PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer
items: miR2Trait: an integrated resource for investigating miRNA-disease associations
items: Impact of cover crop and mulching on soil physical properties and soil nutrients in a citrus orchard
items: A new volute, Ericusa ngayawang sp. nov. (Gastropoda: Volutidae), from the Miocene of South Australia
items: Effects of combination of obesity, diabetes, and hypoxia on inflammatory regulating genes and cytokines in rat pancreatic tissues and serum
items: Characterization of Staphylococcus epidermidis clinical isolates from hospitalized patients with bloodstream infection obtained in two time periods
items: Studying kinematic linkage of finger joints: estimation of kinematics of distal interphalangeal joints during manipulation
items: Theacrine alleviates sepsis-induced acute kidney injury by repressing the activation of NLRP3/Caspase-1 inflammasome
items: Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance
items: Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages

MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer
type: item
type: AcademicArticle
description: Background Recent studies have characterized that microRNA (miRNA) is a suitable candidate for the study of bleomycin/LPS-induced pulmonary fibrosis, but the knowledge on miRNA in bacteria-induced pulmonary fibrosis (BIPF) is limited. Forest musk deer (Moschus berezovskii, FMD) is an important endangered species that has been seriously affected by BIPF. We sought to determine whether miRNA exist that modulates the pathogenesis of BIPF in FMD. Methods High-throughput sequencing and RT-qPCR were used to determine the differentially expressed miRNAs (DEmiRNAs) in the blood of BIPF FMD. The DEmiRNAs were further detected in the blood and lung of BIPF model rat by RT-qPCR, and the targeting relationship between candidate miRNA and its potential target gene was verified by dual-luciferase reporter activity assay. Furthermore, the function of the candidate miRNA was verified in the FMD lung fibroblast cells (FMD-C1). Results Here we found that five dead FMD were suffered from BIPF, and six circulating miRNAs (miR-30g, let-7f-5p, miR-27-3p, miR-25-3p, miR-9-5p and miR-652) were differentially expressed in the blood of the BIPF FMD. Of these, let-7f-5p showed reproducibly lower level in the blood and lung of the BIPF model rat, and the expression levels of PI3K/AKT/COX2 signaling pathway genes (PIK3CA, PDK1, Akt1, IKBKA, NF-κB1 and COX2) were increased in the lung of BIPF model rats, suggesting that there is a potential correlation between BIPF and the PI3K/AKT/COX2 signaling pathway. Notably, using bioinformatic prediction and experimental verification, we demonstrated that let-7f-5p is conserved across mammals, and the seed sequence of let-7f-5p displays perfect complementarity with the 3’ UTR of PIK3CA gene and the expression of the PIK3CA gene was regulated by let-7f-5p. In order to determine the regulatory relationship between let-7f-5p and the PI3K/AKT/COX2 signaling pathway in FMD, we successfully cultured FMD-C1, and found that let-7f-5p could act as a negative regul…
format: application/pdf
format: text/html
creator: Wei Zhao
creator: Jianguo Cheng
creator: Yan Luo
creator: Wenlong Fu
creator: Lei Zhou
creator: Xiang Wang
creator: Yin Wang
creator: Zexiao Yang
creator: Xueping Yao
creator: Meishen Ren
creator: Zhijun Zhong
creator: Xi Wu
creator: Ziwei Ren
creator: Yimeng Li
subject: Biochemistry
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.14097
publisher: PeerJ Inc.
rights: © 2022 Zhao et al.
abstract: Background Recent studies have characterized that microRNA (miRNA) is a suitable candidate for the study of bleomycin/LPS-induced pulmonary fibrosis, but the knowledge on miRNA in bacteria-induced pulmonary fibrosis (BIPF) is limited. Forest musk deer (Moschus berezovskii, FMD) is an important endangered species that has been seriously affected by BIPF. We sought to determine whether miRNA exist that modulates the pathogenesis of BIPF in FMD. Methods High-throughput sequencing and RT-qPCR were used to determine the differentially expressed miRNAs (DEmiRNAs) in the blood of BIPF FMD. The DEmiRNAs were further detected in the blood and lung of BIPF model rat by RT-qPCR, and the targeting relationship between candidate miRNA and its potential target gene was verified by dual-luciferase reporter activity assay. Furthermore, the function of the candidate miRNA was verified in the FMD lung fibroblast cells (FMD-C1). Results Here we found that five dead FMD were suffered from BIPF, and six circulating miRNAs (miR-30g, let-7f-5p, miR-27-3p, miR-25-3p, miR-9-5p and miR-652) were differentially expressed in the blood of the BIPF FMD. Of these, let-7f-5p showed reproducibly lower level in the blood and lung of the BIPF model rat, and the expression levels of PI3K/AKT/COX2 signaling pathway genes (PIK3CA, PDK1, Akt1, IKBKA, NF-κB1 and COX2) were increased in the lung of BIPF model rats, suggesting that there is a potential correlation between BIPF and the PI3K/AKT/COX2 signaling pathway. Notably, using bioinformatic prediction and experimental verification, we demonstrated that let-7f-5p is conserved across mammals, and the seed sequence of let-7f-5p displays perfect complementarity with the 3’ UTR of PIK3CA gene and the expression of the PIK3CA gene was regulated by let-7f-5p. In order to determine the regulatory relationship between let-7f-5p and the PI3K/AKT/COX2 signaling pathway in FMD, we successfully cultured FMD-C1, and found that let-7f-5p could act as a negative regul…
bibliographic citation: Zhao et al. (2022) MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer. PeerJ 10:e14097 https://doi.org/10.7717/peerj.14097
date submitted: 2022-06-07
date accepted: 2022-08-31
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Wei
author list: Agent
  family name: Cheng
  given name: Jianguo
author list: Agent
  family name: Luo
  given name: Yan
author list: Agent
  family name: Fu
  given name: Wenlong
author list: Agent
  family name: Zhou
  given name: Lei
author list: Agent
  family name: Wang
  given name: Xiang
author list: Agent
  family name: Wang
  given name: Yin
author list: Agent
  family name: Yang
  given name: Zexiao
author list: Agent
  family name: Yao
  given name: Xueping
author list: Agent
  family name: Ren
  given name: Meishen
author list: Agent
  family name: Zhong
  given name: Zhijun
author list: Agent
  family name: Wu
  given name: Xi
author list: Agent
  family name: Ren
  given name: Ziwei
author list: Agent
  family name: Li
  given name: Yimeng
doi: 10.7717/peerj.14097
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: ©2022 Zhao et al.
attribution name: Zhao et al.

miR2Trait: an integrated resource for investigating miRNA-disease associations
type: item
type: AcademicArticle
description: MicroRNAs are key components of cellular regulatory networks, and breakdown in miRNA function causes cascading effects leading to pathophenotypes. A better understanding of the role of miRNAs in diseases is essential for human health. Here, we have devised a method for comprehensively mapping the associations between miRNAs and diseases by merging on a common key between two curated omics databases. The resulting bidirectional resource, miR2Trait, is more detailed than earlier catalogs, uncovers new relationships, and includes analytical utilities to interrogate and extract knowledge from these datasets. miR2Trait provides resources to compute the disease enrichment of a user-given set of miRNAs and analyze the miRNA profile of a specified diseasome. Reproducible examples demonstrating use-cases for each of these resource components are illustrated. Furthermore we used these tools to construct pairwise miRNA-miRNA and disease-disease enrichment networks, and identified 23 central miRNAs that could underlie major regulatory functions in the human genome. miR2Trait is available as an open-source command-line interface in Python3 (URL: https://github.com/miR2Trait) with a companion wiki documenting the scripts and data resources developed, under MIT license for commercial and non-commercial use. A minimal web-based implementation has been made available at https://sas.sastra.edu/pymir18. Supplementary information is available at: https://doi.org/10.6084/m9.figshare.8288825.v3.
format: application/pdf
format: text/html
creator: Poornima Babu
creator: Ashok Palaniappan
subject: Bioinformatics
subject: Biotechnology
subject: Computational Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.14146
publisher: PeerJ Inc.
rights: © 2022 Babu and Palaniappan
abstract: MicroRNAs are key components of cellular regulatory networks, and breakdown in miRNA function causes cascading effects leading to pathophenotypes. A better understanding of the role of miRNAs in diseases is essential for human health. Here, we have devised a method for comprehensively mapping the associations between miRNAs and diseases by merging on a common key between two curated omics databases. The resulting bidirectional resource, miR2Trait, is more detailed than earlier catalogs, uncovers new relationships, and includes analytical utilities to interrogate and extract knowledge from these datasets. miR2Trait provides resources to compute the disease enrichment of a user-given set of miRNAs and analyze the miRNA profile of a specified diseasome. Reproducible examples demonstrating use-cases for each of these resource components are illustrated. Furthermore we used these tools to construct pairwise miRNA-miRNA and disease-disease enrichment networks, and identified 23 central miRNAs that could underlie major regulatory functions in the human genome. miR2Trait is available as an open-source command-line interface in Python3 (URL: https://github.com/miR2Trait) with a companion wiki documenting the scripts and data resources developed, under MIT license for commercial and non-commercial use. A minimal web-based implementation has been made available at https://sas.sastra.edu/pymir18. Supplementary information is available at: https://doi.org/10.6084/m9.figshare.8288825.v3.
bibliographic citation: Babu et al. (2022) miR2Trait: an integrated resource for investigating miRNA-disease associations. PeerJ 10:e14146 https://doi.org/10.7717/peerj.14146
date submitted: 2022-06-07
date accepted: 2022-09-07
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Babu
  given name: Poornima
author list: Agent
  family name: Palaniappan
  given name: Ashok
doi: 10.7717/peerj.14146
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: ©2022 Babu and Palaniappan
attribution name: Babu and Palaniappan

Impact of cover crop and mulching on soil physical properties and soil nutrients in a citrus orchard
type: item
type: AcademicArticle
description: Background Cover crops and mulching can ameliorate soil porosity and nutrient availability, but their effects on the physical characteristics and nutrients in the raised bed soils are unclear. Methods The field experiment was conducted in a pomelo orchard from 2019 to 2021, with an area of 1,500 m2. The treatments included control (no cover crop), non-legume cover crop (Commelina communis L.), legume cover crop (Arachis pintoi Krabov & W.C. Gregory), and rice straw mulching (Oryza sativa L.). At the end of each year (2019, 2020, and 2021), soil samples were collected at four different layers (0–10, 10–20, 20–30, and 30–40 cm) in each treatment. Soil bulk density, soil porosity, and the concentration of nutrients in the soil were investigated. Results The results revealed that soil bulk density at two depths, 0–10 and 10–20 cm, was reduced by 0.07 and 0.08 g cm−3 by rice straw mulch and a leguminous cover crop, thus, increasing soil porosity by ~2.74% and ~3.01%, respectively. Soil nutrients (Ca, K, Fe, and Zn) at topsoil (0–10 cm) and subsoil (10–20 cm) layers were not significantly different in the first year, but those nutrients (Ca, K, Fe, and Zn) improved greatly in the second and third years. Conclusions Legume cover crops and straw mulch enhanced soil porosity and plant nutrient availability (Ca, K, Fe, and Zn). These conservation practices best benefit fruit orchards cultivated in the raised bed soils.
format: application/pdf
format: text/html
creator: Tran Van Dung
creator: Ngo Phuong Ngoc
creator: Le Van Dang
creator: Ngo Ngoc Hung
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.14170
publisher: PeerJ Inc.
rights: © 2022 Dung et al.
abstract: Background Cover crops and mulching can ameliorate soil porosity and nutrient availability, but their effects on the physical characteristics and nutrients in the raised bed soils are unclear. Methods The field experiment was conducted in a pomelo orchard from 2019 to 2021, with an area of 1,500 m2. The treatments included control (no cover crop), non-legume cover crop (Commelina communis L.), legume cover crop (Arachis pintoi Krabov & W.C. Gregory), and rice straw mulching (Oryza sativa L.). At the end of each year (2019, 2020, and 2021), soil samples were collected at four different layers (0–10, 10–20, 20–30, and 30–40 cm) in each treatment. Soil bulk density, soil porosity, and the concentration of nutrients in the soil were investigated. Results The results revealed that soil bulk density at two depths, 0–10 and 10–20 cm, was reduced by 0.07 and 0.08 g cm−3 by rice straw mulch and a leguminous cover crop, thus, increasing soil porosity by ~2.74% and ~3.01%, respectively. Soil nutrients (Ca, K, Fe, and Zn) at topsoil (0–10 cm) and subsoil (10–20 cm) layers were not significantly different in the first year, but those nutrients (Ca, K, Fe, and Zn) improved greatly in the second and third years. Conclusions Legume cover crops and straw mulch enhanced soil porosity and plant nutrient availability (Ca, K, Fe, and Zn). These conservation practices best benefit fruit orchards cultivated in the raised bed soils.
bibliographic citation: Dung et al. (2022) Impact of cover crop and mulching on soil physical properties and soil nutrients in a citrus orchard. PeerJ 10:e14170 https://doi.org/10.7717/peerj.14170
date submitted: 2022-05-10
date accepted: 2022-09-12
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dung
  given name: Tran Van
author list: Agent
  family name: Ngoc
  given name: Ngo Phuong
author list: Agent
  family name: Dang
  given name: Le Van
author list: Agent
  family name: Hung
  given name: Ngo Ngoc
doi: 10.7717/peerj.14170
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: © 2022 Dung et al.
attribution name: Dung et al.

A new volute, Ericusa ngayawang sp. nov. (Gastropoda: Volutidae), from the Miocene of South Australia
type: item
type: AcademicArticle
description: Ericusa ngayawang sp. nov. is described from shells preserved in the Middle Miocene Cadell Formation in the western Murray Basin of South Australia. At the time the Murray Basin was part of the Southeastern Australian Marine Biogeographic Province. Ericusa ngayawang is a small heavily costate species of Ericusa with clear affinities to the Early Miocene E. atkinsoni of Victoria and Tasmania but can be distinguished from it by its smaller size, more slender proportions and its heavily costate body whorl. Ericusa atkinsoni and its relative, E. macroptera, inhabited the basins to the east of the Murray Basin during the Late Oligocene and Early Miocene but were extinct there before the end of the Burdigalian Stage of the Early Miocene. The persistence of E. ngayawang into the Langhian Stage of the Middle Miocene is another piece of evidence for partial biogeographic isolation of the western Murray Basin from the rest of the Southeastern Australian Province during the Miocene.
format: application/pdf
format: text/html
creator: Adam M. Yates
subject: Biogeography
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14197
publisher: PeerJ Inc.
rights: © 2022 Yates
abstract: Ericusa ngayawang sp. nov. is described from shells preserved in the Middle Miocene Cadell Formation in the western Murray Basin of South Australia. At the time the Murray Basin was part of the Southeastern Australian Marine Biogeographic Province. Ericusa ngayawang is a small heavily costate species of Ericusa with clear affinities to the Early Miocene E. atkinsoni of Victoria and Tasmania but can be distinguished from it by its smaller size, more slender proportions and its heavily costate body whorl. Ericusa atkinsoni and its relative, E. macroptera, inhabited the basins to the east of the Murray Basin during the Late Oligocene and Early Miocene but were extinct there before the end of the Burdigalian Stage of the Early Miocene. The persistence of E. ngayawang into the Langhian Stage of the Middle Miocene is another piece of evidence for partial biogeographic isolation of the western Murray Basin from the rest of the Southeastern Australian Province during the Miocene.
bibliographic citation: Yates (2022) A new volute, Ericusa ngayawang sp. nov. (Gastropoda: Volutidae), from the Miocene of South Australia. PeerJ 10:e14197 https://doi.org/10.7717/peerj.14197
date submitted: 2022-02-25
date accepted: 2022-09-15
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yates
  given name: Adam M.
doi: 10.7717/peerj.14197
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: © 2022 Yates
attribution name: Yates

Effects of combination of obesity, diabetes, and hypoxia on inflammatory regulating genes and cytokines in rat pancreatic tissues and serum
type: item
type: AcademicArticle
description: Background Obesity and diabetes are becoming increasingly prevalent around the world. Inflammation, oxidative stress, insulin resistance, and glucose intolerance are linked to both obesity and type 2 diabetes, and these disorders are becoming major public health issues globally. Methods This study evaluated the effects of obesity, diabetes, and hypoxia on the levels of pro- and anti-inflammatory cytokines in rats. We divided 120 Wistar rats in two groups, male and female, each including six subgroups: control (CTRL), obese (high-fat diet (HFD)), diabetic (streptozotocin (STZ)-treated), hypoxic (HYX), obese + diabetic (HFD/STZ), and obese + diabetic + hypoxic (HFD/STZ/HYX). We examined the levels of tumor necrosis factor-α (TNF-α), interleukin (IL)-6, IL10, and leptin in pancreatic tissues and serum. Results No significant difference was observed in serum levels of cholesterol, triglycerides, and low-density lipoprotein (LDL) between HYX and CTRL in either sex. However, they were significantly increased, whereas high-density lipoprotein (HDL) was significantly decreased in HFD, STZ, HFD/STZ, and HFD/STZ/HPX compared with CTRL in both sexes. The expression of Tnf-α, Il6, and Lep was significantly upregulated in all subgroups compared with CTRL in both sexes. STZ and HYX showed no significant differences in the expression of these genes between sexes, whereas Tnf-α and Il6 were upregulated in male HFD, HFD/STZ, and HFD/STZ/HYX compared with females. Protein levels showed similar patterns. Combination subgroups, either in the absence or presence of hypoxia, frequently exhibited severe necrosis of endocrine components in pancreatic lobules. The combination of obesity, diabetes, and hypoxia was associated with inflammation, which was verified at the histopathological level.
format: application/pdf
format: text/html
creator: Sarah Albogami
creator: Aziza Hassan
creator: Sekena H. Abdel-Aziem
creator: Saqer Alotaibi
creator: Fayez Althobaiti
creator: Ahmed El-Shehawi
creator: Alaa Alnefaie
creator: Reem Abdulla Alhamed
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.13990
publisher: PeerJ Inc.
rights: © 2022 Albogami et al.
abstract: Background Obesity and diabetes are becoming increasingly prevalent around the world. Inflammation, oxidative stress, insulin resistance, and glucose intolerance are linked to both obesity and type 2 diabetes, and these disorders are becoming major public health issues globally. Methods This study evaluated the effects of obesity, diabetes, and hypoxia on the levels of pro- and anti-inflammatory cytokines in rats. We divided 120 Wistar rats in two groups, male and female, each including six subgroups: control (CTRL), obese (high-fat diet (HFD)), diabetic (streptozotocin (STZ)-treated), hypoxic (HYX), obese + diabetic (HFD/STZ), and obese + diabetic + hypoxic (HFD/STZ/HYX). We examined the levels of tumor necrosis factor-α (TNF-α), interleukin (IL)-6, IL10, and leptin in pancreatic tissues and serum. Results No significant difference was observed in serum levels of cholesterol, triglycerides, and low-density lipoprotein (LDL) between HYX and CTRL in either sex. However, they were significantly increased, whereas high-density lipoprotein (HDL) was significantly decreased in HFD, STZ, HFD/STZ, and HFD/STZ/HPX compared with CTRL in both sexes. The expression of Tnf-α, Il6, and Lep was significantly upregulated in all subgroups compared with CTRL in both sexes. STZ and HYX showed no significant differences in the expression of these genes between sexes, whereas Tnf-α and Il6 were upregulated in male HFD, HFD/STZ, and HFD/STZ/HYX compared with females. Protein levels showed similar patterns. Combination subgroups, either in the absence or presence of hypoxia, frequently exhibited severe necrosis of endocrine components in pancreatic lobules. The combination of obesity, diabetes, and hypoxia was associated with inflammation, which was verified at the histopathological level.
bibliographic citation: Albogami et al. (2022) Effects of combination of obesity, diabetes, and hypoxia on inflammatory regulating genes and cytokines in rat pancreatic tissues and serum. PeerJ 10:e13990 https://doi.org/10.7717/peerj.13990
date submitted: 2022-04-26
date accepted: 2022-08-11
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Albogami
  given name: Sarah
author list: Agent
  family name: Hassan
  given name: Aziza
author list: Agent
  family name: Abdel-Aziem
  given name: Sekena H.
author list: Agent
  family name: Alotaibi
  given name: Saqer
author list: Agent
  family name: Althobaiti
  given name: Fayez
author list: Agent
  family name: El-Shehawi
  given name: Ahmed
author list: Agent
  family name: Alnefaie
  given name: Alaa
author list: Agent
  family name: Alhamed
  given name: Reem Abdulla
doi: 10.7717/peerj.13990
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: ©2022 Albogami et al.
attribution name: Albogami et al.

Characterization of Staphylococcus epidermidis clinical isolates from hospitalized patients with bloodstream infection obtained in two time periods
type: item
type: AcademicArticle
description: Background In recent years Staphylococcus epidermidis has been considered an important and frequent causative agent of health care-associated infections (HAIs), increasing the costs of hospitalization, morbidity, and mortality. Antibiotic resistance and biofilm formation are the most important obstacles in the treatment of infections caused by this microorganism. The aim of this work was to determine the most prevalent STs, as well as the antibiotic resistance profile and biofilm formation of S. epidermidis clinical isolates obtained from hospitalized patients in two hospitals in Acapulco, Guerrero in two time periods. Methods Twenty methicillin-resistant S. epidermidis strains isolated from patients with bacteremia in two hospitals in two time periods were analyzed. Identification and antibiotic susceptibility were performed using the Vitek automated system. Molecular confirmation of the identification and methicillin resistance was performed by duplex PCR of the mecA and nuc genes. Biofilm production was analyzed, and the clonal origin was determined by multilocus sequence typing (MLST). Results We identified 14 antibiotic resistance profiles as well as 13 sequence types (ST), including the new ST761. We also found that ST2 and ST23 were the most prevalent and, together with ST59, were found in both time periods. Seventeen of our clinical isolates were multidrug-resistant, but all of them were sensitive to linezolid and vancomycin, and this was not related to biofilm production. Additionally, we standardized a duplex PCR to identify methicillin-resistant S. epidermidis strains. In conclusion, S. epidermidis STs 2, 23, and 59 were found in both time periods. This study is the first report of S. epidermidis ST761. The clinical isolates obtained in this work showed a high multidrug resistance that is apparently not related to biofilm production.
format: application/pdf
format: text/html
creator: Verónica I. Martínez-Santos
creator: David A. Torres-Añorve
creator: Gabriela Echániz-Aviles
creator: Isela Parra-Rojas
creator: Arturo Ramírez-Peralta
creator: Natividad Castro-Alarcón
subject: Microbiology
subject: Molecular Biology
subject: Hematology
subject: Infectious Diseases
description: doi:10.7717/peerj.14030
publisher: PeerJ Inc.
rights: © 2022 Martínez-Santos et al.
abstract: Background In recent years Staphylococcus epidermidis has been considered an important and frequent causative agent of health care-associated infections (HAIs), increasing the costs of hospitalization, morbidity, and mortality. Antibiotic resistance and biofilm formation are the most important obstacles in the treatment of infections caused by this microorganism. The aim of this work was to determine the most prevalent STs, as well as the antibiotic resistance profile and biofilm formation of S. epidermidis clinical isolates obtained from hospitalized patients in two hospitals in Acapulco, Guerrero in two time periods. Methods Twenty methicillin-resistant S. epidermidis strains isolated from patients with bacteremia in two hospitals in two time periods were analyzed. Identification and antibiotic susceptibility were performed using the Vitek automated system. Molecular confirmation of the identification and methicillin resistance was performed by duplex PCR of the mecA and nuc genes. Biofilm production was analyzed, and the clonal origin was determined by multilocus sequence typing (MLST). Results We identified 14 antibiotic resistance profiles as well as 13 sequence types (ST), including the new ST761. We also found that ST2 and ST23 were the most prevalent and, together with ST59, were found in both time periods. Seventeen of our clinical isolates were multidrug-resistant, but all of them were sensitive to linezolid and vancomycin, and this was not related to biofilm production. Additionally, we standardized a duplex PCR to identify methicillin-resistant S. epidermidis strains. In conclusion, S. epidermidis STs 2, 23, and 59 were found in both time periods. This study is the first report of S. epidermidis ST761. The clinical isolates obtained in this work showed a high multidrug resistance that is apparently not related to biofilm production.
bibliographic citation: Martínez-Santos et al. (2022) Characterization of Staphylococcus epidermidis clinical isolates from hospitalized patients with bloodstream infection obtained in two time periods. PeerJ 10:e14030 https://doi.org/10.7717/peerj.14030
date submitted: 2022-04-11
date accepted: 2022-08-16
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Santos
  given name: Verónica I.
author list: Agent
  family name: Torres-Añorve
  given name: David A.
author list: Agent
  family name: Echániz-Aviles
  given name: Gabriela
author list: Agent
  family name: Parra-Rojas
  given name: Isela
author list: Agent
  family name: Ramírez-Peralta
  given name: Arturo
author list: Agent
  family name: Castro-Alarcón
  given name: Natividad
doi: 10.7717/peerj.14030
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: © 2022 Martínez-Santos et al.
attribution name: Martínez-Santos et al.

Studying kinematic linkage of finger joints: estimation of kinematics of distal interphalangeal joints during manipulation
type: item
type: AcademicArticle
description: The recording of hand kinematics during product manipulation is challenging, and certain degrees of freedom such as distal interphalangeal (DIP) joints are difficult to record owing to limitations of the motion capture systems used. DIP joint kinematics could be estimated by taking advantage of its kinematic linkage with proximal interphalangeal (PIP) and metacarpophalangeal joints. This work analyses this linkage both in free motion conditions and during the performance of 26 activities of daily living. We have studied the appropriateness of different types of linear regressions (several combinations of independent variables and constant coefficients) and sets of data (free motion and manipulation data) to obtain equations to estimate DIP joints kinematics both in free motion and manipulation conditions. Errors that arise when estimating DIP joint angles assuming linear relationships using the equations obtained both from free motion data and from manipulation data are compared for each activity of daily living performed. Estimation using manipulation condition equations implies a lower mean absolute error per task (from 5.87° to 13.67°) than using the free motion ones (from 9° to 17.87°), but it fails to provide accurate estimations when passive extension of DIP joints occurs while PIP is flexed. This work provides evidence showing that estimating DIP joint angles is only recommended when studying free motion or grasps where both joints are highly flexed and when using linear relationships that consider only PIP joint angles.
format: application/pdf
format: text/html
creator: Alba Roda-Sales
creator: Joaquín L. Sancho-Bru
creator: Margarita Vergara
subject: Anatomy and Physiology
subject: Kinesiology
subject: Biomechanics
description: doi:10.7717/peerj.14051
publisher: PeerJ Inc.
rights: © 2022 Roda-Sales et al.
abstract: The recording of hand kinematics during product manipulation is challenging, and certain degrees of freedom such as distal interphalangeal (DIP) joints are difficult to record owing to limitations of the motion capture systems used. DIP joint kinematics could be estimated by taking advantage of its kinematic linkage with proximal interphalangeal (PIP) and metacarpophalangeal joints. This work analyses this linkage both in free motion conditions and during the performance of 26 activities of daily living. We have studied the appropriateness of different types of linear regressions (several combinations of independent variables and constant coefficients) and sets of data (free motion and manipulation data) to obtain equations to estimate DIP joints kinematics both in free motion and manipulation conditions. Errors that arise when estimating DIP joint angles assuming linear relationships using the equations obtained both from free motion data and from manipulation data are compared for each activity of daily living performed. Estimation using manipulation condition equations implies a lower mean absolute error per task (from 5.87° to 13.67°) than using the free motion ones (from 9° to 17.87°), but it fails to provide accurate estimations when passive extension of DIP joints occurs while PIP is flexed. This work provides evidence showing that estimating DIP joint angles is only recommended when studying free motion or grasps where both joints are highly flexed and when using linear relationships that consider only PIP joint angles.
bibliographic citation: Roda-Sales et al. (2022) Studying kinematic linkage of finger joints: estimation of kinematics of distal interphalangeal joints during manipulation. PeerJ 10:e14051 https://doi.org/10.7717/peerj.14051
date submitted: 2022-04-22
date accepted: 2022-08-23
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roda-Sales
  given name: Alba
author list: Agent
  family name: Sancho-Bru
  given name: Joaquín L.
author list: Agent
  family name: Vergara
  given name: Margarita
doi: 10.7717/peerj.14051
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: ©2022 Roda-Sales et al.
attribution name: Roda-Sales et al.

Theacrine alleviates sepsis-induced acute kidney injury by repressing the activation of NLRP3/Caspase-1 inflammasome
type: item
type: AcademicArticle
description: Acute kidney injury (AKI) is a frequent and serious complication of sepsis, which results in a rapid decline of kidney function. Currently, there are no curative therapies for AKI. Theacrine is a purine alkaloid and exerts significant role in regulating inflammation, oxidative stress, and mood elevation. The study aims to evaluate the biological role and potential mechanism of theacrine in septic AKI. The murine and cellular models of septic AKI were established in lipopolysaccharide (LPS)-treated C57BL/6 mice and HK-2 cells, respectively. The effect of theacrine on alleviating septic AKI was assessed after pretreatment with theacrine in vivo and in vitro. We found that theacrine treatment significantly alleviated LPS-induced kidney injury, as evidenced by decreased levels of kidney injury markers (blood urea nitrogen and creatinine), inflammatory factors (IL-1β and IL-18), and cell apoptosis in vivo and in vitro. Mechanistically, theacrine markedly repressed the activation of NOD-like receptor (NLR) pyrin domain-containing protein 3 (NLRP3)inflammasome. As expected, MCC950 (a specific inhibitor of NLRP3) treatment also decreased LPS-induced production of IL-18 and IL-1β and cell apoptosis in HK-2 cells. More important, Nigericin sodiumsalt (a NLRP3 agonist) damaged the effect of theacrine on repressing kidney injury markers (blood urea nitrogen and creatinine), pro-inflammatory cytokines (IL-18 and IL-1β), and cell apoptosis. Taken together, these results demonstrate that theacrine alleviates septic AKI, at least in part by repressing the activation of NLRP3 inflammasome.
format: application/pdf
format: text/html
creator: Maoxian Yang
creator: Peng Shen
creator: Longsheng Xu
creator: Min Kong
creator: Congcong Yu
creator: Yunchao Shi
subject: Biochemistry
subject: Cell Biology
subject: Emergency and Critical Care
subject: Nephrology
description: doi:10.7717/peerj.14109
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Acute kidney injury (AKI) is a frequent and serious complication of sepsis, which results in a rapid decline of kidney function. Currently, there are no curative therapies for AKI. Theacrine is a purine alkaloid and exerts significant role in regulating inflammation, oxidative stress, and mood elevation. The study aims to evaluate the biological role and potential mechanism of theacrine in septic AKI. The murine and cellular models of septic AKI were established in lipopolysaccharide (LPS)-treated C57BL/6 mice and HK-2 cells, respectively. The effect of theacrine on alleviating septic AKI was assessed after pretreatment with theacrine in vivo and in vitro. We found that theacrine treatment significantly alleviated LPS-induced kidney injury, as evidenced by decreased levels of kidney injury markers (blood urea nitrogen and creatinine), inflammatory factors (IL-1β and IL-18), and cell apoptosis in vivo and in vitro. Mechanistically, theacrine markedly repressed the activation of NOD-like receptor (NLR) pyrin domain-containing protein 3 (NLRP3)inflammasome. As expected, MCC950 (a specific inhibitor of NLRP3) treatment also decreased LPS-induced production of IL-18 and IL-1β and cell apoptosis in HK-2 cells. More important, Nigericin sodiumsalt (a NLRP3 agonist) damaged the effect of theacrine on repressing kidney injury markers (blood urea nitrogen and creatinine), pro-inflammatory cytokines (IL-18 and IL-1β), and cell apoptosis. Taken together, these results demonstrate that theacrine alleviates septic AKI, at least in part by repressing the activation of NLRP3 inflammasome.
bibliographic citation: Yang et al. (2022) Theacrine alleviates sepsis-induced acute kidney injury by repressing the activation of NLRP3/Caspase-1 inflammasome. PeerJ 10:e14109 https://doi.org/10.7717/peerj.14109
date submitted: 2022-02-16
date accepted: 2022-09-02
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yang
  given name: Maoxian
author list: Agent
  family name: Shen
  given name: Peng
author list: Agent
  family name: Xu
  given name: Longsheng
author list: Agent
  family name: Kong
  given name: Min
author list: Agent
  family name: Yu
  given name: Congcong
author list: Agent
  family name: Shi
  given name: Yunchao
doi: 10.7717/peerj.14109
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance
type: item
type: AcademicArticle
description: The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization.
format: application/pdf
format: text/html
creator: Alexey A. Kotov
creator: Derek J. Taylor
subject: Biodiversity
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14113
publisher: PeerJ Inc.
rights: © 2022 Kotov and Taylor
abstract: The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization.
bibliographic citation: Kotov et al. (2022) Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance. PeerJ 10:e14113 https://doi.org/10.7717/peerj.14113
date submitted: 2021-11-17
date accepted: 2022-09-02
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kotov
  given name: Alexey A.
author list: Agent
  family name: Taylor
  given name: Derek J.
doi: 10.7717/peerj.14113
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: © 2022 Kotov and Taylor
attribution name: Kotov and Taylor

Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages
type: item
type: AcademicArticle
description: Background Armeniaca sibirica seed kernel oil is rich in oleic acid and linoleic acid, thus holding potential value as a source of high-quality edible oils. However, some regulatory factors involved in fatty acids accumulation in A. sibirica seed kernels remain largely elusive. Thus, the aim of this study was to elucidate the regulatory mechanisms underlying fatty acids biosynthesis in A. sibirica developing seed kernels. Methods Seed kernels from six plants from a single A. sibirica clone were taken at five different developmental stages (days 30, 41, 52, 63, and 73 after anthesis). Fatty acid composition in seed kernel oil was determined by gas chromatography-mass spectrometry (GC-MS). In addition, transcriptome analysis was conducted using second-generation sequencing (SGS) and single-molecule real-time sequencing (SMRT). Results Rapid accumulation of fatty acids occurred throughout the different stages of seed kernels development, with oleic acid and linoleic acid as the main fatty acids. A total of 10,024, 9,803, 6,004, 6,719 and 9,688 unigenes were matched in the Nt, Nr, KOG, GO and KEGG databases, respectively. In the category lipid metabolism, 228 differentially expressed genes (DEGs) were annotated into 13 KEGG pathways. Specific unigenes encoding 12 key enzymes related to fatty acids biosynthesis were determined. Co-expression network analysis identified 11 transcription factors (TFs) and 13 long non-coding RNAs (lncRNAs) which putatively participate in the regulation of fatty acid biosynthesis. This study provides insights into the molecular regulatory mechanisms of fatty acids biosynthesis in A. sibirica developing seed kernels, and enabled the identification of novel candidate factors for future improvement of the production and quality of seed kernel oil by breeding.
format: application/pdf
format: text/html
creator: Yueliang Wu
creator: Wenya Gao
creator: Xinli Li
creator: Shilin Sun
creator: Jian Xu
creator: Xiaoqiong Shi
creator: Huiyan Guo
subject: Agricultural Science
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.14125
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: Background Armeniaca sibirica seed kernel oil is rich in oleic acid and linoleic acid, thus holding potential value as a source of high-quality edible oils. However, some regulatory factors involved in fatty acids accumulation in A. sibirica seed kernels remain largely elusive. Thus, the aim of this study was to elucidate the regulatory mechanisms underlying fatty acids biosynthesis in A. sibirica developing seed kernels. Methods Seed kernels from six plants from a single A. sibirica clone were taken at five different developmental stages (days 30, 41, 52, 63, and 73 after anthesis). Fatty acid composition in seed kernel oil was determined by gas chromatography-mass spectrometry (GC-MS). In addition, transcriptome analysis was conducted using second-generation sequencing (SGS) and single-molecule real-time sequencing (SMRT). Results Rapid accumulation of fatty acids occurred throughout the different stages of seed kernels development, with oleic acid and linoleic acid as the main fatty acids. A total of 10,024, 9,803, 6,004, 6,719 and 9,688 unigenes were matched in the Nt, Nr, KOG, GO and KEGG databases, respectively. In the category lipid metabolism, 228 differentially expressed genes (DEGs) were annotated into 13 KEGG pathways. Specific unigenes encoding 12 key enzymes related to fatty acids biosynthesis were determined. Co-expression network analysis identified 11 transcription factors (TFs) and 13 long non-coding RNAs (lncRNAs) which putatively participate in the regulation of fatty acid biosynthesis. This study provides insights into the molecular regulatory mechanisms of fatty acids biosynthesis in A. sibirica developing seed kernels, and enabled the identification of novel candidate factors for future improvement of the production and quality of seed kernel oil by breeding.
bibliographic citation: Wu et al. (2022) Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages. PeerJ 10:e14125 https://doi.org/10.7717/peerj.14125
date submitted: 2022-06-13
date accepted: 2022-09-06
issued: 2022-10-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Yueliang
author list: Agent
  family name: Gao
  given name: Wenya
author list: Agent
  family name: Li
  given name: Xinli
author list: Agent
  family name: Sun
  given name: Shilin
author list: Agent
  family name: Xu
  given name: Jian
author list: Agent
  family name: Shi
  given name: Xiaoqiong
author list: Agent
  family name: Guo
  given name: Huiyan
doi: 10.7717/peerj.14125
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-04
copyright: ©2022 Wu et al.
attribution name: Wu et al.

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