PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Objective monitoring of functional recovery after total knee and hip arthroplasty using sensor-derived gait measures
items: Comparative mitogenome analysis reveals mitochondrial genome characteristics in eight strains of Beauveria
items: Lack of a genetic cline and temporal genetic stability in an introduced barnacle along the Pacific coast of Japan
items: Ac2-26 attenuates hepatic ischemia-reperfusion injury in mice via regulating IL-22/IL-22R1/STAT3 signaling
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

Objective monitoring of functional recovery after total knee and hip arthroplasty using sensor-derived gait measures
type: item
type: AcademicArticle
description: Background Inertial sensors hold the promise to objectively measure functional recovery after total knee (TKA) and hip arthroplasty (THA), but their value in addition to patient-reported outcome measures (PROMs) has yet to be demonstrated. This study investigated recovery of gait after TKA and THA using inertial sensors, and compared results to recovery of self-reported scores of pain and function. Methods PROMs and gait parameters were assessed before and at two and fifteen months after TKA (n = 24) and THA (n = 24). Gait parameters were compared with healthy individuals (n = 27) of similar age. Gait data were collected using inertial sensors on the feet, lower back, and trunk. Participants walked for two minutes back and forth over a 6m walkway with 180° turns. PROMs were obtained using the Knee Injury and Osteoarthritis Outcome Scores and Hip Disability and Osteoarthritis Outcome Score. Results Gait parameters recovered to the level of healthy controls after both TKA and THA. Early improvements were found in gait-related trunk kinematics, while spatiotemporal gait parameters mainly improved between two and fifteen months after TKA and THA. Compared to the large and early improvements found in of PROMs, these gait parameters showed a different trajectory, with a marked discordance between the outcome of both methods at two months post-operatively. Conclusion Sensor-derived gait parameters were responsive to TKA and THA, showing different recovery trajectories for spatiotemporal gait parameters and gait-related trunk kinematics. Fifteen months after TKA and THA, there were no remaining gait differences with respect to healthy controls. Given the discordance in recovery trajectories between gait parameters and PROMs, sensor-derived gait parameters seem to carry relevant information for evaluation of physical function that is not captured by self-reported scores.
format: application/pdf
format: text/html
creator: Ramon Boekesteijn
creator: José Smolders
creator: Vincent Busch
creator: Noël Keijsers
creator: Alexander Geurts
creator: Katrijn Smulders
subject: Kinesiology
subject: Orthopedics
subject: Surgery and Surgical Specialties
subject: Biomechanics
description: doi:10.7717/peerj.14054
publisher: PeerJ Inc.
rights: © 2022 Boekesteijn et al.
abstract: Background Inertial sensors hold the promise to objectively measure functional recovery after total knee (TKA) and hip arthroplasty (THA), but their value in addition to patient-reported outcome measures (PROMs) has yet to be demonstrated. This study investigated recovery of gait after TKA and THA using inertial sensors, and compared results to recovery of self-reported scores of pain and function. Methods PROMs and gait parameters were assessed before and at two and fifteen months after TKA (n = 24) and THA (n = 24). Gait parameters were compared with healthy individuals (n = 27) of similar age. Gait data were collected using inertial sensors on the feet, lower back, and trunk. Participants walked for two minutes back and forth over a 6m walkway with 180° turns. PROMs were obtained using the Knee Injury and Osteoarthritis Outcome Scores and Hip Disability and Osteoarthritis Outcome Score. Results Gait parameters recovered to the level of healthy controls after both TKA and THA. Early improvements were found in gait-related trunk kinematics, while spatiotemporal gait parameters mainly improved between two and fifteen months after TKA and THA. Compared to the large and early improvements found in of PROMs, these gait parameters showed a different trajectory, with a marked discordance between the outcome of both methods at two months post-operatively. Conclusion Sensor-derived gait parameters were responsive to TKA and THA, showing different recovery trajectories for spatiotemporal gait parameters and gait-related trunk kinematics. Fifteen months after TKA and THA, there were no remaining gait differences with respect to healthy controls. Given the discordance in recovery trajectories between gait parameters and PROMs, sensor-derived gait parameters seem to carry relevant information for evaluation of physical function that is not captured by self-reported scores.
bibliographic citation: Boekesteijn et al. (2022) Objective monitoring of functional recovery after total knee and hip arthroplasty using sensor-derived gait measures. PeerJ 10:e14054 https://doi.org/10.7717/peerj.14054
date submitted: 2022-05-02
date accepted: 2022-08-24
issued: 2022-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boekesteijn
  given name: Ramon
author list: Agent
  family name: Smolders
  given name: José
author list: Agent
  family name: Busch
  given name: Vincent
author list: Agent
  family name: Keijsers
  given name: Noël
author list: Agent
  family name: Geurts
  given name: Alexander
author list: Agent
  family name: Smulders
  given name: Katrijn
doi: 10.7717/peerj.14054
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-28
copyright: ©2022 Boekesteijn et al.
attribution name: Boekesteijn et al.

Comparative mitogenome analysis reveals mitochondrial genome characteristics in eight strains of Beauveria
type: item
type: AcademicArticle
description: Despite the significant progress that has been made in the genome sequencing of Beauveria species, mitochondrial genome (mitogenome) used to examine genetic diversity within fungal populations. Complete mitogenomes of Beauveria species can be easily sequenced and assembled using various sequencing techniques. However, since mitogenome annotations are mainly derived from similar species comparison and software prediction, and are not supported by RNA-seq transcripts data, it leads to problems with the accuracy of mitochondrial annotations and the inability to understand RNA processing. In this study, we assembled and annotated the mitogenome of eight Beauveria strains using Illumina DNA and RNA sequencing data. The circular mitogenome of eight Beauveria strains ranged from 26,850 bp (B. caledonica strain ATCC 64970) to 35,999 bp (B. brongniartii strain GYU-BMZ03), with the intronic insertions accounting for most of the size variation, thus contributing to a total mitochondrial genome (mitogenome) size of 7.01% and 28.95%, respectively. Intron number variations were not directly related to the evolutionary relationship distance. Besides ribosomal protein S3 (rps3), most introns are lost too quickly and lack the stability of protein-coding genes. The short RNA-seq reads from next-generation sequencing can improve the mitochondrial annotation accuracy and help study polycistronic transcripts and RNA processing. The transcription initiation sites may be located in the control region. Most introns do not serve as taxonomic markers and also lack open reading frames (ORFs). We assumed that the poly A tail was added to the polycistronic transcript before splicing and one polycistronic transcript (trnM(1)-trnL(1)-trnA-trnF-trnK-trnL(2)-trnQ-trnH-trnM(2)-nad2-nad3-atp9-cox2-trnR(1)-nad4L-nad5-cob-trnC-cox1-trnR(2)-nad1-nad4-atp8-atp6-rns-trnY-trnD-trnS-trnN-cox3-trnG-nad6-trnV-trnI-trnS-trnW-trnP-rnl(rps3)-trnT-trnE-trnM(3)) was first processed from the mitogenome and was subs…
format: application/pdf
format: text/html
creator: Yu Bai
creator: Xuyuan Gao
creator: Hui Wang
creator: Lin Ye
creator: Xianqun Zhang
creator: Wei Huang
creator: Xiuzhen Long
creator: Kang Yang
creator: Guoyong Li
creator: Jianlin Luo
creator: Jiyue Wang
creator: Yonghao Yu
subject: Evolutionary Studies
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.14067
publisher: PeerJ Inc.
rights: © 2022 Bai et al.
abstract: Despite the significant progress that has been made in the genome sequencing of Beauveria species, mitochondrial genome (mitogenome) used to examine genetic diversity within fungal populations. Complete mitogenomes of Beauveria species can be easily sequenced and assembled using various sequencing techniques. However, since mitogenome annotations are mainly derived from similar species comparison and software prediction, and are not supported by RNA-seq transcripts data, it leads to problems with the accuracy of mitochondrial annotations and the inability to understand RNA processing. In this study, we assembled and annotated the mitogenome of eight Beauveria strains using Illumina DNA and RNA sequencing data. The circular mitogenome of eight Beauveria strains ranged from 26,850 bp (B. caledonica strain ATCC 64970) to 35,999 bp (B. brongniartii strain GYU-BMZ03), with the intronic insertions accounting for most of the size variation, thus contributing to a total mitochondrial genome (mitogenome) size of 7.01% and 28.95%, respectively. Intron number variations were not directly related to the evolutionary relationship distance. Besides ribosomal protein S3 (rps3), most introns are lost too quickly and lack the stability of protein-coding genes. The short RNA-seq reads from next-generation sequencing can improve the mitochondrial annotation accuracy and help study polycistronic transcripts and RNA processing. The transcription initiation sites may be located in the control region. Most introns do not serve as taxonomic markers and also lack open reading frames (ORFs). We assumed that the poly A tail was added to the polycistronic transcript before splicing and one polycistronic transcript (trnM(1)-trnL(1)-trnA-trnF-trnK-trnL(2)-trnQ-trnH-trnM(2)-nad2-nad3-atp9-cox2-trnR(1)-nad4L-nad5-cob-trnC-cox1-trnR(2)-nad1-nad4-atp8-atp6-rns-trnY-trnD-trnS-trnN-cox3-trnG-nad6-trnV-trnI-trnS-trnW-trnP-rnl(rps3)-trnT-trnE-trnM(3)) was first processed from the mitogenome and was subs…
bibliographic citation: Bai et al. (2022) Comparative mitogenome analysis reveals mitochondrial genome characteristics in eight strains of Beauveria. PeerJ 10:e14067 https://doi.org/10.7717/peerj.14067
date submitted: 2022-04-07
date accepted: 2022-08-26
issued: 2022-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Yu
author list: Agent
  family name: Gao
  given name: Xuyuan
author list: Agent
  family name: Wang
  given name: Hui
author list: Agent
  family name: Ye
  given name: Lin
author list: Agent
  family name: Zhang
  given name: Xianqun
author list: Agent
  family name: Huang
  given name: Wei
author list: Agent
  family name: Long
  given name: Xiuzhen
author list: Agent
  family name: Yang
  given name: Kang
author list: Agent
  family name: Li
  given name: Guoyong
author list: Agent
  family name: Luo
  given name: Jianlin
author list: Agent
  family name: Wang
  given name: Jiyue
author list: Agent
  family name: Yu
  given name: Yonghao
doi: 10.7717/peerj.14067
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-28
copyright: ©2022 Bai et al.
attribution name: Bai et al.

Lack of a genetic cline and temporal genetic stability in an introduced barnacle along the Pacific coast of Japan
type: item
type: AcademicArticle
description: Background Large numbers of exotic marine species have been introduced worldwide. Monitoring of introduced species is important to reveal mechanisms underlying their establishment and expansion. Balanus glandula is a common intertidal barnacle native to the northeastern Pacific. However, this species has been introduced to Japan, South America, South Africa, and Europe. While a latitudinal genetic cline is well known in its native range, it is unclear whether such a genetic cline occurs in introduced areas. Twenty years have passed since it was first identified in Japan and its distribution now ranges from temperate to subarctic regions. Methods In the present study, we examined genotypes of cytochrome oxidase subunit I (COI) of mitochondrial (mt)-DNA and elongation factor 1a (EF1) across the distribution of B. glandula in Japan at high and mid intertidal zones. Results At all sampling sites, native northern genotypes are abundant and I did not detect significant effects of latitude, tide levels, or their interaction on genotypic frequencies. Further, I did not detect any change of genotype composition between data collected during a study in 2004 and samples in the present study collected in 2019. Data from the present study offer an important baseline for future monitoring of this species and supply valuable insights into the mechanisms of establishment and expansion of introduced marine species generally.
format: application/pdf
format: text/html
creator: Takefumi Yorisue
subject: Biodiversity
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.14073
publisher: PeerJ Inc.
rights: © 2022 Yorisue
abstract: Background Large numbers of exotic marine species have been introduced worldwide. Monitoring of introduced species is important to reveal mechanisms underlying their establishment and expansion. Balanus glandula is a common intertidal barnacle native to the northeastern Pacific. However, this species has been introduced to Japan, South America, South Africa, and Europe. While a latitudinal genetic cline is well known in its native range, it is unclear whether such a genetic cline occurs in introduced areas. Twenty years have passed since it was first identified in Japan and its distribution now ranges from temperate to subarctic regions. Methods In the present study, we examined genotypes of cytochrome oxidase subunit I (COI) of mitochondrial (mt)-DNA and elongation factor 1a (EF1) across the distribution of B. glandula in Japan at high and mid intertidal zones. Results At all sampling sites, native northern genotypes are abundant and I did not detect significant effects of latitude, tide levels, or their interaction on genotypic frequencies. Further, I did not detect any change of genotype composition between data collected during a study in 2004 and samples in the present study collected in 2019. Data from the present study offer an important baseline for future monitoring of this species and supply valuable insights into the mechanisms of establishment and expansion of introduced marine species generally.
bibliographic citation: Yorisue (2022) Lack of a genetic cline and temporal genetic stability in an introduced barnacle along the Pacific coast of Japan. PeerJ 10:e14073 https://doi.org/10.7717/peerj.14073
date submitted: 2022-05-11
date accepted: 2022-08-27
issued: 2022-09-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yorisue
  given name: Takefumi
doi: 10.7717/peerj.14073
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-28
copyright: © 2022 Yorisue
attribution name: Yorisue

Ac2-26 attenuates hepatic ischemia-reperfusion injury in mice via regulating IL-22/IL-22R1/STAT3 signaling
type: item
type: AcademicArticle
description: Hepatic ischemia-reperfusion injury (HIRI) is one of the major sources of mortality and morbidity associated with hepatic surgery. Ac2-26, a short peptide of Annexin A1 protein, has been proved to have a protective effect against IRI. However, whether it exerts a protective effect on HIRI has not been reported. The HIRI mice model and the oxidative damage model of H2O2-induced AML12 cells were established to investigate whether Ac2-26 could alleviate HIRI by regulating the activation of IL-22/IL-22R1/STAT3 signaling. The protective effect of Ac2-26 was measured by various biochemical parameters related to liver function, apoptosis, inflammatory reaction, mitochondrial function and the expressions of IL-22, IL-22R1, p-STAT3Tyr705. We discovered that Ac2-26 reduced the Suzuki score and cell death rate, and increased the cell viability after HIRI. Moreover, we unraveled that Ac2-26 significantly decreased the number of apoptotic hepatocytes, and the expressions of cleaved-caspase-3 and Bax/Bcl-2 ratio. Furthermore, HIRI increased the contents of malondialdehyde (MDA), NADP+/NADPH ratio and reactive oxygen species (ROS), whereas Ac2-26 decreased them significantly. Additionally, Ac2-26 remarkably alleviated mitochondria dysfunction, which was represented by an increase in the adenosine triphosphate (ATP) content and mitochondrial membrane potential, a decrease in mitochondrial DNA (mtDNA) damage. Finally, we revealed that Ac2-26 pretreatment could significantly inhibit the activation of IL-22/IL22R1/STAT3 signaling. In conclusion, this work demonstrated that Ac2-26 ameliorated HIRI by reducing oxidative stress and inhibiting the mitochondrial apoptosis pathway, which might be closely related to the inhibition of the IL-22/IL22R1/STAT3 signaling pathway.
format: application/pdf
format: text/html
creator: Wanzhen Li
creator: Hongxin Jiang
creator: Chen Bai
creator: Shuna Yu
creator: Yitong Pan
creator: Chenchen Wang
creator: Huiting Li
creator: Ming Li
creator: Yaxin Sheng
creator: Fangfang Chu
creator: Jie Wang
creator: Yuting Chen
creator: Jianguo Li
creator: Jiying Jiang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.14086
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Hepatic ischemia-reperfusion injury (HIRI) is one of the major sources of mortality and morbidity associated with hepatic surgery. Ac2-26, a short peptide of Annexin A1 protein, has been proved to have a protective effect against IRI. However, whether it exerts a protective effect on HIRI has not been reported. The HIRI mice model and the oxidative damage model of H2O2-induced AML12 cells were established to investigate whether Ac2-26 could alleviate HIRI by regulating the activation of IL-22/IL-22R1/STAT3 signaling. The protective effect of Ac2-26 was measured by various biochemical parameters related to liver function, apoptosis, inflammatory reaction, mitochondrial function and the expressions of IL-22, IL-22R1, p-STAT3Tyr705. We discovered that Ac2-26 reduced the Suzuki score and cell death rate, and increased the cell viability after HIRI. Moreover, we unraveled that Ac2-26 significantly decreased the number of apoptotic hepatocytes, and the expressions of cleaved-caspase-3 and Bax/Bcl-2 ratio. Furthermore, HIRI increased the contents of malondialdehyde (MDA), NADP+/NADPH ratio and reactive oxygen species (ROS), whereas Ac2-26 decreased them significantly. Additionally, Ac2-26 remarkably alleviated mitochondria dysfunction, which was represented by an increase in the adenosine triphosphate (ATP) content and mitochondrial membrane potential, a decrease in mitochondrial DNA (mtDNA) damage. Finally, we revealed that Ac2-26 pretreatment could significantly inhibit the activation of IL-22/IL22R1/STAT3 signaling. In conclusion, this work demonstrated that Ac2-26 ameliorated HIRI by reducing oxidative stress and inhibiting the mitochondrial apoptosis pathway, which might be closely related to the inhibition of the IL-22/IL22R1/STAT3 signaling pathway.
bibliographic citation: Li et al. (2022) Ac2-26 attenuates hepatic ischemia-reperfusion injury in mice via regulating IL-22/IL-22R1/STAT3 signaling. PeerJ 10:e14086 https://doi.org/10.7717/peerj.14086
date submitted: 2022-05-26
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: Li
  given name: Wanzhen
author list: Agent
  family name: Jiang
  given name: Hongxin
author list: Agent
  family name: Bai
  given name: Chen
author list: Agent
  family name: Yu
  given name: Shuna
author list: Agent
  family name: Pan
  given name: Yitong
author list: Agent
  family name: Wang
  given name: Chenchen
author list: Agent
  family name: Li
  given name: Huiting
author list: Agent
  family name: Li
  given name: Ming
author list: Agent
  family name: Sheng
  given name: Yaxin
author list: Agent
  family name: Chu
  given name: Fangfang
author list: Agent
  family name: Wang
  given name: Jie
author list: Agent
  family name: Chen
  given name: Yuting
author list: Agent
  family name: Li
  given name: Jianguo
author list: Agent
  family name: Jiang
  given name: Jiying
doi: 10.7717/peerj.14086
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-28
copyright: ©2022 Li et al.
attribution name: Li et al.

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.

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