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{"title":"Energy-Dependent Changes in Ion Mobility Peak Width Reveal Stability Shifts in Ribonucleic Acid Stem Loops.","authors":"Anna G Anders, Jacqueline Anthenien, Ingrid R Kilde, Courteney Dufrene, Markos Koutmos, Brandon T Ruotolo","doi":"10.1021/jasms.5c00064","DOIUrl":"10.1021/jasms.5c00064","url":null,"abstract":"<p><p>Ribonucleic acids (RNAs) are becoming increasingly important to our understanding of cellular biology and our search for new or improved biotherapeutics. However, the dynamic and polydisperse nature of RNAs creates challenges for their structural characterization. Here, we focus on RNA stem-loops (i.e., hairpins), as these are ubiquitous elements of RNA secondary structures. We leverage native ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) to study stem loops isolated from mitochondrial tRNA (tRNA) across a wide range of disease-relevant mutants. While we find that native IM-MS analyses proved capable of tracking stem-loop structure changes upon cofactor-binding and mutation, it remains challenging to evaluate the stabilities of small RNAs using standard RNA CIU workflows. Thus, we explore the ability of energy-dependent changes by IM peak full-width half-maximum (fwhm) values to characterize the stabilities of RNA stem-loops. We find that RNA stem-loop IM fwhm values typically decrease significantly upon activation, with lesser differences detected in Mg²⁺-bound RNA samples in a manner consistent with the stabilization expected under such conditions. We conclude by discussing the potential future applications of IM fwhm analyses in the context of RNA CIU assay development.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"1422-1426"},"PeriodicalIF":3.1,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Broadband Collision-Induced Dissociation Mass Spectrometry Imaging.","authors":"Sumi Krupa, Wiktoria Szuberla, Joanna Nizioł, Anna Ossolińska, Krzysztof Ossoliński, Tomasz Ruman","doi":"10.1021/jasms.5c00045","DOIUrl":"10.1021/jasms.5c00045","url":null,"abstract":"<p><p>This study demonstrates the first application of broadband collision-induced dissociation (bbCID) to mass spectrometry imaging (MSI) for the identification of untargeted metabolites in human tissues. The methodology integrates bbCID with laser ablation-remote atmospheric pressure photoionization/chemical ionization (LARAPPI/CI), enabling the simultaneous acquisition of precursor and fragment ion distributions during MSI for many compounds simultaneously. In this approach, an infrared (IR) laser is used to ablate biological material, which is then ionized in the gas phase by a combination of photoionization and chemical ionization at atmospheric pressure. The method was validated using reference compounds, including thymidine and commonly used synthetic dyes, to assess ionization efficiency, fragmentation behavior, and spatial colocalization of precursor and fragment ions. Subsequently, bbCID-MSI was applied to clinical tissue samples of human bladder and kidney cancer. For the bladder cancer tissue, higher intensities of heptadecanoic acid, docosahexaenoic acid (FA(22:6)), docosapentaenoic acid (FA(22:5)), and FA(16:0) were observed in tumor regions, whereas proline was more abundant in adjacent nontumorous area. In renal cell carcinoma, cancerous regions exhibited elevated levels of polyunsaturated fatty acids such as arachidonic acid (FA(20:4)) and adrenic acid (FA(22:4)), while creatine and serine were enriched in healthy tissue zones. These findings highlight the utility of bbCID-MSI for spatially resolved metabolite analysis and its potential to reveal biologically relevant metabolic alterations associated with cancer.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"1443-1455"},"PeriodicalIF":3.1,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing food by-products macrocomposition by FTIR microspectroscopy.","authors":"Paula Varas Perez, Alexis Fagot, Martijn Heleven, Karen Smeets, Pieter Samyn, Peter Adriaensens, Wouter Marchal, Dries Vandamme","doi":"10.1007/s00216-025-05984-z","DOIUrl":"https://doi.org/10.1007/s00216-025-05984-z","url":null,"abstract":"<p><p>Food by-products offer a promising opportunity for extracting valuable compounds that can be used in the food, pharmaceutical, and polymer industries. However, unpredictable variations in the chemical composition and spatial distribution of the various components within these biological matrices create challenges for new valorization processes. These inconsistencies can lead to variable recovery efficiency and differing quality of extracts. Understanding the chemical composition and spatial distribution of these components is essential, as it will facilitate the effective valorization of these by-products in future applications. Fourier transform infrared (FTIR) microspectroscopy was employed to evaluate the chemical composition and structural organization of industrial food by-products, specifically potato trimmings, carrot pomace, and brewer's spent grain. Frozen sectioning was employed as a sample preparation method. Hierarchical cluster analysis was applied to differentiate the spectral information from the background, allowing the determination of representative average spectra with good reproducibility across sample replicates. Derivative FTIR spectra further revealed previously hidden information by resolving overlapping signals, such as multiple bands in the 1750-1550 cm <math><mmultiscripts><mrow></mrow> <mrow></mrow> <mrow><mo>-</mo> <mrow><mn>1</mn></mrow> </mrow> </mmultiscripts> </math> region, facilitating the assignment of functional groups to compounds of interest such as proteins, lipids, or pectin and the creation of chemical images. However, some macroconstituents exhibited overlapping absorbance peaks, complicating the precise identification of individual components. Despite this limitation, FTIR microspectroscopy provided valuable semi-quantitative information on the composition of these by-products. The results demonstrated that chemical imaging by FTIR microspectroscopy is a valuable tool for food by-product evaluation, providing insight into their composition and supporting the potential for their valorization in industrial applications.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a cloud point extraction method combined with ETAAS and ICP-MS for the preconcentration and quantification of silver as nanoparticles in saline samples.","authors":"María Carmen Barciela-Alonso, Elena Peña-Vázquez, Juan José López-Mayán, Oscar Rodríguez-Arnoso, Pilar Bermejo-Barrera","doi":"10.1007/s00604-025-07330-7","DOIUrl":"https://doi.org/10.1007/s00604-025-07330-7","url":null,"abstract":"<p><p>The increasing industrial use of silver nanoparticles (AgNPs) has led to interest in their determination in different types of environmental complex samples, including saline matrices such as aquaculture waters. A simple, reliable, and green analytical method using instrumentation available in most of the laboratories has been developed for the determination of silver as nanoparticles in saline samples. Cloud point extraction (CPE) was used for the separation of AgNPs from seawater, and silver was then determined in the surfactant-rich extracts by electrothermal atomic absorption spectrometry (ETAAS). Parameters related to ETAAS and the cloud point extraction procedure (Triton X-114 concentration, volume of complexing agent (EDTA), pH and type of buffer, effect of repetitive extraction, matrix modifier, etc) were evaluated. A concentration of Triton X-114 of 12% (v/v), a volume of 750 μL of saturated EDTA, and a pH of 7.0 were selected as the optimum conditions for the separation of AgNPs. Standard addition calibration solutions in a concentration range from 0 to 3.0 μg L^-1 of AgNPs were subjected to the CPE procedure and used for silver determination by ETAAS. The LOD and LOQ were 0.038 and 0.125 μg L^-1 of silver (as AgNPs), respectively. The method is precise (whole procedure 9.7%) and accurate (recovery percentages 99±4%), showing a good selectivity for the extraction of AgNPs, while ionic Ag remains in the aqueous phase. Moreover, the results of size analysis of the nanoparticles in the surfactant extracts of seawater samples spiked with AgNPs (40 and 60 nm) by SP-ICP-MS and TEM were in good agreement.</p>","PeriodicalId":705,"journal":{"name":"Microchimica Acta","volume":"192 8","pages":"470"},"PeriodicalIF":5.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative assessment of the carbon dioxide absorption capacity of vegetation in China, 2000-2020.","authors":"Guoxin Lan, Zhuangzhuang Hou, Yan Wu, Bin Yan, Chuan Fu, Yi Jiang, Xiang Wang, Qiushi Zheng","doi":"10.1007/s11356-025-36692-x","DOIUrl":"https://doi.org/10.1007/s11356-025-36692-x","url":null,"abstract":"<p><p>CO₂ is the main cause of the dramatic increase in greenhouse gases, posing a serious threat to human systems and ecosystems. Most existing studies focus on estimating carbon emissions and carbon sequestration, and there are relatively few studies on the quantitative analysis of CO₂ uptake by vegetation. Therefore, this paper constructed a Carbon Uptake Index (CUI) model based on the carbon estimation model and the Vegetation Carbon sequestration (VCs) model. It was used to estimate the distributional characteristics of carbon absorption in China from 2000 to 2020. Then, the inter-annual variation and spatial aggregation characteristics of carbon absorption were analyzed using linear regression models and spatial autocorrelation, respectively. The results show that from 2000 to 2020, China's carbon uptake as a whole is in an absorptive state, with significant spatial correlation. Inter-annual variability shows an overall decreasing trend, dominated by a slight decreasing trend. The spatial characteristics of carbon absorption are mainly aggregated, with low-low aggregation in the western part of China and high-high aggregation in the southern part. The results of this paper will provide a reasonable reference for China to achieve carbon peak and carbon neutrality.</p>","PeriodicalId":545,"journal":{"name":"Environmental Science and Pollution Research","volume":" ","pages":""},"PeriodicalIF":5.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LncRNAs in hypoxic microenvironment; insight in their impact in cancer biology.","authors":"Beena Briget Kuriakose, Ahmed Hjazi, Raed Obaid Saleh, Ashok Kumar Bishoyi, S Renuka Jyothi, Sami G Almalki, G Sridevi, Kamlesh Chaudhary, Ahmed Hussein Zwamel, O Matchonov","doi":"10.1007/s10142-025-01635-9","DOIUrl":"https://doi.org/10.1007/s10142-025-01635-9","url":null,"abstract":"<p><p>Hypoxia may facilitate metastasis and tumor advancement in solid tumors. Intratumoral hypoxia may facilitate tumor aggressiveness by stabilizing hypoxia-inducible factor-1α (HIF-1α). Various transcriptional and epigenetic pathways modulate hypoxia-stimulated gene expression and tumor progression. Noncoding RNAs longer than 200 nt are long noncoding RNAs (lncRNAs). Current lncRNA profiling in several human tumor types revealed that lncRNA expression and deregulation vary by tumor type and may undergo transcriptional, genomic, and epigenetic modifications. LncRNAs controlled by hypoxia have emerged as a prominent focus in hypoxia-regulated biology due to their ability to influence multiple biological procedures associated with tumorigenesis. Hypoxia-regulated lncRNAs may influence tumor development, growth, anti-apoptosis, migration, invasion, angiogenesis, and tumor metabolism. In this light, hypoxia-inducible lncRNAs could interact with protein/protein complex and chromatin/epigenetic factors and another mechanism, thus favoring tumorigenesis. Conversely, lncRNAs may control hypoxia signaling by stabilizing HIF-1α via several mechanisms. Nonetheless, several undiscovered lncRNAs remain that may mediate or regulate the hypoxia axis. Consequently, the novel lncRNAs modulated by hypoxia or that influence hypoxia signaling have yet to be discovered and thoroughly described. Herein, we aim to classify suitable lncRNA targets to offer a feasible therapeutic modality for hypoxia-driven cancers.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"142"},"PeriodicalIF":3.9,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying intra-urban socio-economic and environmental vulnerability to extreme heat events in Johannesburg, South Africa.","authors":"Craig Parker, Craig Mahlasi, Tamara Govindasamy, Lebohang Radebe, Nicholas Brian Brink, Christopher Jack, Madina Doumbia, Etienne Kouakou, Matthew Chersich, Gueladio Cisse, Sibusisiwe Makhanya","doi":"10.1007/s00484-025-02971-y","DOIUrl":"https://doi.org/10.1007/s00484-025-02971-y","url":null,"abstract":"<p><p>Urban populations face increasing vulnerability to extreme heat events, particularly in rapidly urbanising Global South cities where environmental exposure intersects with socioeconomic inequality and limited healthcare access. This study quantifies heat vulnerability across Johannesburg, South Africa, by integrating high-resolution environmental data with socio-economic and health metrics across 135 urban wards. We examine how historical urban development patterns influence contemporary vulnerability distributions using principal component analysis and spatial statistics. Environmental indicators (Land Surface Temperature (LST), vegetation indices, and thermal field variance) were combined with socioeconomic and health variables (including indicators on crowded dwellings and healthcare access, self-reporting of chronic diseases) in a comprehensive vulnerability assessment. Principal Component Analysis revealed three primary dimensions explaining 56.6% (95% CI: 52.4-60.8%) of the total variance: urban heat exposure (31.5%), health status (12.8%), and socio-economic conditions (12.3%). Built-up areas showed weak but significant correlations with heat indices (ρ = 0.28, p < 0.01), while higher poverty levels demonstrated moderate positive correlations with LST (ρ = 0.41, p < 0.001). The spatial analysis identified significant clustering of vulnerability (Global Moran's I = 0.42, p < 0.001), with distinct high-vulnerability clusters in historically disadvantaged areas. Alexandra Township showed the highest vulnerability(HVI score: 0.87, LST: 29.8 °C ± 0.4 °C, NDVI: 0.08 ± 0.02), with factors characterising the high vulnerability in that area including limited healthcare access and extreme heat exposure. Northern suburbs formed a significant low-vulnerability cluster (Mean HVI = 0.23 ± 0.07, p < 0.001), benefiting from greater vegetation coverage and better healthcare access. These findings demonstrate how historical planning decisions continue to shape contemporary environmental health risks, with vulnerability concentrated in areas of limited healthcare access and high extreme heat exposure. Results suggest the need for targeted interventions that address both environmental and social dimensions of heat vulnerability, particularly focusing on expanding healthcare access in identified hotspots and implementing community-scale green infrastructure in high-risk areas. This study provides an evidence-based framework for prioritising heat-resilience initiatives in rapidly urbanising Global South cities while highlighting the importance of addressing historical inequities in urban adaptation planning.</p>","PeriodicalId":588,"journal":{"name":"International Journal of Biometeorology","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Tomoko Imasaka*,&nbsp;Katsunori Yoshinaga,&nbsp;Cheng-Huang Lin and Totaro Imasaka,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 7","pages":"XXX-XXX 962–968"},"PeriodicalIF":3.1,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/jasms.5c00029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144521939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Increasing Oligonucleotide Sequencing Information and Throughput with Ion Mobility Spectrometry-Mass Spectrometry.","authors":"Jack P Ryan, Gordon W Slysz, Peter Rye, Sarah M Stow, James N Dodds, John Sausen, Erin S Baker","doi":"10.1021/jasms.5c00083","DOIUrl":"10.1021/jasms.5c00083","url":null,"abstract":"<p><p>Synthetic oligonucleotides, such as antisense oligonucleotides or small interfering RNA, are small chain nucleic acid polymers that can be used therapeutically to control gene expression. Watson-Crick base pair interactions provide the primary mode of interaction between synthetic oligonucleotides and their target molecule, and this binding requires accurate, robust, and rapid sequence verification. The development of high-quality synthetic oligonucleotides and comprehensive analytical workflows for their evaluation is therefore essential. Herein, a platform coupling liquid chromatography, ion mobility spectrometry, collision-induced dissociation, and mass spectrometry (LC-IMS-CID-MS) was applied to facilitate oligonucleotide sequence confirmation. Using IMS, multiple charge states of the same oligonucleotide were mobility separated and analyzed simultaneously. Furthermore, all-ion fragmentation was implemented to provide sequence coverage for each charge state using fewer injections than current targeted multiple injection LC-MS methods. The results demonstrated herein denote sequence coverage is generally inversely proportional to oligonucleotide length (<i>i</i>.<i>e</i>., lower fidelity coverage for longer strands), with observed sequence coverages ranging between 40% and 80% for molecules comprised of 20-40 residues. To ease the burden of spectral interpretation and sequence determination for the LC-IMS-CID-MS data, an analysis workflow using the Pacific Northwest National Laboratories (PNNL) preprocessor and Agilent's BioConfirm software was developed.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"1493-1502"},"PeriodicalIF":3.1,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Gabriel F. dosSantos*,&nbsp;Giovanni B. Bevilaqua,&nbsp;Alexis Gilbert,&nbsp;Hugo G. Machado,&nbsp;Maxime Julien,&nbsp;Gesiane S. Lima,&nbsp;Nerilson M. Lima,&nbsp;Júlio C. O. Ribeiro,&nbsp;Alexandre A. Ferreira,&nbsp;Ygor S. Rocha and Boniek Gontijo*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 7","pages":"XXX-XXX 962–968"},"PeriodicalIF":3.1,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/jasms.5c00092","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144521935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}