PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A content analysis of the reliability and quality of Youtube videos as a source of information on health-related post-COVID pain
items: Do pheromone traps help to reduce new attacks of Ips typographus at the local scale after a sanitary cut?
items: Beyond the fish-Daphnia paradigm: testing the potential for pygmy backswimmers (Neoplea striola) to cause trophic cascades in subtropical ponds
items: A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements
items: Nitrate enrichment does not affect enteropathogenic Escherichia coli in aquatic microcosms but may affect other strains present in aquatic habitats
items: Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
items: Presence of leptin and its receptor in the ram reproductive system and in vitro effect of leptin on sperm quality
items: Avoidance of copper by fathead minnows (Pimephales promelas) requires an intact olfactory system
items: What’s the effectiveness of stocking actions in small creeks? The role of water discharge behind hatchery trout downstream movement
items: Improved response inhibition induced by attentional capture is associated with physical activity

A content analysis of the reliability and quality of Youtube videos as a source of information on health-related post-COVID pain
type: item
type: AcademicArticle
description: Background The use of the internet as a source of information has increased during the pandemic, and YouTube has become an increasingly important source of information on Coronavirus disease 2019 (COVID-19). In the long COVID picture, which occurs when symptoms related to COVID-19 last longer than 1 month, pain involving the musculoskeletal system affects the quality of life quite negatively. The aim of this study was to investigate the informational value and quality of YouTube videos related to post-COVID pain. Methods In this study, 180 videos were listed using the search terms “pain after COVID,” “post-COVID pain,” and “long COVID and pain”(15 April 2022). Videos were classified according to video parameters and content analysis. Quality, reliability and accuracy of the videos were determined with the Global Quality Score (GQS), the Journal of American Medical Association (JAMA) Benchmark Criteria and the Modified DISCERN Questionnaire, respectively. Results One hundred videos that met the inclusion criteria were included in the assessment. Of these videos, 74 were found to be of low quality, 14 of moderate quality, and 12 of high quality; 21% contained insufficient data, 73% contained partially sufficient data, and 6% contained completely sufficient data. Videos uploaded by academic sources (66.7%) and physicians (12.5%) made up the majority of the high-quality group. A statistically significant correlation was found between the source of upload and number of views (p = 0.014), likes (p = 0.030), comments (p = 0.007), and video duration (p = 0.004). Video duration was found to have a poor positive correlation with GQS (r = 0.500), JAMA (r = 0.528), and modified DISCERN (r = 0.470) scores (p < 0.001). Conclusion The findings of this study revealed that the majority of YouTube videos on post-COVID pain had low quality and partially sufficient data. High-quality videos were found to have longer durations and were uploaded by academic sources and physicians. The fa…
format: application/pdf
format: text/html
creator: Erkan Ozduran
creator: Sibel Büyükçoban
subject: Anesthesiology and Pain Management
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.14089
publisher: PeerJ Inc.
rights: © 2022 Ozduran and Büyükçoban
abstract: Background The use of the internet as a source of information has increased during the pandemic, and YouTube has become an increasingly important source of information on Coronavirus disease 2019 (COVID-19). In the long COVID picture, which occurs when symptoms related to COVID-19 last longer than 1 month, pain involving the musculoskeletal system affects the quality of life quite negatively. The aim of this study was to investigate the informational value and quality of YouTube videos related to post-COVID pain. Methods In this study, 180 videos were listed using the search terms “pain after COVID,” “post-COVID pain,” and “long COVID and pain”(15 April 2022). Videos were classified according to video parameters and content analysis. Quality, reliability and accuracy of the videos were determined with the Global Quality Score (GQS), the Journal of American Medical Association (JAMA) Benchmark Criteria and the Modified DISCERN Questionnaire, respectively. Results One hundred videos that met the inclusion criteria were included in the assessment. Of these videos, 74 were found to be of low quality, 14 of moderate quality, and 12 of high quality; 21% contained insufficient data, 73% contained partially sufficient data, and 6% contained completely sufficient data. Videos uploaded by academic sources (66.7%) and physicians (12.5%) made up the majority of the high-quality group. A statistically significant correlation was found between the source of upload and number of views (p = 0.014), likes (p = 0.030), comments (p = 0.007), and video duration (p = 0.004). Video duration was found to have a poor positive correlation with GQS (r = 0.500), JAMA (r = 0.528), and modified DISCERN (r = 0.470) scores (p < 0.001). Conclusion The findings of this study revealed that the majority of YouTube videos on post-COVID pain had low quality and partially sufficient data. High-quality videos were found to have longer durations and were uploaded by academic sources and physicians. The fa…
bibliographic citation: Ozduran et al. (2022) A content analysis of the reliability and quality of Youtube videos as a source of information on health-related post-COVID pain. PeerJ 10:e14089 https://doi.org/10.7717/peerj.14089
date submitted: 2022-05-11
date accepted: 2022-08-29
issued: 2022-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ozduran
  given name: Erkan
author list: Agent
  family name: Büyükçoban
  given name: Sibel
doi: 10.7717/peerj.14089
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-28
copyright: © 2022 Ozduran and Büyükçoban
attribution name: Ozduran and Büyükçoban

Do pheromone traps help to reduce new attacks of Ips typographus at the local scale after a sanitary cut?
type: item
type: AcademicArticle
description: The spruce bark beetle, Ips typographus, is causing severe economic losses during epidemic phases triggered by droughts and/or windstorms. Sanitation felling and salvage logging are usually the most recommended strategies to limit the damages. However, any additional control method to limit the economic impact of an outbreak would be welcome. In this respect, the efficiency of pheromone trapping is still controversial or poorly documented. In this 2-year study (2020–2021), at the peak of a severe outbreak in Belgium, we quantified the wood volume and presence/absence of new attacks at 126 sites attacked during the previous year and within 100 m from the initial attack. Each site was randomly allocated to one of three treatments: (1) three crosstraps baited with pheromones, (2) one tree-trap baited with pheromones and treated with an insecticide and (3) control sites with no trapping device. The attacked trees of the previous year were all cut and removed before the start of the experiment and newly attacked trees were removed as they were detected. The trapping devices were only active during spring to target overwintering bark beetles that might have escaped the sanitation cuts and to limit the risk of attracting dispersing beetles from outside the patch during the summer. We found a strong decrease of the attacks relative to the previous year in all treatments, including the controls (more than 50% of the control sites had no new attacks). There was no relationship between the new attacks and the attacks of the previous year. In both years, new attacks were more frequent (presence/absence) in sites with crosstraps (95% Confidence Interval [56–84%] of the sites with new attacks) than in sites with a tree-trap (26–57% - p = 0.02) and to a lesser extent than in control sites (32–63%, p = 0.08). In 2020, the attacked volumes were slightly higher in sites with crosstraps (95% Confidence Interval [3.4–14.2 m³]) than in control sites (0.2–3.5 m³, p = 0.04) and no signifi…
format: application/pdf
format: text/html
creator: Alexandre Kuhn
creator: Louis Hautier
creator: Gilles San Martin
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Zoology
subject: Forestry
description: doi:10.7717/peerj.14093
publisher: PeerJ Inc.
rights: © 2022 Kuhn et al.
abstract: The spruce bark beetle, Ips typographus, is causing severe economic losses during epidemic phases triggered by droughts and/or windstorms. Sanitation felling and salvage logging are usually the most recommended strategies to limit the damages. However, any additional control method to limit the economic impact of an outbreak would be welcome. In this respect, the efficiency of pheromone trapping is still controversial or poorly documented. In this 2-year study (2020–2021), at the peak of a severe outbreak in Belgium, we quantified the wood volume and presence/absence of new attacks at 126 sites attacked during the previous year and within 100 m from the initial attack. Each site was randomly allocated to one of three treatments: (1) three crosstraps baited with pheromones, (2) one tree-trap baited with pheromones and treated with an insecticide and (3) control sites with no trapping device. The attacked trees of the previous year were all cut and removed before the start of the experiment and newly attacked trees were removed as they were detected. The trapping devices were only active during spring to target overwintering bark beetles that might have escaped the sanitation cuts and to limit the risk of attracting dispersing beetles from outside the patch during the summer. We found a strong decrease of the attacks relative to the previous year in all treatments, including the controls (more than 50% of the control sites had no new attacks). There was no relationship between the new attacks and the attacks of the previous year. In both years, new attacks were more frequent (presence/absence) in sites with crosstraps (95% Confidence Interval [56–84%] of the sites with new attacks) than in sites with a tree-trap (26–57% - p = 0.02) and to a lesser extent than in control sites (32–63%, p = 0.08). In 2020, the attacked volumes were slightly higher in sites with crosstraps (95% Confidence Interval [3.4–14.2 m³]) than in control sites (0.2–3.5 m³, p = 0.04) and no signifi…
bibliographic citation: Kuhn et al. (2022) Do pheromone traps help to reduce new attacks of Ips typographus at the local scale after a sanitary cut?. PeerJ 10:e14093 https://doi.org/10.7717/peerj.14093
date submitted: 2022-06-04
date accepted: 2022-08-30
issued: 2022-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuhn
  given name: Alexandre
author list: Agent
  family name: Hautier
  given name: Louis
author list: Agent
  family name: San Martin
  given name: Gilles
doi: 10.7717/peerj.14093
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-28
copyright: © 2022 Kuhn et al.
attribution name: Kuhn et al.

Beyond the fish-Daphnia paradigm: testing the potential for pygmy backswimmers (Neoplea striola) to cause trophic cascades in subtropical ponds
type: item
type: AcademicArticle
description: Trophic cascades, or indirect effects of predators on non-adjacent lower trophic levels, are a classic phenomenon in ecology, and are thought to be strongest in aquatic ecosystems. Most research on freshwater trophic cascades focused on temperate lakes, where fish are present and where Daphnia frequently dominate the zooplankton community. These studies identified that Daphnia often play a key role in facilitating trophic cascades by linking fish to algae with strong food web interactions. However, Daphnia are rare or absent in most tropical and subtropical lowland freshwaters, and fish are absent from small and temporary water bodies, where invertebrates fill the role of top predator. While invertebrate predators are ubiquitous in freshwater systems, most have received little attention in food web research. Therefore, we aimed to test whether trophic cascades are possible in small warmwater ponds where Daphnia are absent and small invertebrates are the top predators. We collected naturally occurring plankton communities from small fishless water bodies in central Texas and propagated them in replicate pond mesocosms. We removed zooplankton from some mesocosms, left the plankton community intact in others, and added one of two densities of the predaceous insect Neoplea striola to others. Following an incubation period, we then compared biomasses of plankton groups to assess food web effects between the trophic levels, including whether Neoplea caused a trophic cascade by reducing zooplankton. The zooplankton community became dominated by copepods which prefer large phytoplankton and exhibit a fast escape response. Perhaps due to these qualities of the copepods and perhaps due to other reasons such as high turbidity impairing predation, no evidence for food web effects were found other than somewhat weak evidence for zooplankton reducing large phytoplankton. More research is needed to understand the behavior and ecology of Neoplea, but trophic cascades may generally …
format: application/pdf
format: text/html
creator: Chase J. Rakowski
creator: Mathew A. Leibold
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14094
publisher: PeerJ Inc.
rights: © 2022 Rakowski and Leibold
abstract: Trophic cascades, or indirect effects of predators on non-adjacent lower trophic levels, are a classic phenomenon in ecology, and are thought to be strongest in aquatic ecosystems. Most research on freshwater trophic cascades focused on temperate lakes, where fish are present and where Daphnia frequently dominate the zooplankton community. These studies identified that Daphnia often play a key role in facilitating trophic cascades by linking fish to algae with strong food web interactions. However, Daphnia are rare or absent in most tropical and subtropical lowland freshwaters, and fish are absent from small and temporary water bodies, where invertebrates fill the role of top predator. While invertebrate predators are ubiquitous in freshwater systems, most have received little attention in food web research. Therefore, we aimed to test whether trophic cascades are possible in small warmwater ponds where Daphnia are absent and small invertebrates are the top predators. We collected naturally occurring plankton communities from small fishless water bodies in central Texas and propagated them in replicate pond mesocosms. We removed zooplankton from some mesocosms, left the plankton community intact in others, and added one of two densities of the predaceous insect Neoplea striola to others. Following an incubation period, we then compared biomasses of plankton groups to assess food web effects between the trophic levels, including whether Neoplea caused a trophic cascade by reducing zooplankton. The zooplankton community became dominated by copepods which prefer large phytoplankton and exhibit a fast escape response. Perhaps due to these qualities of the copepods and perhaps due to other reasons such as high turbidity impairing predation, no evidence for food web effects were found other than somewhat weak evidence for zooplankton reducing large phytoplankton. More research is needed to understand the behavior and ecology of Neoplea, but trophic cascades may generally …
bibliographic citation: Rakowski et al. (2022) Beyond the fish-Daphnia paradigm: testing the potential for pygmy backswimmers (Neoplea striola) to cause trophic cascades in subtropical ponds. PeerJ 10:e14094 https://doi.org/10.7717/peerj.14094
date submitted: 2021-06-30
date accepted: 2022-08-30
issued: 2022-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rakowski
  given name: Chase J.
author list: Agent
  family name: Leibold
  given name: Mathew A.
doi: 10.7717/peerj.14094
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-28
copyright: ©2022 Rakowski and Leibold
attribution name: Rakowski and Leibold

A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements
type: item
type: AcademicArticle
description: Background Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids. Methods To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters. Results A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters. Conclusions We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies.
format: application/pdf
format: text/html
creator: Shaojing Wang
creator: Guoqiang Li
creator: Zitong Liao
creator: Tongtong Liu
creator: Ting Ma
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Data Science
description: doi:10.7717/peerj.14147
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids. Methods To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters. Results A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters. Conclusions We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies.
bibliographic citation: Wang et al. (2022) A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements. PeerJ 10:e14147 https://doi.org/10.7717/peerj.14147
date submitted: 2022-07-19
date accepted: 2022-09-07
issued: 2022-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Shaojing
author list: Agent
  family name: Li
  given name: Guoqiang
author list: Agent
  family name: Liao
  given name: Zitong
author list: Agent
  family name: Liu
  given name: Tongtong
author list: Agent
  family name: Ma
  given name: Ting
doi: 10.7717/peerj.14147
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-28
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Nitrate enrichment does not affect enteropathogenic Escherichia coli in aquatic microcosms but may affect other strains present in aquatic habitats
type: item
type: AcademicArticle
description: Eutrophication of the planet’s aquatic systems is increasing at an unprecedented rate. In freshwater systems, nitrate—one of the nutrients responsible for eutrophication—is linked to biodiversity losses and ecosystem degradation. One of the main sources of freshwater nitrate pollution in New Zealand is agriculture. New Zealand’s pastoral farming system relies heavily on the application of chemical fertilisers. These fertilisers in combination with animal urine, also high in nitrogen, result in high rates of nitrogen leaching into adjacent aquatic systems. In addition to nitrogen, livestock waste commonly carries human and animal enteropathogenic bacteria, many of which can survive in freshwater environments. Two strains of enteropathogenic bacteria found in New Zealand cattle, are K99 and Shiga-toxin producing Escherichia coli (STEC). To better understand the effects of ambient nitrate concentrations in the water column on environmental enteropathogenic bacteria survival, a microcosm experiment with three nitrate-nitrogen concentrations (0, 1, and 3 mg NO3-N /L), two enteropathogenic bacterial strains (STEC O26—human, and K99—animal), and two water types (sterile and containing natural microbiota) was run. Both STEC O26 and K99 reached 500 CFU/10 ml in both water types at all three nitrate concentrations within 24 hours and remained at those levels for the full 91 days of the experiment. Although enteropathogenic strains showed no response to water column nitrate concentrations, the survival of background Escherichia coli, imported as part of the in-stream microbiota did, surviving longer in 1 and 3 mg NO3-N/Lconcentrations (P < 0.001). While further work is needed to fully understand how nitrate enrichment and in-stream microbiota may affect the viability of human and animal pathogens in freshwater systems, it is clear that these two New Zealand strains of STEC O26 and K99 can persist in river water for extended periods alongside some natural microbiota.
format: application/pdf
format: text/html
creator: Meredith T. Davis
creator: Adam D. Canning
creator: Anne C. Midwinter
creator: Russell G. Death
subject: Biochemistry
subject: Ecology
subject: Microbiology
subject: Freshwater Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.13914
publisher: PeerJ Inc.
rights: © 2022 Davis et al.
abstract: Eutrophication of the planet’s aquatic systems is increasing at an unprecedented rate. In freshwater systems, nitrate—one of the nutrients responsible for eutrophication—is linked to biodiversity losses and ecosystem degradation. One of the main sources of freshwater nitrate pollution in New Zealand is agriculture. New Zealand’s pastoral farming system relies heavily on the application of chemical fertilisers. These fertilisers in combination with animal urine, also high in nitrogen, result in high rates of nitrogen leaching into adjacent aquatic systems. In addition to nitrogen, livestock waste commonly carries human and animal enteropathogenic bacteria, many of which can survive in freshwater environments. Two strains of enteropathogenic bacteria found in New Zealand cattle, are K99 and Shiga-toxin producing Escherichia coli (STEC). To better understand the effects of ambient nitrate concentrations in the water column on environmental enteropathogenic bacteria survival, a microcosm experiment with three nitrate-nitrogen concentrations (0, 1, and 3 mg NO3-N /L), two enteropathogenic bacterial strains (STEC O26—human, and K99—animal), and two water types (sterile and containing natural microbiota) was run. Both STEC O26 and K99 reached 500 CFU/10 ml in both water types at all three nitrate concentrations within 24 hours and remained at those levels for the full 91 days of the experiment. Although enteropathogenic strains showed no response to water column nitrate concentrations, the survival of background Escherichia coli, imported as part of the in-stream microbiota did, surviving longer in 1 and 3 mg NO3-N/Lconcentrations (P < 0.001). While further work is needed to fully understand how nitrate enrichment and in-stream microbiota may affect the viability of human and animal pathogens in freshwater systems, it is clear that these two New Zealand strains of STEC O26 and K99 can persist in river water for extended periods alongside some natural microbiota.
bibliographic citation: Davis et al. (2022) Nitrate enrichment does not affect enteropathogenic Escherichia coli in aquatic microcosms but may affect other strains present in aquatic habitats. PeerJ 10:e13914 https://doi.org/10.7717/peerj.13914
date submitted: 2022-05-16
date accepted: 2022-07-27
issued: 2022-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davis
  given name: Meredith T.
author list: Agent
  family name: Canning
  given name: Adam D.
author list: Agent
  family name: Midwinter
  given name: Anne C.
author list: Agent
  family name: Death
  given name: Russell G.
doi: 10.7717/peerj.13914
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-27
copyright: ©2022 Davis et al.
attribution name: Davis et al.

Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
type: item
type: AcademicArticle
description: Background The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the “primer-walking” method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.
format: application/pdf
format: text/html
creator: Regina L. Cunha
creator: Katy R. Nicastro
creator: Gerardo I. Zardi
creator: Celine Madeira
creator: Christopher D. McQuaid
creator: Cymon J. Cox
creator: Rita Castilho
subject: Evolutionary Studies
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13953
publisher: PeerJ Inc.
rights: © 2022 Cunha et al.
abstract: Background The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the “primer-walking” method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.
bibliographic citation: Cunha et al. (2022) Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus. PeerJ 10:e13953 https://doi.org/10.7717/peerj.13953
date submitted: 2022-03-03
date accepted: 2022-08-05
issued: 2022-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cunha
  given name: Regina L.
author list: Agent
  family name: Nicastro
  given name: Katy R.
author list: Agent
  family name: Zardi
  given name: Gerardo I.
author list: Agent
  family name: Madeira
  given name: Celine
author list: Agent
  family name: McQuaid
  given name: Christopher D.
author list: Agent
  family name: Cox
  given name: Cymon J.
author list: Agent
  family name: Castilho
  given name: Rita
doi: 10.7717/peerj.13953
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-26
copyright: © 2022 Cunha et al.
attribution name: Cunha et al.

Presence of leptin and its receptor in the ram reproductive system and in vitro effect of leptin on sperm quality
type: item
type: AcademicArticle
description: Leptin is a 16 kDa hormone encoded by obese (OB) gene in adipocytes. This molecule not only regulates energy metabolism but also plays a role in the reproduction of mammals. Leptin and its receptor (OBR) have been found in male reproductive systems of human, bovine, equine and pig. The effects of leptin on sperm quality vary widely from different research findings. However, the presence of leptin and its receptor in the ram reproductive system and the in vitro effect of leptin on sperm quality have not reported yet. In the present study, we found that the OB was highly expressed in primary and secondary spermatocytes of the testes, OBR was highly expressed in secondary spermatocytes of the testes. The expressions of OB were in stereocilia of epididymis and in columnar cells of epididymal caput and cauda, the expressions of OBR were in columnar cells of epididymis and in stereocilia of epididymal corpus and cauda. The presence of both OB and OBR in testes, epididymis and sperm were confirmed through RT-PCR, immunolocalization and Western blot analyses. The RT-qPCR results indicated OB and OBR had higher expression levels in epididymal sperm than that of the ejaculated sperm in rams. When sperm were treated with 5 ng/mL leptin, the progressive motility (P < 0.01), straight-line velocity (VSL) (P < 0.05), average path velocity (VAP) (P < 0.05), membrane mitochondrial potential (MMP) (P < 0.01) and viability (P < 0.05) significantly increased, while DNA fragmentation index (DFI) and reactive oxygen species (ROS) significantly decreased compared to the control (P < 0.01), and the other semen parameters such as acrosome integrity and acrosome reaction rate had no significant changes between groups (P > 0.05). In conclusion, this is probably the first report describing localization of leptin and its receptors in the reproductive system of rams and their effects on sperm quality parameters. Our findings suggest that 5 ng/mL leptin treatment enhanced sperm motility, viabilit…
format: application/pdf
format: text/html
creator: Yu Gao
creator: Guodong Zhao
creator: Yukun Song
creator: Aerman Haire
creator: Ailing Yang
creator: Xi Zhao
creator: Abulizi Wusiman
subject: Agricultural Science
subject: Biochemistry
subject: Molecular Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.13982
publisher: PeerJ Inc.
rights: © 2022 Gao et al.
abstract: Leptin is a 16 kDa hormone encoded by obese (OB) gene in adipocytes. This molecule not only regulates energy metabolism but also plays a role in the reproduction of mammals. Leptin and its receptor (OBR) have been found in male reproductive systems of human, bovine, equine and pig. The effects of leptin on sperm quality vary widely from different research findings. However, the presence of leptin and its receptor in the ram reproductive system and the in vitro effect of leptin on sperm quality have not reported yet. In the present study, we found that the OB was highly expressed in primary and secondary spermatocytes of the testes, OBR was highly expressed in secondary spermatocytes of the testes. The expressions of OB were in stereocilia of epididymis and in columnar cells of epididymal caput and cauda, the expressions of OBR were in columnar cells of epididymis and in stereocilia of epididymal corpus and cauda. The presence of both OB and OBR in testes, epididymis and sperm were confirmed through RT-PCR, immunolocalization and Western blot analyses. The RT-qPCR results indicated OB and OBR had higher expression levels in epididymal sperm than that of the ejaculated sperm in rams. When sperm were treated with 5 ng/mL leptin, the progressive motility (P < 0.01), straight-line velocity (VSL) (P < 0.05), average path velocity (VAP) (P < 0.05), membrane mitochondrial potential (MMP) (P < 0.01) and viability (P < 0.05) significantly increased, while DNA fragmentation index (DFI) and reactive oxygen species (ROS) significantly decreased compared to the control (P < 0.01), and the other semen parameters such as acrosome integrity and acrosome reaction rate had no significant changes between groups (P > 0.05). In conclusion, this is probably the first report describing localization of leptin and its receptors in the reproductive system of rams and their effects on sperm quality parameters. Our findings suggest that 5 ng/mL leptin treatment enhanced sperm motility, viabilit…
bibliographic citation: Gao et al. (2022) Presence of leptin and its receptor in the ram reproductive system and in vitro effect of leptin on sperm quality. PeerJ 10:e13982 https://doi.org/10.7717/peerj.13982
date submitted: 2022-04-13
date accepted: 2022-08-10
issued: 2022-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Yu
author list: Agent
  family name: Zhao
  given name: Guodong
author list: Agent
  family name: Song
  given name: Yukun
author list: Agent
  family name: Haire
  given name: Aerman
author list: Agent
  family name: Yang
  given name: Ailing
author list: Agent
  family name: Zhao
  given name: Xi
author list: Agent
  family name: Wusiman
  given name: Abulizi
doi: 10.7717/peerj.13982
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-26
copyright: © 2022 Gao et al.
attribution name: Gao et al.

Avoidance of copper by fathead minnows (Pimephales promelas) requires an intact olfactory system
type: item
type: AcademicArticle
description: Fish can detect and respond to a wide variety of cations in their environment, including copper. Most often fish will avoid copper during behavioural trials; however, fish may also show no response or an attraction response, depending on the concentration(s) used. While it may seem intuitive that the response to copper requires olfaction, there is little direct evidence to support this, and what evidence there is remains incomplete. In order to test if olfaction is required for avoidance of copper by fathead minnows (Pimephales promelas) copper-induced movement was compared between fish with an intact olfactory system and fish with induced anosmia. Fish in a control group or a mock-anosmic group avoided copper (approximately 10 µg/L or 62.7 nM copper sulphate) while anosmic fish did not. The evidence demonstrates that an intact olfactory system is required for copper sensing in fish.
format: application/pdf
format: text/html
creator: Rubab Fatima
creator: Robert Briggs
creator: William A. Dew
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Neuroscience
subject: Ecotoxicology
subject: Freshwater Biology
description: doi:10.7717/peerj.13988
publisher: PeerJ Inc.
rights: © 2022 Fatima et al.
abstract: Fish can detect and respond to a wide variety of cations in their environment, including copper. Most often fish will avoid copper during behavioural trials; however, fish may also show no response or an attraction response, depending on the concentration(s) used. While it may seem intuitive that the response to copper requires olfaction, there is little direct evidence to support this, and what evidence there is remains incomplete. In order to test if olfaction is required for avoidance of copper by fathead minnows (Pimephales promelas) copper-induced movement was compared between fish with an intact olfactory system and fish with induced anosmia. Fish in a control group or a mock-anosmic group avoided copper (approximately 10 µg/L or 62.7 nM copper sulphate) while anosmic fish did not. The evidence demonstrates that an intact olfactory system is required for copper sensing in fish.
bibliographic citation: Fatima et al. (2022) Avoidance of copper by fathead minnows (Pimephales promelas) requires an intact olfactory system. PeerJ 10:e13988 https://doi.org/10.7717/peerj.13988
date submitted: 2022-01-26
date accepted: 2022-08-11
issued: 2022-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fatima
  given name: Rubab
author list: Agent
  family name: Briggs
  given name: Robert
author list: Agent
  family name: Dew
  given name: William A.
doi: 10.7717/peerj.13988
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-26
copyright: © 2022 Fatima et al.
attribution name: Fatima et al.

What’s the effectiveness of stocking actions in small creeks? The role of water discharge behind hatchery trout downstream movement
type: item
type: AcademicArticle
description: Fish stocking to enhance freshwater fisheries or to improve the conservation status of endangered fish species is a common practice in many countries. Little is known, however, of the effectiveness of these practices in spite of the high efforts and investments required. The movement of subadult/adult hatchery-released brown trout Salmo trutta L. was studied by passive telemetry in a small tributary of Lake Lugano (i.e., Laveggio Creek, Canton Ticino, Switzerland). Hatchery fish, together with some resident wild individuals sampled during electrofishing surveys, were tagged with Passive Integrated Transponders (PIT) tags. Hatchery fish were released upstream and downstream a submersible monitoring antenna, which was anchored to the streambed in a pass-over orientation. The number of hatchery fish detected daily by the antenna (divided between fish released upstream and downstream the antenna) was analyzed in relation to the daily water discharge, to search for similar patterns in their fluctuation over time. Only the movement of fish released upstream the antenna displayed a significant relationship with water discharge, with the highest number of fish detected during periods of high-water flow, occurring after heavy rains. High-water discharge events had a significant role in hatchery trout downstream movement in our study site, likely acting as a driver for the downstream migration to Lake Lugano. Such events contributed to the poor effectiveness of stocking actions in this small tributary, providing further evidence against stocking strategies based on subadult/adult fish.
format: application/pdf
format: text/html
creator: Stefano Brignone
creator: Vanessa De Santis
creator: Tiziano Putelli
creator: Christophe Molina
creator: Armando Piccinini
creator: Richard A. Carmichael
creator: Pietro Volta
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14069
publisher: PeerJ Inc.
rights: © 2022 Brignone et al.
abstract: Fish stocking to enhance freshwater fisheries or to improve the conservation status of endangered fish species is a common practice in many countries. Little is known, however, of the effectiveness of these practices in spite of the high efforts and investments required. The movement of subadult/adult hatchery-released brown trout Salmo trutta L. was studied by passive telemetry in a small tributary of Lake Lugano (i.e., Laveggio Creek, Canton Ticino, Switzerland). Hatchery fish, together with some resident wild individuals sampled during electrofishing surveys, were tagged with Passive Integrated Transponders (PIT) tags. Hatchery fish were released upstream and downstream a submersible monitoring antenna, which was anchored to the streambed in a pass-over orientation. The number of hatchery fish detected daily by the antenna (divided between fish released upstream and downstream the antenna) was analyzed in relation to the daily water discharge, to search for similar patterns in their fluctuation over time. Only the movement of fish released upstream the antenna displayed a significant relationship with water discharge, with the highest number of fish detected during periods of high-water flow, occurring after heavy rains. High-water discharge events had a significant role in hatchery trout downstream movement in our study site, likely acting as a driver for the downstream migration to Lake Lugano. Such events contributed to the poor effectiveness of stocking actions in this small tributary, providing further evidence against stocking strategies based on subadult/adult fish.
bibliographic citation: Brignone et al. (2022) What’s the effectiveness of stocking actions in small creeks? The role of water discharge behind hatchery trout downstream movement. PeerJ 10:e14069 https://doi.org/10.7717/peerj.14069
date submitted: 2022-07-11
date accepted: 2022-08-27
issued: 2022-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brignone
  given name: Stefano
author list: Agent
  family name: De Santis
  given name: Vanessa
author list: Agent
  family name: Putelli
  given name: Tiziano
author list: Agent
  family name: Molina
  given name: Christophe
author list: Agent
  family name: Piccinini
  given name: Armando
author list: Agent
  family name: Carmichael
  given name: Richard A.
author list: Agent
  family name: Volta
  given name: Pietro
doi: 10.7717/peerj.14069
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-26
copyright: © 2022 Brignone et al.
attribution name: Brignone et al.

Improved response inhibition induced by attentional capture is associated with physical activity
type: item
type: AcademicArticle
description: The ability to stop a response promptly when a stop signal is presented is named response inhibition. It is generally accepted that the process of response inhibition requires a subject to pay attention to the stop instruction and then cancel the action. A wealth of converging evidence suggests that physical activity (PA) can promote response inhibition, but the potential contributions of attentional capture to the relationship between PA and response inhibition are currently unknown. In this study, the standard stop-signal task (SST) and two novel versions of the SST were used to solve this gap. A total of 58 college students were divided into a higher PA group and a lower PA group, respectively. In Experiment 1, the classical SST determined that the participants in the higher PA group displayed a significantly faster stop-signal reaction time (SSRT) than those in the lower PA group. Experiment 2 separated the attentional capture in the SST and revealed that the participants in the higher PA group could detect the signal faster than those in the lower PA group. Experiment 3 further added a stop signal to Experiment 2 and demonstrated that the participants in the higher PA group could more effectively deploy attentional resources to complete the task. Overall, these findings indicate that PA is positively associated with response inhibition and that the positive relationship is associated with effective allocation of attentional resources for faster attentional capture.
format: application/pdf
format: text/html
creator: Hao Zhu
creator: Jiuyang Xu
creator: Yue Zheng
creator: Guiping Jiang
creator: Xinyi Huang
creator: Xiaohuan Tan
creator: Xueping Wu
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.14083
publisher: PeerJ Inc.
rights: © 2022 Zhu et al.
abstract: The ability to stop a response promptly when a stop signal is presented is named response inhibition. It is generally accepted that the process of response inhibition requires a subject to pay attention to the stop instruction and then cancel the action. A wealth of converging evidence suggests that physical activity (PA) can promote response inhibition, but the potential contributions of attentional capture to the relationship between PA and response inhibition are currently unknown. In this study, the standard stop-signal task (SST) and two novel versions of the SST were used to solve this gap. A total of 58 college students were divided into a higher PA group and a lower PA group, respectively. In Experiment 1, the classical SST determined that the participants in the higher PA group displayed a significantly faster stop-signal reaction time (SSRT) than those in the lower PA group. Experiment 2 separated the attentional capture in the SST and revealed that the participants in the higher PA group could detect the signal faster than those in the lower PA group. Experiment 3 further added a stop signal to Experiment 2 and demonstrated that the participants in the higher PA group could more effectively deploy attentional resources to complete the task. Overall, these findings indicate that PA is positively associated with response inhibition and that the positive relationship is associated with effective allocation of attentional resources for faster attentional capture.
bibliographic citation: Zhu et al. (2022) Improved response inhibition induced by attentional capture is associated with physical activity. PeerJ 10:e14083 https://doi.org/10.7717/peerj.14083
date submitted: 2022-07-21
date accepted: 2022-08-29
issued: 2022-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Hao
author list: Agent
  family name: Xu
  given name: Jiuyang
author list: Agent
  family name: Zheng
  given name: Yue
author list: Agent
  family name: Jiang
  given name: Guiping
author list: Agent
  family name: Huang
  given name: Xinyi
author list: Agent
  family name: Tan
  given name: Xiaohuan
author list: Agent
  family name: Wu
  given name: Xueping
doi: 10.7717/peerj.14083
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-26
copyright: © 2022 Zhu et al.
attribution name: Zhu et al.

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