PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Fluconazole worsened lung inflammation, partly through lung microbiome dysbiosis in mice with ovalbumin-induced asthma
items: Deciphering the influence of evolutionary legacy and functional constraints on the patella: an example in modern rhinoceroses amongst perissodactyls
items: Co-applied biochar and drought tolerant PGPRs induced more improvement in soil quality and wheat production than their individual applications under drought conditions
items: Myrmozercon mites are highly host specific: two new species of Myrmozercon Berlese associated with sympatric Camponotus ants in southern Quintana Roo, Mexico
items: Among the world’s smallest vertebrates: a new miniaturized flea-toad (Brachycephalidae) from the Atlantic rainforest
items: Comparative transcriptome analysis of cucumber fruit tissues reveals novel regulatory genes in ascorbic acid biosynthesis
items: Antimicrobial and anti-endotoxin activity of N-acetylcysteine, calcium hydroxide and their combination against Enterococcus faecalis, Escherichia coli and lipopolysaccharides
items: House sparrows do not show a diel rhythm in double-strand DNA damage in erythrocytes
items: The regulation role of calcium channels in mammalian sperm function: a narrative review with a focus on humans and mice
items: Bacterial production of polyhydroxyalkanoates (PHAs) using various waste carbon sources

Fluconazole worsened lung inflammation, partly through lung microbiome dysbiosis in mice with ovalbumin-induced asthma
type: item
type: AcademicArticle
description: Innate immunity in asthma may be influenced by alterations in lung microbiota, potentially affecting disease severity. This study investigates the differences in lung inflammation and microbiome between asthma-ovalbumin (OVA) administered with and without fluconazole treatment in C57BL/6 mice. Additionally, the role of inflammation was examined in an in vitro study using a pulmonary cell line. At 30 days post-OVA administration, allergic asthma mice exhibited increased levels of IgE and IL-4 in serum and lung tissue, higher pathological scores, and elevated eosinophils in bronchoalveolar lavage fluid (BALF) compared to control mice. Asthma inflammation was characterized by elevated serum IL-6, increased lung cytokines (TNF-α, IL-6, IL-10), and higher fungal abundance confirmed by polymerase chain reaction (PCR). Fluconazole-treated asthma mice displayed higher levels of cytokines in serum and lung tissue (TNF-α and IL-6), increased pathological scores, and a higher number of mononuclear cells in BALF, with undetectable fungal levels compared to untreated mice. Lung microbiome analysis revealed similarities between control and asthma mice; however, fluconazole-treated asthma mice exhibited higher Bacteroidota levels, lower Firmicutes, and reduced bacterial abundance. Pro-inflammatory cytokine production was increased in supernatants of the pulmonary cell line (NCI-H292) after co-stimulation with LPS and beta-glucan (BG) compared to LPS alone. Fluconazole treatment in OVA-induced asthma mice exacerbated inflammation, partially due to fungi and Gram-negative bacteria, as demonstrated by LPS+BG-activated pulmonary cells. Therefore, fluconazole should be reserved for treating fungal asthma rather than asthma caused by other etiologies.
format: application/pdf
format: text/html
creator: Jesadakorn Worasilchai
creator: Piyapat Thongchaichayakon
creator: Kittipat Chansri
creator: Supichaya Leelahavanichkul
creator: Vathin Chiewvit
creator: Peerapat Visitchanakun
creator: Poorichaya Somparn
creator: Pratsanee Hiengrach
subject: Microbiology
subject: Allergy and Clinical Immunology
subject: Respiratory Medicine
description: doi:10.7717/peerj.18421
publisher: PeerJ Inc.
rights: © 2024 Worasilchai et al.
abstract: Innate immunity in asthma may be influenced by alterations in lung microbiota, potentially affecting disease severity. This study investigates the differences in lung inflammation and microbiome between asthma-ovalbumin (OVA) administered with and without fluconazole treatment in C57BL/6 mice. Additionally, the role of inflammation was examined in an in vitro study using a pulmonary cell line. At 30 days post-OVA administration, allergic asthma mice exhibited increased levels of IgE and IL-4 in serum and lung tissue, higher pathological scores, and elevated eosinophils in bronchoalveolar lavage fluid (BALF) compared to control mice. Asthma inflammation was characterized by elevated serum IL-6, increased lung cytokines (TNF-α, IL-6, IL-10), and higher fungal abundance confirmed by polymerase chain reaction (PCR). Fluconazole-treated asthma mice displayed higher levels of cytokines in serum and lung tissue (TNF-α and IL-6), increased pathological scores, and a higher number of mononuclear cells in BALF, with undetectable fungal levels compared to untreated mice. Lung microbiome analysis revealed similarities between control and asthma mice; however, fluconazole-treated asthma mice exhibited higher Bacteroidota levels, lower Firmicutes, and reduced bacterial abundance. Pro-inflammatory cytokine production was increased in supernatants of the pulmonary cell line (NCI-H292) after co-stimulation with LPS and beta-glucan (BG) compared to LPS alone. Fluconazole treatment in OVA-induced asthma mice exacerbated inflammation, partially due to fungi and Gram-negative bacteria, as demonstrated by LPS+BG-activated pulmonary cells. Therefore, fluconazole should be reserved for treating fungal asthma rather than asthma caused by other etiologies.
bibliographic citation: Worasilchai et al. (2024) Fluconazole worsened lung inflammation, partly through lung microbiome dysbiosis in mice with ovalbumin-induced asthma. PeerJ 12:e18421 https://doi.org/10.7717/peerj.18421
date submitted: 2024-06-19
date accepted: 2024-10-08
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Worasilchai
  given name: Jesadakorn
author list: Agent
  family name: Thongchaichayakon
  given name: Piyapat
author list: Agent
  family name: Chansri
  given name: Kittipat
author list: Agent
  family name: Leelahavanichkul
  given name: Supichaya
author list: Agent
  family name: Chiewvit
  given name: Vathin
author list: Agent
  family name: Visitchanakun
  given name: Peerapat
author list: Agent
  family name: Somparn
  given name: Poorichaya
author list: Agent
  family name: Hiengrach
  given name: Pratsanee
doi: 10.7717/peerj.18421
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: © 2024 Worasilchai et al.
attribution name: Worasilchai et al.

Deciphering the influence of evolutionary legacy and functional constraints on the patella: an example in modern rhinoceroses amongst perissodactyls
type: item
type: AcademicArticle
description: In mammals, the patella is the biggest sesamoid bone of the skeleton and is of crucial importance in posture and locomotion, ensuring the role of a pulley for leg extensors while protecting and stabilizing the knee joint. Despite its central biomechanical role, the relation between the shape of the patella and functional factors, such as body mass or locomotor habit, in the light of evolutionary legacy are poorly known. Here, we propose a morphofunctional investigation of the shape variation of the patella among modern rhinoceroses and more generally among perissodactyls, this order of ungulates displaying a broad range of body plan, body mass and locomotor habits, to understand how the shape of this sesamoid bone varies between species and relatively to these functional factors. Our investigation, relying on three dimensional geometric morphometrics and comparative analyses, reveals that, within Rhinocerotidae and between the three perissodactyl families, the shape of the patella strongly follows the phylogenetic affinities rather than variations in body mass. The patellar shape is more conservative than initially expected both within and between rhinoceroses, equids and tapirs. The development of a medial angle, engendering a strong mediolateral asymmetry of the patella, appears convergent in rhinoceroses and equids, while tapirs retain a symmetric bone close to the plesiomorphic condition of the order. This asymmetric patella is likely associated with the presence of a “knee locking” mechanism in both equids and rhinos. The emergence of this condition may be related to a shared locomotor habit (transverse gallop) in both groups. Our investigation underlines unexcepted evolutionary constraints on the shape of a sesamoid bone usually considered as mostly driven by functional factors.
format: application/pdf
format: text/html
creator: Christophe Mallet
creator: Alexandra Houssaye
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.18067
publisher: PeerJ Inc.
rights: © 2024 Mallet and Houssaye
abstract: In mammals, the patella is the biggest sesamoid bone of the skeleton and is of crucial importance in posture and locomotion, ensuring the role of a pulley for leg extensors while protecting and stabilizing the knee joint. Despite its central biomechanical role, the relation between the shape of the patella and functional factors, such as body mass or locomotor habit, in the light of evolutionary legacy are poorly known. Here, we propose a morphofunctional investigation of the shape variation of the patella among modern rhinoceroses and more generally among perissodactyls, this order of ungulates displaying a broad range of body plan, body mass and locomotor habits, to understand how the shape of this sesamoid bone varies between species and relatively to these functional factors. Our investigation, relying on three dimensional geometric morphometrics and comparative analyses, reveals that, within Rhinocerotidae and between the three perissodactyl families, the shape of the patella strongly follows the phylogenetic affinities rather than variations in body mass. The patellar shape is more conservative than initially expected both within and between rhinoceroses, equids and tapirs. The development of a medial angle, engendering a strong mediolateral asymmetry of the patella, appears convergent in rhinoceroses and equids, while tapirs retain a symmetric bone close to the plesiomorphic condition of the order. This asymmetric patella is likely associated with the presence of a “knee locking” mechanism in both equids and rhinos. The emergence of this condition may be related to a shared locomotor habit (transverse gallop) in both groups. Our investigation underlines unexcepted evolutionary constraints on the shape of a sesamoid bone usually considered as mostly driven by functional factors.
bibliographic citation: Mallet et al. (2024) Deciphering the influence of evolutionary legacy and functional constraints on the patella: an example in modern rhinoceroses amongst perissodactyls. PeerJ 12:e18067 https://doi.org/10.7717/peerj.18067
date submitted: 2024-02-29
date accepted: 2024-08-19
issued: 2024-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mallet
  given name: Christophe
author list: Agent
  family name: Houssaye
  given name: Alexandra
doi: 10.7717/peerj.18067
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-25
copyright: © 2024 Mallet and Houssaye
attribution name: Mallet and Houssaye

Co-applied biochar and drought tolerant PGPRs induced more improvement in soil quality and wheat production than their individual applications under drought conditions
type: item
type: AcademicArticle
description: Background Plant growth and development can be greatly impacted by drought stress. Suitable plant growth promoting rhizobacteria (PGPR) or biochar (BC) application has been shown to alleviate drought stress for plants. However, their co-application has not been extensively explored in this regard. Methods We isolated bacterial strains from rhizospheric soils of plants from arid soils and characterized them for plant growth promoting characteristics like IAA production and phosphate solubilization as well as for drought tolerance. Three bacterial strains or so called PGPRs, identified as Bacillus thuringiensis, Bacillus tropicus, and Bacillus paramycoides based on their 16S rRNA, were screened for further experiments. Wheat was grown on normal, where soil moisture was maintained at 75% of water holding capacity (WHC), and induced-drought (25% WHC) stressed soil in pots. PGPRs were applied alone or in combination with a biochar derived from pyrolysis of tree wood. Results Drought stress substantially inhibited wheat growth. However, biochar addition under stressed conditions significantly improved the wheat growth and productivity. Briefly, it increased straw yield by 25%, 100-grain weight by 15% and grain yield by 10% compared to the control. Moreover, co-application of biochar with PGPRs B. thuringiensis, B. tropicus and B. paramycoides further enhanced straw yield by 37–41%, 100-grain weight by 30–36%, and grain yield by 22–22.57%, respectively. The co-application also enhanced soil quality by increasing plant-available phosphorus by 4–31%, microbial biomass by 33–45%, and soil K+/Na+ ratio by 41–44%. Conclusion Co-application of PGPRs and biochar alleviated plant drought stress by improving nutrient availability and absorption. Acting as a nutrient reservoir, biochar worked alongside PGPRs, who solubilized nutrients from the former and promoted wheat growth. We recommend that the co-application of suitable PGPRs and biochar is a better technology to produce wheat …
format: application/pdf
format: text/html
creator: Laraib Malik
creator: Sabir Hussain
creator: Muhammad Shahid
creator: Faisal Mahmood
creator: Hayssam M. Ali
creator: Mehreen Malik
creator: Muhammad Sanaullah
creator: Zubda Zahid
creator: Tanvir Shahzad
subject: Environmental Sciences
subject: Agricultural Science
subject: Soil Science
subject: Environmental Impacts
description: doi:10.7717/peerj.18171
publisher: PeerJ Inc.
rights: © 2024 Malik et al.
abstract: Background Plant growth and development can be greatly impacted by drought stress. Suitable plant growth promoting rhizobacteria (PGPR) or biochar (BC) application has been shown to alleviate drought stress for plants. However, their co-application has not been extensively explored in this regard. Methods We isolated bacterial strains from rhizospheric soils of plants from arid soils and characterized them for plant growth promoting characteristics like IAA production and phosphate solubilization as well as for drought tolerance. Three bacterial strains or so called PGPRs, identified as Bacillus thuringiensis, Bacillus tropicus, and Bacillus paramycoides based on their 16S rRNA, were screened for further experiments. Wheat was grown on normal, where soil moisture was maintained at 75% of water holding capacity (WHC), and induced-drought (25% WHC) stressed soil in pots. PGPRs were applied alone or in combination with a biochar derived from pyrolysis of tree wood. Results Drought stress substantially inhibited wheat growth. However, biochar addition under stressed conditions significantly improved the wheat growth and productivity. Briefly, it increased straw yield by 25%, 100-grain weight by 15% and grain yield by 10% compared to the control. Moreover, co-application of biochar with PGPRs B. thuringiensis, B. tropicus and B. paramycoides further enhanced straw yield by 37–41%, 100-grain weight by 30–36%, and grain yield by 22–22.57%, respectively. The co-application also enhanced soil quality by increasing plant-available phosphorus by 4–31%, microbial biomass by 33–45%, and soil K+/Na+ ratio by 41–44%. Conclusion Co-application of PGPRs and biochar alleviated plant drought stress by improving nutrient availability and absorption. Acting as a nutrient reservoir, biochar worked alongside PGPRs, who solubilized nutrients from the former and promoted wheat growth. We recommend that the co-application of suitable PGPRs and biochar is a better technology to produce wheat …
bibliographic citation: Malik et al. (2024) Co-applied biochar and drought tolerant PGPRs induced more improvement in soil quality and wheat production than their individual applications under drought conditions. PeerJ 12:e18171 https://doi.org/10.7717/peerj.18171
date submitted: 2024-01-23
date accepted: 2024-09-03
issued: 2024-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malik
  given name: Laraib
author list: Agent
  family name: Hussain
  given name: Sabir
author list: Agent
  family name: Shahid
  given name: Muhammad
author list: Agent
  family name: Mahmood
  given name: Faisal
author list: Agent
  family name: Ali
  given name: Hayssam M.
author list: Agent
  family name: Malik
  given name: Mehreen
author list: Agent
  family name: Sanaullah
  given name: Muhammad
author list: Agent
  family name: Zahid
  given name: Zubda
author list: Agent
  family name: Shahzad
  given name: Tanvir
doi: 10.7717/peerj.18171
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-25
copyright: ©2024 Malik et al.
attribution name: Malik et al.

Myrmozercon mites are highly host specific: two new species of Myrmozercon Berlese associated with sympatric Camponotus ants in southern Quintana Roo, Mexico
type: item
type: AcademicArticle
description: Two new species of Myrmozercon, M. serratus sp. nov. and M. spatulatus sp. nov., are described based on adults and deutonymphs collected in association with ants in Mexico. They represent the first records of this genus from the Neotropic s.s. faunal region. Both new species are associated with hosts in the genus Camponotus from the same small area of a coastal lagoon, which share the same nesting habit preferences, providing strong evidence for host specificity. All but one colony of C. atriceps hosted mites, whereas they occurred in only half of the colonies of C. rectangularis. There was a significant positive correlation between the abundance of C. atriceps sexual ants and the abundance of mites. We summarize the known host associations for the genus Myrmozercon and discuss host specificity. Larvae of both mite species were collected on the wings of males and gynes suggesting that egg laying occurs on the hosts reproductive caste. Two hypotheses explaining this observation are discussed, larvae may be phoretic on winged sexuals, favoring mite co-dispersal with hosts, or larvae reside on the alates as a refuge from predation.
format: application/pdf
format: text/html
creator: Gabriela Pérez-Lachaud
creator: Hans Klompen
creator: Shahrooz Kazemi
creator: Jean-Paul Lachaud
subject: Animal Behavior
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.18197
publisher: PeerJ Inc.
rights: © 2024 Pérez-Lachaud et al.
abstract: Two new species of Myrmozercon, M. serratus sp. nov. and M. spatulatus sp. nov., are described based on adults and deutonymphs collected in association with ants in Mexico. They represent the first records of this genus from the Neotropic s.s. faunal region. Both new species are associated with hosts in the genus Camponotus from the same small area of a coastal lagoon, which share the same nesting habit preferences, providing strong evidence for host specificity. All but one colony of C. atriceps hosted mites, whereas they occurred in only half of the colonies of C. rectangularis. There was a significant positive correlation between the abundance of C. atriceps sexual ants and the abundance of mites. We summarize the known host associations for the genus Myrmozercon and discuss host specificity. Larvae of both mite species were collected on the wings of males and gynes suggesting that egg laying occurs on the hosts reproductive caste. Two hypotheses explaining this observation are discussed, larvae may be phoretic on winged sexuals, favoring mite co-dispersal with hosts, or larvae reside on the alates as a refuge from predation.
bibliographic citation: Pérez-Lachaud et al. (2024) Myrmozercon mites are highly host specific: two new species of Myrmozercon Berlese associated with sympatric Camponotus ants in southern Quintana Roo, Mexico. PeerJ 12:e18197 https://doi.org/10.7717/peerj.18197
date submitted: 2024-07-03
date accepted: 2024-09-09
issued: 2024-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pérez-Lachaud
  given name: Gabriela
author list: Agent
  family name: Klompen
  given name: Hans
author list: Agent
  family name: Kazemi
  given name: Shahrooz
author list: Agent
  family name: Lachaud
  given name: Jean-Paul
doi: 10.7717/peerj.18197
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-25
copyright: ©2024 Pérez-Lachaud et al.
attribution name: Pérez-Lachaud et al.

Among the world’s smallest vertebrates: a new miniaturized flea-toad (Brachycephalidae) from the Atlantic rainforest
type: item
type: AcademicArticle
description: The genus Brachycephalus includes miniaturized toadlets with two distinct morphotypes: brightly colored species with a bufoniform phenotype and smaller, cryptic species with a leptodactyliform phenotype. The diversity of leptodactyliform species is still underappreciated, and we generally lack fundamental information about their biology. Recent sampling efforts, including DNA analyses and recordings of advertisement calls, have improved our understanding of this group. In the present study, we describe a new species of Brachycephalus, one of the smallest vertebrates known. This new species is distinguished from its congeners by a combination of morphological, bioacoustic, and genetic data. Despite being among the smallest frogs globally (the second smallest amphibian species), it exhibits skeletal traits typical of larger frogs, such as the presence of cranial bones that are lost or fused in other miniature frogs, including other Brachycephalus. Our description underscores how new discoveries within the megadiverse fauna of the Atlantic Forest—a rich biodiversity hotspot—can provide insights into phenotypic variation, including vertebrate body size. By describing this new species, we also aim to revisit the hypothesis that the type series of B. hermogenesi includes two species, potentially including individuals of the species described here.
format: application/pdf
format: text/html
creator: Luís Felipe Toledo
creator: Lucas Machado Botelho
creator: Andres Santiago Carrasco-Medina
creator: Jaimi A. Gray
creator: Julia R. Ernetti
creator: Joana Moura Gama
creator: Mariana Lucio Lyra
creator: David C. Blackburn
creator: Ivan Nunes
creator: Edelcio Muscat
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.18265
publisher: PeerJ Inc.
rights: © 2024 Toledo et al.
abstract: The genus Brachycephalus includes miniaturized toadlets with two distinct morphotypes: brightly colored species with a bufoniform phenotype and smaller, cryptic species with a leptodactyliform phenotype. The diversity of leptodactyliform species is still underappreciated, and we generally lack fundamental information about their biology. Recent sampling efforts, including DNA analyses and recordings of advertisement calls, have improved our understanding of this group. In the present study, we describe a new species of Brachycephalus, one of the smallest vertebrates known. This new species is distinguished from its congeners by a combination of morphological, bioacoustic, and genetic data. Despite being among the smallest frogs globally (the second smallest amphibian species), it exhibits skeletal traits typical of larger frogs, such as the presence of cranial bones that are lost or fused in other miniature frogs, including other Brachycephalus. Our description underscores how new discoveries within the megadiverse fauna of the Atlantic Forest—a rich biodiversity hotspot—can provide insights into phenotypic variation, including vertebrate body size. By describing this new species, we also aim to revisit the hypothesis that the type series of B. hermogenesi includes two species, potentially including individuals of the species described here.
bibliographic citation: Toledo et al. (2024) Among the world’s smallest vertebrates: a new miniaturized flea-toad (Brachycephalidae) from the Atlantic rainforest. PeerJ 12:e18265 https://doi.org/10.7717/peerj.18265
date submitted: 2024-03-01
date accepted: 2024-09-17
issued: 2024-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Toledo
  given name: Luís Felipe
author list: Agent
  family name: Botelho
  given name: Lucas Machado
author list: Agent
  family name: Carrasco-Medina
  given name: Andres Santiago
author list: Agent
  family name: Gray
  given name: Jaimi A.
author list: Agent
  family name: Ernetti
  given name: Julia R.
author list: Agent
  family name: Gama
  given name: Joana Moura
author list: Agent
  family name: Lyra
  given name: Mariana Lucio
author list: Agent
  family name: Blackburn
  given name: David C.
author list: Agent
  family name: Nunes
  given name: Ivan
author list: Agent
  family name: Muscat
  given name: Edelcio
doi: 10.7717/peerj.18265
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-25
copyright: © 2024 Toledo et al.
attribution name: Toledo et al.

Comparative transcriptome analysis of cucumber fruit tissues reveals novel regulatory genes in ascorbic acid biosynthesis
type: item
type: AcademicArticle
description: Ascorbic acid (AsA) is one of the most abundant natural antioxidants, and it is an important indicator of the nutritional value of cucumber fruit. The aim of this study was to elucidate the regulatory mechanism affecting AsA metabolism in cucumber fruit. In this study, the AsA content in the fruit of two cucumber cultivars (H28 and H105) was significantly higher in the exocarp and endocarp than in the mesocarp. To clarify the regulation of AsA in cucumber fruit, the transcriptomes of three fruit tissues (i.e., the exocarp, mesocarp, and endocarp) of two cucumber cultivars (H28 and H105) were sequenced. Transcriptomic profiling combined with transcription factors (TFs) and correlation analysis were performed to reveal that three genes, including CsaV3_5G014110 (phosphomannomutase, PMM), CsaV3_2G004170 (GDP-mannose-3′, 5′-epimerase, GME) and CsaV3_5G006680 (dehydroascorbate reductase, DHAR), were expressed at higher level in the exocarp and endocarp than in the mesocarp. In both two cultivars, CsaV3_4G028360 (ethylene-responsive transcription factor, ERF) was negatively correlated with PMM and GME, and positively correlated with DHAR. CsaV3_6G042110 (ethylene-responsive transcription factor, ERF) was positively correlated with PMM and GME, and negatively correlated with DHAR. CsaV3_6G032360 (mitogen-activated protein kinase, MAPK) as positively correlated with PMM, GME and DHAR. These six genes are considered the key candidate genes for further research. This study provides insight for further study on the regulation of AsA biosynthesis in cucumber fruit and provide potential candidate genes for future genetic improvement of cucumber germplasm with enhanced AsA accumulation.
format: application/pdf
format: text/html
creator: Jun Ren
creator: Shenzao Fu
creator: Hongyao Wang
creator: Wenying Wang
creator: Xin Wang
creator: Haowen Zhang
creator: Zizheng Wang
creator: Min Huang
creator: Zemiao Liu
creator: Chaobiao Wu
creator: Kun Yang
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.18327
publisher: PeerJ Inc.
rights: © 2024 Ren et al.
abstract: Ascorbic acid (AsA) is one of the most abundant natural antioxidants, and it is an important indicator of the nutritional value of cucumber fruit. The aim of this study was to elucidate the regulatory mechanism affecting AsA metabolism in cucumber fruit. In this study, the AsA content in the fruit of two cucumber cultivars (H28 and H105) was significantly higher in the exocarp and endocarp than in the mesocarp. To clarify the regulation of AsA in cucumber fruit, the transcriptomes of three fruit tissues (i.e., the exocarp, mesocarp, and endocarp) of two cucumber cultivars (H28 and H105) were sequenced. Transcriptomic profiling combined with transcription factors (TFs) and correlation analysis were performed to reveal that three genes, including CsaV3_5G014110 (phosphomannomutase, PMM), CsaV3_2G004170 (GDP-mannose-3′, 5′-epimerase, GME) and CsaV3_5G006680 (dehydroascorbate reductase, DHAR), were expressed at higher level in the exocarp and endocarp than in the mesocarp. In both two cultivars, CsaV3_4G028360 (ethylene-responsive transcription factor, ERF) was negatively correlated with PMM and GME, and positively correlated with DHAR. CsaV3_6G042110 (ethylene-responsive transcription factor, ERF) was positively correlated with PMM and GME, and negatively correlated with DHAR. CsaV3_6G032360 (mitogen-activated protein kinase, MAPK) as positively correlated with PMM, GME and DHAR. These six genes are considered the key candidate genes for further research. This study provides insight for further study on the regulation of AsA biosynthesis in cucumber fruit and provide potential candidate genes for future genetic improvement of cucumber germplasm with enhanced AsA accumulation.
bibliographic citation: Ren et al. (2024) Comparative transcriptome analysis of cucumber fruit tissues reveals novel regulatory genes in ascorbic acid biosynthesis. PeerJ 12:e18327 https://doi.org/10.7717/peerj.18327
date submitted: 2024-04-30
date accepted: 2024-09-25
issued: 2024-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ren
  given name: Jun
author list: Agent
  family name: Fu
  given name: Shenzao
author list: Agent
  family name: Wang
  given name: Hongyao
author list: Agent
  family name: Wang
  given name: Wenying
author list: Agent
  family name: Wang
  given name: Xin
author list: Agent
  family name: Zhang
  given name: Haowen
author list: Agent
  family name: Wang
  given name: Zizheng
author list: Agent
  family name: Huang
  given name: Min
author list: Agent
  family name: Liu
  given name: Zemiao
author list: Agent
  family name: Wu
  given name: Chaobiao
author list: Agent
  family name: Yang
  given name: Kun
doi: 10.7717/peerj.18327
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-25
copyright: ©2024 Ren et al.
attribution name: Ren et al.

Antimicrobial and anti-endotoxin activity of N-acetylcysteine, calcium hydroxide and their combination against Enterococcus faecalis, Escherichia coli and lipopolysaccharides
type: item
type: AcademicArticle
description: Background The management of endodontic infections is a complex challenge, mainly due to the involvement of diverse microorganisms and their by-products. This study aimed to evaluate the efficacy of N-acetylcysteine (NAC), calcium hydroxide (Ca(OH)2), and their combined application as intracanal medications in combating Enterococcus faecalis, Escherichia coli, and lipopolysaccharides (LPS) from E. coli. Methods A total of 60 single-rooted human teeth were carefully selected and divided into six groups. These tooth canals were deliberately exposed to E. faecalis (ATCC 29212) and E. coli (ATCC 25922) to induce biofilm formation. Subsequently, the specimens were treated with NAC, Ca(OH)2, or a combination of both substances. Three samples of the root canals were collected at three moments: the first sample (S1) was to confirm the initial contamination, the second sample (S2) was immediately post-instrumentation, and the third sample (S3) was collected after the use of the intracanal medication. The antimicrobial efficacy of these intracanal medications was assessed by enumerating colony-forming units per milliliter (CFU/mL). In addition to this, the kinetic chromogenic Limulus Amebocyte Lysate (LAL) assay by Lonza was used to quantify LPS from E. coli. Data tested for normality; then, Kruskal-Wallis and Friedman tests were used, and Dunn’s for multiple comparisons. Results The findings of this study showed significant reductions in the microbial load of E. faecalis and E. coli by S3. Notably, there were no statistically significant differences among the treatment groups concerning these microorganisms. However, it was observed that only the combination of NAC and Ca(OH)2 led to a noteworthy decrease in the quantity of E. coli’s LPS after 7-days, demonstrating a statistically significant difference from the other treatment groups. NAC + Ca(OH)2 combination, applied for a duration of 7-days, proved to be more suitable in reducing the presence of E. faecalis, E. coli, and…
format: application/pdf
format: text/html
creator: Rayana Duarte Khoury
creator: Amjad Abu Hasna
creator: Carolina Fedel Gagliardi
creator: Renata Marques de Melo Marinho
creator: Cláudio Antonio Talge Carvalho
creator: Eduardo Bresciani
creator: Marcia Carneiro Valera
subject: Microbiology
subject: Dentistry
description: doi:10.7717/peerj.18331
publisher: PeerJ Inc.
rights: © 2024 Khoury et al.
abstract: Background The management of endodontic infections is a complex challenge, mainly due to the involvement of diverse microorganisms and their by-products. This study aimed to evaluate the efficacy of N-acetylcysteine (NAC), calcium hydroxide (Ca(OH)2), and their combined application as intracanal medications in combating Enterococcus faecalis, Escherichia coli, and lipopolysaccharides (LPS) from E. coli. Methods A total of 60 single-rooted human teeth were carefully selected and divided into six groups. These tooth canals were deliberately exposed to E. faecalis (ATCC 29212) and E. coli (ATCC 25922) to induce biofilm formation. Subsequently, the specimens were treated with NAC, Ca(OH)2, or a combination of both substances. Three samples of the root canals were collected at three moments: the first sample (S1) was to confirm the initial contamination, the second sample (S2) was immediately post-instrumentation, and the third sample (S3) was collected after the use of the intracanal medication. The antimicrobial efficacy of these intracanal medications was assessed by enumerating colony-forming units per milliliter (CFU/mL). In addition to this, the kinetic chromogenic Limulus Amebocyte Lysate (LAL) assay by Lonza was used to quantify LPS from E. coli. Data tested for normality; then, Kruskal-Wallis and Friedman tests were used, and Dunn’s for multiple comparisons. Results The findings of this study showed significant reductions in the microbial load of E. faecalis and E. coli by S3. Notably, there were no statistically significant differences among the treatment groups concerning these microorganisms. However, it was observed that only the combination of NAC and Ca(OH)2 led to a noteworthy decrease in the quantity of E. coli’s LPS after 7-days, demonstrating a statistically significant difference from the other treatment groups. NAC + Ca(OH)2 combination, applied for a duration of 7-days, proved to be more suitable in reducing the presence of E. faecalis, E. coli, and…
bibliographic citation: Khoury et al. (2024) Antimicrobial and anti-endotoxin activity of N-acetylcysteine, calcium hydroxide and their combination against Enterococcus faecalis, Escherichia coli and lipopolysaccharides. PeerJ 12:e18331 https://doi.org/10.7717/peerj.18331
date submitted: 2024-05-03
date accepted: 2024-09-25
issued: 2024-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khoury
  given name: Rayana Duarte
author list: Agent
  family name: Abu Hasna
  given name: Amjad
author list: Agent
  family name: Gagliardi
  given name: Carolina Fedel
author list: Agent
  family name: Marinho
  given name: Renata Marques de Melo
author list: Agent
  family name: Carvalho
  given name: Cláudio Antonio Talge
author list: Agent
  family name: Bresciani
  given name: Eduardo
author list: Agent
  family name: Valera
  given name: Marcia Carneiro
doi: 10.7717/peerj.18331
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-25
copyright: © 2024 Khoury et al.
attribution name: Khoury et al.

House sparrows do not show a diel rhythm in double-strand DNA damage in erythrocytes
type: item
type: AcademicArticle
description: DNA damage can be caused by a number of intrinsic and extrinsic factors. A recent study showed that free-living house sparrows (Passer domesticus) have higher DNA damage in the summer than the winter across five different tissues. This result was consistent when house sparrows were brought into captivity and exposed to comparable light cycles, with all other variables held constant. These results generated two hypotheses: (1) seasonal variation in DNA damage is related to circadian regulation and (2) seasonal variation in DNA damage is related to the total number of active hours. To investigate these hypotheses, we first quantified erythrocyte DNA damage in wild-caught house sparrows held in captivity on a 12L:12D light cycle at six points during the day to assess a diel or circadian rhythm but did not find one. We then performed a resonance experiment, in which birds experienced unnatural light cycles, and compared DNA damage in birds held on 6L:6D and 4.5L:7.5D resonance light cycles with their natural counterparts, 12L:12D and 9L:15D, respectively. We assessed corticosterone levels and DNA damage in blood before and after the resonance light cycles and DNA damage in abdominal fat, hippocampus, hypothalamus, and liver after the resonance light cycles. While our second experiment was not able to effectively test our hypotheses, we were able to demonstrate some interesting patterns. Throughout the resonance experiment, baseline corticosterone and testes size increased, consistent with the birds being photostimulated and preparing to breed. Surprisingly, the direction of change of DNA damage throughout the resonance photoperiod differed with tissue, which is not consistent with patterns during the breeding season in the wild. Our data indicate a potential uncoupling of the breeding physiology with the effect on DNA damage due to exposure to a resonance light cycle, which the birds may have interpreted as a skeleton photoperiod. Finally, though we were unable to fully…
format: application/pdf
format: text/html
creator: Emma Rosen
creator: Lily Mikolajczak
creator: Ursula K. Beattie
creator: L. Michael Romero
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.18375
publisher: PeerJ Inc.
rights: © 2024 Rosen et al.
abstract: DNA damage can be caused by a number of intrinsic and extrinsic factors. A recent study showed that free-living house sparrows (Passer domesticus) have higher DNA damage in the summer than the winter across five different tissues. This result was consistent when house sparrows were brought into captivity and exposed to comparable light cycles, with all other variables held constant. These results generated two hypotheses: (1) seasonal variation in DNA damage is related to circadian regulation and (2) seasonal variation in DNA damage is related to the total number of active hours. To investigate these hypotheses, we first quantified erythrocyte DNA damage in wild-caught house sparrows held in captivity on a 12L:12D light cycle at six points during the day to assess a diel or circadian rhythm but did not find one. We then performed a resonance experiment, in which birds experienced unnatural light cycles, and compared DNA damage in birds held on 6L:6D and 4.5L:7.5D resonance light cycles with their natural counterparts, 12L:12D and 9L:15D, respectively. We assessed corticosterone levels and DNA damage in blood before and after the resonance light cycles and DNA damage in abdominal fat, hippocampus, hypothalamus, and liver after the resonance light cycles. While our second experiment was not able to effectively test our hypotheses, we were able to demonstrate some interesting patterns. Throughout the resonance experiment, baseline corticosterone and testes size increased, consistent with the birds being photostimulated and preparing to breed. Surprisingly, the direction of change of DNA damage throughout the resonance photoperiod differed with tissue, which is not consistent with patterns during the breeding season in the wild. Our data indicate a potential uncoupling of the breeding physiology with the effect on DNA damage due to exposure to a resonance light cycle, which the birds may have interpreted as a skeleton photoperiod. Finally, though we were unable to fully…
bibliographic citation: Rosen et al. (2024) House sparrows do not show a diel rhythm in double-strand DNA damage in erythrocytes. PeerJ 12:e18375 https://doi.org/10.7717/peerj.18375
date submitted: 2024-06-12
date accepted: 2024-10-01
issued: 2024-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rosen
  given name: Emma
author list: Agent
  family name: Mikolajczak
  given name: Lily
author list: Agent
  family name: Beattie
  given name: Ursula K.
author list: Agent
  family name: Romero
  given name: L. Michael
doi: 10.7717/peerj.18375
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-25
copyright: ©2024 Rosen et al.
attribution name: Rosen et al.

The regulation role of calcium channels in mammalian sperm function: a narrative review with a focus on humans and mice
type: item
type: AcademicArticle
description: Mammalian sperm are characterized as specialized cells, as their transcriptional and translational processes are largely inactive. Emerging researches indicate that Ca2+ serves as a crucial second messenger in the modulation of various sperm physiological processes, such as capacitation, hyperactivation, and the acrosome reaction. Specifically, sperm-specific calcium channels, including CatSper, voltage-gated calcium channels (VGCCs), store-operated calcium channels (SOCCs), and cyclic nucleotide-gated (CNG) channels, are implicated in the regulation of calcium signaling in mammalian sperm. Calcium stores located in the sperm acrosomes, along with the IP3 receptors in the neck of the redundant nuclear envelope and the mitochondria in the tail, play significant roles in modulating intracellular Ca2+ levels in sperm. However, the functions and mechanisms of these calcium channels in modulating mammalian sperm physiological functions have not yet been well elucidated. Therefore, by focusing on humans and mice, this study aims to provide a comprehensive review of the current advancements in research regarding the roles of calcium signaling and associated calcium channels in regulating sperm function. This endeavor seeks to enhance the understanding of calcium signaling in sperm regulation and to facilitate the development of drugs for the treatment of infertility or as non-hormonal male contraceptives.
format: application/pdf
format: text/html
creator: Yebin Yang
creator: Liu Yang
creator: Xiaoqun Han
creator: Kuaiying Wu
creator: Guangquan Mei
creator: Baojian Wu
creator: Yimin Cheng
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.18429
publisher: PeerJ Inc.
rights: © 2024 Yang et al.
abstract: Mammalian sperm are characterized as specialized cells, as their transcriptional and translational processes are largely inactive. Emerging researches indicate that Ca2+ serves as a crucial second messenger in the modulation of various sperm physiological processes, such as capacitation, hyperactivation, and the acrosome reaction. Specifically, sperm-specific calcium channels, including CatSper, voltage-gated calcium channels (VGCCs), store-operated calcium channels (SOCCs), and cyclic nucleotide-gated (CNG) channels, are implicated in the regulation of calcium signaling in mammalian sperm. Calcium stores located in the sperm acrosomes, along with the IP3 receptors in the neck of the redundant nuclear envelope and the mitochondria in the tail, play significant roles in modulating intracellular Ca2+ levels in sperm. However, the functions and mechanisms of these calcium channels in modulating mammalian sperm physiological functions have not yet been well elucidated. Therefore, by focusing on humans and mice, this study aims to provide a comprehensive review of the current advancements in research regarding the roles of calcium signaling and associated calcium channels in regulating sperm function. This endeavor seeks to enhance the understanding of calcium signaling in sperm regulation and to facilitate the development of drugs for the treatment of infertility or as non-hormonal male contraceptives.
bibliographic citation: Yang et al. (2024) The regulation role of calcium channels in mammalian sperm function: a narrative review with a focus on humans and mice. PeerJ 12:e18429 https://doi.org/10.7717/peerj.18429
date submitted: 2024-06-14
date accepted: 2024-10-08
issued: 2024-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yebin
author list: Agent
  family name: Yang
  given name: Liu
author list: Agent
  family name: Han
  given name: Xiaoqun
author list: Agent
  family name: Wu
  given name: Kuaiying
author list: Agent
  family name: Mei
  given name: Guangquan
author list: Agent
  family name: Wu
  given name: Baojian
author list: Agent
  family name: Cheng
  given name: Yimin
doi: 10.7717/peerj.18429
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-25
copyright: © 2024 Yang et al.
attribution name: Yang et al.

Bacterial production of polyhydroxyalkanoates (PHAs) using various waste carbon sources
type: item
type: AcademicArticle
description: Synthetic plastics are in great demand in society due to their diversified properties, but they cause environmental pollution due to their non-biodegradable nature. Therefore, synthetic plastics are in need to be replaced with biodegradable plastics. Polyhydroxyalkanoates (PHAs), bacterial biopolymers are natural alternative to synthetic plastics. These are present inside the bacterial cytoplasm in granular form. Presently, the production cost of PHA is high due to expensive carbon substrates used in its biosynthesis. Therefore, this study focuses on the cost-effective production of PHA using waste carbon sources. Rice bran and sugarcane molasses were used as the carbon source for PHA production from Bacillus subtilis, Bacillus cereus, Alcaligenes sp. and Pseudomonas aeruginosa. PHA production from these bacterial strains was confirmed through Sudan Black-B screening. With rice bran, as carbon source, the highest PHA yield obtained was for P. aeruginosa, which yielded 93.7% and lowest was 35.5% for B. cereus. Surprisingly, B. cereus produced the highest cell dry mass (0.045 g/L) but its extracted PHA contents were lowest being only 0.02 g/L. Alcaligenes sp. with 0.031 g/L CDM yielded 87.1% PHA. B. subtilis had a CDM 0.029 g/L, 0.02 g/L PHA content and a yield of 69.10%. In the case of sugarcane molasses, P. aeruginosa produced 95% PHA yield, 0.02 g/L CDM, and 0.019 g/L PHA content. Alcaligenes sp. yielded 90.9% PHA, 0.011 g/L CDM, and 0.01 g/L PHA content. B. subtilis produced 91.6% PHA yield, 0.012 g/L CDM, 0.011 g/L PHA content; B. cereus produced 80% PHA yield, 0.015 g/L CDM, 0.012 g/L PHA content at 37 °C, pH 7. Higher concentrations of carbon sources increased the CDM and decreased the PHA yield. The maximum yield of PHA was obtained from sugarcane molasses. 24–48 h of incubation was optimal for B. subtilis and B. cereus, while for Alcaligenes and P. aeruginosa incubation time of 48–96 h was desirable for higher PHA yield. The extracted biopolymers were analyze…
format: application/pdf
format: text/html
creator: Aansa Naseem
creator: Ijaz Rasul
creator: Zulfiqar Ali Raza
creator: Faizan Muneer
creator: Asad ur Rehman
creator: Habibullah Nadeem
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.17936
publisher: PeerJ Inc.
rights: © 2024 Naseem et al.
abstract: Synthetic plastics are in great demand in society due to their diversified properties, but they cause environmental pollution due to their non-biodegradable nature. Therefore, synthetic plastics are in need to be replaced with biodegradable plastics. Polyhydroxyalkanoates (PHAs), bacterial biopolymers are natural alternative to synthetic plastics. These are present inside the bacterial cytoplasm in granular form. Presently, the production cost of PHA is high due to expensive carbon substrates used in its biosynthesis. Therefore, this study focuses on the cost-effective production of PHA using waste carbon sources. Rice bran and sugarcane molasses were used as the carbon source for PHA production from Bacillus subtilis, Bacillus cereus, Alcaligenes sp. and Pseudomonas aeruginosa. PHA production from these bacterial strains was confirmed through Sudan Black-B screening. With rice bran, as carbon source, the highest PHA yield obtained was for P. aeruginosa, which yielded 93.7% and lowest was 35.5% for B. cereus. Surprisingly, B. cereus produced the highest cell dry mass (0.045 g/L) but its extracted PHA contents were lowest being only 0.02 g/L. Alcaligenes sp. with 0.031 g/L CDM yielded 87.1% PHA. B. subtilis had a CDM 0.029 g/L, 0.02 g/L PHA content and a yield of 69.10%. In the case of sugarcane molasses, P. aeruginosa produced 95% PHA yield, 0.02 g/L CDM, and 0.019 g/L PHA content. Alcaligenes sp. yielded 90.9% PHA, 0.011 g/L CDM, and 0.01 g/L PHA content. B. subtilis produced 91.6% PHA yield, 0.012 g/L CDM, 0.011 g/L PHA content; B. cereus produced 80% PHA yield, 0.015 g/L CDM, 0.012 g/L PHA content at 37 °C, pH 7. Higher concentrations of carbon sources increased the CDM and decreased the PHA yield. The maximum yield of PHA was obtained from sugarcane molasses. 24–48 h of incubation was optimal for B. subtilis and B. cereus, while for Alcaligenes and P. aeruginosa incubation time of 48–96 h was desirable for higher PHA yield. The extracted biopolymers were analyze…
bibliographic citation: Naseem et al. (2024) Bacterial production of polyhydroxyalkanoates (PHAs) using various waste carbon sources. PeerJ 12:e17936 https://doi.org/10.7717/peerj.17936
date submitted: 2024-01-29
date accepted: 2024-07-26
issued: 2024-10-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Naseem
  given name: Aansa
author list: Agent
  family name: Rasul
  given name: Ijaz
author list: Agent
  family name: Ali Raza
  given name: Zulfiqar
author list: Agent
  family name: Muneer
  given name: Faizan
author list: Agent
  family name: ur Rehman
  given name: Asad
author list: Agent
  family name: Nadeem
  given name: Habibullah
doi: 10.7717/peerj.17936
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-24
copyright: ©2024 Naseem et al.
attribution name: Naseem et al.

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