PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of the speed on the webbed foot kinematics of mallard (Anas platyrhynchos)
items: Infection of Atlantic tripletail Lobotes surinamensis (Teleostei: Lobotidae) by brain metacercariae Cardiocephaloides medioconiger (Digenea: Strigeidae)
items: Urinary aluminium and its association with autism spectrum disorder in urban preschool children in Malaysia
items: Psychological stress responses to a live performance by professional flamenco dancers
items: A wild rice-derived peptide R14 ameliorates monosodium urate crystals-induced IL-1β secretion through inhibition of NF-κB signaling and NLRP3 inflammasome activation
items: Transcriptomic and metabolomic analysis of autumn leaf color change in Fraxinus angustifolia
items: A new application of multiplex PCR combined with membrane biochip assay for rapid detection of 9 common pathogens in sepsis
items: Contraceptive use among reproductive-age females with disabilities in central Sidama National Regional State, Ethiopia: a multilevel analysis
items: Recent advances on natural depsidones: sources, biosynthesis, structure-activity relationship, and bioactivities
items: Current environmental status of the oyster farms on Lake Kamo in Japan; viral control of the harmful bloom of Heterocapsa circularisquama

Effects of the speed on the webbed foot kinematics of mallard (Anas platyrhynchos)
type: item
type: AcademicArticle
description: In this study, the effect of the speed on the webbed foot locomotion of the mallard was analyzed based on a considerable number of reliable indoor test data. Four adult male mallards were selected for analysis, and the locomotion speed of the mallard was controlled using the treadmill at an accurate and adjustable speed. The locomotion pattern of the webbed foot of the mallard at different speeds was recorded using a high-speed camera. The changes in the position and conformation of the webbed foot during locomotion on a treadmill were tracked and analyzed using Simi-Motion kinematics software. The results indicated that the stride length of the mallard increased, and the stance phase duration was shortened with the increase of the speed, whereas the swing phase duration did not vary significantly. The duty factor decreased with the increase of the mallard speed but not drop below to 0.5, because the mallards flew with their wings, or moved backward relative to the treadmill with the further increase of the speed. Using the energy method to further distinguish gait, and through the percentage of congruity analysis, it was found that between 0.73 and 0.93 m/s, the gait experienced a transition from walking to grounded running, with no significant changes in spatiotemporal parameters. At speeds between 0.93 and 1.6 m/s, mallards adopt a grounded running gait. The instantaneous changes of the tarsometatarso-phalangeal joint (TMTPJ) angle and the intertarsal joint (ITJ) angle at touch-down, mid-stance and lift-off concomitant with the change of the speed were examined with the TMTPJ and ITJ angle as the research objects. Moreover, the continuous changes of the joint angles were examined in a complete stride cycle. The result indicated that the increase of the speed will also make the TMTPJ and ITJ angle change ahead of time in a stride cycle, proving the shortened stance phase duration. The ITJ angle changed much more than the TMTPJ. Thus, the above result reveals that …
format: application/pdf
format: text/html
creator: Dianlei Han
creator: Hairui Liu
creator: Zhiqian Tong
creator: Jiahang Pan
creator: Xinzhong Wang
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.15362
publisher: PeerJ Inc.
rights: © 2023 Han et al.
abstract: In this study, the effect of the speed on the webbed foot locomotion of the mallard was analyzed based on a considerable number of reliable indoor test data. Four adult male mallards were selected for analysis, and the locomotion speed of the mallard was controlled using the treadmill at an accurate and adjustable speed. The locomotion pattern of the webbed foot of the mallard at different speeds was recorded using a high-speed camera. The changes in the position and conformation of the webbed foot during locomotion on a treadmill were tracked and analyzed using Simi-Motion kinematics software. The results indicated that the stride length of the mallard increased, and the stance phase duration was shortened with the increase of the speed, whereas the swing phase duration did not vary significantly. The duty factor decreased with the increase of the mallard speed but not drop below to 0.5, because the mallards flew with their wings, or moved backward relative to the treadmill with the further increase of the speed. Using the energy method to further distinguish gait, and through the percentage of congruity analysis, it was found that between 0.73 and 0.93 m/s, the gait experienced a transition from walking to grounded running, with no significant changes in spatiotemporal parameters. At speeds between 0.93 and 1.6 m/s, mallards adopt a grounded running gait. The instantaneous changes of the tarsometatarso-phalangeal joint (TMTPJ) angle and the intertarsal joint (ITJ) angle at touch-down, mid-stance and lift-off concomitant with the change of the speed were examined with the TMTPJ and ITJ angle as the research objects. Moreover, the continuous changes of the joint angles were examined in a complete stride cycle. The result indicated that the increase of the speed will also make the TMTPJ and ITJ angle change ahead of time in a stride cycle, proving the shortened stance phase duration. The ITJ angle changed much more than the TMTPJ. Thus, the above result reveals that …
bibliographic citation: Han et al. (2023) Effects of the speed on the webbed foot kinematics of mallard (Anas platyrhynchos). PeerJ 11:e15362 https://doi.org/10.7717/peerj.15362
date submitted: 2022-12-09
date accepted: 2023-04-16
issued: 2023-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Dianlei
author list: Agent
  family name: Liu
  given name: Hairui
author list: Agent
  family name: Tong
  given name: Zhiqian
author list: Agent
  family name: Pan
  given name: Jiahang
author list: Agent
  family name: Wang
  given name: Xinzhong
doi: 10.7717/peerj.15362
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-15
copyright: © 2023 Han et al.
attribution name: Han et al.

Infection of Atlantic tripletail Lobotes surinamensis (Teleostei: Lobotidae) by brain metacercariae Cardiocephaloides medioconiger (Digenea: Strigeidae)
type: item
type: AcademicArticle
description: Three juvenile Atlantic tripletail Lobotes surinamensis caught opportunistically in Charleston Harbor (South Carolina, USA) and maintained in captivity for over three months displayed an altered swimming behavior. While no direct causation can be demonstrated herein, fish were infected in their brain by strigeid trematode larvae (metacercariae) of Cardiocephaloides medioconiger, which were identified via ITS2 and 28S ribosomal RNA gene sequencing. Histology showed nonencysted metacercariae within the brain ventricle between the optic tectum and tegmentum, causing distortion of tegmental parenchyma. Aggregates of mononuclear inflammatory cells were in the ventricle adjacent to metacercariae. Metacercarial infection by Cardiocephaloides medioconiger has been reported from the brain and eyes of only two other fish species from the northern US Atlantic coast: the grey mullet Mugil cephalus and silverside Menidia menidia, but this identification is problematic and needs molecular verification. Atlantic tripletail is a new report as a second intermediate host for C. medioconiger and South Carolina is a new locality. Cardiocephaloides species in general have a low host specificity and infection by C. medioconiger could propagate to other fishes and affect neighboring natural ecosystems.
format: application/pdf
format: text/html
creator: Isaure de Buron
creator: Kristina M. Hill-Spanik
creator: Tiffany Baker
creator: Gabrielle Fignar
creator: Jason Broach
subject: Marine Biology
subject: Parasitology
subject: Histology
description: doi:10.7717/peerj.15365
publisher: PeerJ Inc.
rights: © 2023 de Buron et al.
abstract: Three juvenile Atlantic tripletail Lobotes surinamensis caught opportunistically in Charleston Harbor (South Carolina, USA) and maintained in captivity for over three months displayed an altered swimming behavior. While no direct causation can be demonstrated herein, fish were infected in their brain by strigeid trematode larvae (metacercariae) of Cardiocephaloides medioconiger, which were identified via ITS2 and 28S ribosomal RNA gene sequencing. Histology showed nonencysted metacercariae within the brain ventricle between the optic tectum and tegmentum, causing distortion of tegmental parenchyma. Aggregates of mononuclear inflammatory cells were in the ventricle adjacent to metacercariae. Metacercarial infection by Cardiocephaloides medioconiger has been reported from the brain and eyes of only two other fish species from the northern US Atlantic coast: the grey mullet Mugil cephalus and silverside Menidia menidia, but this identification is problematic and needs molecular verification. Atlantic tripletail is a new report as a second intermediate host for C. medioconiger and South Carolina is a new locality. Cardiocephaloides species in general have a low host specificity and infection by C. medioconiger could propagate to other fishes and affect neighboring natural ecosystems.
bibliographic citation: de Buron et al. (2023) Infection of Atlantic tripletail Lobotes surinamensis (Teleostei: Lobotidae) by brain metacercariae Cardiocephaloides medioconiger (Digenea: Strigeidae). PeerJ 11:e15365 https://doi.org/10.7717/peerj.15365
date submitted: 2023-01-10
date accepted: 2023-04-16
issued: 2023-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Buron
  given name: Isaure
author list: Agent
  family name: Hill-Spanik
  given name: Kristina M.
author list: Agent
  family name: Baker
  given name: Tiffany
author list: Agent
  family name: Fignar
  given name: Gabrielle
author list: Agent
  family name: Broach
  given name: Jason
doi: 10.7717/peerj.15365
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-15
copyright: ©2023 de Buron et al.
attribution name: de Buron et al.

Urinary aluminium and its association with autism spectrum disorder in urban preschool children in Malaysia
type: item
type: AcademicArticle
description: Background The presence of aluminium (Al) in the human body may impact brain neurodevelopment and function, and it is thought to contribute to autism spectrum disease (ASD). The main objective of this study was to assess the association between urinary Al and the development of ASD among Malaysian preschool children in the urban city of Kuala Lumpur. Method This was an unmatched case–control study in which children with ASD were recruited from an autism early intervention center and typically developed (TD) children were recruited from government-run nurseries and preschools. Urine samples were collected at home, assembled temporarily at study locations, and transported to the laboratory within 24 h. The Al concentration in the children’s urine samples was determined using inductively coupled plasma mass spectrometry (ICP-MS). Result A total of 155 preschool children; 81 ASD children and 74 TD children, aged 3 to 6 years, were enlisted in the study. This study demonstrated that ASD children had significantly higher urinary Al levels than TD children (median (interquartile range (IQR): 2.89 (6.77) µg/dL versus 0.96 (2.95) µg/dL) (p < 0.001). Higher parental education level, non-Malay ethnicity, male gender, and higher urinary Al level were the significant ASD risk factors (adjusted odds ratio (aOR) >1, p < 0.05). Conclusion A higher urine Al level was discovered to be a significant risk factor for ASD among preschool children in the urban area of Kuala Lumpur, Malaysia.
format: application/pdf
format: text/html
creator: Mohd Shahrol Abd Wahil
creator: Mohd Hasni Ja’afar
creator: Zaleha Md Isa
subject: Toxicology
subject: Neurology
subject: Pediatrics
subject: Public Health
subject: Environmental Health
description: doi:10.7717/peerj.15132
publisher: PeerJ Inc.
rights: © 2023 Abd Wahil et al.
abstract: Background The presence of aluminium (Al) in the human body may impact brain neurodevelopment and function, and it is thought to contribute to autism spectrum disease (ASD). The main objective of this study was to assess the association between urinary Al and the development of ASD among Malaysian preschool children in the urban city of Kuala Lumpur. Method This was an unmatched case–control study in which children with ASD were recruited from an autism early intervention center and typically developed (TD) children were recruited from government-run nurseries and preschools. Urine samples were collected at home, assembled temporarily at study locations, and transported to the laboratory within 24 h. The Al concentration in the children’s urine samples was determined using inductively coupled plasma mass spectrometry (ICP-MS). Result A total of 155 preschool children; 81 ASD children and 74 TD children, aged 3 to 6 years, were enlisted in the study. This study demonstrated that ASD children had significantly higher urinary Al levels than TD children (median (interquartile range (IQR): 2.89 (6.77) µg/dL versus 0.96 (2.95) µg/dL) (p < 0.001). Higher parental education level, non-Malay ethnicity, male gender, and higher urinary Al level were the significant ASD risk factors (adjusted odds ratio (aOR) >1, p < 0.05). Conclusion A higher urine Al level was discovered to be a significant risk factor for ASD among preschool children in the urban area of Kuala Lumpur, Malaysia.
bibliographic citation: Abd Wahil et al. (2023) Urinary aluminium and its association with autism spectrum disorder in urban preschool children in Malaysia. PeerJ 11:e15132 https://doi.org/10.7717/peerj.15132
date submitted: 2022-07-28
date accepted: 2023-03-06
issued: 2023-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abd Wahil
  given name: Mohd Shahrol
author list: Agent
  family name: Ja’afar
  given name: Mohd Hasni
author list: Agent
  family name: Md Isa
  given name: Zaleha
doi: 10.7717/peerj.15132
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-12
copyright: ©2023 Abd Wahil et al.
attribution name: Abd Wahil et al.

Psychological stress responses to a live performance by professional flamenco dancers
type: item
type: AcademicArticle
description: Dance is a high demanding discipline that involves physiological and psychological pressures. The pressure increases when dancers perform in front of an audience that, on a physiological level, can generate hormonal responses similar to those of an athlete before a competition for social status. Low levels of testosterone (T) and high levels of cortisol (C) are related to a decrease in performance and an increase in the risk of injury. Therefore, this study sets out to analyse hormone response patterns in professional flamenco dance performances depending on whether the performances are completed successfully and whether there are differences by sex and professional category. Saliva specimens (2–5 ml) were taken from the participants before and after the performance. Samples were immunoassayed by duplicate to analyze momentary fluctuations in two hormones regularly used in studies with professional athletes. The results showed significant differences in solo dancers’ T responses before and after the performance (p < 0.01), suggesting that the dancing role in the show (soloist or corps the ballet) and responsibility over the performance were important modulators to the hormone responses observed.
format: application/pdf
format: text/html
creator: Rosa de las Heras-Fernández
creator: Guillermo Mendoza
creator: Manuel Jimenez
subject: Diabetes and Endocrinology
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Sports Medicine
description: doi:10.7717/peerj.15282
publisher: PeerJ Inc.
rights: © 2023 De las Heras Fernández et al.
abstract: Dance is a high demanding discipline that involves physiological and psychological pressures. The pressure increases when dancers perform in front of an audience that, on a physiological level, can generate hormonal responses similar to those of an athlete before a competition for social status. Low levels of testosterone (T) and high levels of cortisol (C) are related to a decrease in performance and an increase in the risk of injury. Therefore, this study sets out to analyse hormone response patterns in professional flamenco dance performances depending on whether the performances are completed successfully and whether there are differences by sex and professional category. Saliva specimens (2–5 ml) were taken from the participants before and after the performance. Samples were immunoassayed by duplicate to analyze momentary fluctuations in two hormones regularly used in studies with professional athletes. The results showed significant differences in solo dancers’ T responses before and after the performance (p < 0.01), suggesting that the dancing role in the show (soloist or corps the ballet) and responsibility over the performance were important modulators to the hormone responses observed.
bibliographic citation: de las Heras-Fernández et al. (2023) Psychological stress responses to a live performance by professional flamenco dancers. PeerJ 11:e15282 https://doi.org/10.7717/peerj.15282
date submitted: 2022-12-27
date accepted: 2023-04-03
issued: 2023-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de las Heras-Fernández
  given name: Rosa
author list: Agent
  family name: Mendoza
  given name: Guillermo
author list: Agent
  family name: Jimenez
  given name: Manuel
doi: 10.7717/peerj.15282
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-12
copyright: © 2023 De las Heras Fernández et al.
attribution name: De las Heras Fernández et al.

A wild rice-derived peptide R14 ameliorates monosodium urate crystals-induced IL-1β secretion through inhibition of NF-κB signaling and NLRP3 inflammasome activation
type: item
type: AcademicArticle
description: Gout is an inflammatory arthritis initiated by the deposition of monosodium urate crystals (MSU) around the joints and surrounding tissues. MSU crystals activate the nucleotide-binding oligomerization domain-like receptor containing pyrin domain 3 (NLRP3) inflammasome to the release of interleukin-1β (IL-1β). Gout can have a substantial impact on patient’s quality of life, and currently available medicines are unable to meet all the clinical needs. This study explored anti-gout potentials of the Rice14 (R14) peptide, a peptide derived from leaves of wild rice Oryza minuta. The effects of R14 peptide on IL-1β secretion in THP-1 macrophages with MSU crystals-induced inflammation were examined. Our results clearly showed that the R14 peptide significantly inhibited the secretion of IL-1β in MSU crystals-induced macrophages, and the effects were dose-related. For safety testing, the R14 peptide did not show both cytotoxicity and hemolytic activity. In addition, the R14 peptide strongly suppressed the phospho-IκB-α and nuclear factor kappa-B (NF-κB) p65 proteins in NF-κB signaling pathway, reduced the NLRP3 expression and inhibited the MSU crystals-mediated cleavage of caspase-1 as well as mature IL-1β. The R14 peptide also reduced MSU-triggered intracellular ROS levels in macrophages. Taken together, these results indicated that R14 peptide inhibited MSU crystals-induced IL-1β production through NF-κB and NLRP3 inflammasome activation. Our findings demonstrated that R14 peptide, the newly recognized peptide from wild rice, possessed potent regulatory activity against IL-1β production in MSU crystals-induced inflammation, and we therefore propose that the R14 peptide is a promising molecule with potential clinical application in the treatment of MSU crystals-induced inflammation.
format: application/pdf
format: text/html
creator: Supattra Charoenwutthikun
creator: Kasem Chanjitwiriya
creator: Sittiruk Roytrakul
creator: Duangkamol Kunthalert
subject: Cell Biology
subject: Immunology
subject: Pharmacology
description: doi:10.7717/peerj.15295
publisher: PeerJ Inc.
rights: © 2023 Charoenwutthikun et al.
abstract: Gout is an inflammatory arthritis initiated by the deposition of monosodium urate crystals (MSU) around the joints and surrounding tissues. MSU crystals activate the nucleotide-binding oligomerization domain-like receptor containing pyrin domain 3 (NLRP3) inflammasome to the release of interleukin-1β (IL-1β). Gout can have a substantial impact on patient’s quality of life, and currently available medicines are unable to meet all the clinical needs. This study explored anti-gout potentials of the Rice14 (R14) peptide, a peptide derived from leaves of wild rice Oryza minuta. The effects of R14 peptide on IL-1β secretion in THP-1 macrophages with MSU crystals-induced inflammation were examined. Our results clearly showed that the R14 peptide significantly inhibited the secretion of IL-1β in MSU crystals-induced macrophages, and the effects were dose-related. For safety testing, the R14 peptide did not show both cytotoxicity and hemolytic activity. In addition, the R14 peptide strongly suppressed the phospho-IκB-α and nuclear factor kappa-B (NF-κB) p65 proteins in NF-κB signaling pathway, reduced the NLRP3 expression and inhibited the MSU crystals-mediated cleavage of caspase-1 as well as mature IL-1β. The R14 peptide also reduced MSU-triggered intracellular ROS levels in macrophages. Taken together, these results indicated that R14 peptide inhibited MSU crystals-induced IL-1β production through NF-κB and NLRP3 inflammasome activation. Our findings demonstrated that R14 peptide, the newly recognized peptide from wild rice, possessed potent regulatory activity against IL-1β production in MSU crystals-induced inflammation, and we therefore propose that the R14 peptide is a promising molecule with potential clinical application in the treatment of MSU crystals-induced inflammation.
bibliographic citation: Charoenwutthikun et al. (2023) A wild rice-derived peptide R14 ameliorates monosodium urate crystals-induced IL-1β secretion through inhibition of NF-κB signaling and NLRP3 inflammasome activation. PeerJ 11:e15295 https://doi.org/10.7717/peerj.15295
date submitted: 2022-10-05
date accepted: 2023-04-04
issued: 2023-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Charoenwutthikun
  given name: Supattra
author list: Agent
  family name: Chanjitwiriya
  given name: Kasem
author list: Agent
  family name: Roytrakul
  given name: Sittiruk
author list: Agent
  family name: Kunthalert
  given name: Duangkamol
doi: 10.7717/peerj.15295
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-12
copyright: ©2023 Charoenwutthikun et al.
attribution name: Charoenwutthikun et al.

Transcriptomic and metabolomic analysis of autumn leaf color change in Fraxinus angustifolia
type: item
type: AcademicArticle
description: Fraxinus angustifolia is a type of street tree and shade tree with ornamental value. It has a beautiful shape and yellow or reddish purple autumn leaves, but its leaf color formation mechanism and molecular regulation network need to be studied. In this study, we integrated the metabolomes and transcriptomes of stage 1 (green leaf) and stage 2 (red-purple leaf) leaves at two different developmental stages to screen differential candidate genes and metabolites related to leaf color variation. The results of stage 1 and stage 2 transcriptome analysis showed that a total of 5,827 genes were differentially expressed, including 2,249 upregulated genes and 3,578 downregulated genes. Through functional enrichment analysis of differentially expressed genes, we found that they were involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, pigment metabolism, carotene metabolism, terpenoid biosynthesis, secondary metabolite biosynthesis, pigment accumulation, and other biological processes. By measuring the metabolites of Fraxinus angustifolia leaves, we found the metabolites closely related to the differentially expressed genes in two different periods of Fraxinus angustifolia, among which flavonoid compounds were the main differential metabolites. Through transcriptome and metabolomics data association analysis, we screened nine differentially expressed genes related to anthocyanins. Transcriptome and qRT-PCR results showed that these nine genes showed significant expression differences in different stages of the sample, and we speculate that they are likely to be the main regulatory factors in the molecular mechanism of leaf coloration. This is the first time that we have analyzed the transcriptome combination metabolome in the process of leaf coloration of Fraxinus angustifolia, which has important guiding significance for directional breeding of colored-leaf Fraxinus species and will also give new insights for enriching the landscape.
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format: text/html
creator: Yanlong Wang
creator: Jinpeng Zhen
creator: Xiaoyu Che
creator: Kang Zhang
creator: Guowei Zhang
creator: Huijuan Yang
creator: Jing Wen
creator: Jinxin Wang
creator: Jiming Wang
creator: Bo He
creator: Ailong Yu
creator: Yanhui Li
creator: Zhigang Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
subject: Synthetic Biology
description: doi:10.7717/peerj.15319
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Fraxinus angustifolia is a type of street tree and shade tree with ornamental value. It has a beautiful shape and yellow or reddish purple autumn leaves, but its leaf color formation mechanism and molecular regulation network need to be studied. In this study, we integrated the metabolomes and transcriptomes of stage 1 (green leaf) and stage 2 (red-purple leaf) leaves at two different developmental stages to screen differential candidate genes and metabolites related to leaf color variation. The results of stage 1 and stage 2 transcriptome analysis showed that a total of 5,827 genes were differentially expressed, including 2,249 upregulated genes and 3,578 downregulated genes. Through functional enrichment analysis of differentially expressed genes, we found that they were involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, pigment metabolism, carotene metabolism, terpenoid biosynthesis, secondary metabolite biosynthesis, pigment accumulation, and other biological processes. By measuring the metabolites of Fraxinus angustifolia leaves, we found the metabolites closely related to the differentially expressed genes in two different periods of Fraxinus angustifolia, among which flavonoid compounds were the main differential metabolites. Through transcriptome and metabolomics data association analysis, we screened nine differentially expressed genes related to anthocyanins. Transcriptome and qRT-PCR results showed that these nine genes showed significant expression differences in different stages of the sample, and we speculate that they are likely to be the main regulatory factors in the molecular mechanism of leaf coloration. This is the first time that we have analyzed the transcriptome combination metabolome in the process of leaf coloration of Fraxinus angustifolia, which has important guiding significance for directional breeding of colored-leaf Fraxinus species and will also give new insights for enriching the landscape.
bibliographic citation: Wang et al. (2023) Transcriptomic and metabolomic analysis of autumn leaf color change in Fraxinus angustifolia. PeerJ 11:e15319 https://doi.org/10.7717/peerj.15319
date submitted: 2023-01-10
date accepted: 2023-04-10
issued: 2023-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yanlong
author list: Agent
  family name: Zhen
  given name: Jinpeng
author list: Agent
  family name: Che
  given name: Xiaoyu
author list: Agent
  family name: Zhang
  given name: Kang
author list: Agent
  family name: Zhang
  given name: Guowei
author list: Agent
  family name: Yang
  given name: Huijuan
author list: Agent
  family name: Wen
  given name: Jing
author list: Agent
  family name: Wang
  given name: Jinxin
author list: Agent
  family name: Wang
  given name: Jiming
author list: Agent
  family name: He
  given name: Bo
author list: Agent
  family name: Yu
  given name: Ailong
author list: Agent
  family name: Li
  given name: Yanhui
author list: Agent
  family name: Wang
  given name: Zhigang
doi: 10.7717/peerj.15319
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-12
copyright: ©2023 Wang et al.
attribution name: Wang et al.

A new application of multiplex PCR combined with membrane biochip assay for rapid detection of 9 common pathogens in sepsis
type: item
type: AcademicArticle
description: Rapid and accurate identification of specific sepsis pathogens is critical for patient treatment and disease control. This study aimed to establish a new application for the rapid identification of common pathogens in patients with suspected sepsis and evaluate its role in clinical application. A multiplex PCR assay was designed to simultaneously amplify specific conserved regions of nine common pathogenic microorganisms in sepsis, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumonia, and Candida albicans. The PCR products were analyzed by a membrane biochip. The analytical sensitivity of the assay was determined at a range of 5–100 copies/reaction for each standard strain, and the detection range was 20–200 cfu/reaction in a series dilution of simulated clinical samples at different concentrations. Out of the 179 clinical samples, the positive rate for pathogens detected by the membrane biochip assay and blood culture method was 20.11% (36/179) and 18.44% (33/179), respectively. However, by comparing the positive rate of the nine common pathogens we detected, the membrane biochip assay tended to be more sensitive than the blood culture method (20.11% vs 15.64%). The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the membrane biochip assay were 92.9%, 93.2%, 72.2% and 98.6%, respectively. Generally, this multiplex PCR combined membrane biochip assay can be used to detect major sepsis pathogens, and is useful for early initiation of effective antimicrobial treatment, and is feasible for sepsis pathogens identification in routine clinical practice.
format: application/pdf
format: text/html
creator: Yun Li
creator: LuJie Zhao
creator: Jingye Wang
creator: Peipei Qi
creator: Zhongfa Yang
creator: Xiangyu Zou
creator: Fujun Peng
creator: Shengguang Li
subject: Microbiology
subject: Epidemiology
description: doi:10.7717/peerj.15325
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Rapid and accurate identification of specific sepsis pathogens is critical for patient treatment and disease control. This study aimed to establish a new application for the rapid identification of common pathogens in patients with suspected sepsis and evaluate its role in clinical application. A multiplex PCR assay was designed to simultaneously amplify specific conserved regions of nine common pathogenic microorganisms in sepsis, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumonia, and Candida albicans. The PCR products were analyzed by a membrane biochip. The analytical sensitivity of the assay was determined at a range of 5–100 copies/reaction for each standard strain, and the detection range was 20–200 cfu/reaction in a series dilution of simulated clinical samples at different concentrations. Out of the 179 clinical samples, the positive rate for pathogens detected by the membrane biochip assay and blood culture method was 20.11% (36/179) and 18.44% (33/179), respectively. However, by comparing the positive rate of the nine common pathogens we detected, the membrane biochip assay tended to be more sensitive than the blood culture method (20.11% vs 15.64%). The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the membrane biochip assay were 92.9%, 93.2%, 72.2% and 98.6%, respectively. Generally, this multiplex PCR combined membrane biochip assay can be used to detect major sepsis pathogens, and is useful for early initiation of effective antimicrobial treatment, and is feasible for sepsis pathogens identification in routine clinical practice.
bibliographic citation: Li et al. (2023) A new application of multiplex PCR combined with membrane biochip assay for rapid detection of 9 common pathogens in sepsis. PeerJ 11:e15325 https://doi.org/10.7717/peerj.15325
date submitted: 2022-11-15
date accepted: 2023-04-10
issued: 2023-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yun
author list: Agent
  family name: Zhao
  given name: LuJie
author list: Agent
  family name: Wang
  given name: Jingye
author list: Agent
  family name: Qi
  given name: Peipei
author list: Agent
  family name: Yang
  given name: Zhongfa
author list: Agent
  family name: Zou
  given name: Xiangyu
author list: Agent
  family name: Peng
  given name: Fujun
author list: Agent
  family name: Li
  given name: Shengguang
doi: 10.7717/peerj.15325
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-12
copyright: © 2023 Li et al.
attribution name: Li et al.

Contraceptive use among reproductive-age females with disabilities in central Sidama National Regional State, Ethiopia: a multilevel analysis
type: item
type: AcademicArticle
description: Background Contraceptive use is an important and cost-effective intervention to prevent unwanted pregnancies. People with disabilities face discrimination when it comes to using contraception and are doubly burdened by unwanted pregnancies. However, the status of contraceptive use and associated factors among reproductive-aged females with disabilities was not adequately determined in Ethiopia. Objective This study aimed to assess contraceptive use and associated factors among reproductive-age females with disabilities in Dale and Wonsho districts and Yirgalem city administration of central Sidama National Regional State, Ethiopia. Methods A community-based cross-sectional study was conducted among randomly selected 620 reproductive-age females with disabilities living in the selected districts from June 20 to July 15, 2022. The data were collected through face-to-face interviewing techniques using a structured questionnaire. A multilevel logistic regression analysis model was employed to analyze the data. The adjusted odds ratio (AOR) with a 95% confidence interval (CI) was used to report the measures of associations. Results In this study, 27.3% (95% CI [23.8%–31.0%]) of the reproductive-age females with disabilities were current contraceptive users. Regarding the methods, 82 (48.5%) of the reproductive-age females with disabilities used implants. Having good contraceptive knowledge (AOR = 9.03; 95% CI [4.39–18.6]), transport accessibility to health facilities (AOR = 2.28; 95% CI [1.32–3.94]), being an adult (25 to 34 years old) (AOR = 3.04; 95% CI [1.53–6.04]), having a hearing disability (AOR = 0.38; 95% CI [0.18, 0.79]), having paralysis of the extremities (AOR = 0.06; 95% CI [0.03–0.12]), and wheel-chaired disability (AOR = 0.10; 95% CI [0.05–0.22]) were factors associated with contraceptive use. Conclusion Contraceptive use among reproductive-age females with disabilities is low. Transport accessibility, contraceptive knowledge, being in the age groups of 25 …
format: application/pdf
format: text/html
creator: Zelalem Tenaw
creator: Taye Gari
creator: Achamyelesh Gebretsadik
subject: Drugs and Devices
subject: Global Health
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.15354
publisher: PeerJ Inc.
rights: © 2023 Tenaw et al.
abstract: Background Contraceptive use is an important and cost-effective intervention to prevent unwanted pregnancies. People with disabilities face discrimination when it comes to using contraception and are doubly burdened by unwanted pregnancies. However, the status of contraceptive use and associated factors among reproductive-aged females with disabilities was not adequately determined in Ethiopia. Objective This study aimed to assess contraceptive use and associated factors among reproductive-age females with disabilities in Dale and Wonsho districts and Yirgalem city administration of central Sidama National Regional State, Ethiopia. Methods A community-based cross-sectional study was conducted among randomly selected 620 reproductive-age females with disabilities living in the selected districts from June 20 to July 15, 2022. The data were collected through face-to-face interviewing techniques using a structured questionnaire. A multilevel logistic regression analysis model was employed to analyze the data. The adjusted odds ratio (AOR) with a 95% confidence interval (CI) was used to report the measures of associations. Results In this study, 27.3% (95% CI [23.8%–31.0%]) of the reproductive-age females with disabilities were current contraceptive users. Regarding the methods, 82 (48.5%) of the reproductive-age females with disabilities used implants. Having good contraceptive knowledge (AOR = 9.03; 95% CI [4.39–18.6]), transport accessibility to health facilities (AOR = 2.28; 95% CI [1.32–3.94]), being an adult (25 to 34 years old) (AOR = 3.04; 95% CI [1.53–6.04]), having a hearing disability (AOR = 0.38; 95% CI [0.18, 0.79]), having paralysis of the extremities (AOR = 0.06; 95% CI [0.03–0.12]), and wheel-chaired disability (AOR = 0.10; 95% CI [0.05–0.22]) were factors associated with contraceptive use. Conclusion Contraceptive use among reproductive-age females with disabilities is low. Transport accessibility, contraceptive knowledge, being in the age groups of 25 …
bibliographic citation: Tenaw et al. (2023) Contraceptive use among reproductive-age females with disabilities in central Sidama National Regional State, Ethiopia: a multilevel analysis. PeerJ 11:e15354 https://doi.org/10.7717/peerj.15354
date submitted: 2022-12-23
date accepted: 2023-04-13
issued: 2023-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tenaw
  given name: Zelalem
author list: Agent
  family name: Gari
  given name: Taye
author list: Agent
  family name: Gebretsadik
  given name: Achamyelesh
doi: 10.7717/peerj.15354
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-12
copyright: ©2023 Tenaw et al.
attribution name: Tenaw et al.

Recent advances on natural depsidones: sources, biosynthesis, structure-activity relationship, and bioactivities
type: item
type: AcademicArticle
description: Depsidones are a class of polyphenolic polyketides that have been proposed to be biosynthesized from oxidative coupling of esters of two polyketidic benzoic acid derivatives. They are principally encountered in fungi and lichens. In addition to their diversified structural features, they revealed varied bioactivities such as antimicrobial, antimalarial, cytotoxic, anti-inflammatory, anti-Helicobacter pylori, antimycobacterial, antihypertensive, anti-diarrheal, antidiabetic, phytotoxic, anti-HIV, anti-osteoclastogenic, and butyrylcholinesterase, tyrosinase, hyaluronidase, and acetylcholinesterase inhibition. The current work was targeted to provide an overview on the naturally reported depsidones from various sources in the period from 2018 to the end of 2022 including their structures, biosynthesis, sources, and bioactivities, as well as the reported structure-activity relationship and semisynthetic derivatives. A total of 172 metabolites with 87 references were reviewed. The reported findings unambiguously demonstrated that these derivatives could be promising leads for therapeutic agents. However, further in-vivo evaluation of their potential biological properties and mechanistic investigations are needed.
format: application/pdf
format: text/html
creator: Maan T. Khayat
creator: Kholoud F. Ghazawi
creator: Waad A. Samman
creator: Aisha A. Alhaddad
creator: Gamal A. Mohamed
creator: Sabrin RM Ibrahim
subject: Biochemistry
subject: Bioengineering
subject: Mycology
description: doi:10.7717/peerj.15394
publisher: PeerJ Inc.
rights: © 2023 Khayat et al.
abstract: Depsidones are a class of polyphenolic polyketides that have been proposed to be biosynthesized from oxidative coupling of esters of two polyketidic benzoic acid derivatives. They are principally encountered in fungi and lichens. In addition to their diversified structural features, they revealed varied bioactivities such as antimicrobial, antimalarial, cytotoxic, anti-inflammatory, anti-Helicobacter pylori, antimycobacterial, antihypertensive, anti-diarrheal, antidiabetic, phytotoxic, anti-HIV, anti-osteoclastogenic, and butyrylcholinesterase, tyrosinase, hyaluronidase, and acetylcholinesterase inhibition. The current work was targeted to provide an overview on the naturally reported depsidones from various sources in the period from 2018 to the end of 2022 including their structures, biosynthesis, sources, and bioactivities, as well as the reported structure-activity relationship and semisynthetic derivatives. A total of 172 metabolites with 87 references were reviewed. The reported findings unambiguously demonstrated that these derivatives could be promising leads for therapeutic agents. However, further in-vivo evaluation of their potential biological properties and mechanistic investigations are needed.
bibliographic citation: Khayat et al. (2023) Recent advances on natural depsidones: sources, biosynthesis, structure-activity relationship, and bioactivities. PeerJ 11:e15394 https://doi.org/10.7717/peerj.15394
date submitted: 2023-02-09
date accepted: 2023-04-20
issued: 2023-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khayat
  given name: Maan T.
author list: Agent
  family name: Ghazawi
  given name: Kholoud F.
author list: Agent
  family name: Samman
  given name: Waad A.
author list: Agent
  family name: Alhaddad
  given name: Aisha A.
author list: Agent
  family name: Mohamed
  given name: Gamal A.
author list: Agent
  family name: Ibrahim
  given name: Sabrin RM
doi: 10.7717/peerj.15394
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-12
copyright: © 2023 Khayat et al.
attribution name: Khayat et al.

Current environmental status of the oyster farms on Lake Kamo in Japan; viral control of the harmful bloom of Heterocapsa circularisquama
type: item
type: AcademicArticle
description: Lake Kamo is an enclosed, low-inflow estuary connected to the open sea that is famous for oyster farming in Japan. In the fall of 2009, this lake experienced its first bloom of the dinoflagellate Heterocapsa circularisquama, which selectively kills bivalve mollusks. This species has been detected exclusively in southwestern Japan. The completely unexpected outbreak of H. circularisquama in the northern region is believed to have been caused by the contamination of purchased seedlings with this species. The water quality and nutrient data collected by our group from July through October over the past 10 years revealed that the environment of Lake Kamo has not changed significantly. However, in the open water around Sado Island, where Lake Kamo is located, the water temperature has increased by 1.80 °C in the last 100 years, which is equivalent to 2–3-fold the world average. This has resulted in a rise in the sea level, which is expected to further deteriorate the water exchange between Lake Kamo and the open sea and low dissolved oxygen in the bottom layer of the Lake and the associated dissolution of nutrients from the bottom sediment. Therefore, seawater exchange has become insufficient and the lake has become nutrient rich, making it prone to the establishment of microorganisms, such as H. circularisquama, once they have been introduced. We developed a method to mitigate the damage caused by the bloom by spraying sediments containing the H. circularisquama RNA virus (HcRNAV), which infects H. circularisquama. After ∼10 years of performing various verification tests, including field trials, this method was used at the Lake in 2019. During the 2019 H. circularisquama growth season, a small amount of sediment containing HcRNAV was sprayed on the lake three times, which resulted in a decrease in H. circularisquama and an increase in HcRNAV, indicating that this method is effective in diminishing the bloom.
format: application/pdf
format: text/html
creator: Natsuko Nakayama
creator: Saho Kitatsuji
creator: Masami Hamaguchi
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Molecular Biology
subject: Virology
subject: Zoology
description: doi:10.7717/peerj.14813
publisher: PeerJ Inc.
rights: © 2023 Nakayama et al.
abstract: Lake Kamo is an enclosed, low-inflow estuary connected to the open sea that is famous for oyster farming in Japan. In the fall of 2009, this lake experienced its first bloom of the dinoflagellate Heterocapsa circularisquama, which selectively kills bivalve mollusks. This species has been detected exclusively in southwestern Japan. The completely unexpected outbreak of H. circularisquama in the northern region is believed to have been caused by the contamination of purchased seedlings with this species. The water quality and nutrient data collected by our group from July through October over the past 10 years revealed that the environment of Lake Kamo has not changed significantly. However, in the open water around Sado Island, where Lake Kamo is located, the water temperature has increased by 1.80 °C in the last 100 years, which is equivalent to 2–3-fold the world average. This has resulted in a rise in the sea level, which is expected to further deteriorate the water exchange between Lake Kamo and the open sea and low dissolved oxygen in the bottom layer of the Lake and the associated dissolution of nutrients from the bottom sediment. Therefore, seawater exchange has become insufficient and the lake has become nutrient rich, making it prone to the establishment of microorganisms, such as H. circularisquama, once they have been introduced. We developed a method to mitigate the damage caused by the bloom by spraying sediments containing the H. circularisquama RNA virus (HcRNAV), which infects H. circularisquama. After ∼10 years of performing various verification tests, including field trials, this method was used at the Lake in 2019. During the 2019 H. circularisquama growth season, a small amount of sediment containing HcRNAV was sprayed on the lake three times, which resulted in a decrease in H. circularisquama and an increase in HcRNAV, indicating that this method is effective in diminishing the bloom.
bibliographic citation: Nakayama et al. (2023) Current environmental status of the oyster farms on Lake Kamo in Japan; viral control of the harmful bloom of Heterocapsa circularisquama. PeerJ 11:e14813 https://doi.org/10.7717/peerj.14813
date submitted: 2022-08-30
date accepted: 2023-01-06
issued: 2023-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nakayama
  given name: Natsuko
author list: Agent
  family name: Kitatsuji
  given name: Saho
author list: Agent
  family name: Hamaguchi
  given name: Masami
doi: 10.7717/peerj.14813
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-11
copyright: ©2023 Nakayama et al.
attribution name: Nakayama et al.

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