title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=684 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: When does self-report of pain occur?: A study of older adults link: https://peerj.com/articles/13716 last-modified: 2022-07-19 description: Technologies for self-care can drive participatory health and promote independence of older adults. One self-care activity is regularly measuring and registering personal health indicators (self-reporting). Older adults may benefit from this practice, as they are more likely to have chronic health issues and have specific self-monitoring needs. However, self-reporting technologies are usually not designed specifically for them. Pain is usually measured using patient reports compiled during medical appointments, although this process may be affected by memory bias and under reporting of fluctuating pain. To address these issues, we introduced a simple tangible interface to self-report pain levels and conducted a three-hour evaluation with 24 older adults. The goal of this study was to identify whether specific activities, activity levels or pain levels trigger older adults to self-report their pain level, besides to understand how older adults would use such a device. Within the limited time frame of the experiment, the majority of our participants chose to report pain when they felt it most, not reporting lower levels of pain. No evidence was found to suggest a relationship between the reporting of pain and the activity (or activity level). Several design insights intended to improve the design of technologies are provided. creator: Iyubanit Rodríguez creator: Gabriela Cajamarca creator: Valeria Herskovic uri: https://doi.org/10.7717/peerj.13716 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rodríguez et al. title: Diversity and distribution of air-breathing sea slug genus Peronia Fleming, 1822 (Gastropoda: Onchidiidae) in southern Japanese waters link: https://peerj.com/articles/13720 last-modified: 2022-07-19 description: Species of the genus Peronia Fleming, 1822, are air-breathing onchidiid sea slugs that inhabit intertidal reef flats of temperate to tropical zones. In the Ryukyu Islands of southern subtropical Japan, Peronia species are a traditional food source for local people. To date, there have been three species recorded around Okinawajima Island; P. verruculata and P. peronii, along with recently described P. okinawensis, which was described as possibly endemic to Okinawajima Island. This study aimed to map the distribution ranges of these three Peronia species within the Ryukyu Islands using molecular analyses in order to understand the specific distribution of each species. Since Peronia species are generally indistinguishable by gross external morphology, a DNA barcoding approach was employed to identify specimens. The molecular data showed that there are four species present in the Ryukyu Islands. P. verruculata (unit #1 sensuDayrat et al., 2020) was dominant at almost all locations, while P. peronii was present in much lower numbers than P. verruculata, but found across a relatively wide range in the Ryukyu Islands. We newly record P. okinawensis and P. setoensis from Amami Oshima Island and from several places around Okinawajima Island, and also identified high levels of genetic variation within P. setoensis. Peronia okinawensis and P. setoensis have been thought to be endemic to Okinawajima Island and to Honshu, mainland Japan, respectively. However, as both species were observed around Okinawajima and Amami Oshima islands, other islands of the Ryukyus are also likely to harbor these species, and their distribution ranges are wider than previously thought. Based on the results from molecular analyses, we provide general descriptions of each species. Sizes of specimens were consistently smaller for P. setoensis and relatively larger for P. peronii specimens. On the other hand, P. verruculata and P. okinawensis had similar size ranges, but P. okinawensis had comparatively much more distinct papillae. This study revealed that the Ryukyu Islands are the only region currently known with four sympatric Peronia species, and this work provides a basis for future research on these Peronia species throughout the northwest Pacific Ocean, representing the first step in more effective management of the local Peronia fisheries in the Ryukyu Islands. creator: Iori Mizukami creator: Chloé Julie Loïs Fourreau creator: Sakine Matsuo creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.13720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mizukami et al. title: Comparative genomic analysis of the COBRA genes in six Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri) link: https://peerj.com/articles/13723 last-modified: 2022-07-19 description: COBRA-Like (COBL) genes encode a glycosylphosphatidylinositol (GPI) anchoring protein unique to plants. In current study, 87 COBRA genes were identified in 6 Rosaceae species, including Pyrus bretschneideri (16 genes), Malus domestica (22 genes), Fragaria vesca (13 genes), Prunus mume (11 genes), Rubus occidentalis (13 genes) and Prunus avium (12 genes). We revealed the evolution of the COBRA gene in six Rosaceae species by phylogeny, gene structure, conservative sequence, hydrophobicity analysis, gene replication events and sliding window analysis. In addition, based on the analysis of expression patterns in pear fruit combined with bioinformatics, we identified PbCOBL12 and PbCOBL13 as potential genes regulating secondary cell wall (SCW) formation during pear stone cell development. This study aimed to understand the evolutionary relationship of the COBRA gene in Rosaceae species, clarify the potential function of COBRA in pear fruit development, and provide essential theoretical basis and gene resources for improving pear fruit quality through genetical modification mechanism. creator: Yu Zhao creator: Xueqiang Su creator: Xinya Wang creator: Mengna Wang creator: Xiaofeng Feng creator: Muhammad Aamir Manzoor creator: Yongping Cai uri: https://doi.org/10.7717/peerj.13723 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhao et al. title: Adaptive multi-paddock grazing management’s influence on soil food web community structure for: increasing pasture forage production, soil organic carbon, and reducing soil respiration rates in southeastern USA ranches link: https://peerj.com/articles/13750 last-modified: 2022-07-19 description: BackgroundMeasurement of two grazing management’s influence on pasture productivity, soil food web structure, soil organic carbon and soil microbial respiration efficiency was conducted on five southeastern US, across-the-fence ranch pairs to compare adaptive multi-paddock grazing (AMP) management, using short grazing events with planned, adaptive recovery periods, to conventional grazing (CG) management, with continuous grazing at low stock density.MethodologyA point-in-time experimental field analysis was conducted to compare five AMP or CG ranch pairs to better understand the influence of grazing management on (a) standing crop biomass productivity; (b) soil food web community population, structure and functionality; (c) soil organic carbon accrual; and d) soil-C (CO2) respiration kinetics.ResultsAMP grazing systems outperformed CG systems by generating: (a) 92.68 g m−2 more standing crop biomass (SCB), promoting 46% higher pasture photosynthetic capacity (Two sample Mann-Whitney; Z = 6.1836; no DF in MW; p = 6.26 × 10−10; Effect size = 0.35) (b) a strong positive linear relationship of SCB with fungal biomass (R = 0.9915; F(1,3) = 175.35; p = 0.015); fungal to bacterial (F:B) biomass ratio (R = 0.9616; F(1,3) = 36.75; p = 0.009) and a soil food web proxy (R = 0.9616; F(1,3) = 36.75; p = 0.009) and a concurrent very strong inverse relationship with bacteria biomass (R = −0.946; F(1,3) = 25.56; p = 0.015); (c) significant predator/prey interactions with an inverse relationship with bacterial population biomass (R =  − 0.946; F(1,3) = 25.56; p = 0.015) and a positive relationship with total protozoa enumeration (R = 0.9826; F(1,3) = 83.68; p = 0.003) when compared to SCB; (d) a 19.52% reduction in soil C (CO2) respiration rates (Two sample t-test; T = −2.3581; DF = 52.3541; p = 0.0221; Effect size = 0.59); and (e) a 20.6% increase in soil organic carbon (SOC) in the top 10 cm of soil profile (Two sample Mann–Whitney; Z = 2.6507; no DF in MW; p = 0.008; Effect size = 0.24). Rancher conversion to AMP grazing strategies would appear to regenerate soil food web population, structure, diversity and biological functionality helping to improve: carbon flow into plant biomass, buildup of soil carbon, predator/prey nutrient cycling and soil microbial respiration efficiency while offering improved climate resilience and a strategy to increase the capture and storage of atmospheric CO2 in soils of the world’s rangeland. creator: David C. Johnson creator: Richard Teague creator: Steven Apfelbaum creator: Ry Thompson creator: Peter Byck uri: https://doi.org/10.7717/peerj.13750 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Johnson et al. title: Plastic debris in plastic-mulched soil—a screening study from western Germany link: https://peerj.com/articles/13781 last-modified: 2022-07-19 description: BackgroundAgricultural plastic mulches offer great benefits such as higher yields and lower pesticide use. Yet, plastic mulches may disintegrate over time and fragment into smaller debris. Such plastic debris is expected to remain in the field after removal of the plastic mulch and thus contributes to soil contamination with plastics.MethodTo investigate this, we collected soil samples at 0–10 cm and 10–40 cm depth from three fields covered with black mulch film for three consecutive years. Three fields without any reported plastic use served as control. Visual plastic debris > 1 cm (macroplastics) was collected from the soil surface. Mesoplastics between 2 mm and 1 cm were density separated from the sampled soil using saturated NaCl solution and analyzed by Fourier-transform infrared spectroscopy. Debris ≤ 2 mm (microplastics) was dispersed from 50 g soil using sodium hexametaphosphate solution followed by the aforementioned density separation. The separated polyethylene (PE), polypropylene (PP), and polystyrene (PS) were quantified via solvent-based pyrolysis–gas chromatography/mass spectrometry (Py–GC/MS).ResultsWith 89–206 fragments ha−1, the majority of macroplastics were located in fields previously covered with mulch films. 80% of the collected specimen were identified as black PE film. The number of mesoplastics in plastic-mulched soil was 2.3 particles kg−1, while only 1.0 particles kg−1 were found in the reference fields. Py–GC/MS revealed microplastic levels of up to 13 mg kg−1. The PE content was significantly higher in plastic-mulched fields than in reference fields.DiscussionAlthough the identified plastic levels are lower than those reported in comparable studies, our results still suggest that plastic mulching functions as a source of plastic debris in agricultural systems. Due to its severely restricted degradability, these plastics are likely to accumulate in soil in the long term and further fragment into smaller and smaller debris. creator: Zacharias Steinmetz creator: Heike Schröder uri: https://doi.org/10.7717/peerj.13781 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Steinmetz and Schröder title: Coral micro-fragmentation assays for optimizing active reef restoration efforts link: https://peerj.com/articles/13653 last-modified: 2022-07-18 description: The global decline of coral reefs has driven considerable interest in active coral restoration. Despite their importance and dominance on mature reefs, relatively few coral restoration projects use slower growth forms like massive and encrusting coral species. Micro-fragmentation can increase coral cover by orders of magnitude faster than natural growth, which now allows cultivation of slow growing massive forms and shows promise and flexibility for active reef restoration. However, the major causes of variation in growth and survival of outplanted colonies remain poorly understood. Here, we report simple outplanting assays to aid in active reef restoration of slower growing species and increase the likelihood of restoration success. We used two different micro-fragmentation assays. Pyramid assays were used to examine variation associated with fragment size (ranging from ≈1–9 cm2), nursery residence time (for both in-situ and ex-situ nurseries), and 2D vs. 3D measurements of growth. Block assays were used to examine spatial variation among individual performance at outplanting sites in the field. We found 2D and 3D measurements correlated well, so measured survivorship and growth using top-down planar images for two of the main Hawaiian reef building corals, the plating Montipora capitata and the massive Porites compressa. Pyramid assays housed and outplanted from the in-situ nursery showed no effect of residence time or size on overall survivorship or growth for either species. Results from the ex-situ nursery, however, varied by species, with P. compressa again showing no effect of nursery residence time or size on survivorship or growth. In contrast, nursery culture resulted in improved survivorship of small M. capitata fragments, but net growth showed a weak positive effect of nursery time for medium fragments. Small fragments still suffered higher mortality than either medium or large fragments. Due to their lower mortality, medium fragments (≈3 cm2) appear to be the best compromise between growth and survivorship for outplanting. Likewise, given weak positive gains relative to the investment, our results suggest that it could be more cost-effective to simply outplant medium fragments as soon as possible, without intermediate culture in a nursery. Furthermore, the block assay revealed significant differences in survivorship and growth among sites for individuals of both species, emphasizing the importance of considering spatial variation in coral survival and growth following outplanting. These results highlight the value of using short-term micro-fragmentation assays prior to outplanting to assess size, and location specific performance, optimizing the efficiency of active reef restoration activities and maximizing the probability of success for active coral restoration projects. creator: Ingrid S.S. Knapp creator: Zac H. Forsman creator: Austin Greene creator: Erika C. Johnston creator: Claire E. Bardin creator: Norton Chan creator: Chelsea Wolke creator: David Gulko creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.13653 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Knapp et al. title: Active ingredients and molecular targets of Taraxacum mongolicum against hepatocellular carcinoma: network pharmacology, molecular docking, and molecular dynamics simulation analysis link: https://peerj.com/articles/13737 last-modified: 2022-07-18 description: BackgroundTaraxacum mongolicum (TM) is a widely used herb. Studies have reported that TM exhibits growth-inhibitory and apoptosis-inducing on multiple tumors, including hepatocellular carcinoma (HCC). The active ingredients, targets, and molecular mechanisms of TM against HCC need to be further elucidated.MethodsWe identified the active ingredients and targets of TM via HERB, PubChem, SwissADME, SwissTargetPrediction, and PharmMapper. We searched HCC targets from GeneCards, Comparative Toxicogenomics Database (CTD), and DisGeNET. Then, the intersection of drug targets and disease targets was uploaded to the STRING database to construct protein-protein interactions (PPI) networking whose topology parameters were analyzed in Cytoscape software to screen hub targets. Next, we used Metascape for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and we employed AutoDock vina, AMBER18 and PyMOL software along with several auxiliary tools for molecular docking and molecular dynamics (MD) simulation. Finally, based on the in silico findings, cellular experiments were conducted to investigate the effect of TM on HSP90AA1 gene expression.ResultsA total of 228 targets and 35 active ingredients were identified. Twenty two hub targets were selected through PPI networking construction for further investigation. The enrichment analysis showed that protein kinase binding, mitogenactivated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways were mainly involved. Molecular docking and MD simulation results supported good interaction between HSP90 protein and Austricin/Quercetin. The in vitro assay showed that TM inhibited the proliferation of HepG2 cells and the expression of HSP90AA1 gene.ConclusionsThis study is the first to use network pharmacology, molecular docking, MD simulation and cellular experiments to elucidate the active ingredients, molecular targets, and key biological pathways responsible for TM anti-HCC, providing a theoretical basis for further research. creator: Yanfeng Zheng creator: Shaoxiu Ji creator: Xia Li creator: Quansheng Feng uri: https://doi.org/10.7717/peerj.13737 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zheng et al. title: Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris) link: https://peerj.com/articles/13753 last-modified: 2022-07-18 description: The gut microbiota has key physiological functions in host adaptation, although little is known about the seasonal changes in the composition and diversity of the gut microbiota in deer. In this study, seasonal variations (grassy and withering season) in the gut microbiota of white-lipped deer (Cervus albirostris), which lives in alpine environments, were explored through 16S rRNA high-throughput sequencing based on sixteen fecal samples collected from Gansu Qilian Mountain National Nature Reserve in China. At the phylum level, Firmicutes, Bacteroidota, and Actinobacteriota dominated the grassy season, while Firmicutes, Proteobacteria, and Actinobacteriota dominated the withering season. At the genus level, Carnobacterium dominated the grassy season, while Arthrobacter and Acinetobacter dominated the withering season. Alpha diversity results (Shannon: P = 0.01, ACE: P = 0.00, Chao1: P = 0.00) indicated that there was a difference in the diversity and richness of the gut microbiota between the two seasons, with higher diversity in the grassy season than in the withering season. Beta diversity results further indicated that there was a significant difference in the community structure between the two seasons (P = 0.001). In summary, the composition, diversity, and community structure of the gut microbiota showed significant seasonal variations, which could be explained by variations in the seasonal food availability, composition, diversity, and nutrition due to phenological alternations. The results of this study indicate that the gut microbiota can adapt to changes in the environment and provide the scientific basis for health assessment of white-lipped deer. creator: Zhangqiang You creator: Jing Deng creator: Jialin Liu creator: Junhua Fu creator: Huan Xiong creator: Wei Luo creator: Jianli Xiong uri: https://doi.org/10.7717/peerj.13753 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 You et al. title: Structural and functional characteristics of soil microbial community in a Pinus massoniana forest at different elevations link: https://peerj.com/articles/13504 last-modified: 2022-07-15 description: Shifts in forest soil microbial communities over altitudinal gradients have long been attracting scientific interest. The distribution patterns of different soil microbial communities along altitudinal gradients in subtropical mountain forest ecosystems remain unclear. To better understand the changes in soil microbial communities along an altitude gradient, we used Illumina MiSeq metagenome sequencing technology to survey the soil microbial communities in a Pinus massoniana forest at four elevations (Mp1000, Mp1200, Mp1400, Mp1600) and in a tea garden in Guizhou Leigong Mountain in Southwestern China. We observed that the richness of bacteria, fungi, and viruses in the soil microbial community changed in a unimodal pattern with increasing elevation while that of Archaea first increased significantly, then decreased, and finally increased again. Euryarchaeota and Thaumarchaeota were the predominant Archaea, Proteobacteria and Acidobacteria were the predominant bacterial groups, Ascomycota and Basidiomycota were the predominant fungal groups, and Myoviridae, Podoviridae, and Siphoviridae were the predominant virus groups. Amino acid transport and metabolism, energy production and conversion, signal transduction mechanisms, and DNA replication, restructuring and repair were the predominant categories as per NOG function gene-annotation. Carbohydrate metabolism, global and overview map, amino acid metabolism, and energy metabolism were predominant categories in the KEGG pathways. Glycosyl transferase and glycoside hydrolase were predominant categories among carbohydrate enzyme-functional genes. Cluster, redundancy, and co-occurring network analyses showed obvious differences in the composition, structure, and function of different soil microbial communities along the altitudinal gradient studied. Our findings indicate that the different soil microbial communities along the altitudinal gradient have different distribution patterns, which may provide a better understanding of the mechanisms that determine microbial life in a mid-subtropical mountain forest ecosystem. creator: Jian Zhang creator: Ming Xu creator: Xiao Zou creator: Jin Chen uri: https://doi.org/10.7717/peerj.13504 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Muscone improves hypoxia/reoxygenation (H/R)-induced neuronal injury by blocking HMGB1/TLR4/NF-κB pathway via modulating microRNA-142 link: https://peerj.com/articles/13523 last-modified: 2022-07-15 description: Previous reports have indicated that natural muscone has neuroprotective effects against cerebral hypoxia injury; however, little is known in regards to its pharmacological mechanism. In this study, we tried to evaluate the neuroprotective effects and mechanisms of muscone against cerebral hypoxia injury using an in vitro model. The cerebral hypoxia injury cell model was produced by hypoxia/reoxygenation (H/R). The cell viability and apoptosis were measured using the cell counting Kit-8 and the Annexin V-FITC/PI Apoptosis Detection kit, respectively. To screen microRNAs regulated by muscone, we analyzed the gene expression datasets of GSE84216 retrieved from gene expression omnibus (GEO). Here, it was demonstrated that muscone treatment significantly alleviated the cell apoptosis, oxidative stress and inflammation in H/R-exposed neurons. Subsequently, through analyzing GSE84216 from the GEO database, miR-142-5p was markedly upregulated by treatment of muscone in this cell model of cerebral hypoxia injury. Further experiments revealed that downregulation of miR-142-5p eliminated the neuroprotective effects of muscone against H/R induced neuronal injury. Additionally, high mobility group box 1 (HMGB1), an important inflammatory factor, was identified as a direct target of miR-142-5p in neurons. Meanwhile, we further demonstrated that muscone could reduce the expression of HMGB1 by upregulating miR-142-5p expression, which subsequently resulted in the inactivation of TLR4/NF-κB pathway, finally leading to the improvement of cell injury in H/R-exposed neurons. Overall, we demonstrate for the first time that muscone treatment alleviates cerebral hypoxia injury in in vitro experiments through blocking activation of the TLR4/NF-κB signaling pathway by targeting HMGB1, suggesting that muscone may serve as a potential therapeutic drug for treating cerebral hypoxia injury. creator: Weihua Ren creator: Fucheng Zhao creator: Yanru Han creator: Zhenzhou Liu creator: Jianli Zhai creator: Kui Jia uri: https://doi.org/10.7717/peerj.13523 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ren et al.