title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=183 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The influence of rhizosphere microbial diversity on the accumulation of active compounds in farmed Scutellaria baicalensis link: https://peerj.com/articles/18749 last-modified: 2024-12-24 description: Rhizosphere microorganisms are important factors affecting herb quality and secondary metabolite accumulation. In this study, we investigated the diversity of rhizosphere microbial communities (bacteria and fungi) and their correlations with soil physicochemical properties and active compounds of Scutellaria baicalensis (baicalin, oroxindin, baicalein, wogonin, and oroxylin A) from cultivated Scutellaria baicalensis with three different origins via high-throughput sequencing and correlation analysis to further clarify the role of soil factors in the accumulation of the active compounds of Scutellaria baicalensis. The results are summarized as follows. A total of 28 dominant bacterial genera, such as Arthrobacter, Rubrobacter, Microvirga, and Sphingomonas, and 42 dominant fungal genera, such as Alternaria, Spegazzinia, and Minimedusa, were detected. The soil microbial communities associated with cultivated Scutellaria baicalensis were very diverse, but there were some differences in the relative abundances of microbial taxa. Correlation analysis revealed that the bacterial genera Rubrobacter, Ellin6055, Gaiella, norank__f__norank__o___norank__c__bacteriap25, unclassified__f__Micromonosporaceae, norank__f__ Gemmatimonadaceae, Arthrobacter, and Sphingomonas and the fungal genera Tausonia, Minimedusa, Cercospora, Botrytis, Alternaria, Boeremia, Titaea, Solicoccozyma, and Mortierella were positively or negatively correlated with each active component of Scutellaria baicalensis and were important genera affecting the accumulation of the active compounds of Scutellaria baicalensis and correlated with soil physiochemistry to different degrees. These results suggest that rhizosphere microorganisms may play a role in the accumulation of active compounds in medicinal plants and provide a scientific basis for guiding the cultivation of Scutellaria baicalensis, developing biofertilizers, and improving the quality of Scutellaria baicalensis medicinal materials. creator: Ping Dong creator: Yang Lu creator: Jia Bai creator: Chunying Zhao creator: Zhongsi Li creator: Yu Cao creator: Yingzhe Li uri: https://doi.org/10.7717/peerj.18749 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dong et al. title: New findings of Dunyu (Eugaleaspiformes, Galeaspida) from the Xiaoxi Formation in South China and their biostratigraphic significance link: https://peerj.com/articles/18760 last-modified: 2024-12-24 description: New discoveries of the late Silurian fossil fish Dunyu (Eugaleaspidae, Eugaleaspiformes, Galeaspida), Dunyu tianlu sp. nov. and Dunyu sp., are described from the Xiaoxi Formation in Xiushan of Chongqing and Xiushui of Jiangxi, China respectively. D. tianlu sp. nov. can be distinguished from D. longiforus and D. xiushanensis in its nearly equal preorbital and postorbital regions of the headshield. As the currently only known genus of Eugaleaspiformes during the late Silurian, Dunyu not only displays a large morphological difference with galeaspids from both the early Silurian and Early Devonian but also occupies a phylogenetic position that is far from the root of Eugaleaspiformes, which indicates that the lineages nested between Yongdongaspidae and Eugaleaspidae should have diversified before the early Ludlow, even during the Telychian. Discovery of new specimens of Dunyu provides direct evidence on the genus level for the correlation of the late Ludlow strata between the margin and interior of the Yangtze Platform, further supporting that the central part of the Yangtze Platform suffered from widespread transgression in the late Silurian. creator: Qiang Li creator: Xianren Shan creator: Zhikun Gai creator: Yang Chen creator: Lijian Peng creator: Jiaqi Zheng creator: Xianghong Lin creator: Wenjin Zhao creator: Min Zhu uri: https://doi.org/10.7717/peerj.18760 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: An efficient propagation system through stem cuttings of a multipurpose plant—Ficus tikoua Bur link: https://peerj.com/articles/18768 last-modified: 2024-12-24 description: Ficus tikoua Bur., a versatile plant with medicinal, edible, landscaping, and ecological applications, holds significant economic value and boasts a long-standing history of utilization in China. Despite its robust adaptability, rapid growth, and extensive distribution, the current research gap concerning the physiological mechanisms underlying stem cutting propagation hampers the development of efficient strategies for commercial-scale propagation of F. tikoua, particularly for large-scale cultivation. To address this, we investigated the effects of habitat heterogeneity, physiological indicators, and environmental factors on the cutting propagation of F. tikoua. Stem segments were collected from grassland, sandy, rocky and understory habitats in the field and subjected to comprehensive analyses using a two-factor mixed experimental design and progressive group experiments. Our findings indicate that stem segments of F. tikoua with a length of 10 cm and a diameter of 0.5∼0.7 cm exhibited the highest shoot induction rate and total multiplication coefficient. Optimal results were achieved with a vertical burial depth of 5∼7 cm. Stem segments aged 2∼3 years produced the highest number of seedlings, and the most suitable propagation period for cuttings was from March to April. The best substrate-habitat combinations for overall seeding yield were grassland-T4 (loam: light substrate: humus = 2:1:1), sandy-T6 (loam: light substrate: humus = 2:3:1), rocky-T5 (loam: light substrate: humus = 2:2:1), understory-T3 (loam: light substrate: humus = 1:1:1), respectively. Mantel test analyses revealed that the ability of F. tikoua cuttings from different habitats to form adventitious roots (ARs) largely determined the functional traits associated with cutting propagation. Overall, our results suggest that stem segment from grassland habitat are the most suitable for F. tikoua cutting propagation, with a loam: light substrate: humus ratio of 2:1:1 being the most favorable substrate. In contrast, F. tikoua from rocky habitat is not suitable for cutting propagation, particularly for large-scale seedling production. creator: Tinghong Tan creator: Yu Peng creator: Biling An creator: Fan Gao creator: Yanni Sun creator: Chuandong Yang creator: Hong Yang creator: Zhihong Lu uri: https://doi.org/10.7717/peerj.18768 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tan et al. title: Effects of nitrogen doses on stomatal characteristics, chlorophyll content, and agronomic traits in wheat (Triticum aestivum L.) link: https://peerj.com/articles/18792 last-modified: 2024-12-24 description: It is very important to determine the chlorophyll content (SPAD) and nitrogen (N) requirement in order to increase the seed yield and nutritional quality of wheat. This research was carried out with three N doses (0, 50, 100 kg ha−1) and nine wheat cultivars (Alpu-2001, Soyer-02, Kate-A1, Bezostaja-1, Altay-2000, Müfitbey, Nacibey, Harmankaya-99 and Sönmez-2001) during 2-years field condition according to factorial randomized complete block design and three replications. In this study, with the increase of N dose (N50), seed yield increased by 13%, plant height by 10.8%, 1,000 seed weight by 10.5% compared to control plants (N0). The increase of N dose from 50 kg ha−1 to 100 kg gave lower increase rates in the same criteria (11.7%, 11.4%, 10.3%, respectively). However, the spike number per plant, spikelet number in spike, seed number in spike, spike length showed statistically significant differences between N doses and varieties. Boost of N doses caused a significant increase compared to plants without N application. The chlorophyll content and flag leaf area index were determined at three growth times (1st growth time; early, 2nd growth time; the middle and end of flowering, 3rd growth time; with a 10-day interval). Chlorophyll content was significantly (p < 0.01) affected by the N dose, variety and growth time. As N doses increased, chlorophyll content increased, and it was higher at both N doses compared with N0. The chlorophyll content had the highest rates (30.22%) at 1st growth time and it decreased as the growth period progressed. N doses, varieties and their interactions had significant effects on the flag leaf area index. The highest flag leaf area index (41.9 cm2) was determined from variety Bezostaja-1 and 100 kg ha−1 N dose treatment. The effect of N dose was found significantly on abaxial and adaxial stomata width-length and epidermal cells. The adaxial and abaxial stomata width were higher than N0 at both N levels. The highest adaxial and abaxial stomata width- length was obtained from 100 kg ha−1 N dose. As nitrogen concentration increased, both stomatal density and stomatal index increased. The stomatal index varied between 19% and 36%. The lowest stomata density had appeared in the 100 kg ha−1 N dose and Bezostaja-1 variety. As a result, stomatal characteristics, chlorophyll content, and agronomic traits of wheat were significantly affected by increasing N doses. creator: Fatih Oner uri: https://doi.org/10.7717/peerj.18792 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Oner title: Evaluating techniques for determining elasmobranch body size: a review of current methodologies link: https://peerj.com/articles/18646 last-modified: 2024-12-23 description: There is global awareness that many species of elasmobranchs (sharks and rays) have life history characteristics that make them susceptible to overexploitation. The study of these animals is critical, as it contributes to increasing knowledge of these specimens and aids in their conservation. In particular, growth rate, age, fecundity, and size at maturity are key parameters for defining management and conservation strategies in elasmobranchs. Biometric data collection allows these parameters to be determined and considered in the evaluation of population demography. Over the last decades, several methodologies for measuring elasmobranch size have evolved, progressing from traditional capture-based methods to sophisticated, non-intrusive photographic techniques. The present review aims to understand and analyse all the existing non-invasive techniques that currently allow the collection of zoometric data in elasmobranchs and, later, to highlight the advantages and limitations of each technique, with comments on their application to fieldwork. To this end, 49 articles were selected, encompassing seven measurement techniques: photogrammetry using distance to the individual, bar photogrammetry, laser photogrammetry, stereo-DOV, stereo-BRUV, stereo-ROV, and aerial photogrammetry. Globally, the last four techniques are excellent alternatives to methods that involve animal capture or death, as they are practical, simple to use, minimally invasive, and potentially highly accurate. Each technique’s requirements related to equipment and cost, limitations, and distinctive features are presented here and summarized to guide researchers on what’s available and how to select the most appropriate for their studies. creator: Ana S. Ferreira creator: Márcia A. Naré creator: Joana I. Robalo creator: Núria D. Baylina uri: https://doi.org/10.7717/peerj.18646 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ferreira et al. title: DNA metabarcoding reveals diet diversity and niche partitioning by two sympatric herbivores in summer link: https://peerj.com/articles/18665 last-modified: 2024-12-23 description: BackgroundFood provides essential nutrients and energy necessary for animals to sustain life activities. Accordingly, dietary niche analysis facilitates the exploration of foraging strategies and interspecific relationships among wildlife. The vegetation succession has reduced understory forage resources (i.e., shrubs and herbs) available to sika deer (Cervus nippon kopschi). Little is known about the summer foraging strategies or the interspecific relationship between sika deer and Reeves’ muntjac (Muntiacus reevesi).MethodsThe present study used high-throughput sequencing and DNA metabarcoding techniques to investigate the feeding habits and interspecific relationships between sika deer and Reeves’ muntjac in our study.ResultsA total of 458 amplicon sequence variants (ASVs) were identified from fecal samples, with 88 ASVs (~19.21%) unique to sika deer and 52 ASVs (~11.35%) unique to Reeves’ muntjac, suggesting the consumption and utilization of specific food items for the two species. The family Rosaceae was the most abundant for both species, especially Rubus spp. and Smilax china. Alpha diversity (local species richness) indicated that the dietary species richness of sika deer was higher than that of Reeves’ muntjac, but the difference was not statistically significant. Sika deer also exhibited a higher evenness index (J′ = 0.514) than Reeves’ muntjac (J′ = 0.442). Linear discriminant effect size analysis revealed significant differences in forage plants between the two herbivores. The niche breadths of sika deer and Reeves’ muntjac were 11.36 and 14.06, respectively, and the dietary niche overlap index was 0.44. Our findings indicate the diet partitioning primarily manifested in the differentiation of food items and the proportion, which ultimately reduces the overlap of nutritional niches and helps avoid conflicts resulting from resource utilization. This study provides a deeper insight into the diversity of foraging strategies and the interspecific relationship of herbivores from the food dimension. creator: Ruofei Li creator: Dandan Wang creator: Zhiming Cao creator: Yuqin Liu creator: Wenguo Wu creator: Wuhua Liu creator: Jianwen Zhan creator: Yongtao Xu uri: https://doi.org/10.7717/peerj.18665 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Identification of the whole genome of alternative splicing and RNA-binding proteins involved in nintedanib-induced apoptosis in gastric cancer cells link: https://peerj.com/articles/18697 last-modified: 2024-12-23 description: BackgroundIt has been demonstrated that nintedanib can inhibit the proliferation of gastric cancer cells, but the specific mechanism of action is unclear.ObjectiveInvestigating the changes of key factors involved in gene transcription and post-transcriptional regulation during the process of treating gastric cancer with nintedanib.MethodsIn this study, we performed transcriptome sequencing on gastric cancer cell groups treated with nintedanib and control groups. The SUVA (Splice sites Usage Variation Analysis) software was used to identify differential alternative splicing (AS) events between the nintedanib-treated group and the control group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to assess the functional differences and pathways associated with these events. Finally, a co-expression regulatory network of differentially expressed RNA-binding proteins (RBPs) and differentially spliced genes was established. Results: A total of 915 differential AS events were identified between the two groups, and these differential genes were closely related to the apoptosis pathway. Further analysis revealed that differential RBPs (TAGLN2, TAGLN, SRSF6, PKM, SRSF2, NOC2L, IPO4, C1QBP, DHX9) may affect the anti-proliferative effect of nintedanib on gastric cancer cells by regulating downstream genes involved in cell proliferation and angiogenesis (NR4A1, BBC3, IFI27) through alternative splicing.ConclusionThis study systematically identified important changes in alternative splicing and RNA-binding proteins during the process of nintedanib-induced apoptosis in gastric cancer cells. It innovatively revealed the mechanisms of action of nintedanib in gastric cancer cells and expanded the selection of new targets for gastric cancer treatment. creator: Xiaohua Dong creator: Zhilong Liu creator: Miao Yu creator: Xiaojun Yang creator: Hui Cai uri: https://doi.org/10.7717/peerj.18697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dong et al. title: Quality of life and subjective well-being comparison between traumatic, nontraumatic chronic spinal cord injury, and healthy individuals in China link: https://peerj.com/articles/18709 last-modified: 2024-12-23 description: BackgroundDifferentiating between traumatic and non-traumatic spinal cord injuries (NT-SCI) is critical, as these classifications may significantly impact patients’ health outcomes and overall well-being, potentially resulting in differences in treatment protocols and therapeutic efficacy.ObjectiveThis study aims to compare the quality of life (QoL) and satisfaction with life (SWL) among individuals with traumatic spinal cord injuries (T-SCI), NT-SCI, and the healthy population in China.MethodA quantitative, cross-sectional survey was conducted between July and December 2020 in the Rehabilitation and Physiotherapy Department of Tongji Hospital, Hubei University of Science and Technology. The World Health Organization Quality of Life Brief Version (WHOQOL-BREF) and the Satisfaction with Life Scale (SWLS) were administered to evaluate QoL and subjective well-being (SWB). An independent t-test was performed to assess differences within the SCI population, while Pearson’s correlation coefficient was utilized to explore relationships between the WHOQOL-BREF domains and the SWLS. Multiple linear regression analysis was applied to identify key determinants influencing World Health Organization Quality of Life (WHOQOL) domain scores and overall SWLS score.ResultParticipants with NT-SCI exhibited significant differences in overall health as measured by the WHOQOL-BREF domains compared to those with T-SCI (p < 0.05). Both the NT-SCI and T-SCI groups demonstrated lower mean scores across all four WHOQOL-BREF domains compared to healthy individuals. No significant differences were observed between the NT-SCI and T-SCI groups in the SWLS, although both groups scored lower than the healthy population. Additionally, SWB was moderately positively correlated with QoL (p < 0.01). Collectively, the predictor variables explained 22.28% of the variance in physical health, 6.43% in psychological health, 28.67% in social health, and 25.68% in environmental health. Furthermore, the independent variables accounted for approximately 22.67% of the variance in the SWLS.ConclusionsIndividuals with NT-SCI experience significantly worse overall health outcomes compared to those with T-SCI, although both groups report QoL and life satisfaction than healthy individuals. No significant differences in life satisfaction were found between two groups. Additionally, SWB shows a moderate positive correlation with QoL, highlighting the close relationship between mental and physical health in SCI populations. creator: Ruba Altahla creator: Jamal Alshorman creator: Sayed Zulfiqar Ali-Shah creator: Mohammad Nasb creator: Xu Tao uri: https://doi.org/10.7717/peerj.18709 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Altahla et al. title: Spatial heterogeneity of soil properties in planted mixed forests in the rocky desertification areas of the Wuling Mountain link: https://peerj.com/articles/18724 last-modified: 2024-12-23 description: In this study, experiments were conducted on soil samples collected from depths of 0–15 cm, 15–30 cm, and 30–50 cm at the National Long-term Scientific Research Base for the Comprehensive Management of Rocky Desertification in the Wuling Mountains. The aim was to determine the physicochemical indexes and explore the nature and spatial heterogeneity of the soil of the planted mixed forests within the rocky desertification area of the Wuling Mountain. Various analytical methods were employed, including descriptive statistical analysis, correlation analysis, analysis of variance, principal component analysis, spatial interpolation analysis, and kriging interpolation, to fit the optimal model of the semi-variance function of soil physicochemical properties and analyze the model’s parameters. The results indicated that soil physical and chemical properties varied with depth and were generally correlated. The relationship between soil organic matter and total nitrogen content was the closest. Additionally, there was a certain degree of correlation between soils at different depths in the vertical profile, generally the correlation between layer B (15–30 cm) and layer C (30–50 cm) > that between layer A (0–15 cm) and layer B (15–30 cm) > that between layer A (0–15 cm) and layer C (30–50 cm). The weighting coefficients of the principal components of soil physicochemical properties indicated that soil organic matter, nitrogen, phosphorus, potassium, pH, total porosity, and capillary porosity are key factors in the soil properties of karst desertification areas. The spatial variability of soil physicochemical properties at different depths ranged from 21.91 to 87.59 m, and the abutment ratio (Co/Co+C) of these properties ranged from 12.99% to 89.53%. Using kriging interpolation in ArcGIS, the spatial distribution pattern of soil physical and chemical properties was mapped, revealing that these indicators were distributed with heterogeneous patches of various sizes and shapes. Therefore, the degree of rocky desertification significantly influences the spatial distribution pattern of soil physical and chemical properties. creator: Ziqian Pan creator: Yanyan Dong creator: Gongxiu He creator: Tongtong Guo creator: Ninghua Zhu uri: https://doi.org/10.7717/peerj.18724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Pan et al. title: Malignant behaviors and immune response in melanoma: Epstein-Barr virus induced gene 3 as a therapeutic target based on an in-vitro exploration link: https://peerj.com/articles/18730 last-modified: 2024-12-23 description: BackgroundEpstein-Barr virus induced gene 3 (EBI3), a member of the IL-12 family, is known to be involved in malignant progression in a variety of cancers, but its role in melanoma is unclear. The aim of this study was to explore the effects of EBI3 on the malignant phenotype melanoma to reveal its potential as a therapeutic target.MethodsIn this study, we used bioinformatics to analyze the expression of EBI3 in pan-cancer and verified its expression level in melanoma cells by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Subsequently, the effects of EBI3 knockdown on cell proliferation, migration and invasion were detected using the Cell Counting Kit-8 (CCK-8) and Transwell assays. Changes in immune-related cytokines were detected by ELISA, and macrophage polarization was observed using immunofluorescence. Finally, the phosphorylation levels of signaling pathways such as Smad3, STAT6 and cGAS-STING were analyzed by Western blot.ResultsEBI3 was evidently highly-expressed in melanoma, and silencing of EBI3 could visibly suppress the survival and migration/invasion of melanoma cells, concurrent with the increased levels of BAX and CDH1 and the decreased expressions of BCL2 and CDH2. Meanwhile, EBI3 knockdown diminished the phosphorylation levels of both Smad3 and STAT6 and the levels of immune response-relevant cytokines in melanoma cells, while aggravating the macrophage M1 polarization and the expression of cGAS, p-STING and p-IRE1 α in THP-1 monocyte-derived macrophages co-cultured with EBI3-silenced melanoma cells.ConclusionThis study filled the blank on the involvement of EBI3 in melanoma, hinting the possibility of controlling EBI3 as a therapeutic strategy in the management of melanoma. creator: Ying Zhang creator: Fengrui Cheng creator: Xingrui Cai creator: Jingping Wu uri: https://doi.org/10.7717/peerj.18730 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al.