PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p
items: Foliar nutrient concentrations of six northern hardwood species responded to nitrogen and phosphorus fertilization but did not predict tree growth
items: Nickel mine soil is a potential source for soybean plant growth promoting and heavy metal tolerant rhizobia
items: Strategic decision making and prediction differences in autism
items: Changes in primary metabolites and volatile organic compounds in cotton seedling leaves exposed to silver ions and silver nanoparticles revealed by metabolomic analysis
items: DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera)
items: Changes in serum amino acid levels in non-small cell lung cancer: a case-control study in Chinese population
items: Population biological traits of Periophthalmus chrysospilos Bleeker, 1853 in the Vietnamese Mekong Delta
items: Change of intestinal microbiota in mice model of bronchopulmonary dysplasia
items: https://peerj.com/articles/13307

lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p
type: item
type: AcademicArticle
description: Background Bone mesenchymal stem cells (BMSCs) have good osteogenic differentiation potential and have become ideal seed cells in bone tissue engineering. However, the osteogenic differentiation ability of BMSCs gradually weakens with age, and the regulatory mechanism is unclear. Method We conducted a bioinformatics analysis, dual-luciferase reporter (DLR) experiment, and RNA binding protein immunoprecipitation (RIP) to explore the hub genes that may affect BMSC functions. Results The expression level of long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (Malat1) was significantly higher in the BMSCs from elderly than younger mice, while miR-129-5p showed the opposite trend. The results of alkaline phosphatase staining, quantitative reverse transcription PCR and western blot experiments indicated that inhibiting the expression of Malat1 inhibits the osteogenic differentiation of BMSCs. This effect can be reversed by reducing the expression of miR-129-5p. Additionally, DLR and RIP experiments confirmed that Malat1 acts as a sponge for miR-129-5p. Conclusion Overall, our study findings indicated that lncRNA Malat1 may play a critical role in maintaining the osteoblast differentiation potential of BMSCs by sponging miR-129-5p.
format: application/pdf
format: text/html
creator: Junhao Yin
creator: Zhanglong Zheng
creator: Xiaoli Zeng
creator: Yijie Zhao
creator: Zexin Ai
creator: Miao Yu
creator: Yang’ou Wu
creator: Jirui Jiang
creator: Jia Li
creator: Shengjiao Li
subject: Bioinformatics
subject: Cell Biology
subject: Genetics
subject: Genomics
subject: Orthopedics
description: doi:10.7717/peerj.13355
publisher: PeerJ Inc.
rights: © 2022 Yin et al.
abstract: Background Bone mesenchymal stem cells (BMSCs) have good osteogenic differentiation potential and have become ideal seed cells in bone tissue engineering. However, the osteogenic differentiation ability of BMSCs gradually weakens with age, and the regulatory mechanism is unclear. Method We conducted a bioinformatics analysis, dual-luciferase reporter (DLR) experiment, and RNA binding protein immunoprecipitation (RIP) to explore the hub genes that may affect BMSC functions. Results The expression level of long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (Malat1) was significantly higher in the BMSCs from elderly than younger mice, while miR-129-5p showed the opposite trend. The results of alkaline phosphatase staining, quantitative reverse transcription PCR and western blot experiments indicated that inhibiting the expression of Malat1 inhibits the osteogenic differentiation of BMSCs. This effect can be reversed by reducing the expression of miR-129-5p. Additionally, DLR and RIP experiments confirmed that Malat1 acts as a sponge for miR-129-5p. Conclusion Overall, our study findings indicated that lncRNA Malat1 may play a critical role in maintaining the osteoblast differentiation potential of BMSCs by sponging miR-129-5p.
bibliographic citation: Yin et al. (2022) lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p. PeerJ 10:e13355 https://doi.org/10.7717/peerj.13355
date submitted: 2022-01-25
date accepted: 2022-04-08
issued: 2022-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Junhao
author list: Agent
  family name: Zheng
  given name: Zhanglong
author list: Agent
  family name: Zeng
  given name: Xiaoli
author list: Agent
  family name: Zhao
  given name: Yijie
author list: Agent
  family name: Ai
  given name: Zexin
author list: Agent
  family name: Yu
  given name: Miao
author list: Agent
  family name: Wu
  given name: Yang’ou
author list: Agent
  family name: Jiang
  given name: Jirui
author list: Agent
  family name: Li
  given name: Jia
author list: Agent
  family name: Li
  given name: Shengjiao
doi: 10.7717/peerj.13355
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-22
copyright: ©2022 Yin et al.
attribution name: Yin et al.

Foliar nutrient concentrations of six northern hardwood species responded to nitrogen and phosphorus fertilization but did not predict tree growth
type: item
type: AcademicArticle
description: Foliar chemistry can be useful for diagnosing soil nutrient availability and plant nutrient limitation. In northern hardwood forests, foliar responses to nitrogen (N) addition have been more often studied than phosphorus (P) addition, and the interactive effects of N and P addition have rarely been described. In the White Mountains of central New Hampshire, plots in ten forest stands of three age classes across three sites were treated annually beginning in 2011 with 30 kg N ha−1 y−1 or 10 kg P ha−1 y−1 or both or neither–a full factorial design. Green leaves of American beech (Fagus grandifolia Ehrh.), pin cherry (Prunus pensylvanica L.f.), red maple (Acer rubrum L.), sugar maple (A. saccharum Marsh.), white birch (Betula papyrifera Marsh.), and yellow birch (B. alleghaniensis Britton) were sampled pre-treatment and 4–6 years post-treatment in two young stands (last cut between 1988–1990), four mid-aged stands (last cut between 1971–1985) and four mature stands (last cut between 1883–1910). In a factorial analysis of species, stand age class, and nutrient addition, foliar N was 12% higher with N addition (p < 0.001) and foliar P was 45% higher with P addition (p < 0.001). Notably, P addition reduced foliar N concentration by 3% (p = 0.05), and N addition reduced foliar P concentration by 7% (p = 0.002). When both nutrients were added together, foliar P was lower than predicted by the main effects of N and P additions (p = 0.08 for N × P interaction), presumably because addition of N allowed greater use of P for growth. Foliar nutrients did not differ consistently with stand age class (p ≥ 0.11), but tree species differed (p ≤ 0.01), with the pioneer species pin cherry having the highest foliar nutrient concentrations and the greatest responses to nutrient addition. Foliar calcium (Ca) and magnesium (Mg) concentrations, on average, were 10% (p < 0.001) and 5% lower (p = 0.01), respectively, with N addition, but were not affected by P addition (p = 0.35 for Ca and p …
format: application/pdf
format: text/html
creator: Daniel S. Hong
creator: Kara E. Gonzales
creator: Timothy J. Fahey
creator: Ruth D. Yanai
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.13193
publisher: PeerJ Inc.
rights: © 2022 Hong et al.
abstract: Foliar chemistry can be useful for diagnosing soil nutrient availability and plant nutrient limitation. In northern hardwood forests, foliar responses to nitrogen (N) addition have been more often studied than phosphorus (P) addition, and the interactive effects of N and P addition have rarely been described. In the White Mountains of central New Hampshire, plots in ten forest stands of three age classes across three sites were treated annually beginning in 2011 with 30 kg N ha−1 y−1 or 10 kg P ha−1 y−1 or both or neither–a full factorial design. Green leaves of American beech (Fagus grandifolia Ehrh.), pin cherry (Prunus pensylvanica L.f.), red maple (Acer rubrum L.), sugar maple (A. saccharum Marsh.), white birch (Betula papyrifera Marsh.), and yellow birch (B. alleghaniensis Britton) were sampled pre-treatment and 4–6 years post-treatment in two young stands (last cut between 1988–1990), four mid-aged stands (last cut between 1971–1985) and four mature stands (last cut between 1883–1910). In a factorial analysis of species, stand age class, and nutrient addition, foliar N was 12% higher with N addition (p < 0.001) and foliar P was 45% higher with P addition (p < 0.001). Notably, P addition reduced foliar N concentration by 3% (p = 0.05), and N addition reduced foliar P concentration by 7% (p = 0.002). When both nutrients were added together, foliar P was lower than predicted by the main effects of N and P additions (p = 0.08 for N × P interaction), presumably because addition of N allowed greater use of P for growth. Foliar nutrients did not differ consistently with stand age class (p ≥ 0.11), but tree species differed (p ≤ 0.01), with the pioneer species pin cherry having the highest foliar nutrient concentrations and the greatest responses to nutrient addition. Foliar calcium (Ca) and magnesium (Mg) concentrations, on average, were 10% (p < 0.001) and 5% lower (p = 0.01), respectively, with N addition, but were not affected by P addition (p = 0.35 for Ca and p …
bibliographic citation: Hong et al. (2022) Foliar nutrient concentrations of six northern hardwood species responded to nitrogen and phosphorus fertilization but did not predict tree growth. PeerJ 10:e13193 https://doi.org/10.7717/peerj.13193
date submitted: 2021-06-21
date accepted: 2022-03-09
issued: 2022-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Daniel S.
author list: Agent
  family name: Gonzales
  given name: Kara E.
author list: Agent
  family name: Fahey
  given name: Timothy J.
author list: Agent
  family name: Yanai
  given name: Ruth D.
doi: 10.7717/peerj.13193
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-21
copyright: ©2022 Hong et al.
attribution name: Hong et al.

Nickel mine soil is a potential source for soybean plant growth promoting and heavy metal tolerant rhizobia
type: item
type: AcademicArticle
description: Mine soil is not only barren but also contaminated by some heavy metals. It is unclear whether some rhizobia survived under extreme conditions in the nickel mine soil. Therefore, this study tries to isolate some effective soybean plant growth promoting and heavy metal resistant rhizobia from nickel mine soil, and to analyze their diversity. Soybean plants were used to trap rhizobia from the nickel mine soil. A total of 21 isolates were preliminarily identified as rhizobia, which were clustered into eight groups at 87% similarity level using BOXA1R-PCR fingerprinting technique. Four out of the eight representative isolates formed nodules on soybean roots with effectively symbiotic nitrogen-fixing and plant growth promoting abilities in the soybean pot experiment. Phylogenetic analysis of 16S rRNA, four housekeeping genes (atpD-recA-glnII-rpoB) and nifH genes assigned the symbiotic isolates YN5, YN8 and YN10 into Ensifer xinjiangense and YN11 into Rhizobium radiobacter, respectively. They also showed different tolerance levels to the heavy metals including cadmium, chromium, copper, nickel, and zinc. It was concluded that there were some plant growth promoting and heavy metal resistant rhizobia with the potential to facilitate phytoremediation and alleviate the effects of heavy metals on soybean cultivation in nickel mine soil, indicating a novel evidence for further exploring more functional microbes from the nickel mine soil.
format: application/pdf
format: text/html
creator: Han Liu
creator: Yongliang Cui
creator: Jie Zhou
creator: Petri Penttinen
creator: Jiahao Liu
creator: Lan Zeng
creator: Qiang Chen
creator: Yunfu Gu
creator: Likou Zou
creator: Ke Zhao
creator: Quanju Xiang
creator: Xiumei Yu
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.13215
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Mine soil is not only barren but also contaminated by some heavy metals. It is unclear whether some rhizobia survived under extreme conditions in the nickel mine soil. Therefore, this study tries to isolate some effective soybean plant growth promoting and heavy metal resistant rhizobia from nickel mine soil, and to analyze their diversity. Soybean plants were used to trap rhizobia from the nickel mine soil. A total of 21 isolates were preliminarily identified as rhizobia, which were clustered into eight groups at 87% similarity level using BOXA1R-PCR fingerprinting technique. Four out of the eight representative isolates formed nodules on soybean roots with effectively symbiotic nitrogen-fixing and plant growth promoting abilities in the soybean pot experiment. Phylogenetic analysis of 16S rRNA, four housekeeping genes (atpD-recA-glnII-rpoB) and nifH genes assigned the symbiotic isolates YN5, YN8 and YN10 into Ensifer xinjiangense and YN11 into Rhizobium radiobacter, respectively. They also showed different tolerance levels to the heavy metals including cadmium, chromium, copper, nickel, and zinc. It was concluded that there were some plant growth promoting and heavy metal resistant rhizobia with the potential to facilitate phytoremediation and alleviate the effects of heavy metals on soybean cultivation in nickel mine soil, indicating a novel evidence for further exploring more functional microbes from the nickel mine soil.
bibliographic citation: Liu et al. (2022) Nickel mine soil is a potential source for soybean plant growth promoting and heavy metal tolerant rhizobia. PeerJ 10:e13215 https://doi.org/10.7717/peerj.13215
date submitted: 2022-01-20
date accepted: 2022-03-13
issued: 2022-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Han
author list: Agent
  family name: Cui
  given name: Yongliang
author list: Agent
  family name: Zhou
  given name: Jie
author list: Agent
  family name: Penttinen
  given name: Petri
author list: Agent
  family name: Liu
  given name: Jiahao
author list: Agent
  family name: Zeng
  given name: Lan
author list: Agent
  family name: Chen
  given name: Qiang
author list: Agent
  family name: Gu
  given name: Yunfu
author list: Agent
  family name: Zou
  given name: Likou
author list: Agent
  family name: Zhao
  given name: Ke
author list: Agent
  family name: Xiang
  given name: Quanju
author list: Agent
  family name: Yu
  given name: Xiumei
doi: 10.7717/peerj.13215
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-21
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Strategic decision making and prediction differences in autism
type: item
type: AcademicArticle
description: Background Several theories in autism posit that common aspects of the autism phenotype may be manifestations of an underlying differentiation in predictive abilities. The present study investigates this hypothesis in the context of strategic decision making in autistic participants compared to a control group. Method Autistic individuals (43 adults, 35 male) and a comparison group (42 adults, 35 male) of age and gender matched individuals, played a modified version of the prisoner’s dilemma (PD) task where they were asked, if capable, to predict their opponents’ move. The predictive performance of the two groups was assessed. Results Overall, participants in the autism group had a significantly lower number of correct predictions. Moreover, autistic participants stated, significantly more frequently than the comparison group, that they were unable to make a prediction. When attempting a prediction however, the success ratio did not differ between the two groups. Conclusions These findings indicate that there is a difference in prediction performance between the two groups. Although our task design does not allow us to identify whether this difference is due to difficulty to form a prediction or a reluctance in registering one, these findings could justify a role for prediction in strategic decision making during the PD task.
format: application/pdf
format: text/html
creator: Vasileios Mantas
creator: Artemios Pehlivanidis
creator: Katerina Papanikolaou
creator: Vasileia Kotoula
creator: Charalambos Papageorgiou
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13328
publisher: PeerJ Inc.
rights: © 2022 Mantas et al.
abstract: Background Several theories in autism posit that common aspects of the autism phenotype may be manifestations of an underlying differentiation in predictive abilities. The present study investigates this hypothesis in the context of strategic decision making in autistic participants compared to a control group. Method Autistic individuals (43 adults, 35 male) and a comparison group (42 adults, 35 male) of age and gender matched individuals, played a modified version of the prisoner’s dilemma (PD) task where they were asked, if capable, to predict their opponents’ move. The predictive performance of the two groups was assessed. Results Overall, participants in the autism group had a significantly lower number of correct predictions. Moreover, autistic participants stated, significantly more frequently than the comparison group, that they were unable to make a prediction. When attempting a prediction however, the success ratio did not differ between the two groups. Conclusions These findings indicate that there is a difference in prediction performance between the two groups. Although our task design does not allow us to identify whether this difference is due to difficulty to form a prediction or a reluctance in registering one, these findings could justify a role for prediction in strategic decision making during the PD task.
bibliographic citation: Mantas et al. (2022) Strategic decision making and prediction differences in autism. PeerJ 10:e13328 https://doi.org/10.7717/peerj.13328
date submitted: 2021-10-15
date accepted: 2022-04-04
issued: 2022-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mantas
  given name: Vasileios
author list: Agent
  family name: Pehlivanidis
  given name: Artemios
author list: Agent
  family name: Papanikolaou
  given name: Katerina
author list: Agent
  family name: Kotoula
  given name: Vasileia
author list: Agent
  family name: Papageorgiou
  given name: Charalambos
doi: 10.7717/peerj.13328
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-21
copyright: © 2022 Mantas et al.
attribution name: Mantas et al.

Changes in primary metabolites and volatile organic compounds in cotton seedling leaves exposed to silver ions and silver nanoparticles revealed by metabolomic analysis
type: item
type: AcademicArticle
description: In the area of climate change, nanotechnology provides handy tools for improving crop production and assuring sustainability in global agricultural system. Due to excellent physiological and biochemical properties, silver nanoparticles (AgNPs) have been widely studied for potential use in agriculture. However, there are concerns about the mechanism of the toxic effects of the accumulation of AgNPs on crop growth and development. In this study, the impacts of AgNPs on cotton (Gossypium hirsutum) seedlings were evaluated by integrating physiological and comprehensive metabolomic analyses. Potting-soil-grown, two-week-old cotton seedlings were foliar-exposed to 5 mg/plant AgNP or 0.02 mg/plant Ag+ (equivalent to the free Ag+ released from AgNPs). Primary metabolites and volatile organic compounds (VOCs) were identified by gas chromatography–mass spectrometry (GC-MS) and solid-phase microextraction (SPME) GC-MS, respectively. AgNPs inhibited the photosynthetic capacity of the cotton leaves. The metabolic spectrum analysis identified and quantified 73 primary metabolites and 45 VOCs in cotton leaves. Both treatments significantly changed the metabolite profiles of plant leaves. Among the primary metabolites, AgNPs induced marked changes in amino acids, sugars and sugar alcohols. Among the VOCs, 13 volatiles, mainly aldehydes, alkanes and terpenoids, were specifically altered only in response to AgNPs. In summary, our study showed that the comprehensive influence of AgNPs on primary metabolites and VOCs was not merely attributed to the released Ag+ but was caused by AgNP-specific effects on cotton leaves. These results provide important knowledge about the physiological and chemical changes in cotton leaves upon exposure to AgNPs and offer a new insight for supporting the sustainable use of AgNPs in agriculture.
format: application/pdf
format: text/html
creator: Yong Yang
creator: PengMeng Du
creator: Wenjie Lai
creator: Liyan Yin
creator: Yuanhao Ding
creator: Zhonghua Li
creator: Haiyan Hu
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.13336
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: In the area of climate change, nanotechnology provides handy tools for improving crop production and assuring sustainability in global agricultural system. Due to excellent physiological and biochemical properties, silver nanoparticles (AgNPs) have been widely studied for potential use in agriculture. However, there are concerns about the mechanism of the toxic effects of the accumulation of AgNPs on crop growth and development. In this study, the impacts of AgNPs on cotton (Gossypium hirsutum) seedlings were evaluated by integrating physiological and comprehensive metabolomic analyses. Potting-soil-grown, two-week-old cotton seedlings were foliar-exposed to 5 mg/plant AgNP or 0.02 mg/plant Ag+ (equivalent to the free Ag+ released from AgNPs). Primary metabolites and volatile organic compounds (VOCs) were identified by gas chromatography–mass spectrometry (GC-MS) and solid-phase microextraction (SPME) GC-MS, respectively. AgNPs inhibited the photosynthetic capacity of the cotton leaves. The metabolic spectrum analysis identified and quantified 73 primary metabolites and 45 VOCs in cotton leaves. Both treatments significantly changed the metabolite profiles of plant leaves. Among the primary metabolites, AgNPs induced marked changes in amino acids, sugars and sugar alcohols. Among the VOCs, 13 volatiles, mainly aldehydes, alkanes and terpenoids, were specifically altered only in response to AgNPs. In summary, our study showed that the comprehensive influence of AgNPs on primary metabolites and VOCs was not merely attributed to the released Ag+ but was caused by AgNP-specific effects on cotton leaves. These results provide important knowledge about the physiological and chemical changes in cotton leaves upon exposure to AgNPs and offer a new insight for supporting the sustainable use of AgNPs in agriculture.
bibliographic citation: Yang et al. (2022) Changes in primary metabolites and volatile organic compounds in cotton seedling leaves exposed to silver ions and silver nanoparticles revealed by metabolomic analysis. PeerJ 10:e13336 https://doi.org/10.7717/peerj.13336
date submitted: 2022-01-31
date accepted: 2022-04-05
issued: 2022-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yong
author list: Agent
  family name: Du
  given name: PengMeng
author list: Agent
  family name: Lai
  given name: Wenjie
author list: Agent
  family name: Yin
  given name: Liyan
author list: Agent
  family name: Ding
  given name: Yuanhao
author list: Agent
  family name: Li
  given name: Zhonghua
author list: Agent
  family name: Hu
  given name: Haiyan
doi: 10.7717/peerj.13336
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-21
copyright: ©2022 Yang et al.
attribution name: Yang et al.

DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera)
type: item
type: AcademicArticle
description: Background The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy. Methods A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies. Results Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin…
format: application/pdf
format: text/html
creator: Dora Hlebec
creator: Ignac Sivec
creator: Martina Podnar
creator: Mladen Kučinić
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13213
publisher: PeerJ Inc.
rights: © 2022 Hlebec et al.
abstract: Background The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy. Methods A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies. Results Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin…
bibliographic citation: Hlebec et al. (2022) DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera). PeerJ 10:e13213 https://doi.org/10.7717/peerj.13213
date submitted: 2021-12-27
date accepted: 2022-03-12
issued: 2022-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hlebec
  given name: Dora
author list: Agent
  family name: Sivec
  given name: Ignac
author list: Agent
  family name: Podnar
  given name: Martina
author list: Agent
  family name: Kučinić
  given name: Mladen
doi: 10.7717/peerj.13213
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-20
copyright: © 2022 Hlebec et al.
attribution name: Hlebec et al.

Changes in serum amino acid levels in non-small cell lung cancer: a case-control study in Chinese population
type: item
type: AcademicArticle
description: Background Previous studies have shown the alteration of amino acid (AA) profile in patients with non-small cell lung cancer (NSCLC). However, there is little data regarding AA profile in NSCLC in Chinese population. The aim of this study was to evaluate AA profile in Chinese NSCLC patients, explore its utility in sample classification and further discuss its related metabolic pathways. Methods The concentrations of 22 AAs in serum samples from 200 patients with NSCLC and 202 healthy controls were determined by liquid chromatography-tandem mass spectrometer (LC-MS/MS). AA levels in different tumor stages and histological types were also discussed. The performance of AA panel in classifying the cases and controls was evaluated in the training data set and validation data set based on the receiver operating characteristic (ROC) curve, and the important metabolic pathways were identified. Results The concentrations of tryptophan (Trp), phenylalanine (Phe), isoleucine (Ile), glycine (Gly), serine (Ser), aspartic acid (Asp), asparagine (Asn), cystein (Cys), glutamic acid (Glu), ornithine (Orn) and citrulline (Cit) were significantly altered in NSCLC patients compared with controls (all P-FDR < 0.05). Among these, four AAs including Asp, Cys, Glu and Orn were substantially up-regulated in NSCLC patients (FC ≥ 1.2). AA levels were significantly altered in patients with late-stage NSCLC, but not in those with early-stage when comparing with healthy controls. In terms of histological type, these AAs were altered in both adenocarcinoma and squamous cell carcinoma. For discrimination of NSCLC from controls, the area under the ROC curve (AUC) was 0.80 (95% CI [0.74–0.85]) in the training data set and 0.79 (95%CI [0.71–0.87]) in the validation data set. The AUCs for early-stage and late-stage NSCLC were 0.75 (95% CI [0.68–0.81]) and 0.86 (95% CI [0.82–0.91]), respectively. Moreover, the model showed a better performance in the classification of squamous cell carcinoma (AUC = 0.9…
format: application/pdf
format: text/html
creator: Ke Liu
creator: Jiaoyuan Li
creator: Tingting Long
creator: Yi Wang
creator: Tongxin Yin
creator: Jieyi Long
creator: Ying Shen
creator: Liming Cheng
subject: Biochemistry
subject: Epidemiology
subject: Oncology
subject: Respiratory Medicine
subject: Metabolic Sciences
description: doi:10.7717/peerj.13272
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Background Previous studies have shown the alteration of amino acid (AA) profile in patients with non-small cell lung cancer (NSCLC). However, there is little data regarding AA profile in NSCLC in Chinese population. The aim of this study was to evaluate AA profile in Chinese NSCLC patients, explore its utility in sample classification and further discuss its related metabolic pathways. Methods The concentrations of 22 AAs in serum samples from 200 patients with NSCLC and 202 healthy controls were determined by liquid chromatography-tandem mass spectrometer (LC-MS/MS). AA levels in different tumor stages and histological types were also discussed. The performance of AA panel in classifying the cases and controls was evaluated in the training data set and validation data set based on the receiver operating characteristic (ROC) curve, and the important metabolic pathways were identified. Results The concentrations of tryptophan (Trp), phenylalanine (Phe), isoleucine (Ile), glycine (Gly), serine (Ser), aspartic acid (Asp), asparagine (Asn), cystein (Cys), glutamic acid (Glu), ornithine (Orn) and citrulline (Cit) were significantly altered in NSCLC patients compared with controls (all P-FDR < 0.05). Among these, four AAs including Asp, Cys, Glu and Orn were substantially up-regulated in NSCLC patients (FC ≥ 1.2). AA levels were significantly altered in patients with late-stage NSCLC, but not in those with early-stage when comparing with healthy controls. In terms of histological type, these AAs were altered in both adenocarcinoma and squamous cell carcinoma. For discrimination of NSCLC from controls, the area under the ROC curve (AUC) was 0.80 (95% CI [0.74–0.85]) in the training data set and 0.79 (95%CI [0.71–0.87]) in the validation data set. The AUCs for early-stage and late-stage NSCLC were 0.75 (95% CI [0.68–0.81]) and 0.86 (95% CI [0.82–0.91]), respectively. Moreover, the model showed a better performance in the classification of squamous cell carcinoma (AUC = 0.9…
bibliographic citation: Liu et al. (2022) Changes in serum amino acid levels in non-small cell lung cancer: a case-control study in Chinese population. PeerJ 10:e13272 https://doi.org/10.7717/peerj.13272
date submitted: 2021-09-20
date accepted: 2022-03-23
issued: 2022-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Ke
author list: Agent
  family name: Li
  given name: Jiaoyuan
author list: Agent
  family name: Long
  given name: Tingting
author list: Agent
  family name: Wang
  given name: Yi
author list: Agent
  family name: Yin
  given name: Tongxin
author list: Agent
  family name: Long
  given name: Jieyi
author list: Agent
  family name: Shen
  given name: Ying
author list: Agent
  family name: Cheng
  given name: Liming
doi: 10.7717/peerj.13272
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-20
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Population biological traits of Periophthalmus chrysospilos Bleeker, 1853 in the Vietnamese Mekong Delta
type: item
type: AcademicArticle
description: Periophthalmus chrysospilos is an amphibious fish living in mudflats from eastern India to Indonesia, including the Vietnamese Mekong Delta. Population biological traits play an important role in fishery assessment, but understanding is limited for this species. In total 1,031 specimens were caught in two regions covering four provinces, including the TVST (Duyen Hai, Tra Vinh and Tran De, Soc Trang) and BLCM (Dong Hai, Bac Lieu and Dam Doi, Ca Mau). Results found that the sex ratio was close to 1:1. The parameters of the von Bertalanffy in TVST were L∞ = 12.8 cm, K = 0.41 yr−1, t0 = −0.10 yr and in BLCM were 12.7 cm, 0.38 yr−1 and −0.08 yr, respectively. Although the growth coefficient (Φ′) in BLCM (1.79), was lower than that in TVST (1.83), the species shared a similar size at first capture (7.9 cm in TVST and 7.9 cm in BLCM). The species suffered from heavy pressure of fishing in TVST as fishing mortality in TVST (2.32 yr−1) was higher than that in BLCM (1.38 yr−1), leading to the higher total mortality (Z = 3.60 yr−1) in TVST compared to BLCM (Z = 2.59 yr−1). By contrast, the species showed similar natural mortality over both sites (1.20 yr−1 in TVST and 1.22 yr−1 in BLCM). The Periophthalmus chrysospilos population was reasonably exploited because E values (0.64 in TVST and 0.53 in BLCM) were lower than E10 (0.706 in BTTV and 0.705 in STBL). Nonetheless, to avoid the consequences of overfishing, some sustainable fisheries practices should be implemented, such as protecting mangrove forests, restricting fishing during the recruitment period, using appropriate fishing tools and increasing mesh size.
format: application/pdf
format: text/html
creator: Quang Minh Dinh
creator: Ton Huu Duc Nguyen
creator: Tien Thi Kieu Nguyen
creator: Tran Thi Huyen Lam
creator: Ngon Trong Truong
creator: Dinh Dac Tran
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13289
publisher: PeerJ Inc.
rights: © 2022 Dinh et al.
abstract: Periophthalmus chrysospilos is an amphibious fish living in mudflats from eastern India to Indonesia, including the Vietnamese Mekong Delta. Population biological traits play an important role in fishery assessment, but understanding is limited for this species. In total 1,031 specimens were caught in two regions covering four provinces, including the TVST (Duyen Hai, Tra Vinh and Tran De, Soc Trang) and BLCM (Dong Hai, Bac Lieu and Dam Doi, Ca Mau). Results found that the sex ratio was close to 1:1. The parameters of the von Bertalanffy in TVST were L∞ = 12.8 cm, K = 0.41 yr−1, t0 = −0.10 yr and in BLCM were 12.7 cm, 0.38 yr−1 and −0.08 yr, respectively. Although the growth coefficient (Φ′) in BLCM (1.79), was lower than that in TVST (1.83), the species shared a similar size at first capture (7.9 cm in TVST and 7.9 cm in BLCM). The species suffered from heavy pressure of fishing in TVST as fishing mortality in TVST (2.32 yr−1) was higher than that in BLCM (1.38 yr−1), leading to the higher total mortality (Z = 3.60 yr−1) in TVST compared to BLCM (Z = 2.59 yr−1). By contrast, the species showed similar natural mortality over both sites (1.20 yr−1 in TVST and 1.22 yr−1 in BLCM). The Periophthalmus chrysospilos population was reasonably exploited because E values (0.64 in TVST and 0.53 in BLCM) were lower than E10 (0.706 in BTTV and 0.705 in STBL). Nonetheless, to avoid the consequences of overfishing, some sustainable fisheries practices should be implemented, such as protecting mangrove forests, restricting fishing during the recruitment period, using appropriate fishing tools and increasing mesh size.
bibliographic citation: Dinh et al. (2022) Population biological traits of Periophthalmus chrysospilos Bleeker, 1853 in the Vietnamese Mekong Delta. PeerJ 10:e13289 https://doi.org/10.7717/peerj.13289
date submitted: 2021-12-22
date accepted: 2022-03-28
issued: 2022-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dinh
  given name: Quang Minh
author list: Agent
  family name: Nguyen
  given name: Ton Huu Duc
author list: Agent
  family name: Nguyen
  given name: Tien Thi Kieu
author list: Agent
  family name: Lam
  given name: Tran Thi Huyen
author list: Agent
  family name: Truong
  given name: Ngon Trong
author list: Agent
  family name: Tran
  given name: Dinh Dac
doi: 10.7717/peerj.13289
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-20
copyright: © 2022 Dinh et al.
attribution name: Dinh et al.

Change of intestinal microbiota in mice model of bronchopulmonary dysplasia
type: item
type: AcademicArticle
description: Background Gut microbiota has been proposed to be related to the pathogenesis of pulmonary diseases such as asthma and lung cancer, according to the gut-lung axis. However, little is known about the roles of gut microbiota in the pathogenesis of bronchopulmonary dysplasia (BPD). This study was designed to investigate the changes of gut microbiota in neonatal mice with BPD. Methods BPD model was induced through exposure to high concentration of oxygen. Hematoxylin and eosin (H&E) staining was utilized to determine the modeling efficiency. Stool samples were collected from the distal colon for the sequencing of V3–V4 regions of 16S rRNA, in order to analyze the gut microbiota diversity. Results Alpha diversity indicated that there were no statistical differences in the richness of gut microbiota between BPD model group and control group on day 7, 14 and 21. Beta diversity analysis showed that there were statistical differences in the gut microbiota on day 14 (R = 0.368, p = 0.021). Linear discriminant analysis effect size (LEfSe) showed that there were 22 markers with statistical differences on day 14 (p < 0.05), while those on day 7 and 21 were 3 and 4, respectively. Functional prediction analysis showed that the top three metabolic pathways were signal transduction (PFDR = 0.037), glycan biosynthesis and metabolism (PFDR = 0.032), and metabolism of terpenoids and polyketides (PFDR = 0.049). Conclusions BPD mice showed disorder of gut microbiota, which may involve specific metabolic pathways in the early stage. With the progression of neonatal maturity, the differences of the gut microbiota between the two groups would gradually disappear.
format: application/pdf
format: text/html
creator: Tianqun Fan
creator: Ling Lu
creator: Rong Jin
creator: Aihua Sui
creator: Renzheng Guan
creator: Fengjing Cui
creator: Zhenghai Qu
creator: Dongyun Liu
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.13295
publisher: PeerJ Inc.
rights: © 2022 Fan et al.
abstract: Background Gut microbiota has been proposed to be related to the pathogenesis of pulmonary diseases such as asthma and lung cancer, according to the gut-lung axis. However, little is known about the roles of gut microbiota in the pathogenesis of bronchopulmonary dysplasia (BPD). This study was designed to investigate the changes of gut microbiota in neonatal mice with BPD. Methods BPD model was induced through exposure to high concentration of oxygen. Hematoxylin and eosin (H&E) staining was utilized to determine the modeling efficiency. Stool samples were collected from the distal colon for the sequencing of V3–V4 regions of 16S rRNA, in order to analyze the gut microbiota diversity. Results Alpha diversity indicated that there were no statistical differences in the richness of gut microbiota between BPD model group and control group on day 7, 14 and 21. Beta diversity analysis showed that there were statistical differences in the gut microbiota on day 14 (R = 0.368, p = 0.021). Linear discriminant analysis effect size (LEfSe) showed that there were 22 markers with statistical differences on day 14 (p < 0.05), while those on day 7 and 21 were 3 and 4, respectively. Functional prediction analysis showed that the top three metabolic pathways were signal transduction (PFDR = 0.037), glycan biosynthesis and metabolism (PFDR = 0.032), and metabolism of terpenoids and polyketides (PFDR = 0.049). Conclusions BPD mice showed disorder of gut microbiota, which may involve specific metabolic pathways in the early stage. With the progression of neonatal maturity, the differences of the gut microbiota between the two groups would gradually disappear.
bibliographic citation: Fan et al. (2022) Change of intestinal microbiota in mice model of bronchopulmonary dysplasia. PeerJ 10:e13295 https://doi.org/10.7717/peerj.13295
date submitted: 2021-07-16
date accepted: 2022-03-28
issued: 2022-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Tianqun
author list: Agent
  family name: Lu
  given name: Ling
author list: Agent
  family name: Jin
  given name: Rong
author list: Agent
  family name: Sui
  given name: Aihua
author list: Agent
  family name: Guan
  given name: Renzheng
author list: Agent
  family name: Cui
  given name: Fengjing
author list: Agent
  family name: Qu
  given name: Zhenghai
author list: Agent
  family name: Liu
  given name: Dongyun
doi: 10.7717/peerj.13295
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-20
copyright: © 2022 Fan et al.
attribution name: Fan et al.

https://peerj.com/articles/13307
type: item
type: AcademicArticle
title: Modification of the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes by availability of emergency cash reserves: findings from a nationally-representative survey in Thailand
description: Background Studies have suggested that economic distress is associated with behavioral health outcomes, while availability of cash reserves for emergencies is associated with a reduction in economic distress. The objective of this study was to assess the extent that the availability of emergency cash reserves modified the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes in the general adult population of Thailand. Methods We conducted a nationally-representative phone-based survey in late April 2021. Survey questions included questions on experience of economic distress, and a question on what participants would do to cover a 5,000 Thai Bahts (THB) emergency expense within one week, anxiety and depression screening questions, and questions regarding sleep, exercise, gambling, smoking, and drinking behaviors. We analyzed data using descriptive statistics and multivariate logistic regression analyses with adjustment for complex survey designs, and stratified analyses with assessment of heterogeneity of odds ratios between strata and assessment of additive and multiplicative interactions. Results A total of 1,555 individuals from 15 provinces participated in the survey (participation rate = 68.3%). Approximately 19.6% ± 1.0% of the participants reported that they would cover the 5,000 THB emergency expense only with cash or cash equivalent without resorting to other means. Experience of economic distress was associated with anxiety disorder after adjusting for covariables (Adjusted Odds Ratio (OR) = 2.47; 95% CI [1.45–4.19]). There was no evidence that availability of emergency cash reserves significantly modified the stated association, nor the association between experience of economic distress and other outcomes. However, with regard to anxiety disorder, depressive symptoms and history of gambling in past 30 days, the p-for-trend values (p-for-trend < 0.001) suggested that those with emergency cash reser…
format: application/pdf
format: text/html
creator: Wit Wichaidit
creator: Chayapisika Prommanee
creator: Sasira Choocham
creator: Rassamee Chotipanvithayakul
creator: Sawitri Assanangkornchai
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.13307
publisher: PeerJ Inc.
rights: © 2022 Wichaidit et al.
abstract: Background Studies have suggested that economic distress is associated with behavioral health outcomes, while availability of cash reserves for emergencies is associated with a reduction in economic distress. The objective of this study was to assess the extent that the availability of emergency cash reserves modified the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes in the general adult population of Thailand. Methods We conducted a nationally-representative phone-based survey in late April 2021. Survey questions included questions on experience of economic distress, and a question on what participants would do to cover a 5,000 Thai Bahts (THB) emergency expense within one week, anxiety and depression screening questions, and questions regarding sleep, exercise, gambling, smoking, and drinking behaviors. We analyzed data using descriptive statistics and multivariate logistic regression analyses with adjustment for complex survey designs, and stratified analyses with assessment of heterogeneity of odds ratios between strata and assessment of additive and multiplicative interactions. Results A total of 1,555 individuals from 15 provinces participated in the survey (participation rate = 68.3%). Approximately 19.6% ± 1.0% of the participants reported that they would cover the 5,000 THB emergency expense only with cash or cash equivalent without resorting to other means. Experience of economic distress was associated with anxiety disorder after adjusting for covariables (Adjusted Odds Ratio (OR) = 2.47; 95% CI [1.45–4.19]). There was no evidence that availability of emergency cash reserves significantly modified the stated association, nor the association between experience of economic distress and other outcomes. However, with regard to anxiety disorder, depressive symptoms and history of gambling in past 30 days, the p-for-trend values (p-for-trend < 0.001) suggested that those with emergency cash reser…
bibliographic citation: Wichaidit et al. (2022) Modification of the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes by availability of emergency cash reserves: findings from a nationally-representative survey in Thailand. PeerJ 10:e13307 https://doi.org/10.7717/peerj.13307
date submitted: 2021-06-25
date accepted: 2022-03-30
issued: 2022-04-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wichaidit
  given name: Wit
author list: Agent
  family name: Prommanee
  given name: Chayapisika
author list: Agent
  family name: Choocham
  given name: Sasira
author list: Agent
  family name: Chotipanvithayakul
  given name: Rassamee
author list: Agent
  family name: Assanangkornchai
  given name: Sawitri
doi: 10.7717/peerj.13307
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-20
copyright: © 2022 Wichaidit et al.
attribution name: Wichaidit et al.

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