PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2
items: Maximum aerobic speed, maximum oxygen consumption, and running spatiotemporal parameters during an incremental test among middle- and long-distance runners and endurance non-running athletes
items: Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales
items: The soccer season: performance variations and evolutionary trends
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

Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2
type: item
type: AcademicArticle
description: Background A variety of proteins including epigenetic factors are involved in the differentiation of human bone marrow mesenchymal stem cells. These cells also exhibited an epigenetic plasticity that enabled them to trans-differentiate from adipocytes to osteoblasts (and vice versa) after commitment. Further in-depth study of their epigenetic alterations may make sense. Methods Chromatin Immunoprecipitation-PCR (ChIP-PCR) was used to detect the methylation enrichment status of H3K9me2 in the Runx2 promoter, alizarin red and alkaline phosphatase (ALP) staining were used to detect osteogenic differentiation and mineralization ability, western blot and quantitative RT-PCR were used to measure the differential expression of osteogenesis-related proteins and genes. Recombinant Lentivirus mediated gain-of-function and loss-of-function study. The scale of epigenetic modification was detected by laser confocal. Results Our results showed that compared with human bone marrow mesenchymal stem cells (hBMSCs) without osteogenic differentiation treatment, hBMSCs after osteogenic differentiation significantly promoted osteogenic differentiation and mRNA expression such as JMJD2B/KDM4B, osteogenesis-related genes like Runx2 and FAM210A in hBMSCs cells, suggesting that upregulation of JMJD2B/KDM4B is involved in the promoting effect of osteogenesis. After overexpression and silencing expression of JMJD2B, we found a completely opposite and significant difference in mRNA expression of osteogenesis-related genes and staining in hBMSCs. Overexpression of JMJD2B/KDM4B significantly promoted osteogenic differentiation, suggesting that JMJD2B/KDM4B could promote osteogenesis. In addition, ChIP-PCR showed that overexpression of JMJD2B/KDM4B significantly reversed the methylation enrichment status of H3K9me2 in Runx2 promoter. Furthermore, overexpression of JMJD2B/KDM4B significantly reverses the inhibitory effect of BIX01294 on H3K9me2, suggesting that JMJD2B/KDM4B regulates the osteogeni…
format: application/pdf
format: text/html
creator: Pan Kang
creator: Zhiming Wu
creator: Yuxi Huang
creator: Zhen Luo
creator: Shaochuan Huo
creator: Qunqun Chen
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13862
publisher: PeerJ Inc.
rights: © 2022 Kang et al.
abstract: Background A variety of proteins including epigenetic factors are involved in the differentiation of human bone marrow mesenchymal stem cells. These cells also exhibited an epigenetic plasticity that enabled them to trans-differentiate from adipocytes to osteoblasts (and vice versa) after commitment. Further in-depth study of their epigenetic alterations may make sense. Methods Chromatin Immunoprecipitation-PCR (ChIP-PCR) was used to detect the methylation enrichment status of H3K9me2 in the Runx2 promoter, alizarin red and alkaline phosphatase (ALP) staining were used to detect osteogenic differentiation and mineralization ability, western blot and quantitative RT-PCR were used to measure the differential expression of osteogenesis-related proteins and genes. Recombinant Lentivirus mediated gain-of-function and loss-of-function study. The scale of epigenetic modification was detected by laser confocal. Results Our results showed that compared with human bone marrow mesenchymal stem cells (hBMSCs) without osteogenic differentiation treatment, hBMSCs after osteogenic differentiation significantly promoted osteogenic differentiation and mRNA expression such as JMJD2B/KDM4B, osteogenesis-related genes like Runx2 and FAM210A in hBMSCs cells, suggesting that upregulation of JMJD2B/KDM4B is involved in the promoting effect of osteogenesis. After overexpression and silencing expression of JMJD2B, we found a completely opposite and significant difference in mRNA expression of osteogenesis-related genes and staining in hBMSCs. Overexpression of JMJD2B/KDM4B significantly promoted osteogenic differentiation, suggesting that JMJD2B/KDM4B could promote osteogenesis. In addition, ChIP-PCR showed that overexpression of JMJD2B/KDM4B significantly reversed the methylation enrichment status of H3K9me2 in Runx2 promoter. Furthermore, overexpression of JMJD2B/KDM4B significantly reverses the inhibitory effect of BIX01294 on H3K9me2, suggesting that JMJD2B/KDM4B regulates the osteogeni…
bibliographic citation: Kang et al. (2022) Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2. PeerJ 10:e13862 https://doi.org/10.7717/peerj.13862
date submitted: 2021-11-29
date accepted: 2022-07-18
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Pan
author list: Agent
  family name: Wu
  given name: Zhiming
author list: Agent
  family name: Huang
  given name: Yuxi
author list: Agent
  family name: Luo
  given name: Zhen
author list: Agent
  family name: Huo
  given name: Shaochuan
author list: Agent
  family name: Chen
  given name: Qunqun
doi: 10.7717/peerj.13862
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: ©2022 Kang et al.
attribution name: Kang et al.

Maximum aerobic speed, maximum oxygen consumption, and running spatiotemporal parameters during an incremental test among middle- and long-distance runners and endurance non-running athletes
type: item
type: AcademicArticle
description: Background Maximal aerobic speed (MAS) is a useful parameter to assess aerobic capacity and estimate training intensity in middle- and long-distance runners. However, whether middle- and long-distance runners reach different levels of MAS compared to other endurance athletes with similar V̇O2max has not been previously studied. Therefore, we aimed to compare V̇O2max, MAS and spatiotemporal parameters between sub-elite middle- and long-distance runners (n = 6) and endurance non-runners (n = 6). In addition, we aimed to compare the maximal blood lactate concentration [BLa] experienced by participants after conducting these tests. Methods Telemetric portable respiratory gas analysis, contact and flight time, and stride length and rate were measured using a 5-m contact platform during an incremental test at a synthetic athletics track. V̇O2, heart rate, respiratory quotient values in any 15 s average period during the test were measured. [BLa] was analyzed after the test . Running spatiotemporal parameters were recorded at the last two steps of each 400 m lap. A coefficient of variation (%CV) was calculated for each spatiotemporal variable in each participant from 8 km h−1 onwards. Results Whereas runners reported faster MAS (21.0 vs. 18.2 km h−1) than non-runners (p = 0.0001, ES = 3.0), no differences were found for V̇O2max and maximum blood lactate concentration during the running tests (p > 0.05). While significant increases in flight time and stride length and frequency (p < 0.001, 0.52 ≤ ${\eta }_{p}^{2}$ η p 2 ≤ 0.8) were observed throughout the tests, decreases in contact time (p < 0.001, ${\eta }_{p}^{2}=0.9$ η p 2 = 0 . 9 ) were reported. Runners displayed a greater %CV (p = 0.015) in stride length than non-runners. We conclude that middle- and long-distance runners can achieve a faster MAS compared to non-running endurance athletes despite exhibiting a similar V̇O2max. This superior performance may be associated to a greater mechanical efficiency. Overall, run…
format: application/pdf
format: text/html
creator: Arturo Casado
creator: José Luis Tuimil
creator: Xavier Iglesias
creator: Miguel Fernández-del-Olmo
creator: Pedro Jiménez-Reyes
creator: Rafael Martín-Acero
creator: Ferran A. Rodríguez
subject: Kinesiology
subject: Respiratory Medicine
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.14035
publisher: PeerJ Inc.
rights: © 2022 Casado et al.
abstract: Background Maximal aerobic speed (MAS) is a useful parameter to assess aerobic capacity and estimate training intensity in middle- and long-distance runners. However, whether middle- and long-distance runners reach different levels of MAS compared to other endurance athletes with similar V̇O2max has not been previously studied. Therefore, we aimed to compare V̇O2max, MAS and spatiotemporal parameters between sub-elite middle- and long-distance runners (n = 6) and endurance non-runners (n = 6). In addition, we aimed to compare the maximal blood lactate concentration [BLa] experienced by participants after conducting these tests. Methods Telemetric portable respiratory gas analysis, contact and flight time, and stride length and rate were measured using a 5-m contact platform during an incremental test at a synthetic athletics track. V̇O2, heart rate, respiratory quotient values in any 15 s average period during the test were measured. [BLa] was analyzed after the test . Running spatiotemporal parameters were recorded at the last two steps of each 400 m lap. A coefficient of variation (%CV) was calculated for each spatiotemporal variable in each participant from 8 km h−1 onwards. Results Whereas runners reported faster MAS (21.0 vs. 18.2 km h−1) than non-runners (p = 0.0001, ES = 3.0), no differences were found for V̇O2max and maximum blood lactate concentration during the running tests (p > 0.05). While significant increases in flight time and stride length and frequency (p < 0.001, 0.52 ≤ ${\eta }_{p}^{2}$ η p 2 ≤ 0.8) were observed throughout the tests, decreases in contact time (p < 0.001, ${\eta }_{p}^{2}=0.9$ η p 2 = 0 . 9 ) were reported. Runners displayed a greater %CV (p = 0.015) in stride length than non-runners. We conclude that middle- and long-distance runners can achieve a faster MAS compared to non-running endurance athletes despite exhibiting a similar V̇O2max. This superior performance may be associated to a greater mechanical efficiency. Overall, run…
bibliographic citation: Casado et al. (2022) Maximum aerobic speed, maximum oxygen consumption, and running spatiotemporal parameters during an incremental test among middle- and long-distance runners and endurance non-running athletes. PeerJ 10:e14035 https://doi.org/10.7717/peerj.14035
date submitted: 2022-06-09
date accepted: 2022-08-18
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Casado
  given name: Arturo
author list: Agent
  family name: Tuimil
  given name: José Luis
author list: Agent
  family name: Iglesias
  given name: Xavier
author list: Agent
  family name: Fernández-del-Olmo
  given name: Miguel
author list: Agent
  family name: Jiménez-Reyes
  given name: Pedro
author list: Agent
  family name: Martín-Acero
  given name: Rafael
author list: Agent
  family name: Rodríguez
  given name: Ferran A.
doi: 10.7717/peerj.14035
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: ©2022 Casado et al.
attribution name: Casado et al.

Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales
type: item
type: AcademicArticle
description: Bistorta vivipara is a widespread herbaceous perennial plant with a discontinuous pattern of distribution in arctic, alpine, subalpine and boreal habitats across the northern Hemisphere. Studies of the fungi associated with the roots of B. vivipara have mainly been conducted in arctic and alpine ecosystems. This study examined the fungal diversity and specificity from root tips of B. vivipara in two local mountain ecosystems as well as on a global scale. Sequences were generated by Sanger sequencing of the internal transcribed spacer (ITS) region followed by an analysis of accurately annotated nuclear segments including ITS1-5.8S-ITS2 sequences available from public databases. In total, 181 different UNITE species hypotheses (SHs) were detected to be fungi associated with B. vivipara, 73 of which occurred in the Bavarian Alps and nine in the Swabian Alps–with one SH shared among both mountains. In both sites as well as in additional public data, individuals of B. vivipara were found to contain phylogenetically diverse fungi, with the Basidiomycota, represented by the Thelephorales and Sebacinales, being the most dominant. A comparative analysis of the diversity of the Sebacinales associated with B. vivipara and other co-occurring plant genera showed that the highest number of sebacinoid SHs were associated with Quercus and Pinus, followed by Bistorta. A comparison of B. vivipara with plant families such as Ericaceae, Fagaceae, Orchidaceae, and Pinaceae showed a clear trend: Only a few species were specific to B. vivipara and a large number of SHs were shared with other co-occurring non-B. vivipara plant species. In Sebacinales, the majority of SHs associated with B. vivipara belonged to the ectomycorrhiza (ECM)-forming Sebacinaceae, with fewer SHs belonging to the Serendipitaceae encompassing diverse ericoid–orchid–ECM–endophytic associations. The large proportion of non-host-specific fungi able to form a symbiosis with other non-B. vivipara plants could suggest tha…
format: application/pdf
format: text/html
creator: Max Emil Schön
creator: Kessy Abarenkov
creator: Sigisfredo Garnica
subject: Biodiversity
subject: Ecology
subject: Mycology
description: doi:10.7717/peerj.14047
publisher: PeerJ Inc.
rights: © 2022 Schön et al.
abstract: Bistorta vivipara is a widespread herbaceous perennial plant with a discontinuous pattern of distribution in arctic, alpine, subalpine and boreal habitats across the northern Hemisphere. Studies of the fungi associated with the roots of B. vivipara have mainly been conducted in arctic and alpine ecosystems. This study examined the fungal diversity and specificity from root tips of B. vivipara in two local mountain ecosystems as well as on a global scale. Sequences were generated by Sanger sequencing of the internal transcribed spacer (ITS) region followed by an analysis of accurately annotated nuclear segments including ITS1-5.8S-ITS2 sequences available from public databases. In total, 181 different UNITE species hypotheses (SHs) were detected to be fungi associated with B. vivipara, 73 of which occurred in the Bavarian Alps and nine in the Swabian Alps–with one SH shared among both mountains. In both sites as well as in additional public data, individuals of B. vivipara were found to contain phylogenetically diverse fungi, with the Basidiomycota, represented by the Thelephorales and Sebacinales, being the most dominant. A comparative analysis of the diversity of the Sebacinales associated with B. vivipara and other co-occurring plant genera showed that the highest number of sebacinoid SHs were associated with Quercus and Pinus, followed by Bistorta. A comparison of B. vivipara with plant families such as Ericaceae, Fagaceae, Orchidaceae, and Pinaceae showed a clear trend: Only a few species were specific to B. vivipara and a large number of SHs were shared with other co-occurring non-B. vivipara plant species. In Sebacinales, the majority of SHs associated with B. vivipara belonged to the ectomycorrhiza (ECM)-forming Sebacinaceae, with fewer SHs belonging to the Serendipitaceae encompassing diverse ericoid–orchid–ECM–endophytic associations. The large proportion of non-host-specific fungi able to form a symbiosis with other non-B. vivipara plants could suggest tha…
bibliographic citation: Schön et al. (2022) Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales. PeerJ 10:e14047 https://doi.org/10.7717/peerj.14047
date submitted: 2021-09-02
date accepted: 2022-08-22
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schön
  given name: Max Emil
author list: Agent
  family name: Abarenkov
  given name: Kessy
author list: Agent
  family name: Garnica
  given name: Sigisfredo
doi: 10.7717/peerj.14047
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: © 2022 Schön et al.
attribution name: Schön et al.

The soccer season: performance variations and evolutionary trends
type: item
type: AcademicArticle
description: The physiological demands of soccer challenge the entire spectrum of the response capacity of the biological systems and fitness requirements of the players. In this review we examined variations and evolutionary trends in body composition, neuromuscular and endurance-related parameters, as well as in game-related physical parameters of professional players. Further, we explore aspects relevant for training monitoring and we reference how different training stimulus and situational variables (e.g., competition exposure) affect the physiological and performance parameters of players. Generally, improvements of small magnitude in non- (non-CMJ) and countermovement-based jumps (CMJBased) and in the sprint acceleration (ACCPhase) and maximal velocity phase (MVPhase) are observed from start of preparation phase (PPS) to beginning of competition phase (BCP). A greater magnitude of increases is observed in physiological and endurance performance measures within this period; moderate magnitude in sub-maximal intensity exercise (velocity at fixed blood lactate concentrations; V2–4mmol/l) and large magnitude in VO2max, maximal aerobic speed (MAS) and intense intermittent exercise performance (IE). In the middle of competition phase (MCP), small (CMJBased and ACCPhase), moderate (non-CMJ; MVPhase; VO2max; sub-maximal exercise) and large (MAS and IE) improvements were observed compared to PPS. In the end of competition period (ECP), CMJBased and MVPhase improve to a small extent with non-CMJ, and ACCPhase, VO2max, MAS, sub-maximal intensity exercise and IE revealing moderate increments compared to PPS. Although less investigated, there are generally observed alterations of trivial magnitude in neuromuscular and endurance-related parameters between in-season assessments; only substantial alterations are examined for IE and sub-maximal exercise performance (decrease and increase of small magnitude, respectively) from BCP to MCP and in VO2max and IE (decrements of small magnitude)…
format: application/pdf
format: text/html
creator: Joao Renato Silva
subject: Anatomy and Physiology
subject: Kinesiology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.14082
publisher: PeerJ Inc.
rights: © 2022 Silva
abstract: The physiological demands of soccer challenge the entire spectrum of the response capacity of the biological systems and fitness requirements of the players. In this review we examined variations and evolutionary trends in body composition, neuromuscular and endurance-related parameters, as well as in game-related physical parameters of professional players. Further, we explore aspects relevant for training monitoring and we reference how different training stimulus and situational variables (e.g., competition exposure) affect the physiological and performance parameters of players. Generally, improvements of small magnitude in non- (non-CMJ) and countermovement-based jumps (CMJBased) and in the sprint acceleration (ACCPhase) and maximal velocity phase (MVPhase) are observed from start of preparation phase (PPS) to beginning of competition phase (BCP). A greater magnitude of increases is observed in physiological and endurance performance measures within this period; moderate magnitude in sub-maximal intensity exercise (velocity at fixed blood lactate concentrations; V2–4mmol/l) and large magnitude in VO2max, maximal aerobic speed (MAS) and intense intermittent exercise performance (IE). In the middle of competition phase (MCP), small (CMJBased and ACCPhase), moderate (non-CMJ; MVPhase; VO2max; sub-maximal exercise) and large (MAS and IE) improvements were observed compared to PPS. In the end of competition period (ECP), CMJBased and MVPhase improve to a small extent with non-CMJ, and ACCPhase, VO2max, MAS, sub-maximal intensity exercise and IE revealing moderate increments compared to PPS. Although less investigated, there are generally observed alterations of trivial magnitude in neuromuscular and endurance-related parameters between in-season assessments; only substantial alterations are examined for IE and sub-maximal exercise performance (decrease and increase of small magnitude, respectively) from BCP to MCP and in VO2max and IE (decrements of small magnitude)…
bibliographic citation: Silva (2022) The soccer season: performance variations and evolutionary trends. PeerJ 10:e14082 https://doi.org/10.7717/peerj.14082
date submitted: 2022-07-01
date accepted: 2022-08-29
issued: 2022-10-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Joao Renato
doi: 10.7717/peerj.14082
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-05
copyright: © 2022 Silva
attribution name: Silva

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.

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