title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=359 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Molecular cloning and characterization of farnesyl diphosphate synthase from Rosa rugosa Thunb associated with salinity stress link: https://peerj.com/articles/16929 last-modified: 2024-02-29 description: Rosa rugosa, a renowned ornamental plant, is cultivated for its essential oil containing valuable monoterpenes, sesquiterpenes, and other compounds widely used in the floriculture industry. Farnesyl diphosphate synthase (FPPS) is a key enzyme involved in the biosynthesis of sesquiterpenes and triterpenes for abiotic or biotic stress. In this study, we successfully cloned and characterized a full-length FPPS- encoding cDNA identified as RrFPPS1 using RT-PCR from R. rugosa. Phylogenetic analysis showed that RrFPPS1 belonged to the angiosperm-FPPS clade. Transcriptomic and RT-qPCR analyses revealed that the RrFPPS1 gene had tissue-specific expression patterns. Subcellular localization analysis using Nicotiana benthamiana leaves showed that RrFPPS1 was a cytoplasmic protein. In vitro enzymatic assays combined with GC-MS analysis showed that RrFPPS1 produced farnesyl diphosphate (FPP) using isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) as substrates to provide a precursor for sesquiterpene and triterpene biosynthesis in the plant. Additionally, our research found that RrFPPS1 was upregulated under salt treatment. These substantial findings contribute to an improved understanding of terpene biosynthesis in R. rugosa and open new opportunities for advancements in horticultural practices and fragrance industries by overexpression of the RrFPPS1 gene in vivo increased FPP production and subsequently led to elevated sesquiterpene yields in the future. The knowledge gained from this study can potentially lead to the development of enhanced varieties of R. rugosa with improved aroma, medicinal properties, and resilience to environmental stressors. creator: Guo Wei creator: Yudie Chen creator: Jianwen Wang creator: Liguo Feng uri: https://doi.org/10.7717/peerj.16929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wei et al. title: Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer link: https://peerj.com/articles/16935 last-modified: 2024-02-29 description: BackgroundTriple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with high heterogeneity, poor prognosis, and a low 10-year survival rate of less than 50%. Although cellular senescence displays extensive effects on cancer, the comprehensions of cellular senescence-related characteristics in TNBC patients remains obscure.MethodSingle-cell RNA sequencing (scRNA-seq) data were analyzed by Seurat package. Scores for cellular senescence-related pathways were computed by single-sample gene set enrichment analysis (ssGSEA). Subsequently, unsupervised consensus clustering was performed for molecular cluster identification. Immune scores of patients in The Cancer Genome Atlas (TCGA) dataset and associated immune cell scores were calculated using Estimation of STromal and Immune cells in MAlignantTumours using Expression data (ESTIMATE) and Microenvironment Cell Populations-counter (MCP-counter), Tumor Immune Estimation Resource (TIMER) and Estimating the Proportion of Immune and Cancer cells (EPIC) methods, respectively. Immunotherapy scores were assessed using TIDE. Furthermore, feature genes were identified by univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses; these were used to construct a risk model. Additionally, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and transwell assay were conducted for in vitro validation of hub genes.ResultTNBC was classified into three subtypes based on cellular senescence-related pathways as clusters 1, 2, and 3. Specifically, cluster 1 showed the best prognosis, followed by cluster 2 and cluster 3. The levels of gene expression in cluster 2 were the lowest, whereas these were the highest in cluster 3. Moreover, clusters 1 and 3 showed a high degree of immune infiltration. TIDE scores were higher for cluster 3, suggesting that immune escape was more likely in patients with the cluster 3 subtype who were less likely to benefit from immunotherapy. Next, the TNBC risk model was constructed and validated. RT-qPCR revealed that prognostic risk genes (MMP28, ACP5 and KRT6A) were up-regulated while protective genes (CT83) were down-regulated in TNBC cell lines, validating the results of the bioinformatics analysis. Meanwhile, cellular experiments revealed that ACP5 could promote the migration and invasion abilities in two TNBC cell lines. Finally, we evaluated the validity of prognostic models for assessing TME characteristics and TNBC chemotherapy response.ConclusionIn conclusion, these findings help to assess the efficacy of targeted therapies in patients with different molecular subtypes, have practical applications for subtype-specific treatment of TNBC patients, and provide information on prognostic factors, as well as guidance for the revelation of the molecular mechanisms by which senescence-associated genes influence TNBC progression. creator: Tengfei Cao creator: Mengjie Huang creator: Xinyue Huang creator: Tian Tang uri: https://doi.org/10.7717/peerj.16935 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cao et al. title: The destructive subterranean termite Reticulitermes flavipes (Blattodea: Rhinotermitidae) can colonize arid territories link: https://peerj.com/articles/16936 last-modified: 2024-02-29 description: Reticulitermes flavipes, one of the most destructive subterranean termite species, has been detected for the first time in an arid territory: Lanzarote (Canary Islands, Spain). This invasive species was introduced into several countries but never such a dry region. Although there are places with presence of this termite at similar or even higher temperatures, none has annual rainfall (10.1 mm) as low as Lanzarote. On this island it is present in semi-desert, near an affected urban area. Distribution, genetic, climate and host-plant data are evaluated to track and understand its invasion process in the archipelago. creator: David Hernández-Teixidor creator: Aura Pérez-Morín creator: Juan Pestano creator: David Mora creator: Silvia Fajardo uri: https://doi.org/10.7717/peerj.16936 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hernández-Teixidor et al. title: Prognostic value of RNA methylation-related genes in gastric adenocarcinoma based on bioinformatics link: https://peerj.com/articles/16951 last-modified: 2024-02-29 description: BackgroundGastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer.MethodsIn this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR).ResultsIn total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics.ConclusionOur study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy. creator: Xionghui He creator: Xiang Chen creator: Changcheng Yang creator: Wei Wang creator: Hening Sun creator: Junjie Wang creator: Jincheng Fu creator: Huaying Dong uri: https://doi.org/10.7717/peerj.16951 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 He et al. title: Transformation of the pectoral girdle in pennaraptorans: critical steps in the formation of the modern avian shoulder joint link: https://peerj.com/articles/16960 last-modified: 2024-02-29 description: Important transformations of the pectoral girdle are related to the appearance of flight capabilities in the Dinosauria. Previous studies on this topic focused mainly on paravians yet recent data suggests flight evolved in dinosaurs several times, including at least once among non-avialan paravians. Thus, to fully explore the evolution of flight-related avian shoulder girdle characteristics, it is necessary to compare morphology more broadly. Here, we present information from pennaraptoran specimens preserving pectoral girdle elements, including all purportedly volant taxa, and extensively compare aspects of the shoulder joint. The results show that many pectoral girdle modifications appear during the evolution from basal pennaraptorans to paravians, including changes in the orientation of the coracoid body and the location of the articulation between the furcula and scapula. These modifications suggest a change in forelimb range of motion preceded the origin of flight in paravians. During the evolution of early avialans, additional flight adaptive transformations occur, such as the separation of the scapula and coracoid and reduction of the articular surface between these two bones, reduction in the angle between these two elements, and elongation of the coracoid. The diversity of coracoid morphologies and types of articulations joining the scapula-coracoid suggest that each early avialan lineage evolved these features in parallel as they independently evolved more refined flight capabilities. In early ornithothoracines, the orientation of the glenoid fossa and location of the acrocoracoid approaches the condition in extant birds, suggesting a greater range of motion in the flight stroke, which may represent the acquisition of improved powered flight capabilities, such as ground take-off. The formation of a new articulation between the coracoid and furcula in the Ornithuromorpha is the last step in the formation of an osseous triosseal canal, which may indicate the complete acquisition of the modern flight apparatus. These morphological transitions equipped birds with a greater range of motion, increased and more efficient muscular output and while at the same time transmitting the increased pressure being generated by ever more powerful flapping movements in such a way as to protect the organs. The driving factors and functional adaptations of many of these transitional morphologies are as yet unclear although ontogenetic transitions in forelimb function observed in extant birds provide an excellent framework through which we can explore the behavior of Mesozoic pennaraptorans. creator: Qian Wu creator: Jingmai K. O’Connor creator: Shiying Wang creator: Zhonghe Zhou uri: https://doi.org/10.7717/peerj.16960 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wu et al. title: A Cellular Potts Model of the interplay of synchronization and aggregation link: https://peerj.com/articles/16974 last-modified: 2024-02-29 description: We investigate the behavior of systems of cells with intracellular molecular oscillators (“clocks”) where cell-cell adhesion is mediated by differences in clock phase between neighbors. This is motivated by phenomena in developmental biology and in aggregative multicellularity of unicellular organisms. In such systems, aggregation co-occurs with clock synchronization. To account for the effects of spatially extended cells, we use the Cellular Potts Model (CPM), a lattice agent-based model. We find four distinct possible phases: global synchronization, local synchronization, incoherence, and anti-synchronization (checkerboard patterns). We characterize these phases via order parameters. In the case of global synchrony, the speed of synchronization depends on the adhesive effects of the clocks. Synchronization happens fastest when cells in opposite phases adhere the strongest (“opposites attract”). When cells of the same clock phase adhere the strongest (“like attracts like”), synchronization is slower. Surprisingly, the slowest synchronization happens in the diffusive mixing case, where cell-cell adhesion is independent of clock phase. We briefly discuss potential applications of the model, such as pattern formation in the auditory sensory epithelium. creator: Rose Una creator: Tilmann Glimm uri: https://doi.org/10.7717/peerj.16974 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Una and Glimm title: Downsizing a heavyweight: factors and methods that revise weight estimates of the giant fossil whale Perucetus colossus link: https://peerj.com/articles/16978 last-modified: 2024-02-29 description: Extremes in organismal size have broad interest in ecology and evolution because organismal size dictates many traits of an organism’s biology. There is particular fascination with identifying upper size extremes in the largest vertebrates, given the challenges and difficulties of measuring extant and extinct candidates for the largest animal of all time, such as whales, terrestrial non-avian dinosaurs, and extinct marine reptiles. The discovery of Perucetus colossus, a giant basilosaurid whale from the Eocene of Peru, challenged many assumptions about organismal extremes based on reconstructions of its body weight that exceeded reported values for blue whales (Balaenoptera musculus). Here we present an examination of a series of factors and methodological approaches to assess reconstructing body weight in Perucetus, including: data sources from large extant cetaceans; fitting published body mass estimates to body outlines; testing the assumption of isometry between skeletal and body masses, even with extrapolation; examining the role of pachyostosis in body mass reconstructions; addressing method-dependent error rates; and comparing Perucetus with known physiological and ecological limits for living whales, and Eocene oceanic productivity. We conclude that Perucetus did not exceed the body mass of today’s blue whales. Depending on assumptions and methods, we estimate that Perucetus weighed 60–70 tons assuming a length 17 m. We calculated larger estimates potentially as much as 98–114 tons at 20 m in length, which is far less than the direct records of blue whale weights, or the 270 ton estimates that we calculated for body weights of the largest blue whales measured by length. creator: Ryosuke Motani creator: Nicholas D. Pyenson uri: https://doi.org/10.7717/peerj.16978 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Motani and Pyenson title: H2O2 promotes trimming-induced tillering by regulating energy supply and redox status in bermudagrass link: https://peerj.com/articles/16985 last-modified: 2024-02-29 description: Tillering/branching pattern plays a significant role in determining the structure and diversity of grass, and trimming has been found to induce tillering in turfgrass. Recently, it has been reported that hydrogen peroxide (H2O2) regulates axillary bud development. However, the role of H2O2 in trimming-induced tillering in bermudagrass, a kind of turfgrass, remains unclear. Our study unveils the significant impact of trimming on promoting the sprouting and growth of tiller buds in stolon nodes, along with an increase in the number of tillers in the main stem. This effect is accompanied by spatial-temporal changes in cytokinin and sucrose content, as well as relevant gene expression in axillary buds. In addition, the partial trimming of new-born tillers results in an increase in sucrose and starch reserves in their leaves, which can be attributed to the enhanced photosynthesis capacity. Importantly, trimming promotes a rapid H2O2 burst in the leaves of new-born tillers and axillary stolon buds. Furthermore, exogenous application of H2O2 significantly increases the number of tillers after trimming by affecting the expression of cytokinin-related genes, bolstering photosynthesis potential, energy reserves and antioxidant enzyme activity. Taken together, these results indicate that both endogenous production and exogenous addition of H2O2 enhance the inductive effects of trimming on the tillering process in bermudagrass, thus helping boost energy supply and maintain the redox state in newly formed tillers. creator: Shuang Li creator: Yanling Yin creator: Jianmin Chen creator: Xinyu Cui creator: Jinmin Fu uri: https://doi.org/10.7717/peerj.16985 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Microbiota associated with urban forests link: https://peerj.com/articles/16987 last-modified: 2024-02-29 description: Urban forests are essential for maintaining urban ecological stability. As decomposers, soil microorganisms play an indispensable role in the stability of urban forest ecosystems, promoting the material cycle of the ecosystems. This study used high-throughput sequencing technology to explore the bacteria in six forest stands, including Phyllostachys edulis (ZL), Metasequoia glyptostroboides (SSL), Cornus officinalis (SZY), mixed broad-leaved shrub forest (ZKG), mixed pine and cypress forest (SBL), and mixed broad-leaved tree forest (ZKQ). Meanwhile, the differences in fungal communities were investigated. The results show that ZL has the highest alpha diversity of bacterial communities, while its fungal community is the lowest; Proteobacteria is the most abundant bacterial phylum in the six forest stands; ZKQ has the highest fungal diversity. In addition, soil microbial communities are affected by environmental factors. Soil pH, organic matter (SOM), and available phosphorus (AP) significantly influence the compositions of urban forest soil microbial communities. This study revealed the differences in bulk soil (BS) microbial community structures among six forest stands and the relationship between environmental factors and soil microbial communities, which has important guiding significance for creating healthy and stable urban forests with profound ecological benefits. creator: Xin Wan creator: Runyang Zhou creator: Yingdan Yuan creator: Wei Xing creator: Sian Liu uri: https://doi.org/10.7717/peerj.16987 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wan et al. title: The application of two drainage angles in neurocritical care patients with complicated pneumonia: a randomized controlled trial link: https://peerj.com/articles/16997 last-modified: 2024-02-29 description: BackgroundAlthough head elevation is an early first-line treatment for elevated intracranial pressure (ICP), the use of the head-down or prone position in managing neurocritical patients is controversial because a change in a position directly affects the intracranial and cerebral perfusion pressure, which may cause secondary brain injury and affect patient outcomes. This study compared the effects of two postural drainage positions (30° head-up tilt and 0° head flat) on the prognosis of neurocritical care patients with complicated pneumonia and a clinical pulmonary infection score (CPIS) ≥5 points to provide a reference for selecting appropriate postural drainage positions for patients with pneumonia in neurocritical care units.MethodsA prospective randomized controlled study was conducted with 62 neurocritical care patients with complicated pneumonia. The patients were categorized into control (=31) and experimental (=31) groups in a 1:1 ratio using a simple randomized non-homologous pairing method. Emphasis was placed on matching the baseline characteristics of the two groups, including patient age, sex, height, weight, Glasgow Coma Scale score, heart rate, mean arterial pressure, cough reflex, and mechanical ventilation usage to ensure comparability. Both groups received bundled care for artificial airway management. The control group maintained a standard postural drainage position of 0° head-flat, whereas the experimental group maintained a 30° head-up tilt. The efficacy of the nursing intervention was evaluated by comparing the CPIS and other therapeutic indicators between the two groups after postural drainage.ResultsAfter the intervention, the within-group comparison showed a significant decrease in the CPIS (P < 0.001); procalcitonin levels showed a significant decreasing trend (P < 0.05); the arterial oxygen pressure significantly increased (P < 0.05); the oxygenation index significantly increased (P < 0.001); and the aspiration risk score showed a significant decreasing trend (P < 0.001). A between-group comparison showed no significant differences in any of the indicators before and after the intervention (P < 0.05).ConclusionPostural drainage positions of 30° head-up tilt and 0° head-flat can improve the CPIS and oxygenation in patients without adverse effects. Therefore, we recommend that patients under neurological intensive care and having pneumonia be drained in a 30° head-up tilt position with good centralized care of the lung infection.Trial registrationThe study, “Study of Angles of Postural Drainage in Neurocritical Patients with Pneumonia,” was registered in the Protocol Registration Data Element Definitions for Interventional Study database (# ChiCTR2100042155); date of registration: 2021-01-14. creator: Anna Zhao creator: Huangrong Zeng creator: Hui Yin creator: Jinlin Wang creator: Wenming Yuan creator: Chao Li creator: Yan Zhong creator: Lanlan Ma creator: Chongmao Liao creator: Hong Zeng creator: Yan Li uri: https://doi.org/10.7717/peerj.16997 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al.