title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=38 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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 title: Role of necroptosis in pulpitis: integration of bacterial infection, immune imbalance, and oxidative stress link: https://peerj.com/articles/20209 last-modified: 2025-10-20 description: BackgroundPulpitis is a common oral inflammatory condition driven by bacterial infection, immune imbalance, and oxidative stress, often involving pro-inflammatory cell death within the dental pulp. Necroptosis—a regulated, caspase-independent form of cell death mediated by the receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed-lineage kinase domain-like protein (MLKL)—has garnered growing interest in various infectious and inflammatory diseases. However, its specific role in pulpitis remains underexplored.Aim of the studyThis review aims to explore how bacterial infection, immune imbalance, and oxidative stress synergistically activate necroptosis, and proposes for the first time that excessive activation of necroptosis may contribute to the progression of pulpitis.MethodologyA narrative review was conducted using PubMed, Web of Science, and Google Scholar. Searches employed the keywords “pulpitis”, “necroptosis”, and related MeSH terms, combined with Boolean operators.ResultsBased on a comprehensive review of the existing literature, this review is the first to propose that the integration of bacterial infection, immune imbalance, and oxidative stress may contribute to the progression of pulpitis from reversible inflammation to irreversible necrosis.ConclusionBacterial infection in pulpitis may activate necroptosis through the Toll-Like Receptor 4 (TLR4)-RIPK3 pathway, leading to the release of damage-associated molecular patterns (DAMPs) that disrupt immune homeostasis, while mitochondrial dysfunction-induced ROS further aggravates oxidative stress. These interacting mechanisms may collectively exacerbate pulpal inflammation and tissue damage, ultimately resulting in irreversible pulpitis. Accordingly, targeting necroptosis pathways may offer a promising therapeutic approach for pulpitis. creator: Xuefei Wang creator: Yaying Wang creator: Zhenyu Pang creator: Peiyao Gong creator: Xuyi Ma creator: Yuhao Qiu creator: Jianzhen Li creator: Lianjie Peng creator: Zhichao Liu uri: https://doi.org/10.7717/peerj.20209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: DNA metabarcoding of mites from small soil samples: limited agreement with morphological identifications but improved results from long-read sequencing link: https://peerj.com/articles/20205 last-modified: 2025-10-20 description: The characterization of soil mite (Acari) communities traditionally follows morphological identifications of specimens extracted from soil, which is a highly laborious and time-consuming process. Metabarcoding has become an increasingly utilized approach for species identification from environmental DNA (eDNA) samples, but whether the metabarcoding approaches align with the morphological identification data on soil mites has rarely been addressed. Here, we examine the congruence of soil mite communities between morphological and metabarcoding datasets. The morphological dataset was generated by extracting mite specimens from the soil samples, whereas molecular datasets represent two types of cytochrome c oxidase subunit I (COI) amplicons produced directly from soil eDNA (from 0.2 g and 2 g soil samples) and sequenced with Illumina (313 base pairs amplicons) and PacBio (658 base pairs amplicons) platforms. We found that specimen extraction from soil samples, followed by morphological identification, yielded the highest number of mite species. Despite significantly lower mite richness in the metabarcoding datasets, PacBio datasets provided more reliable community profiles that aligned strongly with the morphological data. This indicates that soil sample quantities generally used for microbial analyses are also informative in studying soil faunal communities. Furthermore, our results indicate that methodological choices (herein PacBio vs. Illumina) have a greater influence on mite community detection than the amount of input soil used for DNA extraction. Interestingly, the patterns of the entire metazoan community in the metabarcoding datasets strongly mirrored those of the morphologically identified mite communities alone, indicating that soil mites serve as a powerful ecological indicator group. creator: Sirle Varusk creator: Kaarel Sammet creator: Manikandan Ariyan creator: Khairiah Mubarak Alwutayd creator: Sten Anslan uri: https://doi.org/10.7717/peerj.20205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Varusk et al. title: Alpha-centractin is a novel substrate of SETD3 methyltransferase in vitro link: https://peerj.com/articles/20195 last-modified: 2025-10-20 description: BackgroundThe SETD3 enzyme, a protein histidine methyltransferase, catalyzes the Nτ-methylation of the histidine 73 residue in β-actin. This post-translational modification is important for maintaining cytoskeleton integrity, and actin remains the only known substrate of this methyltransferase to date. However, SETD3 was also postulated to play a role in the regulation of processes that are not directly related to actin homeostasis, such as cell cycle control and response to hypoxic conditions. These findings suggest that actin may not be the sole substrate of SETD3 methyltransferase. Here, we demonstrate that SETD3 methylates additional proteins in human cells, and α-centractin (ACTR1A) may be one of them.MethodsThree different human SETD3 knockout cell lines (HAP1, HeLa, HEK293T) were generated with the CRISPR/Cas9 method and used as a source of SETD3 substrates. Fluorography was used to detect the SETD3-dependent methylation of proteins present in cell lysates, while the TurboID biotin ligase proximity labeling technique was used to isolate proteins that interact with SETD3. The molecular identity of the proteins was determined by mass spectrometry and the activity of recombinant SETD3 towards potential substrates was tested using a radiochemical assay.ResultsFluorography revealed that SETD3 methylates at least five novel proteins besides β-actin in HAP1 cells. TurboID proximity labeling identified α-centractin, a key dynactin subunit, as an SETD3 interactor and an in vitro methylation target, suggesting that SETD3 potentially regulates not only actin cytoskeleton dynamics but also dynein-mediated intracellular transport. creator: Apolonia Witecka creator: Paulina Emmel creator: Klaudia Ślusarczyk creator: Julia Z. Kamińska creator: Michał Zaród creator: Takao Ishikawa creator: Jakub Drożak uri: https://doi.org/10.7717/peerj.20195 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Witecka et al.