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DIA Quantitative Proteomic Analysis Reveals Early Proteomic Responses to Honeybee-Derived Melittin in Murine Breast Cancer Cells. DIA定量蛋白质组学分析揭示了小鼠乳腺癌细胞对蜜蜂来源的蜂毒素的早期蛋白质组学反应。
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191727
Junling Zhu, Wenhua Xu, He Zang, Yunzhen Yang, Nian Fan, Yuwei Zhang, Yaqin Gao, Jianfeng Qiu, Dafu Chen, Rui Guo
{"title":"DIA Quantitative Proteomic Analysis Reveals Early Proteomic Responses to Honeybee-Derived Melittin in Murine Breast Cancer Cells.","authors":"Junling Zhu, Wenhua Xu, He Zang, Yunzhen Yang, Nian Fan, Yuwei Zhang, Yaqin Gao, Jianfeng Qiu, Dafu Chen, Rui Guo","doi":"10.3390/biology15191727","DOIUrl":"10.3390/biology15191727","url":null,"abstract":"<p><p>Breast cancer remains a major clinical challenge because of its molecular heterogeneity, therapeutic resistance, and disease recurrence. Melittin, the principal bioactive peptide of honeybee venom, exhibits antitumor activity in multiple experimental models; however, its early proteome-wide effects in breast cancer cells remain incompletely characterized. In this study, E0771 murine mammary carcinoma cells were exposed to melittin for 15 min. Colony formation and CCK-8 assays using 0-8 μg/mL melittin showed concentration-dependent reductions in clonogenic capacity and cell viability. For DIA-based quantitative proteomic profiling, E0771 cells were treated with 4 μg/mL melittin for 15 min. Among 9748 quantified protein entries, 339 proteins met the exploratory criteria for candidate differential abundance, including 114 up-regulated and 225 down-regulated candidates. GO and KEGG analyses associated these candidate proteins with cell junctions, cytoskeletal organization, protein kinase-related functions, metabolic processes, and cell-death-associated pathways. A STRING-derived association network containing 132 nodes and 216 edges further prioritized CASP8, RPS27A, ANXA5, and PIK3CA as relatively high-connectivity candidates. Collectively, these findings describe early proteomic responses to short-term melittin exposure and provide candidate proteins and biological processes for subsequent mechanistic validation rather than establishing causal molecular mechanisms.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149196409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Immersed Weight Measurements: A Useful Tool for Estimating Size and Predicting Wet and Dry Body Component Weights of the Sea Cucumber Cucumaria frondosa. 沉重测量:估算海参大小和预测湿体和干体成分重量的有用工具。
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191737
Robert Trenholm, Jean-François Hamel, Deepika Dave, Annie Mercier
{"title":"Immersed Weight Measurements: A Useful Tool for Estimating Size and Predicting Wet and Dry Body Component Weights of the Sea Cucumber <i>Cucumaria frondosa</i>.","authors":"Robert Trenholm, Jean-François Hamel, Deepika Dave, Annie Mercier","doi":"10.3390/biology15191737","DOIUrl":"10.3390/biology15191737","url":null,"abstract":"<p><p>The commercial dendrochirotid holothuroid <i>Cucumaria frondosa</i> is characterized by large variability in size, weight, and volume, primarily due to morphological plasticity, which makes the species difficult to assess and describe reliably, especially in a non-destructive way. Here, three different methods for assessing immersed weight were compared. Direct measurement (using a submerged basket attached to a load cell) proved to be the most reliable, showing strong predictive power for body wall dry weights (r<sup>2</sup> = 0.86). A proximate-composition-based model incorporating component-specific densities was used to explore how variation in biochemical composition, particularly lipid content in female gonads, may influence overall body density and buoyancy. This study also highlighted the importance of accounting for internal fluid density, including fluid within the coelom and respiratory tree, in interpreting immersed weight measurements. Standardization methods, including conversion mathematical formulas, were developed, tested, and demonstrated, supporting broader application of immersed weight in both research and fisheries contexts. Overall, immersed weight standardized to a common fluid density offers a promising, non-destructive approach for assessing <i>C. frondosa</i> and potentially other sea cucumber species, with applications in monitoring body-component changes, growth studies, stock assessment, and sustainable fisheries management.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149196387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
How Phylogenies Inferred from 46 Mitochondrial Genomes Informed the Systematics of the Australasian Genus of Ticks, Bothriocroton, with the Description of Three New Species. 从46个线粒体基因组推断的系统发育如何为澳大利亚蜱属Bothriocroton的系统分类学提供信息,并描述了三个新种。
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191733
Samuel Kelava, Mingeun Cho, Finlay G Mills, Dayana Barker, Yurie Taya, Alexander W Gofton, Iffy Glendinning, Amber Gillett, Peggy Rismiller, Yukari Horio, Aiko Ohnuma, Ernest J M Teo, Ryo Nakao, Stephen C Barker
{"title":"How Phylogenies Inferred from 46 Mitochondrial Genomes Informed the Systematics of the Australasian Genus of Ticks, <i>Bothriocroton</i>, with the Description of Three New Species.","authors":"Samuel Kelava, Mingeun Cho, Finlay G Mills, Dayana Barker, Yurie Taya, Alexander W Gofton, Iffy Glendinning, Amber Gillett, Peggy Rismiller, Yukari Horio, Aiko Ohnuma, Ernest J M Teo, Ryo Nakao, Stephen C Barker","doi":"10.3390/biology15191733","DOIUrl":"10.3390/biology15191733","url":null,"abstract":"<p><strong>Background: </strong>We revised the taxonomy and identification of the species of the genus <i>Bothriocroton</i> in light of entire mitochondrial genomes and nuclear rRNA genes, scanning electron microscopy, and light microscopy.</p><p><strong>Methods: </strong>(i) phylogenetic trees inferred from entire mitochondrial genomes and nuclear rRNA genes, (ii) species delimitation analyses (ABGD and bPTP), and (iii) the study of morphology by scanning electron microscopy (SEM) and light microscopy.</p><p><strong>Results: </strong>The most complete picture of the <i>Bothriocroton</i> ticks so far. Thirty-five new mitochondrial genomes and 27 partial 18S-28S rDNA sequences were generated. Phylogenetic analyses recovered seven well-supported clades corresponding to species-level lineages. Intraspecific genetic divergence ranged from 0.14 to 1.16%, whereas interspecific divergence ranged from 4.94 to 21.75%. Three new species were described, and the morphological diagnosis of other species was improved by redescribing two other species. In addition, we updated and improved the morphological dichotomous keys to male and female ticks. Conclusions and prospects: The routine genotyping of <i>Bothriocroton</i> ticks to identify species and to confirm provisional identifications of species from their morphology is an alternative to the morphological identification of closely related <i>Bothriocroton</i> ticks.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spatiotemporal Patterns of Five Sympatric Ungulates in the Tangjiahe National Nature Reserve, Sichuan, China. 唐家河国家级自然保护区五种同域有蹄类动物的时空格局
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191729
Jiayuan Hu, Mei Xiao, Mingfu Li, Zhisong Yang, Yanfei Chen, Lingyu Liu, Jiao Liao, Weichao Zheng
{"title":"Spatiotemporal Patterns of Five Sympatric Ungulates in the Tangjiahe National Nature Reserve, Sichuan, China.","authors":"Jiayuan Hu, Mei Xiao, Mingfu Li, Zhisong Yang, Yanfei Chen, Lingyu Liu, Jiao Liao, Weichao Zheng","doi":"10.3390/biology15191729","DOIUrl":"10.3390/biology15191729","url":null,"abstract":"<p><p>Ungulates serve as a critical link between primary producers and higher-level consumers, and play an irreplaceable role in maintaining the structural and functional integrity of forest ecosystems. Understanding the spatiotemporal niche differentiation of sympatric ungulates is of great guiding significance for forest biodiversity conservation and refined habitat management. Based on camera-trapping data collected across the entire Tangjiahe National Nature Reserve from 2022 to 2024, this study systematically analyzed the relative detection intensity, multi-scale activity rhythms, spatiotemporal niche overlap characteristics, and environmental response patterns of five sympatric ungulate species: the Chinese takin (<i>Budorcas tibetana</i>), Chinese serow (<i>Capricornis milneedwardsii</i>), Chinese goral (<i>Naemorhedus griseus</i>), tufted deer (<i>Elaphodus cephalophus</i>), and forest musk deer (<i>Moschus berezovskii</i>). The results showed that the relative detection intensity of the five ungulates exhibited a three-tiered hierarchical pattern, with the Chinese takin showing the highest relative detection intensity and the Chinese serow and forest musk deer showing the lowest detection rates. Fitted diel activity curves were characterized mainly by crepuscular bimodal patterns, whereas forest musk deer showed a predominantly nocturnal unimodal pattern; the DI of Chinese serow showed no statistically supported overall bias between the predefined daytime and nighttime windows. Seasonal overlap coefficients and activity curves indicated species-specific seasonal adjustment, with Chinese serow showing the greatest cold-warm-season divergence and Chinese goral the highest seasonal similarity. The three widely distributed species displayed moderate to high spatiotemporal overlap, whereas the two narrowly distributed species showed pronounced differentiation in spatial-use patterns. Generalized additive models further revealed species-specific nonlinear associations with environmental variables, with elevation and distance to roads emerging as the most consistent predictors across all five species. These findings characterize the spatiotemporal niche differentiation pattern of sympatric ungulates in the Minshan Mountains, and offer a scientific basis for targeted monitoring and conservation of species with low detection rates, habitat zoning optimization, and seasonally adaptive regulation of human disturbance within the nature reserve.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrated Phytoremediation and Microbial Mitigation Strategies for Sustainable Restoration of Toxic Metal-Contaminated Soils. 有毒金属污染土壤可持续修复的植物修复与微生物缓解综合策略
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191732
Inès Hammami, Mohamed Abdelaal, Ibtisam M Ababutain, Sumayah I Alsanie, Ghadah H Al Hawas, Azzah I Alghamdi, Nadiyah M Alqazlan, Ruba A Alghamdi, Fajir M Alsubaie, Joaher Y Alnabbat
{"title":"Integrated Phytoremediation and Microbial Mitigation Strategies for Sustainable Restoration of Toxic Metal-Contaminated Soils.","authors":"Inès Hammami, Mohamed Abdelaal, Ibtisam M Ababutain, Sumayah I Alsanie, Ghadah H Al Hawas, Azzah I Alghamdi, Nadiyah M Alqazlan, Ruba A Alghamdi, Fajir M Alsubaie, Joaher Y Alnabbat","doi":"10.3390/biology15191732","DOIUrl":"10.3390/biology15191732","url":null,"abstract":"<p><p>Toxic metal contamination of soil remains a critical global challenge due to the persistence, bioaccumulation, and irreversible toxicity of these metals. Cadmium (Cd), lead (Pb), mercury (Hg), arsenic (As), chromium (Cr) and nickel (Ni) are the most common toxic metals that threaten food security, ecosystem stability, and human health. While conventional physicochemical remediation technologies provide rapid pollutant removal, they are constrained by high economic costs, secondary pollution risks, and long-term soil degradation. Biological approaches, particularly phytoremediation and microbial mitigation, offer environmentally compatible alternatives; however, their field-scale performance is often limited by low biomass production, restricted metal bioavailability, microbial instability, and heterogeneous soil conditions. This review critically synthesizes recent advances that move beyond standalone biological strategies toward integrated, multi-scale remediation frameworks. We evaluate the mechanistic basis and performance of nano-assisted phytoremediation, biochar-mediated stabilization, omics-guided plant-microbe optimization, and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein systems (CRISPR/Cas) for enhancing metal transport, chelator biosynthesis, antioxidant defense, and microbial detoxification pathways. Emerging evidence indicates that nano-enabled amendments and biochar composites can reduce bioavailable Cd fractions by up to 75%, while omics-driven microbial consortia and targeted genome editing improve tolerance and accumulation efficiency in key crops such as rice and sorghum. Importantly, we assess translational barriers including nanoparticle ecotoxicity, off-target genome effects, regulatory constraints, biomass disposal, and life-cycle sustainability that currently limit large-scale deployment. By integrating mechanistic insights with field validation data, risk assessment considerations, and technology readiness evaluation, this review proposes a conceptual roadmap for scalable, eco-efficient soil restoration. The convergence of nanotechnology, systems biology, microbiome engineering, and precision genome editing represents a transformative pathway for next-generation remediation strategies capable of restoring contaminated soil while safeguarding environmental and public health.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149196702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
JAK3-Mediated Structural Remodeling of β-Catenin Suppresses Epithelial-Mesenchymal Transition: Insights from In Silico Modeling. jak3介导的β-Catenin结构重塑抑制上皮-间质转化:来自计算机模型的见解
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191738
Jugal Kishore Das, Jayshree Mishra, Narendra Kumar
{"title":"JAK3-Mediated Structural Remodeling of β-Catenin Suppresses Epithelial-Mesenchymal Transition: Insights from In Silico Modeling.","authors":"Jugal Kishore Das, Jayshree Mishra, Narendra Kumar","doi":"10.3390/biology15191738","DOIUrl":"10.3390/biology15191738","url":null,"abstract":"<p><strong>Introduction: </strong>Janus kinase 3 (JAK3) is a non-receptor tyrosine kinase that phosphorylates multiple proteins, including β-catenin, a critical component of adherens junctions (AJs). We previously demonstrated that JAK3-mediated phosphorylation of β-catenin regulates its basolateral localization and preserves epithelial barrier integrity. However, the structural basis underlying JAK3-β-catenin interactions and their role in epithelial-mesenchymal transition (EMT) remains unclear.</p><p><strong>Methodology: </strong>Here, we employed homology modeling, molecular docking, and structural simulations to investigate phosphorylation-dependent interactions between JAK3 and β-catenin.</p><p><strong>Results: </strong>Our analysis revealed that Src-mediated phosphorylation at Y654 induces conformational remodeling of the β-catenin N-terminal domain (NTD), creating a favorable interface for JAK3 binding and shifting its interaction from the armadillo repeat domain to the NTD. Subsequent JAK3-mediated phosphorylation at Y30, Y64, and Y86 restores β-catenin conformation, stabilizes the E-cadherin/β-catenin complex, and limits nuclear translocation. Phosphomimetic analyses identified distinct structural contributions of these residues.</p><p><strong>Conclusions: </strong>Collectively, these findings reveal a sequential Src-JAK3 phosphorylation mechanism that maintains AJ integrity and suppresses EMT, providing potential therapeutic insights into epithelial cancer progression.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent Advances in Plastic Waste Biodegradation: Microorganisms, Enzymes, Invertebrates, and Evidence Standards. 塑料废物生物降解的最新进展:微生物、酶、无脊椎动物和证据标准。
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191726
Key-Seem Phang, Chou-Min Chong, Yan Chen, Jiun-Yan Loh
{"title":"Recent Advances in Plastic Waste Biodegradation: Microorganisms, Enzymes, Invertebrates, and Evidence Standards.","authors":"Key-Seem Phang, Chou-Min Chong, Yan Chen, Jiun-Yan Loh","doi":"10.3390/biology15191726","DOIUrl":"10.3390/biology15191726","url":null,"abstract":"<p><p>The uncontrolled and rapidly increasing use of synthetic polymers has created persistent environmental contamination. Millions of tonnes of plastic waste accumulate annually, and fragmentation generates microplastics that threaten terrestrial and aquatic ecosystems and may affect human health. Biodegradation has therefore attracted attention as a complementary strategy for plastic-waste management. Reported biological agents include bacteria and fungi, their enzymes, and plastic-consuming invertebrates such as mealworms and waxworms. This review synthesizes evidence on microbial, enzymatic, and invertebrate-mediated degradation of common synthetic polymers and examines the physicochemical changes used to assess degradation, including changes in molecular weight, surface morphology, hydrophilicity, functional groups, and mineralization products. It also considers biodegradable polymers derived wholly or partly from renewable feedstocks as alternatives to conventional petroleum-based plastics. Emphasis is placed on the evidence required to demonstrate genuine biodegradation, because surface damage, biofilm formation, or mass loss alone can be misleading. Current research gaps, methodological limitations, and priorities for standardized, reproducible testing are discussed to support the development of credible biological approaches to plastic-waste reduction.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Refined Mapping of Endothelial Cells, Brain Pericytes and Astrocytes Proteomes via Subcellular Fractionation and DDA Mass Spectrometry. 通过亚细胞分离和DDA质谱技术精确定位内皮细胞、脑周细胞和星形胶质细胞蛋白质组。
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191724
Océane Dusailly, Camille Menaceur Vandenbroucke, Johan Hachani, Sophie Duban-Deweer, Fumitaka Shimizu, Takashi Kanda, Yannis Karamanos, Fabien Gosselet, Laurence Fenart, Julien Saint-Pol
{"title":"Refined Mapping of Endothelial Cells, Brain Pericytes and Astrocytes Proteomes via Subcellular Fractionation and DDA Mass Spectrometry.","authors":"Océane Dusailly, Camille Menaceur Vandenbroucke, Johan Hachani, Sophie Duban-Deweer, Fumitaka Shimizu, Takashi Kanda, Yannis Karamanos, Fabien Gosselet, Laurence Fenart, Julien Saint-Pol","doi":"10.3390/biology15191724","DOIUrl":"10.3390/biology15191724","url":null,"abstract":"<p><p>Proteomic profiling of brain microvascular cells, i.e., endothelial cells, brain pericytes, and glial cells, is essential for understanding their distinct roles in the neurovascular unit. In this study, we present a comparative data-dependent acquisition (DDA) analysis of endothelial cells (ECs), brain pericytes (BPs), and astrocytes (ACs), using both whole-cell lysates (WCL) and subcellular fractionation. Analysis of the WCL identified 2000-2300 proteins per cell type, revealing distinct biological signatures consistent with the known function of each cell type. Compared to the standard WCL protocol, subcellular fractionation significantly increased the depth of the proteome (by up to 93%), particularly for membrane and insoluble proteins. Functional enrichment analysis revealed sharper biological associations: angiogenesis in ECs, cell cycle regulation in BPs, and lipid metabolism in ACs. However, the results also revealed that the sampling method impacts the interpretation of cell-type specificity. For example, a disintegrin and metalloprotease 10 (ADAM10) appeared EC-specific in WCL data but was broadly detected after fractionation. Likewise, Glial Fibrillary Acidic Protein (GFAP) was unexpectedly identified in ECs, reflecting its transient expression in immature cells. To overcome such biases, we generated an integrative reference proteome for each cell type by combining data from different sampling strategies. These include 3605 proteins for ECs, 3378 for BPs, and 3976 for ACs, with consistent representation of membrane-associated sub-proteomes. This study highlights the importance of integrating sampling methods and considering cell differentiation status when interpreting proteomic data. It also provides valuable reference datasets for future neurovascular research.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PiProteline: An R Package for Integrated Proteomics Data Analysis, from Label-Free Quantitation to Systems Biology. PiProteline:一个集成蛋白质组学数据分析的R包,从无标签定量到系统生物学。
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191723
Andrea Lomagno, Saleh Hamed, Ishak Yusuf, Pietro Luigi Mauri, Dario Di Silvestre
{"title":"PiProteline: An R Package for Integrated Proteomics Data Analysis, from Label-Free Quantitation to Systems Biology.","authors":"Andrea Lomagno, Saleh Hamed, Ishak Yusuf, Pietro Luigi Mauri, Dario Di Silvestre","doi":"10.3390/biology15191723","DOIUrl":"10.3390/biology15191723","url":null,"abstract":"<p><p>The demand for user-friendly applications to support biologists in analyzing high-throughput proteomics data remains a pressing challenge. Given the complexity and the multiple intermediate steps involved, this process is time-consuming and often requires specialized computational skills. To simplify and accelerate the exploration of proteomics data, we present PiProteline, an R package designed to operate on high-dimensional data matrices assembled from the output of any search engine commonly used in bottom-up proteomics experiments. In addition to data preprocessing and descriptive statistics, PiProteline enables label-free quantitation, functional enrichment, and systems biology analyses. It supports both unweighted and weighted protein-protein interaction (PPI) network topological analyses for the identification of critical nodes, such as hubs and bottlenecks. By integrating multiple computational approaches, PiProteline accelerates the selection of potentially relevant protein signatures, providing insights into the molecular mechanisms characterizing the investigated systems. This information facilitates the formulation of new hypotheses and the design of targeted experiments, ultimately reducing costs and advancing translational medicine. PiProteline is available as an open-source R package via GitHub, as a Shiny application, and via Zenodo.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nano-Zinc Iron Oxide Elicits Oxidative Stress-Driven Midgut Damage and Developmental Suppression in Bombyx mori. 纳米氧化锌引起家蚕氧化应激驱动的中肠损伤和发育抑制。
IF 4.3 3区 生物学
Biology-Basel Pub Date : 2026-10-01 DOI: 10.3390/biology15191731
Zhen He, Jiaying Lin, Bing Chen, Liang Huang, Cui Yu, Hui Ai, Fan Wu
{"title":"Nano-Zinc Iron Oxide Elicits Oxidative Stress-Driven Midgut Damage and Developmental Suppression in <i>Bombyx mori</i>.","authors":"Zhen He, Jiaying Lin, Bing Chen, Liang Huang, Cui Yu, Hui Ai, Fan Wu","doi":"10.3390/biology15191731","DOIUrl":"10.3390/biology15191731","url":null,"abstract":"<p><p>The silkworm, <i>Bombyx mori</i>, a key economic insect, has been employed as a model organism to investigate the toxicological effects and underlying mechanisms of zinc iron oxide nanoparticle exposure on its growth and development, midgut tissue structure, and physiological functions. Exposure to zinc iron oxide inhibited larval growth and development, which was accompanied by pathological alterations in the midgut, including a reduction in columnar cells, vacuolation, chromatin condensation, microvilli shedding, and disrupted tight junctions, which directly impaired the intestinal barrier integrity and nutrient absorption. Furthermore, zinc iron oxide exposure resulted in elevated reactive oxygen species levels, decreased superoxide dismutase and glutathione contents, and increased catalase activity, indicating the activation of oxidative stress. This stress-induced mitochondrial response, characterized by the observation of autophagic vesicles, suggests the potential mitophagy of activation in action to zinc iron oxide exposure, thereby preserving cellular homeostasis. This was also associated with the downregulation of most genes involved in purine metabolism, the peroxisome, the biosynthesis of amino acids, the ribosome pathway, and carbon metabolism pathways, leading to reduced protein synthesis and energy supply, ultimately resulting in larval developmental retardation. This study elucidates the intestinal-targeted toxicity of zinc iron oxide nanoparticles in lepidopteran insects, providing direct in vivo experimental evidence for evaluating the ecological risk of zinc iron oxide in sericulture environments. Furthermore, it offers a novel research avenue for developing intestinal intervention strategies aimed at mitigating the toxic effects of nanomaterials and ensuring the stability of economically important traits in silkworms.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"15 19","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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