title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=643 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2 link: https://peerj.com/articles/13862 last-modified: 2022-10-05 description: BackgroundA 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.MethodsChromatin 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.ResultsOur 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 osteogenic differentiation of hBMSCs by changing the methylation status of H3K9me2 at the Runx2 promoter.ConclusionsTaken together, these results suggest that JMJD2B/ KDM4B may induce the osteogenic differentiation of hBMSCs by regulating the methylation level of H3K9me2 at the Runx2 promoter. creator: Pan Kang creator: Zhiming Wu creator: Yuxi Huang creator: Zhen Luo creator: Shaochuan Huo creator: Qunqun Chen uri: https://doi.org/10.7717/peerj.13862 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kang et al. title: 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 link: https://peerj.com/articles/14035 last-modified: 2022-10-05 description: BackgroundMaximal 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.MethodsTelemetric 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.ResultsWhereas 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 ≤ ${\eta }_{p}^{2}$ηp2 ≤ 0.8) were observed throughout the tests, decreases in contact time (p < 0.001, ${\eta }_{p}^{2}=0.9$ηp2=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, runners displayed a greater ability to modify stride length to achieve fast speeds, which may be related to a more mechanically efficient pattern of spatiotemporal parameters than non-runners. 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 uri: https://doi.org/10.7717/peerj.14035 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Casado et al. title: Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales link: https://peerj.com/articles/14047 last-modified: 2022-10-05 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 that the high fungal diversity in B. vivipara comes from an active recruitment of their associates from the co-occurring vegetation. The non-host-specificity suggests that this strategy may offer ecological advantages; specifically, linkages with generalist rather than specialist fungi. Proximity to co-occurring non-B. vivipara plants can maximise the fitness of B. vivipara, allowing more rapid and easy colonisation of the available habitats. creator: Max Emil Schön creator: Kessy Abarenkov creator: Sigisfredo Garnica uri: https://doi.org/10.7717/peerj.14047 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Schön et al. title: The soccer season: performance variations and evolutionary trends link: https://peerj.com/articles/14082 last-modified: 2022-10-05 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) from MCP to ECP. Match performance may vary during the season. Although, the variability between studies is clear for TD, VHSR and sprint, all the studies observed substantial increments in HSR between MCP and ECP. Finally, studies examining evolutionary trends by means of exercise and competition performance measures suggests of a heightened importance of neuromuscular factors. In conclusion, during the preseason players “recover” body composition profile and neuromuscular and endurance competitive capacity. Within in-season, and more robustly towards ECP, alterations in neuromuscular performance seem to be force-velocity dependent, and in some cases, physiological determinants and endurance performance may be compromised when considering other in-season moments. Importantly, there is a substantial variability in team responses that can be observed during in-season. Consequently, this informs on the need to both provide a regular training stimulus and adequate monitorization throughout the season. creator: Joao Renato Silva uri: https://doi.org/10.7717/peerj.14082 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Silva title: MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer link: https://peerj.com/articles/14097 last-modified: 2022-10-05 description: BackgroundRecent 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.MethodsHigh-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).ResultsHere 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 regulator for the PI3K/Akt/COX2 signaling pathway in FMD-C1. Collectively, this study not only provided a study strategy for non-invasive research in pulmonary disease in rare animals, but also laid a foundation for further research in BIPF. 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 uri: https://doi.org/10.7717/peerj.14097 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhao et al. title: miR2Trait: an integrated resource for investigating miRNA-disease associations link: https://peerj.com/articles/14146 last-modified: 2022-10-05 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. creator: Poornima Babu creator: Ashok Palaniappan uri: https://doi.org/10.7717/peerj.14146 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Babu and Palaniappan title: Impact of cover crop and mulching on soil physical properties and soil nutrients in a citrus orchard link: https://peerj.com/articles/14170 last-modified: 2022-10-05 description: BackgroundCover 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.MethodsThe 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.ResultsThe 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.ConclusionsLegume 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. creator: Tran Van Dung creator: Ngo Phuong Ngoc creator: Le Van Dang creator: Ngo Ngoc Hung uri: https://doi.org/10.7717/peerj.14170 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Dung et al. title: A new volute, Ericusa ngayawang sp. nov. (Gastropoda: Volutidae), from the Miocene of South Australia link: https://peerj.com/articles/14197 last-modified: 2022-10-05 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. creator: Adam M. Yates uri: https://doi.org/10.7717/peerj.14197 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yates title: Effects of combination of obesity, diabetes, and hypoxia on inflammatory regulating genes and cytokines in rat pancreatic tissues and serum link: https://peerj.com/articles/13990 last-modified: 2022-10-04 description: BackgroundObesity 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.MethodsThis 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.ResultsNo 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. 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 uri: https://doi.org/10.7717/peerj.13990 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Albogami et al. title: Characterization of Staphylococcus epidermidis clinical isolates from hospitalized patients with bloodstream infection obtained in two time periods link: https://peerj.com/articles/14030 last-modified: 2022-10-04 description: BackgroundIn 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.MethodsTwenty 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).ResultsWe 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. 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 uri: https://doi.org/10.7717/peerj.14030 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Martínez-Santos et al.