Analytical biochemistry最新文献_第10页

Mismatch-sensitive DNA hybridization controlled by inchworm-type peptide nucleic acid–PEG conjugates 尺蠖型肽核酸- peg偶联物控制错配敏感DNA杂交

IF 2.5 4区生物学

Analytical biochemistry Pub Date : 2025-12-01 Epub Date: 2025-09-04 DOI: 10.1016/j.ab.2025.115967

Toshihiko Sakurai , Yusuke Hamashita , Takahiro Shibata

{"title":"Mismatch-sensitive DNA hybridization controlled by inchworm-type peptide nucleic acid–PEG conjugates","authors":"Toshihiko Sakurai , Yusuke Hamashita , Takahiro Shibata","doi":"10.1016/j.ab.2025.115967","DOIUrl":"10.1016/j.ab.2025.115967","url":null,"abstract":"<div><div>The duplex-forming behavior of an inchworm-type PNA–PEG conjugate (i-PPc), engineered for the selective recognition of point mutations in DNA, was assessed through thermodynamic analysis employing UV melting curves and circular dichroism spectroscopy. The i-PPc demonstrated the ability to form stable duplexes exclusively with fully complementary DNA sequences, while no hybridization with single-base mismatched sequences. This binary on/off hybridization behavior was maintained even under physiologically relevant conditions (37 °C), thereby illustrating the exceptional point mutation discrimination capability of i-PPc. The behavior observed can be ascribed to the distinctive structure of i-PPc, wherein two PNA segments, possessing intrinsically different duplex-forming stabilities—high and low—are covalently linked via a flexible PEG linker. The high-stability PNA segment functions as the primary recognition domain for point mutations, thereby defining the sequence specificity of duplex formation. Conversely, the low-stability segment contributes cooperatively to the overall duplex stabilization only when the high-stability segment successfully hybridizes with the target DNA. This cooperative mechanism underlies the sequence-selective duplex formation of i-PPc, highlighting its potential as a highly specific probe for DNA mutation diagnostics. These findings indicate that i-PPc represents a promising platform for point mutation detection and nucleic acid-based molecular diagnostics grounded in DNA hybridization under physiological conditions.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"707 ","pages":"Article 115967"},"PeriodicalIF":2.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145003703","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}

引用次数: 0

Development of species-specific PCR for authentication of medicinal plant Bupleuri Radix and its common adulterants 药用植物柴胡及其常见掺假物种特异性PCR鉴定方法的建立

IF 2.5 4区生物学

Analytical biochemistry Pub Date : 2025-12-01 Epub Date: 2025-08-14 DOI: 10.1016/j.ab.2025.115963

Hui Tian , Xiuna Zhang , Chi Ma , Yidi Yang , Jing Fang , Fanna Qu , Lihong Yang

{"title":"Development of species-specific PCR for authentication of medicinal plant Bupleuri Radix and its common adulterants","authors":"Hui Tian , Xiuna Zhang , Chi Ma , Yidi Yang , Jing Fang , Fanna Qu , Lihong Yang","doi":"10.1016/j.ab.2025.115963","DOIUrl":"10.1016/j.ab.2025.115963","url":null,"abstract":"<div><div>Bupleuri Radix is a widely used herbal plant, and its official source recognized by Chinese pharmacopoeia is the dried roots of <em>Bupleurum chinense</em> DC. or <em>Bupleurum scorzonerifolium</em> Willd. Although two species share core therapeutic functions, differences in the types of chemical components lead to different clinical applications. Currently, two species have not been distinguished in pharmacopeial standards. Therefore, we hypothesize prescribing them separately based on the pharmacological characteristics may provide better clinical efficacy. Additionally, <em>Bupleurum marginatum</em> Wall. ex DC. var stenophyllum (Wolff) Shan et Y. Li, and <em>Bupleurum bicaule</em> Helm were often misused as Bupleuri Radix. To address above issues, we developed species-specific PCR targeting ITS region. The observed fragments of 252bp, 183bp, 272bp and 165bp correspond to <em>B. chinense, B. scorzonerifolium, B. marginatum</em> var. <em>stenophyllum, and B. bicaule</em> respectively. The PCR exhibited strong discriminative capability, even when analyzing artificial adulterate samples. Furthermore, analysis of commercial samples validated the accuracy of the species information. In summary, the species-specific PCR enables accurate authentication of Bupleuri Radix and common adulterants in the market. It provides a practical tool for quality control of Bupleuri Radix and supports standardization of herbal medicine production.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"707 ","pages":"Article 115963"},"PeriodicalIF":2.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858519","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}

引用次数: 0

Boron nitride quantum dot-based fluorescent sensor for carbamazepine determination in exhaled breath condensate 氮化硼量子点荧光传感器测定呼出液中卡马西平

IF 2.5 4区生物学

Analytical biochemistry Pub Date : 2025-12-01 Epub Date: 2025-08-26 DOI: 10.1016/j.ab.2025.115964

Saba Ershadi , Maryam Khoubnasabjafari , Vahid Jouyban-Gharamaleki , Elaheh Rahimpour , Abolghasem Jouyban

{"title":"Boron nitride quantum dot-based fluorescent sensor for carbamazepine determination in exhaled breath condensate","authors":"Saba Ershadi , Maryam Khoubnasabjafari , Vahid Jouyban-Gharamaleki , Elaheh Rahimpour , Abolghasem Jouyban","doi":"10.1016/j.ab.2025.115964","DOIUrl":"10.1016/j.ab.2025.115964","url":null,"abstract":"<div><div>Carbamazepine is a widely prescribed antiepileptic drug with a narrow therapeutic index, necessitating precise monitoring to avoid toxicity and ensure therapeutic efficacy. This study presents a fluorescence-based nanosensor using boron nitride quantum dots (BNQDs) for the rapid and sensitive detection of carbamazepine in exhaled breath condensate (EBC). BNQDs were prepared via a simple hydrothermal technique and characterized using transmission electron microscopy, dynamic light scattering, energy-dispersive X-ray, and attenuated total reflectance-Fourier transform infrared techniques. The sensor exhibited a concentration-dependent quenching of BNQD fluorescence upon carbamazepine addition, with a linear response range of 0.2–2.4 μg mL<sup>−1</sup> and a low detection limit of 0.05 μg mL<sup>−1</sup>. Stern–Volmer analysis confirmed a dynamic quenching mechanism. The nanosensor also demonstrated high selectivity against common co-administered drugs and was successfully applied to real EBC samples collected from patients receiving carbamazepine therapy. This BNQD-based sensing platform offered a rapid, cost-effective, and user-friendly approach for the non-invasive therapeutic drug monitoring of carbamazepine.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"707 ","pages":"Article 115964"},"PeriodicalIF":2.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144920129","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}

引用次数: 0

K-SNOpred: Identification of protein S-nitrosylation sites through word embedding features and machine learning K-SNOpred：通过词嵌入特征和机器学习识别蛋白质s -亚硝基化位点。

IF 2.5 4区生物学

Analytical biochemistry Pub Date : 2025-12-01 Epub Date: 2025-08-06 DOI: 10.1016/j.ab.2025.115952

Tasmin Karim , Md Shazzad Hossain Shaon , Md Mamun Ali , Sobhy M. Ibrahim , Mst Shapna Akter , Kawsar Ahmed , Francis M. Bui , Li Chen , Mohammad Ali Moni

{"title":"K-SNOpred: Identification of protein S-nitrosylation sites through word embedding features and machine learning","authors":"Tasmin Karim , Md Shazzad Hossain Shaon , Md Mamun Ali , Sobhy M. Ibrahim , Mst Shapna Akter , Kawsar Ahmed , Francis M. Bui , Li Chen , Mohammad Ali Moni","doi":"10.1016/j.ab.2025.115952","DOIUrl":"10.1016/j.ab.2025.115952","url":null,"abstract":"<div><div>Protein S-nitrosylation (SNO) is a process involving the covalent modification of cysteine residues by nitric oxide (NO) and its derivatives. Numerous studies have demonstrated that SNO is significantly involved in cell function and pathophysiology. The identification of SNO sites is significant in clarifying their function in cellular physiology, disease processes, and potential treatment strategies, rendering it of paramount importance in medical science. This study developed a machine learning (ML) model named “K-SNOpred” and found notable performance in identifying SNO sites using the Latent Semantic Analysis (LSA) feature embedding system. After collecting dbSNO and RecSNO datasets from the literature search, we applied three feature embedding systems: Doc2vec, FastText, and LSA on each dataset. The study employed various ML models and assessed their performance using multiple evaluation metrics through independent testing and 10-fold cross-validation. The evaluation's outcomes demonstrate that the proposed model achieved an accuracy of 87.56 % and an AUC score of 95.06 %, outperforming existing state-of-the-art (SOTA) models by nearly 10 % in accuracy and 6 % in AUC. Furthermore, the model demonstrated balanced sensitivity and specificity, indicating its ability to detect both positive and negative SNO sites accurately. The outstanding performance of the K-SNOpred model demonstrates its high potential for clinical use and its applicability in the biotechnology field.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"707 ","pages":"Article 115952"},"PeriodicalIF":2.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803266","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}

引用次数: 0

Easy reference-guided assembly of nanopore whole plasmid sequencing datasets 易于参考引导组装纳米孔全质粒测序数据集。

IF 2.5 4区生物学

Analytical biochemistry Pub Date : 2025-12-01 Epub Date: 2025-09-05 DOI: 10.1016/j.ab.2025.115970

Vinita Sharma , Naiyu Jiang , Yukihiro Nagashima , Hisashi Koiwa

引用次数: 0

Proton-coupled electron transfer in hallachrome, a natural 1,2 anthraquinone: Linking electrochemical properties to biological activity 一种天然1,2蒽醌——汉那色胺的质子耦合电子转移：将电化学性质与生物活性联系起来。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-11-01 Epub Date: 2025-07-11 DOI: 10.1016/j.ab.2025.115945

Felice C. Simeone

引用次数: 0

A modular and universal platform for neutralizing-antibody profiling by quantifying antigen-receptor interactions via qPCR 通过qPCR定量抗原-受体相互作用的中和抗体分析的模块化和通用平台

IF 2.5 4区生物学

Analytical biochemistry Pub Date : 2025-11-01 Epub Date: 2025-07-30 DOI: 10.1016/j.ab.2025.115951

Xia Li , Qi Chen , Yating Zhu , Haofei Hong , Zhifang Zhou , Zhimeng Wu , Jie Shi

{"title":"A modular and universal platform for neutralizing-antibody profiling by quantifying antigen-receptor interactions via qPCR","authors":"Xia Li , Qi Chen , Yating Zhu , Haofei Hong , Zhifang Zhou , Zhimeng Wu , Jie Shi","doi":"10.1016/j.ab.2025.115951","DOIUrl":"10.1016/j.ab.2025.115951","url":null,"abstract":"<div><div>Rapid and accurate detection of neutralizing antibody (nAb) is essential for assessing vaccine efficacy and immune protection against infectious diseases. In the present study, we developed a neutralization-antibody detection qPCR platform (NAD-qPCR) that quantifies nAb potency by integrating antigen-receptor binding specificity with qPCR sensitivity. Using the SARS-CoV-2 nAb as a proof-of-concept target, this system comprised a hybrid probe with the viral RBD as an antigen module covalently conjugated to a reporter DNA, and magnetic beads functionalized with the ACE2 mimic mini-protein as a receptor module, thereby recapitulating the natural antigen-receptor interactions. With this design, the neutralizing capability of nAb against the antigen was transformed into a competitive reduction of the probe binding and DNA amplification signal by qPCR. The NAD-qPCR demonstrated robust performance in quantifying commercial SARS-CoV-2 nAb with a LOD of 4 ng/μL. Furthermore, it was demonstrated to be capable of effectively profiling a large number of vaccinated donor serum with broad neutralization activity. Notably, the hybrid probe and the capture beads were designed modularly, which allows for straightforward adaptation to other pathogens by replacing the module component. This platform offers a rapid, high-throughput, and universally applicable approach for nAb detection in vaccine development and immune monitoring.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"706 ","pages":"Article 115951"},"PeriodicalIF":2.5,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756934","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}

引用次数: 0

Simultaneous multi-element determination in whole blood and urine via dual-mode ICP-MS 双模式ICP-MS同时测定全血和尿液中的多元素。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-11-01 Epub Date: 2025-07-11 DOI: 10.1016/j.ab.2025.115941

Yan Li , Jian-Yuan Zhong , Ya-qi Mo , Li-mei Qin , Michael Aschner , Yue-ming Jiang

{"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":"2025-11-01","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}

引用次数: 0

Mass spectrometric identification of novel truncated α-synuclein species following optimized immunoprecipitation from human brain tissue 优化免疫沉淀后人脑组织中新型截断α-突触核蛋白的质谱鉴定。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-11-01 Epub Date: 2025-07-09 DOI: 10.1016/j.ab.2025.115942

Kim-Thanh Van , Fatimah Nabeebaccus , Foudil Lamari , Susana Boluda , François Fenaille , Nicolas Villain , François Becher

{"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":"2025-11-01","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}

引用次数: 0

Spectroscopic method for measuring activity of cis-aconitate decarboxylase, an important metabolic regulator of immune responses 测定免疫反应重要代谢调节因子顺式乌头酸脱羧酶活性的光谱方法

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-11-01 Epub Date: 2025-07-11 DOI: 10.1016/j.ab.2025.115944

Kevin Knowlan, Cody L. Hoop, Nadya I. Tarasova

引用次数: 0