems, but L. pneumophila is often able to survive these treatments due to both bacterium-intrinsic and environmental factors. Previous work has established an experimental evolution system to model the observations of increased heat resistance in repeatedly but unsuccessfully pasteurized L. pneumophila populations. Here, we show rapid fixation of novel alleles in lineages selected for resistance to heat shock and shifts in mutational profile related to increases in the temperature of selection. Gene-level and nucleotide-level parallelisms between independently-evolving lineages show the centrality of the DnaJ/DnaK chaperone system in the heat resistance of L. pneumophila. Inference of epistatic interactions through reverse genetics shows an unexpected interaction between DnaJ/DnaK and the polyhydroxybutyrate-accumulation energy storage mechanism used by the species to survive long-term starvation in low-nutrient environments.
format: application/pdf
format: text/html
creator: Jeffrey Liang
creator: Sebastien P. Faucher
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.17197
publisher: PeerJ Inc.
rights: © 2024 Liang and Faucher
abstract: Waterborne transmission of the bacterium Legionella pneumophila has emerged as a major cause of severe nosocomial infections of major public health impact. The major route of transmission involves the uptake of aerosolized bacteria, often from the contaminated hot water systems of large buildings. Public health regulations aimed at controlling the mesophilic pathogen are generally concerned with acute pasteurization and maintaining high temperatures at the heating systems and throughout the plumbing of hot water systems, but L. pneumophila is often able to survive these treatments due to both bacterium-intrinsic and environmental factors. Previous work has established an experimental evolution system to model the observations of increased heat resistance in repeatedly but unsuccessfully pasteurized L. pneumophila populations. Here, we show rapid fixation of novel alleles in lineages selected for resistance to heat shock and shifts in mutational profile related to increases in the temperature of selection. Gene-level and nucleotide-level parallelisms between independently-evolving lineages show the centrality of the DnaJ/DnaK chaperone system in the heat resistance of L. pneumophila. Inference of epistatic interactions through reverse genetics shows an unexpected interaction between DnaJ/DnaK and the polyhydroxybutyrate-accumulation energy storage mechanism used by the species to survive long-term starvation in low-nutrient environments.
bibliographic citation: Liang et al. (2024) Interactions between chaperone and energy storage networks during the evolution of Legionella pneumophila under heat shock. PeerJ 12:e17197 https://doi.org/10.7717/peerj.17197
date submitted: 2023-11-27
date accepted: 2024-03-14
issued: 2024-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Jeffrey
author list: Agent
  family name: Faucher
  given name: Sebastien P.
doi: 10.7717/peerj.17197
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-30
copyright: © 2024 Liang and Faucher
attribution name: Liang and Faucher

The low survival rate of European hare leverets in arable farmland: evidence from the predation experiment
type: item
type: AcademicArticle
description: The low survival rate of leverets may significantly contribute to steep population declines and slow recovery of European hares (Lepus europaeus). However, the leveret survival rate in farmlands with different landscape structures is poorly understood, and the existing evidence comes mainly from Western Europe. In this study, we explored the survival of leveret hare dummies along linear semi-natural habitats in homogeneous Central European arable farmland during the main part of the European hare reproduction period (March–April) in 2019 and 2020. The survival rate of hare leverets during the 14-day period was only 22.2%, and all predation events were recorded during the first six days of the experiment. Mammalian predators were responsible for 53.1% of predation events, avian predators for 40.8%, and agricultural operations for 6.1%. The red fox (Vulpes vulpes) was the dominant predator in our study area and was the primary cause of leveret dummy mortality (32.7%), but it also had the highest use-intensity and visit frequency of all of the study plots. Predation by avian predators was associated with patches of lower vegetation height and cover (such as plowed fields) and during daylight hours, whereas the opposite was true for mammalian predators. We propose that improving the habitat quality of arable landscapes by increasing the proportion and quality of extensively used non-farmed habitats (e.g., set-asides, wildflower areas, extensive meadows, fallow land, and semi-natural habitats on arable land) providing cover and shelter for leverets could be an effective management measure for reducing predation risk on leverets.
format: application/pdf
format: text/html
creator: Jan Cukor
creator: Jan Riegert
creator: Aleksandra Krivopalova
creator: Zdeněk Vacek
creator: Martin Šálek
subject: Agricultural Science
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.17235
publisher: PeerJ Inc.
rights: © 2024 Cukor et al.
abstract: The low survival rate of leverets may significantly contribute to steep population declines and slow recovery of European hares (Lepus europaeus). However, the leveret survival rate in farmlands with different landscape structures is poorly understood, and the existing evidence comes mainly from Western Europe. In this study, we explored the survival of leveret hare dummies along linear semi-natural habitats in homogeneous Central European arable farmland during the main part of the European hare reproduction period (March–April) in 2019 and 2020. The survival rate of hare leverets during the 14-day period was only 22.2%, and all predation events were recorded during the first six days of the experiment. Mammalian predators were responsible for 53.1% of predation events, avian predators for 40.8%, and agricultural operations for 6.1%. The red fox (Vulpes vulpes) was the dominant predator in our study area and was the primary cause of leveret dummy mortality (32.7%), but it also had the highest use-intensity and visit frequency of all of the study plots. Predation by avian predators was associated with patches of lower vegetation height and cover (such as plowed fields) and during daylight hours, whereas the opposite was true for mammalian predators. We propose that improving the habitat quality of arable landscapes by increasing the proportion and quality of extensively used non-farmed habitats (e.g., set-asides, wildflower areas, extensive meadows, fallow land, and semi-natural habitats on arable land) providing cover and shelter for leverets could be an effective management measure for reducing predation risk on leverets.
bibliographic citation: Cukor et al. (2024) The low survival rate of European hare leverets in arable farmland: evidence from the predation experiment. PeerJ 12:e17235 https://doi.org/10.7717/peerj.17235
date submitted: 2023-09-25
date accepted: 2024-03-22
issued: 2024-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cukor
  given name: Jan
author list: Agent
  family name: Riegert
  given name: Jan
author list: Agent
  family name: Krivopalova
  given name: Aleksandra
author list: Agent
  family name: Vacek
  given name: Zdeněk
author list: Agent
  family name: Šálek
  given name: Martin
doi: 10.7717/peerj.17235
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-30
copyright: ©2024 Cukor et al.
attribution name: Cukor et al.

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