Pub Date : 2025-07-11DOI: 10.1016/j.ab.2025.115945
Felice C. Simeone
Hallachrome is a 1,2-anthraquinone secreted by marine polychaete worms whose toxicity and antimicrobial properties have been reported; the origin of this biological activity, however, remains elusive. Voltammetric studies reveal reversible redox behavior in the pH range 1–10, consistent with a two-electron, two-proton (2e−/2H+) mechanism. The electron-donating substituents in hallachrome (hydroxyl and methyl groups) stabilize the protonated hydroquinone form and result in a substantial cathodic shift of 0.4–0.5 V compared to unsubstituted 1,2-benzoquinone.
The electrochemical analysis reveals that hallachrome (redox potential −0.12 V vs. SHE at pH 7) might be capable, from a thermodynamic point of view, of oxidizing key cellular antioxidants, including NADH (−0.32 V), NADPH (−0.32 V), and glutathione (−0.24 V). These findings provide fundamental insights into the structure-activity relationships governing quinone electrochemistry and establish a foundation for understanding hallachrome's biological activity.
Hallachrome是一种由海洋多毛类蠕虫分泌的1,2-蒽醌，其毒性和抗菌特性已被报道；然而，这种生物活性的起源仍然难以捉摸。伏安研究表明，在pH值1 ~ 10范围内，其氧化还原行为是可逆的，符合双电子、双质子（2e-/2H+）机制。hallachrome中的给电子取代基（羟基和甲基）稳定了质子化对苯二酚的形式，与未取代的1,2-苯醌相比，导致了0.4-0.5 V的阴极位移。电化学分析表明，从热力学角度来看，hallachrome （pH = 7时氧化还原电位-0.12 V vs. SHE）可能能够氧化关键的细胞抗氧化剂，包括NADH (-0.32 V), NADPH （-0.32 V）和谷胱甘肽（-0.24 V）。这些发现为研究醌类电化学的构效关系提供了基础，并为进一步了解hallachrome的生物活性奠定了基础。
{"title":"Proton-coupled electron transfer in hallachrome, a natural 1,2 anthraquinone: Linking electrochemical properties to biological activity","authors":"Felice C. Simeone","doi":"10.1016/j.ab.2025.115945","DOIUrl":"10.1016/j.ab.2025.115945","url":null,"abstract":"<div><div>Hallachrome is a 1,2-anthraquinone secreted by marine polychaete worms whose toxicity and antimicrobial properties have been reported; the origin of this biological activity, however, remains elusive. Voltammetric studies reveal reversible redox behavior in the pH range 1–10, consistent with a two-electron, two-proton (2e<sup>−</sup>/2H<sup>+</sup>) mechanism. The electron-donating substituents in hallachrome (hydroxyl and methyl groups) stabilize the protonated hydroquinone form and result in a substantial cathodic shift of 0.4–0.5 V compared to unsubstituted 1,2-benzoquinone.</div><div>The electrochemical analysis reveals that hallachrome (redox potential −0.12 V vs. SHE at pH 7) might be capable, from a thermodynamic point of view, of oxidizing key cellular antioxidants, including NADH (−0.32 V), NADPH (−0.32 V), and glutathione (−0.24 V). These findings provide fundamental insights into the structure-activity relationships governing quinone electrochemistry and establish a foundation for understanding hallachrome's biological activity.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"706 ","pages":"Article 115945"},"PeriodicalIF":2.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625290","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}
Pub Date : 2025-07-11DOI: 10.1016/j.ab.2025.115941
Yan Li , Jian-Yuan Zhong , Ya-qi Mo , Li-mei Qin , Michael Aschner , Yue-ming Jiang
The content of elements in the body has a significant relationship with human health. However, the wide variation in the concentrations of different elements in blood or urine poses challenges for accurate detection. This study presents a dual-mode ICP-MS methodology integrating kinetic energy discrimination (KED) and dynamic reaction cell (DRC) technologies, specifically designed to address the analytical challenge of quantifying 22 physiologically critical elements (Be, V, Cr, Mn, Fe, Ca, Mg, Ba, Co, Cd, Cu, Zn, As, Se, Ti, Sr, Ni, Mo, Sn, Sb, Tl, Pb) spanning six orders of magnitude in concentration (μg/L to g/L) within complex biological matrices. Rejection parameter q (RPq) adjusts the low-mass cutoff, while rejection parameter a (RPa) controls the high-mass cutoff. Optimizing both extends the low-interference dynamic range. The method's core innovation lies in the synchronized optimization of quadrupole parameters RPa and RPq, which enables simultaneous suppression of matrix-derived polyatomic interferences while maintaining linear detector response across ultra-wide dynamic ranges. The method employs a dual-mode analysis approach: (1) In urine analysis, the KED-He mode is suitable for analyzing all elements. (2) In whole blood analysis, DRC-NH3 mode is used for interference-prone elements (Mn, Cr, Ca), and KED-He mode is used for the remaining elements. Strategic optimization of quadrupole rejection parameters (RPa/RPq) achieved intra-day precision of 0.5–7.2 % (blood) and 1.6–5.5 % (urine), with inter-day variations ≤9.6 %, demonstrating robust performance for multi-element profiling across clinically relevant concentration ranges.
{"title":"Simultaneous multi-element determination in whole blood and urine via dual-mode ICP-MS","authors":"Yan Li , Jian-Yuan Zhong , Ya-qi Mo , Li-mei Qin , Michael Aschner , Yue-ming Jiang","doi":"10.1016/j.ab.2025.115941","DOIUrl":"10.1016/j.ab.2025.115941","url":null,"abstract":"<div><div>The content of elements in the body has a significant relationship with human health. However, the wide variation in the concentrations of different elements in blood or urine poses challenges for accurate detection. This study presents a dual-mode ICP-MS methodology integrating kinetic energy discrimination (KED) and dynamic reaction cell (DRC) technologies, specifically designed to address the analytical challenge of quantifying 22 physiologically critical elements (Be, V, Cr, Mn, Fe, Ca, Mg, Ba, Co, Cd, Cu, Zn, As, Se, Ti, Sr, Ni, Mo, Sn, Sb, Tl, Pb) spanning six orders of magnitude in concentration (μg/L to g/L) within complex biological matrices. Rejection parameter q (RPq) adjusts the low-mass cutoff, while rejection parameter a (RPa) controls the high-mass cutoff. Optimizing both extends the low-interference dynamic range. The method's core innovation lies in the synchronized optimization of quadrupole parameters RPa and RPq, which enables simultaneous suppression of matrix-derived polyatomic interferences while maintaining linear detector response across ultra-wide dynamic ranges. The method employs a dual-mode analysis approach: (1) In urine analysis, the KED-He mode is suitable for analyzing all elements. (2) In whole blood analysis, DRC-NH<sub>3</sub> mode is used for interference-prone elements (Mn, Cr, Ca), and KED-He mode is used for the remaining elements. Strategic optimization of quadrupole rejection parameters (RPa/RPq) achieved intra-day precision of 0.5–7.2 % (blood) and 1.6–5.5 % (urine), with inter-day variations ≤9.6 %, demonstrating robust performance for multi-element profiling across clinically relevant concentration ranges.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"706 ","pages":"Article 115941"},"PeriodicalIF":2.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625291","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}
Pub Date : 2025-07-11DOI: 10.1016/j.ab.2025.115944
Kevin Knowlan, Cody L. Hoop, Nadya I. Tarasova
Cis-aconitate decarboxylase (ACOD1) is a key enzyme converting cis-aconitate to itaconate, which has therapeutic potential for inflammatory diseases. Existing methods to measure ACOD1 activity and itaconate are often expensive and complex. We developed a novel, high-throughput spectrophotometric assay using the Fürth-Herrmann reaction. Our method quantifies ACOD1-catalyzed itaconate production by leveraging distinct absorbance ratios of cis-aconitate and itaconate at 386 nm and 440 nm. We optimized parameters, characterized human ACOD1 kinetics, and determined an IC50 for citraconate consistent with previous reports. This simple, fast, and reliable assay, requiring only a UV–Vis spectrophotometer, will accelerate screening for ACOD1 modulators, speeding up therapeutic development.
{"title":"Spectroscopic method for measuring activity of cis-aconitate decarboxylase, an important metabolic regulator of immune responses","authors":"Kevin Knowlan, Cody L. Hoop, Nadya I. Tarasova","doi":"10.1016/j.ab.2025.115944","DOIUrl":"10.1016/j.ab.2025.115944","url":null,"abstract":"<div><div><em>Cis</em>-aconitate decarboxylase (ACOD1) is a key enzyme converting <em>cis</em>-aconitate to itaconate, which has therapeutic potential for inflammatory diseases. Existing methods to measure ACOD1 activity and itaconate are often expensive and complex. We developed a novel, high-throughput spectrophotometric assay using the Fürth-Herrmann reaction. Our method quantifies ACOD1-catalyzed itaconate production by leveraging distinct absorbance ratios of <em>cis</em>-aconitate and itaconate at 386 nm and 440 nm. We optimized parameters, characterized human ACOD1 kinetics, and determined an IC<sub>50</sub> for citraconate consistent with previous reports. This simple, fast, and reliable assay, requiring only a UV–Vis spectrophotometer, will accelerate screening for ACOD1 modulators, speeding up therapeutic development.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"706 ","pages":"Article 115944"},"PeriodicalIF":2.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144614768","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}
Pub Date : 2025-07-11DOI: 10.1016/j.ab.2025.115931
Xu Yang , Bowei Han , Jie Huang , Min Zhang , Shi Weng , Guojun Ouyang , Wanqing Han , Wenyu Wang , Li Zhang , Juanjuan Chen , Juan Du , Yingsong Wu , Xuexi Yang
Objective
Fragile X syndrome is mainly caused by the expansion of GC-rich cytosine-guanine-guanine (CGG) repeat in FMR1 5′UTR region, as well as rare gene point mutations or deletions in its open reading frame. Currently, third-generation long-read sequencing is a potential technology for simultaneously detecting CGG repeat expansions, point mutations, and deletions. However, a major challenge remains in obtaining the target long-fragment CGG repeat region with ultra-high GC content for sequencing.
Methods
We developed a novel approach combining long-fragment ultra-high GC polymerase chain reaction (PCR) amplification with Oxford Nanopore sequencing to detect the full spectrum of FMR1 5′UTR CGG repeat mutations. The method was validated using 10 standard cell line samples (males: nnormal = 1, nintermediate = 1, npre-mutation = 1, and nfull mutation = 2; females: nnormal = 1, nintermediate = 1, npre-mutation = 2, and nfull mutation = 1) and 53 retrospective clinical blood samples (males: nnormal = 7, npre-mutation = 3, nfull mutation = 15, and nmosaicmutaion = 2; females: nnormal = 9, npre-mutation = 13, and nfull mutation = 4).
Results
Our method demonstrated that the 100 % concordance with the triplet repeat-primed PCR and Southern blot analysis in genotyping 10 cell line samples and 53 clinical samples. Additionally, CGG repeat numbers showed strong correlation with reference mehods (male cell lines, n = 5, R2 = 0.9996; female cell lines, n = 5, R2 = 0.9972; clinical male samples, n = 26, R2 = 1.0000; clinical female samples, n = 25, R2 = 0.9854).
Conclusion
This study presents a simple and cost-effective strategy for preparing FMR1 5′UTR CGG repeat regions with long-fragment ultra-high GC content for third-generation sequencing. The approach could serve as a model for detecting other challenging disorders caused by short tandem repeat expansions, such as myotonic dystrophy and Huntington’ s disease.
{"title":"Oxford Nanopore third generation sequencing for analysis of FMR1 5′UTR CGG repeat expansions","authors":"Xu Yang , Bowei Han , Jie Huang , Min Zhang , Shi Weng , Guojun Ouyang , Wanqing Han , Wenyu Wang , Li Zhang , Juanjuan Chen , Juan Du , Yingsong Wu , Xuexi Yang","doi":"10.1016/j.ab.2025.115931","DOIUrl":"10.1016/j.ab.2025.115931","url":null,"abstract":"<div><h3>Objective</h3><div>Fragile X syndrome is mainly caused by the expansion of GC-rich cytosine-guanine-guanine (CGG) repeat in <em>FMR1</em> 5′UTR region, as well as rare gene point mutations or deletions in its open reading frame. Currently, third-generation long-read sequencing is a potential technology for simultaneously detecting CGG repeat expansions, point mutations, and deletions. However, a major challenge remains in obtaining the target long-fragment CGG repeat region with ultra-high GC content for sequencing.</div></div><div><h3>Methods</h3><div>We developed a novel approach combining long-fragment ultra-high GC polymerase chain reaction (PCR) amplification with Oxford Nanopore sequencing to detect the full spectrum of <em>FMR1</em> 5′UTR CGG repeat mutations. The method was validated using 10 standard cell line samples (males: n<sub>normal</sub> = 1, n<sub>intermediate</sub> = 1, n<sub>pre-mutation</sub> = 1, and n<sub>full mutation</sub> = 2; females: n<sub>normal</sub> = 1, n<sub>intermediate</sub> = 1, n<sub>pre-mutation</sub> = 2, and n<sub>full mutation</sub> = 1) and 53 retrospective clinical blood samples (males: n<sub>normal</sub> = 7, n<sub>pre-mutation</sub> = 3, n<sub>full mutation</sub> = 15, and n<sub>mosaic</sub> <sub>mutaion</sub> = 2; females: n<sub>normal</sub> = 9, n<sub>pre-mutation</sub> = 13, and n<sub>full mutation</sub> = 4).</div></div><div><h3>Results</h3><div>Our method demonstrated that the 100 % concordance with the triplet repeat-primed PCR and Southern blot analysis in genotyping 10 cell line samples and 53 clinical samples. Additionally, CGG repeat numbers showed strong correlation with reference mehods (male cell lines, n = 5, R<sup>2</sup> = 0.9996; female cell lines, n = 5, R<sup>2</sup> = 0.9972; clinical male samples, n = 26, R<sup>2</sup> = 1.0000; clinical female samples, n = 25, R<sup>2</sup> = 0.9854).</div></div><div><h3>Conclusion</h3><div>This study presents a simple and cost-effective strategy for preparing <em>FMR1</em> 5′UTR CGG repeat regions with long-fragment ultra-high GC content for third-generation sequencing. The approach could serve as a model for detecting other challenging disorders caused by short tandem repeat expansions, such as myotonic dystrophy and Huntington’ s disease.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"706 ","pages":"Article 115931"},"PeriodicalIF":2.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625289","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}
Pub Date : 2025-07-09DOI: 10.1016/j.ab.2025.115942
Kim-Thanh Van , Fatimah Nabeebaccus , Foudil Lamari , Susana Boluda , François Fenaille , Nicolas Villain , François Becher
α-synuclein is a protein central to neurodegenerative diseases, and its functions are affected by multiple posttranslational modifications. Mass spectrometry is powerful for the characterization of α-synuclein forms but requires prior efficient immunoprecipitation conditions. In this study, we refined the immunoprecipitation of α-synuclein from human brain tissues by evaluating key parameters that influence recovery and specificity. We assessed the performance of tosyl-activated magnetic beads versus sheep antibody beads, identifying the optimal bead type for enhanced binding efficiency. Various elution conditions were rigorously tested to maximize protein yield. We also evaluated a range of antibodies specific to α-synuclein and delineated the effects of antibody amount and bead volume on the recovery of α-synuclein. The optimized immunoprecipitation protocol was effectively combined with high-resolution mass spectrometry for characterizing brain-derived α-synuclein from Parkinson's disease patients and controls. The assay identified a total of 38 N- or C-terminal truncated α-synuclein forms, including 22 novel sites. Our findings provide analytical tools for the reliable enrichment and characterization of α-synuclein from complex biological matrices, with potential applications in biomarker discovery and the investigation of pathogenic mechanisms underlying synucleinopathies.
{"title":"Mass spectrometric identification of novel truncated α-synuclein species following optimized immunoprecipitation from human brain tissue","authors":"Kim-Thanh Van , Fatimah Nabeebaccus , Foudil Lamari , Susana Boluda , François Fenaille , Nicolas Villain , François Becher","doi":"10.1016/j.ab.2025.115942","DOIUrl":"10.1016/j.ab.2025.115942","url":null,"abstract":"<div><div>α-synuclein is a protein central to neurodegenerative diseases, and its functions are affected by multiple posttranslational modifications. Mass spectrometry is powerful for the characterization of α-synuclein forms but requires prior efficient immunoprecipitation conditions. In this study, we refined the immunoprecipitation of α-synuclein from human brain tissues by evaluating key parameters that influence recovery and specificity. We assessed the performance of tosyl-activated magnetic beads versus sheep antibody beads, identifying the optimal bead type for enhanced binding efficiency. Various elution conditions were rigorously tested to maximize protein yield. We also evaluated a range of antibodies specific to α-synuclein and delineated the effects of antibody amount and bead volume on the recovery of α-synuclein. The optimized immunoprecipitation protocol was effectively combined with high-resolution mass spectrometry for characterizing brain-derived α-synuclein from Parkinson's disease patients and controls. The assay identified a total of 38 N- or C-terminal truncated α-synuclein forms, including 22 novel sites. Our findings provide analytical tools for the reliable enrichment and characterization of α-synuclein from complex biological matrices, with potential applications in biomarker discovery and the investigation of pathogenic mechanisms underlying synucleinopathies.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"706 ","pages":"Article 115942"},"PeriodicalIF":2.6,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615792","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}
Pub Date : 2025-07-09DOI: 10.1016/j.ab.2025.115939
Jianmin Yang, Kai Tang, Shuyan Xiong, Liang Shi, Aidong Tang
Iodine deficiency or excess impacts thyroid health, necessitating accurate urinary iodine monitoring. However, existing detection methods face challenges including complicated sample handling, poor anti-interference ability, and the detection range does not cover the range of human urinary iodine concentration. Conventional iodide ion-selective electrode is based on polycrystalline membranes, which has high detection limit and is susceptible to chloride ion interference. It is also not suitable for accurate detection of human urinary iodine. In this study, we introduced a single-crystal AgI electrode for rapid and interference-free detection of urinary iodine. The dense (220) crystal plane of the single-crystal AgI electrode provided excellent selectivity and sensitivity, with a detection limit as low as 59 μg L−1 and good linearity in the range of 100–1000 μg L−1. This fully covers the optimal range of urinary iodine concentrations recommended by the World Health Organization (100–500 μg L−1). Importantly, the single-crystal AgI electrode has excellent resistance to chloride interference, which is a significant improvement over conventional polycrystallaline iodide ion-selective electrodes. Our results show that the electrode has excellent precision, stability and accuracy without interference from common urine ions. This work addresses the limitations of existing methods and provides a rapid, inexpensive and reliable method for urinary iodine testing.
{"title":"Rapid and accurate detection of urinary iodine by single crystal silver iodide sensor","authors":"Jianmin Yang, Kai Tang, Shuyan Xiong, Liang Shi, Aidong Tang","doi":"10.1016/j.ab.2025.115939","DOIUrl":"10.1016/j.ab.2025.115939","url":null,"abstract":"<div><div>Iodine deficiency or excess impacts thyroid health, necessitating accurate urinary iodine monitoring. However, existing detection methods face challenges including complicated sample handling, poor anti-interference ability, and the detection range does not cover the range of human urinary iodine concentration. Conventional iodide ion-selective electrode is based on polycrystalline membranes, which has high detection limit and is susceptible to chloride ion interference. It is also not suitable for accurate detection of human urinary iodine. In this study, we introduced a single-crystal AgI electrode for rapid and interference-free detection of urinary iodine. The dense (220) crystal plane of the single-crystal AgI electrode provided excellent selectivity and sensitivity, with a detection limit as low as 59 μg L<sup>−1</sup> and good linearity in the range of 100–1000 μg L<sup>−1</sup>. This fully covers the optimal range of urinary iodine concentrations recommended by the World Health Organization (100–500 μg L<sup>−1</sup>). Importantly, the single-crystal AgI electrode has excellent resistance to chloride interference, which is a significant improvement over conventional polycrystallaline iodide ion-selective electrodes. Our results show that the electrode has excellent precision, stability and accuracy without interference from common urine ions. This work addresses the limitations of existing methods and provides a rapid, inexpensive and reliable method for urinary iodine testing.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"706 ","pages":"Article 115939"},"PeriodicalIF":2.6,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144604946","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}
Pub Date : 2025-07-08DOI: 10.1016/j.ab.2025.115940
Xiaofang Zheng , Daikun Zheng , Linfeng Zheng , Peng Wang , Yong Liu , Xixi You , Xiaoling Zheng , Xinyuan Cao , Jiao Luo , Wansong Chen , Guoli Li , Ruizi Peng
Unraveling tumor-associated membrane proteins' spatial proximity holds a significance for clinically relevant multiple biomarker detection. Herein, based on aptamer binding to target proteins in clinical formalin-fixed paraffin-embedded (FFPE) tissue samples, we developed aptamer-tethered auto-cycling proximity recording (APR) probes as a proof-of-concept methodology for biosensing membrane proteins' spatial proximity. This APR enables continuous and repetitive recording of spatial neighboring pairs of DNA probes in FFPE breast cancer tissue samples in situ, without altering the probes themselves. Finally, this aptamer-based auto-cycling proximity recorder is able to identify spatial proximity of three membrane proteins in FFPE breast cancer tissues. Our research establishes a foundation for proximity-driven biosensing platform and provides a perspective for exploration in aptamer-based bioimaging in clinical tissue samples.
{"title":"Multi-protein-triggered, aptamer-tethered auto-cycling proximity recorder in formalin-fixed paraffin-embedded tissues","authors":"Xiaofang Zheng , Daikun Zheng , Linfeng Zheng , Peng Wang , Yong Liu , Xixi You , Xiaoling Zheng , Xinyuan Cao , Jiao Luo , Wansong Chen , Guoli Li , Ruizi Peng","doi":"10.1016/j.ab.2025.115940","DOIUrl":"10.1016/j.ab.2025.115940","url":null,"abstract":"<div><div>Unraveling tumor-associated membrane proteins' spatial proximity holds a significance for clinically relevant multiple biomarker detection. Herein, based on aptamer binding to target proteins in clinical formalin-fixed paraffin-embedded (FFPE) tissue samples, we developed aptamer-tethered auto-cycling proximity recording (APR) probes as a proof-of-concept methodology for biosensing membrane proteins' spatial proximity. This APR enables continuous and repetitive recording of spatial neighboring pairs of DNA probes in FFPE breast cancer tissue samples in situ, without altering the probes themselves. Finally, this aptamer-based auto-cycling proximity recorder is able to identify spatial proximity of three membrane proteins in FFPE breast cancer tissues. Our research establishes a foundation for proximity-driven biosensing platform and provides a perspective for exploration in aptamer-based bioimaging in clinical tissue samples.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"706 ","pages":"Article 115940"},"PeriodicalIF":2.6,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144605504","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}
Pub Date : 2025-06-30DOI: 10.1016/j.ab.2025.115930
Xueqiang Wu , Xuyang Pu , Yinmei Zhang , Heming Wu , Zhikang Yu , Wei He , Yibiao Chen
This study presents a novel Terminal Self-Competitive Nucleic Acid Probe (TSCP) for rapid, precise detection of mutant and wild-type gene sequences. The TSCP probe employs overlapping binding domains and inhibition strands, enabling highly specific competitive hybridization. Combined with hybridization chain reaction (HCR) for signal amplification, the method achieves nanomolar sensitivity without requiring proteases, temperature control, or complex instrumentation. Experimental validation in blood samples demonstrated distinct fluorescent signals for mutant and wild-type sequences, allowing accurate target differentiation. The probe is cost-effective and scalable, as it only requires nucleic acid synthesis for new mutations, ensuring rapid adaptation to emerging variants. This straightforward, versatile approach facilitates simultaneous detection of genetic variations, making it highly suitable for molecular diagnostics and genetic research. Its high specificity, rapid response, and low-cost production underscore its potential as a practical tool for advancing mutation detection in clinical and research settings. By eliminating the need for specialized equipment and enabling quick deployment, the TSCP-based method offers a widely accessible solution for identifying genetic mutations, enhancing both diagnostic accuracy and research efficiency.
{"title":"A nucleic acid-based strategy for highly specific discrimination between mutant and wild-type sequences","authors":"Xueqiang Wu , Xuyang Pu , Yinmei Zhang , Heming Wu , Zhikang Yu , Wei He , Yibiao Chen","doi":"10.1016/j.ab.2025.115930","DOIUrl":"10.1016/j.ab.2025.115930","url":null,"abstract":"<div><div>This study presents a novel Terminal Self-Competitive Nucleic Acid Probe (TSCP) for rapid, precise detection of mutant and wild-type gene sequences. The TSCP probe employs overlapping binding domains and inhibition strands, enabling highly specific competitive hybridization. Combined with hybridization chain reaction (HCR) for signal amplification, the method achieves nanomolar sensitivity without requiring proteases, temperature control, or complex instrumentation. Experimental validation in blood samples demonstrated distinct fluorescent signals for mutant and wild-type sequences, allowing accurate target differentiation. The probe is cost-effective and scalable, as it only requires nucleic acid synthesis for new mutations, ensuring rapid adaptation to emerging variants. This straightforward, versatile approach facilitates simultaneous detection of genetic variations, making it highly suitable for molecular diagnostics and genetic research. Its high specificity, rapid response, and low-cost production underscore its potential as a practical tool for advancing mutation detection in clinical and research settings. By eliminating the need for specialized equipment and enabling quick deployment, the TSCP-based method offers a widely accessible solution for identifying genetic mutations, enhancing both diagnostic accuracy and research efficiency.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"705 ","pages":"Article 115930"},"PeriodicalIF":2.6,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551708","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}
Pub Date : 2025-06-28DOI: 10.1016/j.ab.2025.115929
Qing Zhang , You-Hang Hu , Yu Zhou , Jun Hu , Xiao-Gen Zhou , Biao Zhang
Protein-protein interactions (PPIs) play a pivotal role in numerous biological processes. Accurate identification of the amino acid residues involved in these interactions is essential for understanding the functional mechanisms of proteins. To effectively integrate both structure and sequence information, we propose a new interaction site predictor, TargetPPI, which leverages bidirectional long short-term memory networks (Bi-LSTM), convolutional neural networks (CNN), and Edge Aggregation through Graph Attention layers with Node Similarity (EGR-NS) neural networks. In TargetPPI, CNN and Bi-LSTM are first employed to extract the global and local feature information, respectively. The combination of global and local features is then used as node embeddings in the graph derived from the protein structure. We have also extracted six discriminative structural features as edge features in the graph. Additionally, a mean ensemble strategy is used to integrate multiple prediction models with diverse model parameters into the final model, resulting in more accurate PPIs prediction performance. Benchmarked results on seven independent testing datasets demonstrate that, compared to most of the state-of-the-art methods, TargetPPI achieves higher accuracy, precision, and Matthews Correlation Coefficient (MCC) values on average, specifically, 84.3 %, 57.6 %, and 0.383, respectively. The source code of TargetPPI is freely available at https://github.com/bukkeshuo/TargetPPI.
{"title":"Improving protein-protein interaction site prediction using graph neural network and structure profiles","authors":"Qing Zhang , You-Hang Hu , Yu Zhou , Jun Hu , Xiao-Gen Zhou , Biao Zhang","doi":"10.1016/j.ab.2025.115929","DOIUrl":"10.1016/j.ab.2025.115929","url":null,"abstract":"<div><div>Protein-protein interactions (PPIs) play a pivotal role in numerous biological processes. Accurate identification of the amino acid residues involved in these interactions is essential for understanding the functional mechanisms of proteins. To effectively integrate both structure and sequence information, we propose a new interaction site predictor, TargetPPI, which leverages bidirectional long short-term memory networks (Bi-LSTM), convolutional neural networks (CNN), and Edge Aggregation through Graph Attention layers with Node Similarity (EGR-NS) neural networks. In TargetPPI, CNN and Bi-LSTM are first employed to extract the global and local feature information, respectively. The combination of global and local features is then used as node embeddings in the graph derived from the protein structure. We have also extracted six discriminative structural features as edge features in the graph. Additionally, a mean ensemble strategy is used to integrate multiple prediction models with diverse model parameters into the final model, resulting in more accurate PPIs prediction performance. Benchmarked results on seven independent testing datasets demonstrate that, compared to most of the state-of-the-art methods, TargetPPI achieves higher accuracy, precision, and Matthews Correlation Coefficient (MCC) values on average, specifically, 84.3 %, 57.6 %, and 0.383, respectively. The source code of TargetPPI is freely available at <span><span>https://github.com/bukkeshuo/TargetPPI</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"705 ","pages":"Article 115929"},"PeriodicalIF":2.6,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526110","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}
Pub Date : 2025-06-27DOI: 10.1016/j.ab.2025.115928
Dimitrios Tsikas
In quantitative analyses, thousands of compounds are extracted from a biological matrix in addition to the analytes of interest and can affect their quantification by many different effects. They are widely known as matrix effects (ME). A frequently used approach in LC-MS/MS to quantify ME is performing two series of analyses, that is 1) in the biological sample, and 2) in analyte solutions in water, organic solvents and/or in mixtures of them, and by comparing the slope values of the two standard curves. This article suggests a new approach for the quantification of ME in GC-MS using isotopologs, namely their specific peak area. The approach is exemplified for amino acids, representing an important group of physiological substances, for human serum and urine, two capital matrices in biological analysis.
{"title":"Assessment of matrix effects in quantitative GC-MS by using isotopologs","authors":"Dimitrios Tsikas","doi":"10.1016/j.ab.2025.115928","DOIUrl":"10.1016/j.ab.2025.115928","url":null,"abstract":"<div><div>In quantitative analyses, thousands of compounds are extracted from a biological matrix in addition to the analytes of interest and can affect their quantification by many different effects. They are widely known as matrix effects (ME). A frequently used approach in LC-MS/MS to quantify ME is performing two series of analyses, that is 1) in the biological sample, and 2) in analyte solutions in water, organic solvents and/or in mixtures of them, and by comparing the slope values of the two standard curves. This article suggests a new approach for the quantification of ME in GC-MS using isotopologs, namely their specific peak area. The approach is exemplified for amino acids, representing an important group of physiological substances, for human serum and urine, two capital matrices in biological analysis.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"705 ","pages":"Article 115928"},"PeriodicalIF":2.6,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144510654","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}
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