Time-dependent effect of intense capsule-coffee and bleaching on the color of resin-infiltrated enamel white spot lesions: an in vitro study
Background and Objectives White spot lesions (WSLs) are a common problem that can be conservatively managed by resin infiltration. Consumption of dark beverages such as coffee causes staining of dental hard tissues, which can deteriorate the esthetic qualities of treated WSLs. The aims of this study were to investigate the effect of dark coffee heavy consumption on ICON® resin infiltrated WSLs and the influence of bleaching on them after staining. Methods Twenty surfaces from sound human extracted third molars were used in the study. Two square-shaped buccal and lingual window areas had artificially created WSLs (received buccal resin infiltration afterward). Using VITA Easyshade, the baseline ΔE was recorded. Espresso coffee was used to immerse all surfaces for 8 days. The color coordinates according to CIE LAB were recorded for all surfaces at 2, 4, 6, and 8 days of immersion, and ΔE was calculated at each timepoint. After 8 days, in-office bleaching was applied to all surfaces according to the manufacturer’s instructions and the color. Coordinates and ΔE were recorded. For statistical analysis, an independent sample t-test was used to compare each group. A general linear mixed model (GLMM) repeated measure ANOVA was applied for statistical analysis of L*and changes due to staining over time. Results Analysis of time as a main effect on the L values of surfaces was statistically highly significant (p < 0.01). The interaction of time with surfaces under investigation and type of surface (test vs. control) as a main effect were non-significant (p = 0.47 and p = 0.35, respectively). Bleaching showed a significant difference in color lightness in both test and control surfaces compared to the mean L value at 8 days of staining (p < 0.01). Conclusion Capsule-coffee consumption gradually influences the esthetic of resin infiltration on treated teeth. However, bleaching materials might restore an esthetic shade.
Yeslam et al. (2022) Time-dependent effect of intense capsule-coffee and bleaching on the color of resin-infiltrated enamel white spot lesions: an in vitro study. PeerJ 10:e14135 https://doi.org/10.7717/peerj.14135
Genomic differences between sequence types 1 and 104 of Streptococcus suis Serotype 2
Background Streptococcus suis is a zoonotic pathogen that can cause invasive infections in humans who are in close contact with infected pigs or contaminated pork-derived products. S. suis serotype 2 sequence type (ST) 1 strains are mostly associated with meningitis, whereas ST104 strains are mostly recovered from sepsis cases in humans. No data are available for comparison of the ST1 and ST104 strains at the genomic level, particularly concerning virulence-associated genes. Thus, genomic comparison of both STs was performed in this study. Methods An ST1 isolate (ID26154) from the cerebrospinal fluid of a patient with meningitis and an ST104 isolate (ID24525) from the blood of a patient with sepsis were subjected to shotgun pyrosequencing using the 454 GS Junior System. Genomic comparison was conducted between the ST1 isolate and the ST104 isolate using the Artemis Comparison Tool (ACT) to identify the region of differences (RDs) between ST1 and ST104. Results Fifty-eight RDs were unique to the ST104 genome and were mainly involved in metabolism and cell functional activities, cell wall anchored proteins, bacteriophages and mobile genetic elements, ABC-type transporters, two-component signal transductions, and lantibiotic proteins. Some virulence genes mostly found in ST1 strains were also present in the ST104 genome. Whole-genome comparison is a powerful tool for identifying genomic region differences between different STs of S. suis serotype 2, leading to the identification of the molecular basis of virulence involved in the pathogenesis of the infection.
Kerdsin et al. (2022) Genomic differences between sequence types 1 and 104 of Streptococcus suis Serotype 2. PeerJ 10:e14144 https://doi.org/10.7717/peerj.14144
Shallow epifaunal sea cucumber densities and their relationship with the benthic community in the Okinawa Islands
Sea cucumbers are important ecological engineers in marine ecosystems. However, the fishery demand of some species, especially large-epifaunal and commercially used (LEC) sea cucumbers, has risen drastically, resulting in serious depletion of local populations for many species. Despite this problem, basic ecological data on sea cucumbers, such as population densities and preferred habitats, are often still insufficient. Here, we report on the population densities of multiple LEC sea cucumber species, and their ambient benthic communities at eight sites around Okinawa Islands. Further, we discuss the correspondence between sea cucumber densities and the surrounding coral communities. Our results show two sites within national or quasi-national parks, Aka and Manza, where stricter rules have been placed on fisheries and land reclamation compared to other areas, had the highest and third highest sea cucumber population densities among sites, respectively. Holothuria atra was observed at all survey sites and made up the majority of sea cucumber populations at all sites except for Chatan and Sesoko, where Holothuria leucospilota and Stichopus chloronotus were most abundant, respectively. Regarding the relationships between benthic composition and LEC sea cucumber species, S. chloronotus was significantly correlated with dead corals, scleractinian corals, and coralline algae. As well, H. leucospilota had significant correlations with rubble. Although there were no significant correlations between any specific scleractinian coral genus and sea cucumber densities, S. chloronotus was marginally insignificant with Platygyra and Psammocora. Notably, medium- to highly valued species were sparse in our surveys, and most of them appeared at only one site. Additionally, at one site (Odo), only three LEC sea cucumber individuals were observed. Combining these facts with relatively low population densities around the Okinawa Islands compared to densities reported in previous research from the Indo-West Pacific Ocean region, we conclude that Okinawan LEC sea cucumber populations have been and are being impacted by high levels of direct (e.g., overexploitation, as well as coastal development) and indirect anthropogenic pressure (e.g., decreasing water quality). To address the current situation, repeated monitoring and more detailed investigations to reveal the drivers that determine LEC sea cucumber species aggregations and population densities are urgently needed, along with more robust management of remaining LEC sea cucumber populations.
Hamamoto et al. (2022) Shallow epifaunal sea cucumber densities and their relationship with the benthic community in the Okinawa Islands. PeerJ 10:e14181 https://doi.org/10.7717/peerj.14181
Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2
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 osteogenic differentiation of hBMSCs by changing the methylation status of H3K9me2 at the Runx2 promoter. Conclusions Taken 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.
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
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
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, 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.
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
Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales
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.
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
The soccer season: performance variations and evolutionary trends
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.
Silva (2022) The soccer season: performance variations and evolutionary trends. PeerJ 10:e14082 https://doi.org/10.7717/peerj.14082
MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer
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 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.
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
miR2Trait: an integrated resource for investigating miRNA-disease associations
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.
Babu et al. (2022) miR2Trait: an integrated resource for investigating miRNA-disease associations. PeerJ 10:e14146 https://doi.org/10.7717/peerj.14146
Impact of cover crop and mulching on soil physical properties and soil nutrients in a citrus orchard
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.
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