title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=40
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Functions of wheat ncRNAs in pathogen defense and stress adaptation
link: https://peerj.com/articles/20142
last-modified: 2025-10-22
description: In organisms, non-coding RNAs (ncRNAs) are key regulatory elements that modulate, the expression of genes involved in diverse biological traits. Among them, micro RNAs (miRNAs), small interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs) have become major research focuses. Wheat, the world’s most widely grown crop, occupies 17% of global cultivated land and supplies ∼55% of the world’s carbohydrates. Understanding the roles, identification, and mechanisms of wheat ncRNAs is essential for both basic research and crop improvement. Through systematic searches of PubMed, Web of Science, and EndNote databases, this study identified 182 publications related to wheat ncRNAs. Based on predefined criteria—research relevance and publication timeframe (2015–2025)—70 high-quality studies were selected for in-depth analysis. This review comprehensively summarizes recent advances in ncRNA research (focusing on lncRNAs and small RNAs) in relation to wheat diseases, pests, and responses to biotic and abiotic stress. By integrating traditional classification with functional characterization, we developed a comprehensive analytical framework encompassing “molecular characteristics-biotic stress–abiotic stress”. Furthermore, this review consolidates multi-omics high-throughput data and online ncRNA databases. The integration of multi-omics technologies aims to provide both a theoretical foundation and novel strategies for wheat genetic improvement.
creator: Yongji Yang
creator: Yi Hu
creator: Tao Li
creator: Qi You
uri: https://doi.org/10.7717/peerj.20142
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2025 Yang et al.

title: Effects of four different times of day on various aspects of maximal short-term physical performance in young soccer players
link: https://peerj.com/articles/20065
last-modified: 2025-10-22
description: The time of day (TOD) has a significant influence on physical performance through circadian rhythms, which regulate body temperature, muscle function, and hormone levels. While extensively studied in adults, the impact of TOD on adolescent athletes remains underexplored. This study aimed to investigate the effects of TOD on maximal short-term physical performance in adolescent soccer players, to guide evidence-based decisions regarding the structuring of training and competition schedules. Nineteen male adolescent soccer players (mean age: 14.58 ± 0.7 years) participated in a randomized trial, performing at four TOD sessions (08:00 h, 11:00 h, 15:00 h, and 18:00 h) with recovery periods of at least 48 hours between sessions. Performance metrics included oral temperature (OT), medicine ball throw (MBT), 5-meter sprint (5m-T), 20-meter sprint (20m-T), Illinois Agility Test (IAT), and Illinois Agility Test with Ball (IAT-B). Results revealed significant TOD effects. OT increased notably from 08:00 to 18:00 (p < 0.001). Physical performance metrics (MBT, 5m-T, 20m-T, IAT, and IAT-B) improved significantly at 11:00, 15:00, and 18:00 (all p < 0.05) relative to 08:00. The 18:00 session consistently produced the highest performance levels. At the same time, no significant differences were observed between 11:00 and 15:00 (all p > 0.05). Our results suggest that time of day significantly influences short-term maximal physical performance in adolescent male soccer players, with peak performance levels consistently observed in the late afternoon (18:00 h). This appears to reflect diurnal variations in core temperature, hormonal activity, and neuromuscular readiness, which likely enhance sprint speed, agility, and explosive power at this time. These findings indicate that coaches and youth sport practitioners should consider scheduling high-intensity training sessions and performance assessments in the late afternoon to optimize physiological conditions for training and evaluation. Aligning training and competition timing with circadian rhythms may therefore support improved athletic output and more accurate performance monitoring in youth soccer settings.
creator: Houda Bougrine
creator: Nidhal Nasser
creator: Imed Gandouzi
creator: Halil ibrahim Ceylan
creator: Majdi Bouazizi
creator: Thierry Paillard
creator: Ismail Dergaa
creator: Valentina Stefanica
creator: Abderraouf Ben Abderrahman
uri: https://doi.org/10.7717/peerj.20065
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2025 Bougrine et al.

title: Using natural landscape and instream habitat to identify stream reference groups for bioassessment
link: https://peerj.com/articles/20234
last-modified: 2025-10-21
description: BackgroundGrouping streams into reference groups based on their similarities is a critical component of developing multi-metric indices to evaluate biotic integrity. The use of level III ecoregions is a common approach that has been successful for many geopolitical regions. However, the diversity in ecoregions across the state of Oklahoma results in excessive complexity in the application of reference groups. In this study, we sought to simplify Oklahoma’s reference groups by considering the natural drivers of species distribution in wadeable streams.MethodsWe used two K-means clustering algorithms to create hierarchical stream groups. In the first K-means analysis, we grouped wadeable streams using several climatic and geologic features expected to influence fish distributions across the state (Tier I). Next, we subdivided the stream groups identified in the Tier I analysis based on water chemistry and instream habitat (Tier II). We used classification trees and between class multivariate analyses to validate and understand the resulting groups and define them as ‘stream archetypes’ based on distinguishing habitat characteristics.ResultsThe two K-means analyses resulted in six groups that represented both regional differences and reach-scale geomorphological differences. We determined that there were two regions, West and East that were primarily distinguished by mean annual precipitation. Tier II clustering identified Plains and Valley stream groups in both the East and West regions. These groups represented shallow, run-dominated, sand bed streams, and relatively deep, pool dominated, silty streams, respectively. The East region possessed two additional stream groups (i.e., Hills and Highlands groups), each with rocky substrate and riffle channel units that broke up the runs and pools in the stream. Of these, the Hills group was more prone to having pools than runs and had low nutrient concentrations compared to the Highlands group. We found that the six groups explained variability in habitat and water chemistry as well as the previous 13 ecoregion-based reference groups. Further, we confirmed that the groups were not the result of common anthropogenic influences on stream ecosystems. The six groups were subsequently organized into three stream archetypes, Plains (East and West), Valley (East and West) and Rocky (Hills and Highlands). We expect these six hierarchical stream groups and three archetypes to be useful in evaluating biotic communities in Oklahoma moving forward.
creator: Joseph J. Dyer
creator: Daniel Dvorett
creator: Joseph Flotemersch
uri: https://doi.org/10.7717/peerj.20234
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2025 Dyer et al.

title: Integrative bioinformatics analysis identifies C1orf198 as a novel prognostic biomarker in colorectal cancer
link: https://peerj.com/articles/20227
last-modified: 2025-10-21
description: Colorectal cancer (CRC) is a leading cause of cancer-related mortality, necessitating the identification of novel prognostic biomarkers to improve patient management. In this study, we integrated bioinformatics analyses and experimental validation to explore the role of C1orf198 in CRC. Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) revealed significantly upregulated C1orf198 mRNA in CRC tissues compared to normal counterparts, confirmed by immunohistochemistry (IHC) in clinical samples. High C1orf198 expression correlated with advanced tumor stages (T, N, M) and poor survival outcomes, including shorter overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). Functional enrichment analyses highlighted involvement in extracellular matrix organization, cell adhesion, and oncogenic signaling pathways such as PI3K-AKT and focal adhesion. Immune infiltration analysis showed positive correlations with stromal/immune scores and M2 macrophage infiltration, linking C1orf198 to tumor microenvironment (TME) remodeling. Notably, C1orf198 was strongly associated with cytokines CXCL12 and receptors CXCR5, which mirrored its immune cell correlations. Collectively, our findings identify C1orf198 as a potential prognostic biomarker in CRC, implicating its role in TME modulation and oncogenic progression.
creator: Changjiang Yang
creator: Xuhua Geng
creator: Zihan Zhao
uri: https://doi.org/10.7717/peerj.20227
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2025 Yang et al.

title: Effect of harvest on the agronomic, mineral and antioxidant profile of three oregano species (Origanum onites L., Origanum vulgare L. ssp. hirtum, and Origanum acutidens (Hand.-Mazz.) Ietswaart)
link: https://peerj.com/articles/20223
last-modified: 2025-10-21
description: This study primarily aims to examine the variations in plant characteristics, micro- and macronutrient levels, heavy metal content, and antioxidant properties (2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), and 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)), along with antioxidant compounds such as phenolics and flavonoids, across different oregano species cultivated under identical ecological conditions. Origanum vulgare demonstrated the highest fresh (292.25 g/plant) and dry herbage yield (153.34 g/plant). The antioxidant activity varied significantly depending on the oregano species and harvest time. Origanum acutidens showed the highest DPPH radical scavenging activity during the early flowering stage. Conversely, Origanum onites L. displayed the lowest antioxidant activities, as measured by DPPH assay, during the same developmental phase. O. vulgare exhibited the strongest ABTS activity (0.997 mg TE/g dry weight (DW)) in the early flowering stage. Antioxidant activity in O. onites tended to decrease from pre-flowering to full flowering across all assays. Total phenolic content followed a similar trend, with O. vulgare reaching a maximum value at early flowering. Total flavonoid content was highest in O. acutidens during later development stages. The most abundant macronutrients, based on their average values of different harvest times, were calcium (Ca), potassium (K), magnesium (Mg), and phosphorus (P), respectively. The micro, macronutrient, and heavy metal content varied significantly between oregano species and across harvest periods within the same species. Heavy metal levels in oregano samples generally fell below WHO safety limits, except for cobalt (Co) and Chromium (Cr). Multivariate statistical techniques, including principal component analysis (PCA) and correlation analysis, were utilized to elucidate the interrelationships among oregano species, plant characteristics, antioxidant capacity, and mineral composition, thereby providing a comprehensive assessment of the factors governing oregano’s qualitative and nutritional characteristics. These findings emphasize the critical role of oregano species and harvest timing in determining plant growth, antioxidant characteristics, and nutritional properties.
creator: Tansu Uskutoğlu
uri: https://doi.org/10.7717/peerj.20223
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2025 Uskutoğlu

title: Stream baseline conditions shape functional responses to wastewater: evidence from insect-dominated sites
link: https://peerj.com/articles/20193
last-modified: 2025-10-21
description: Wastewater treatment plants (WWTP) are a crucial part of modern day infrastructure, cleaning about half of our global wastewater. However, the emergence of micropollutants and higher frequencies of extreme weather events pose unprecedented challenges for society and biodiversity. Conventionally treated wastewater and altered flow regimes create environmental boundaries in rivers, impacting aquatic communities. Previous studies revealed pronounced taxonomic changes in freshwater invertebrate communities in response to WWTP effluents. To explore whether these shifts extend to functional diversity, we studied 338 communities upstream and downstream of 169 WWTPs using commonly applied functional diversity metrics. Surprisingly, we found no clear changes in functional alpha and beta diversity metrics, or community weighted means (CWM), suggesting that trait redundancy offsets the functional impact of the previously observed species turnover. However, in streams dominated by Ephemeroptera, Plecoptera and Trichoptera (EPT), we found more pronounced shifts in CWMs, indicating that the extent of functional changes depends on the baseline condition of the streams. EPT-dominated site-pairs showed significant shifts in traits related to reproduction, dispersal, and feeding, including increased occurrences of ovoviviparity and interstitial locomotion potentially as an avoidance mechanism of high flow and low oxygen saturation. Further, shifts in shredding and absorbing feeding types, aquatic passive dispersal, and hololimnic life cycles might be forms of adaptation to increased nutrient concentrations and reduced intermittency induced by WWTPs. These findings demonstrate that functional responses to wastewater inputs can remain undetected due to the noise inherent in large datasets and are often absent as a result of functional redundancy. In contrast, significant changes emerge in communities dominated by sensitive species, underscoring the value of trait-based approaches for detecting context-dependent ecological impacts.
creator: Daniel Enns
creator: Nathan Jay Baker
creator: Jörg Oehlmann
creator: Jonas Jourdan
uri: https://doi.org/10.7717/peerj.20193
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2025 Enns et al.

title: Impacts of tropical cyclones on Northwest Atlantic seabirds: insights from a Category 1 hurricane
link: https://peerj.com/articles/20157
last-modified: 2025-10-21
description: Tropical cyclones are annual occurrences in the western North Atlantic Ocean, where many seabird species are vulnerable to the environmental factors associated with extreme weather events. We summarize the history of tropical cyclones in Newfoundland, Canada, which hosts globally significant populations of seabirds. We examine the interactions that historical tropical cyclones have had with breeding seabirds by plotting the temporal association of Category 1 hurricanes with the breeding phenology of colonial seabirds in Newfoundland and identifying which major colonies have fallen within the pathways of these hurricanes. As a case study, we explore how Hurricane Larry (2021) coincided with increased stranding and mortality of Northern Gannets and Leach’s Storm-Petrels. The breeding seasons of Northern Gannets and Leach’s Storm-Petrels overlapped with all Category 1 hurricanes making landfall in Newfoundland from 1851 to 2024, whereby the central pathways of at least one hurricane passed over the six large Leach’s Storm-Petrel colonies and at least one of the Northern Gannet colonies. For Northern Gannets, a notable stranding and mortality event occurred with at least 146 stranded and 130 dead from September 13 to 24, 2021. For Leach’s Storm-Petrels, 19 birds were observed stranded and 16 died from September 10 to 14, 2021, which was higher than strandings and deaths reported during this period in 2020, 2022, 2023, and 2024. As global climate change drives shifts in the timing, frequency, severity, and attributes of tropical cyclones, we raise the concern that the impacts of tropical cyclones on breeding seabirds may worsen and lead to high mortality in some years.
creator: Tori V. Burt
creator: Robert J. Blackmore
creator: Sydney M. Collins
creator: Kyle J. N. d’Entremont
creator: Christopher R. E. Ward
creator: Joshua Cunningham
creator: Cerren Richards
creator: Fiona Le Taro
creator: Sabina I. Wilhelm
creator: Amanda E. Bates
creator: Stephanie Avery-Gomm
creator: William A. Montevecchi
uri: https://doi.org/10.7717/peerj.20157
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2025 Burt et al.

title: Effectiveness of seed dispersal by foxes in areas with different human disturbances in southern Chile
link: https://peerj.com/articles/20150
last-modified: 2025-10-21
description: Frugivorous mammals play a key role in forest regeneration by dispersing seeds yet their effectiveness can vary with landscape disturbance and the native or exotic status of the plant species. In the temperate forests of southern Chile, we evaluated the seed dispersal efficiency (SDE) of foxes (Lycalopex spp.) for native and exotic fleshy-fruited plants across 10 sites spanning a gradient from less to more disturbed landscapes. SDE was assessed though two components: quantity (frequency of feces containing seeds and number of seeds per plant species) and quality (proportion of viable seeds and their germination success under natural conditions). Between November 2022 and July 2023, we collected 199 fox fecal samples, of which 131 contained seeds. In total, we recovered of 23,012 seeds from three native species (Aristotelia chilensis, Gaultheria mucronata, Ugni molinae) and three exotic species (Prunus spp., Malus sylvestris, Rubus ulmifolius). Native seeds were more frequently found in feces from less disturbed landscapes, whereas exotic species exhibited more variable patterns. Seed viability was generally high and unaffected by landscape type, although germination rates were higher in less disturbed areas. Notably, G. mucronata failed to germinate in more disturbed landscapes despite high viability. Conversely, U. molinae showed significantly greater SDE in more disturbed areas due to higher seed quantity and germination. These findings demonstrate that foxes are effective seed dispersers of both native and exotic species, with their effectiveness shaped by landscape type and plant species. Our results highlight the dual ecological role of generalist frugivores in supporting native plant regeneration while potentially facilitating the spread of exotic species. We recommend that future conservation and restoration efforts consider these dynamics when managing fragmented temperate forests.
creator: Onaylis Triay-Limonta
creator: Rocío Paleo-López
creator: Camila J. Stuardo
creator: Carolina S. Ugarte
creator: Carlos E. Valdivia
creator: Constanza Napolitano
uri: https://doi.org/10.7717/peerj.20150
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2025 Triay-Limonta et al.

title: Efficacy and optimal dosage of various exercises for migraine: a multilevel network and dose-response meta-analysis
link: https://peerj.com/articles/20254
last-modified: 2025-10-20
description: BackgroundTo elucidate the relative efficacy of diverse exercise modalities for migraine and quantify the optimal therapeutic dosage.MethodA systematic search was conducted across four electronic databases from their inception to May 2025. Two reviewers independently performed data extraction and risk of bias assessment. A multilevel network meta-analysis (ML-NMA) integrated with a dose-response analysis was employed to comprehensively compare these interventions.ResultsTwenty-seven randomized controlled trials (RCTs) (n = 1,611) were included. The most effective interventions were combined aerobic+resistance exercise (g =  − 1.85, 95% credible interval (CrI): [−2.53 to −1.18]; surface under the cumulative ranking curve (SUCRA) = 0.91), followed by resistance exercise (g =  − 1.45, 95% CrI [−1.79 to −1.10]; SUCRA = 0.81), yoga (g =  − 0.35, 95% CrI [−0.63 to −0.06]; SUCRA = 0.49), and tai chi (g =  − 0.48, 95% CrI [−0.91 to −0.05]; SUCRA = 0.46). The dose-response analysis identified an optimal therapeutic window of 300-600 metabolic equivalent of task (MET)-min/week, an intensity of 4.5–5.5 METs, and a duration of 8–10 weeks. The overall certainty of evidence was rated from very low to low.ConclusionCombined aerobic+resistance exercise, resistance exercise, tai chi, and yoga represent promising therapeutic options for migraine. The optimal dose was identified as approximately 70–135 minutes of moderate-intensity or 45–90 minutes of vigorous-intensity activity weekly, for 8–10 weeks. These findings, however, must be interpreted with caution due to the low quality of the underlying evidence.
creator: Jingyi Xie
creator: Yupeng Lin
creator: Bin Wang
uri: https://doi.org/10.7717/peerj.20254
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2025 Xie et al.

title: Genome-wide identification of calcium-dependent protein kinase (CDPK) family members in Phaseolus vulgaris L. and expression analysis during abiotic stresses
link: https://peerj.com/articles/20217
last-modified: 2025-10-20
description: BackgroundCalcium-dependent protein kinases (CDPKs) are a family of enzymes that are essential in plant signaling pathways. These kinases are activated in response to changes in calcium ion (Ca2+) concentration under stress conditions. Although CDPK gene families have been investigated in various plants, comprehensive genome-wide analyses and expression studies of CDPK genes in Phaseolus vulgaris L. under abiotic stress have not yet been performed. The objective of this research is to perform a genome-wide analysis of the CDPK gene family in common bean and evaluate the expression patterns of these genes under salt and drought stress conditions.MethodsThis study presents a comprehensive bioinformatics analysis focusing on the phylogenetic relationships, chromosomal distribution, gene structures, conserved motifs, promoter regulatory elements, and expression profiles under salt and drought stress conditions of the CDPK gene family in common bean.ResultsIn this study, 25 PvCDPK genes were identified in the common bean genome. The lengths of proteins vary between 298 and 582 amino acids (aa), and their molecular weights (kDa) range from 33.43 kDa to 65.13 kDa. The majority of the PvCDPKs located on a total of eight chromosomes have six introns. Phylogenetic analysis revealed that PvCDPK proteins are grouped into three major clades along with Arabidopsis thaliana and Glycine max orthologs. The divergence times for six pairs of segmentally duplicated genes ranged from 48.94 million years ago (MYA) to 65.57 MYA, while tandem duplicates ranged from 32.09 to 84.95 MYA.ConclusionsComparative expression analysis of PvCDPK genes revealed varying expression levels depending on the two common bean cultivars. Furthermore, these observations suggest that PvCDPK genes could be essential for the growth and development of common beans in response to abiotic stresses such as drought and salt. This is the first study to investigate the CDPK gene family in common bean, and the identified genes obtained can be directly evaluated as candidate genes for marker-assisted selection or gene editing approaches. In addition, the findings are expected to contribute to the development of resilient cultivars capable of withstanding climate change.
creator: Gülşen Güçlü
uri: https://doi.org/10.7717/peerj.20217
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2025 Güçlü