Analytical biochemistry最新文献

Comparative assessment of four virus neutralization assays for detection of SARS-CoV-2 neutralizing antibodies.

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-04-03 DOI: 10.1016/j.ab.2025.115860

Faezeh Maghsood, Navid Dashti, Tannaz Bahadori, Forough Golsaz-Shirazi, Christiane Moog, Mohammad Mehdi Amiri, Fazel Shokri

{"title":"Comparative assessment of four virus neutralization assays for detection of SARS-CoV-2 neutralizing antibodies.","authors":"Faezeh Maghsood, Navid Dashti, Tannaz Bahadori, Forough Golsaz-Shirazi, Christiane Moog, Mohammad Mehdi Amiri, Fazel Shokri","doi":"10.1016/j.ab.2025.115860","DOIUrl":"https://doi.org/10.1016/j.ab.2025.115860","url":null,"abstract":"<p><p>Neutralizing antibodies (NAbs) targeting receptor-binding domain (RBD) or spike of SARS-CoV-2 play an important role in blocking virus entry to the host cells and detecting their levels is critical for the assessment of humoral protective immune response following vaccination or recovery from SARS-CoV-2 infection. Here, we compared the performance of four virus neutralization tests to measure neutralizing antibodies in various sample types. We analyzed 25 serum samples obtained from mice or rabbits immunized with different vaccine platforms, and also 11 mouse anti-RBD monoclonal antibodies (MAbs) using surrogate virus neutralization test (SVNT), pseudovirus neutralization test (PVNT), conventional virus neutralization test (CVNT), and one-step or two-step inhibition flowcytometry virus neutralization test (IFVNT). All four VNTs showed significant correlations with each other, though PVNT and CVNT displayed significantly lower limit of detection (LoD) compared to the other two assays. In conclusion, our findings indicate that all four VNT assays give valid and accurate results and could be employed to determine the level of SARS-CoV-2 neutralizing monoclonal and polyclonal antibodies.</p>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":" ","pages":"115860"},"PeriodicalIF":2.6,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787545","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

A predictive model for MGMT promoter methylation status in glioblastoma based on terahertz spectral data

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-29 DOI: 10.1016/j.ab.2025.115850

Minghui Du , Xianhao Wu , Zhiyan Sun , Rui Tao , Peiyuan Sun , Shaowen Zheng , Zhaohui Zhang , Tianyao Zhang , Xiaoyan Zhao , Pei Yang

引用次数: 0

Development of Pt/Au/PPy-COOH multisegmental nanowires modified label-free impedimetric immunosensor to determine mucin 1 (MUC1)

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-28 DOI: 10.1016/j.ab.2025.115857

Baha Öndeş, Deniz Aktaş Uygun

{"title":"Development of Pt/Au/PPy-COOH multisegmental nanowires modified label-free impedimetric immunosensor to determine mucin 1 (MUC1)","authors":"Baha Öndeş, Deniz Aktaş Uygun","doi":"10.1016/j.ab.2025.115857","DOIUrl":"10.1016/j.ab.2025.115857","url":null,"abstract":"<div><div>In this study, a label-free nanowire-based impedimetric immunosensor was developed for the purpose of determining cancer biomarkers mucin 1 (MUC1). Nanowires were selected for sensor modification due to their high catalytic properties and high enzyme loading capacity. The synthesis, characterization, and application of Pt/Au/PPy-COOH nanowires to modify SPE electrodes were conducted. The nanowire-based immunosensors developed as a result of this research demonstrated a broad linear working range for MUC1 (20–3000 fg/mL), a low LOD value (0.244 fg/mL), and a low LOQ value (0.815 fg/mL). The nanowire-based immunosensor exhibited several notable characteristics. Firstly, it demonstrated excellent reproducibility, selectivity, and long-term stability. Furthermore, it demonstrated notable regenerative capabilities. It is noteworthy that the sensor exhibited the capability to detect MUC1 in commercial human serum samples, even in the presence of interfering agents. The affordability, simplicity, and expeditious analysis of nanowire-based immunosensors render them more appealing than alternative commercial kits. Consequently, these sensors hold considerable promise for clinical applications.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115857"},"PeriodicalIF":2.6,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143746500","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

One-step cascade method via glucose oxidase-copper ion complex for detecting glucose using a portable device

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-28 DOI: 10.1016/j.ab.2025.115856

Qingxi Wu, Hongxuan Zhang, Li Fu, Li Jia

{"title":"One-step cascade method via glucose oxidase-copper ion complex for detecting glucose using a portable device","authors":"Qingxi Wu, Hongxuan Zhang, Li Fu, Li Jia","doi":"10.1016/j.ab.2025.115856","DOIUrl":"10.1016/j.ab.2025.115856","url":null,"abstract":"<div><div>In this study, a one-step cascade fluorescence method was developed for the detection of glucose in honey, based on the glucose oxidase-copper ion complexes (GOx@Cu<sup>2+</sup>). These complexes exhibit dual enzymatic activities—glucose oxidase and peroxidase-like activities—which enable them to catalyze a cascade reaction. This reaction involves the oxidation of glucose and <em>o</em>-phenylenediamine (OPD), leading to the formation of 2,3-diaminophenazine (oxOPD), a compound with fluorescent properties. The proposed method overcomes the challenges of pH mismatch between enzymes and streamlines the testing process, eliminating the need for nanomaterial preparation and reducing the detection time to just 20 min. The feasibility of the method was validated by analyzing three honey samples, achieving recoveries between 96.4 % and 106 %, with relative standard deviations of less than 1.9 %. The selectivity and accuracy of the method were verified by capillary electrophoresis in three honey samples. Moreover, a self-designed portable device was introduced to enable on-site glucose detection.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115856"},"PeriodicalIF":2.6,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143738747","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

scCorrect: Cross-modality label transfer from scRNA-seq to scATAC-seq using domain adaptation

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-27 DOI: 10.1016/j.ab.2025.115847

Yan Liu , Wenyi Pei , Li Chen , Yu Xia , He Yan , Xiaohua Hu

{"title":"scCorrect: Cross-modality label transfer from scRNA-seq to scATAC-seq using domain adaptation","authors":"Yan Liu , Wenyi Pei , Li Chen , Yu Xia , He Yan , Xiaohua Hu","doi":"10.1016/j.ab.2025.115847","DOIUrl":"10.1016/j.ab.2025.115847","url":null,"abstract":"<div><div>Cell type annotation in single-cell chromatin accessibility sequencing (scATAC-seq) is crucial for enabling researchers to identify subpopulations of cells associated with specific diseases, elucidate gene regulatory networks, and discover markers indicative of disease states. The prevailing approach for cell type annotation in single-cell research involves transferring well-delineated cell types from single-cell RNA sequencing (scRNA-seq) data to scATAC-seq data using a label propagation algorithm. However, the inherent modal discrepancies (i.e.biological interpretation) between scRNA-seq and scATAC-seq data, coupled with the intrinsic sparsity and high dimensionality of scATAC-seq data, pose significant challenges to the efficacy of this strategy. To address these challenges, we introduce a novel neural network framework, scCorrect, which operates in two distinct phases. In the first phase, scCorrect aligns the scRNA-seq and scATAC-seq datasets, generating initial annotation results. The second phase involves training a corrective network specifically designed to amend any erroneous annotations produced during the first phase. Empirical tests across multiple datasets have demonstrated that scCorrect consistently achieves superior recognition accuracy, underscoring its significant potential to enhance disease-related research in humans.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115847"},"PeriodicalIF":2.6,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741996","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

Chitosan-stabilized copper oxide nanoparticles: A novel colorimetric approach for ascorbic acid sensing

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-27 DOI: 10.1016/j.ab.2025.115855

Nazish Kanwal , Mansoor Khan , Saeed Ahmad Khan , Ahmed Bari , Essam A. Ali , Wei Sun , Tanzila Rehman , Umar Nishan , Amir Badshah

{"title":"Chitosan-stabilized copper oxide nanoparticles: A novel colorimetric approach for ascorbic acid sensing","authors":"Nazish Kanwal , Mansoor Khan , Saeed Ahmad Khan , Ahmed Bari , Essam A. Ali , Wei Sun , Tanzila Rehman , Umar Nishan , Amir Badshah","doi":"10.1016/j.ab.2025.115855","DOIUrl":"10.1016/j.ab.2025.115855","url":null,"abstract":"<div><div>Ascorbic acid is implicated in various diseases such as scurvy, oxidative stress, cardiovascular diseases, etc. Herein, for the first time, a simple and efficient strategy was used to synthesize cross-linked chitosan-stabilized copper oxide nanoparticles (CuO@C-CS) as a non-toxic and biodegradable-based approach. Various spectroscopic techniques, including FTIR, XRD, SEM, EDX, TGA, and elemental mapping, confirmed the synthesis of the material. The synthesized nanozyme (CuO@C-CS) was used as a peroxidase mimic for the detection of ascorbic acid, through the chromogenic substrate 3,3′,5,5′-tetramethylbenzidine (TMB) with the assistance of hydrogen peroxide. The synthesized mimic enzyme transforms colorless TMB into oxTMB. The sensing of ascorbic acid was achieved through the peroxidase-like inhibitory activity of the mimic enzyme along with the reduction of oxTMB. The sensor system was fine-tuned, and it showed a limit of detection, a limit of quantification, a linear range, and regression coefficient values of 0.24 μM, 0.80 μM, 1–96 μM, and 0.999, respectively. The fabricated sensor was very selective in the presence of various potential interferents. The proposed sensor was successfully applied to commercially available orange juices for the qualitative and quantitative determination of ascorbic acid. The sensor can be used for the determination of ascorbic acid in biomedical and food samples.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115855"},"PeriodicalIF":2.6,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724182","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

Novel network construction algorithm for the study of similarity and differential mechanisms between different clinical treatments: From key metabolites to the related genes for personalized therapy of breast cancer

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-26 DOI: 10.1016/j.ab.2025.115852

Xin Huang , Hanjun Cai , Xinyu He , Yong Wang , Yang Zhou

{"title":"Novel network construction algorithm for the study of similarity and differential mechanisms between different clinical treatments: From key metabolites to the related genes for personalized therapy of breast cancer","authors":"Xin Huang , Hanjun Cai , Xinyu He , Yong Wang , Yang Zhou","doi":"10.1016/j.ab.2025.115852","DOIUrl":"10.1016/j.ab.2025.115852","url":null,"abstract":"<div><div>Breast cancer (BC) is the most common diagnosed cancer in the female population. Different near-infrared (NIR)-based technologies have been generally applied for BC clinical treatment. In this study, a novel network construction algorithm based on molecular vertical relationship (NCVR) was proposed to identify key network signals for clinical personalized treatment. In NCVR, the molecular vertical relationship that can be characterized in simple terms was proposed for network construction, thereby facilitating to better advance clinical decision making. To effectively measure the discriminative ability of molecular vertical relationship between different physiological and pathological stages, the joint probability mass function was constructed using sample frequency which can reduce the influence of sample variability caused by individual differences and the probability of over fitting caused by the high complexity of molecular expression data. NCVR was successfully employed to analyze the similarities and differences of living organisms treated by different treatment patterns (i.e., NIR and apoferritin-conjugated cypate (Cy@AFT) + NIR) on BC. The results of similarity analysis indicated that the reprogramming of cellular lipid and energy metabolism may be responsible for the BC cell death induced by treatments. Experimental results of difference analysis suggested that the disruptions in cholesterol metabolism, ferroptosis and severe lipid metabolism imbalances etc. contribute to the enhanced effectiveness of BC treatment with Cy@AFT + NIR. Then, analysis results of genes related to the selected key metabolites further provided deep insights into pathological alterations associated with BC development and illustrated why the performance of Cy@AFT + NIR therapy is better than that of NIR therapy.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115852"},"PeriodicalIF":2.6,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143725015","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

Low-speed centrifugation based isolation and self-priming mediated chain extension based fluorescent quantification of Pseudomonas aeruginosa

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-26 DOI: 10.1016/j.ab.2025.115853

Lili Pian, Duoduo Liu, Dongmiao Chen, Tingting Shen, Congrong Wang

{"title":"Low-speed centrifugation based isolation and self-priming mediated chain extension based fluorescent quantification of Pseudomonas aeruginosa","authors":"Lili Pian, Duoduo Liu, Dongmiao Chen, Tingting Shen, Congrong Wang","doi":"10.1016/j.ab.2025.115853","DOIUrl":"10.1016/j.ab.2025.115853","url":null,"abstract":"<div><div>Infections acquired at home and hospital are rather prevalent, and the incidence of these infections has been on the rise in recent years due to the growing elderly population. Infections caused by <em>Pseudomonas aeruginosa</em> (<em>P. aeruginosa</em>) pose a significant risk to human health and are prevalent among patients in hospitals and nursing homes. Consequently, it is imperative to devise an innovative and fluorescent method for analyzing <em>P. aeruginosa</em> to facilitate the early identification of home-acquired pneumonia. However, it is difficult to isolate and simultaneously quantify <em>P. aeruginosa</em> using most of the currently available methods. We present a novel platform that combines aptamer recognition-based aggregation of target bacteria with self-priming induced chain extension for signal amplification. This approach facilitates low-speed centrifugation-based isolation and simultaneous quantification of <em>P. aeruginosa</em>. The chain displacement procedure is incorporated for signal amplification, providing the approach with a broad detection range of six orders of magnitude and a low detection limit of 2.4 cfu/mL. In addition to its exceptional sensitivity, the method demonstrates commendable selectivity for the detection of <em>P. aeruginosa</em>, rendering it a viable instrument for identifying home-acquired pneumonia caused by <em>P. aeruginosa</em> and facilitating the early management of <em>P. aeruginosa</em> infections in the emergency department.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115853"},"PeriodicalIF":2.6,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741995","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

MIP-based electrochemical sensor with machine learning for accurate ZIKV detection in protein- and glucose-rich urine

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-26 DOI: 10.1016/j.ab.2025.115854

Wannisa Sukjee , Pichai Sirisangsawang , Chutima Thepparit , Prasert Auewarakul , Tasawan Puttasakul , Chak Sangma

{"title":"MIP-based electrochemical sensor with machine learning for accurate ZIKV detection in protein- and glucose-rich urine","authors":"Wannisa Sukjee , Pichai Sirisangsawang , Chutima Thepparit , Prasert Auewarakul , Tasawan Puttasakul , Chak Sangma","doi":"10.1016/j.ab.2025.115854","DOIUrl":"10.1016/j.ab.2025.115854","url":null,"abstract":"<div><div>Nowadays, a multitude of biosensors are being developed worldwide. However, a significant challenge arises when these biosensors are tested in real sample environments, as many of them fail to perform as expected. This can lead to ambiguous results and raise concerns about their reliability. In many cases, further data analysis is required to enhance the clarity and meaningfulness of the outputs. In this study, we investigated the acrylamide-methacrylic acid-methyl methacrylate-vinylpyrrolidone copolymer for fabrication of molecularly imprinted polymers, aimed at developing electrochemical sensors for the direct detection Zika virus in urine. Here, Zika virus detection by the biosensor in three types of urine possibly found in clinical samples including normal, high glucose (glucose >540 mg/dL) and high protein urines (protein >100 mg/dL). The results show that the signal obtained from normal urine increased with virus concentration, while it decreased in urine with high glucose or high protein level. Support vector machine was introduced to unify two opposite trends and resolve ambiguity of the data. It was able to sift through the noise and extract valuable information, thereby improving the reliability and achieved 91 % accuracy in detecting the analyte spiked into real patient samples.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115854"},"PeriodicalIF":2.6,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143738746","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

A site-specific fluorogenic probe for protein disulfide isomerase A1

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-25 DOI: 10.1016/j.ab.2025.115851

Yuli Zhuang , Danqi Hong , Wenjie Lang , Yinyan Xuan , Liquan Zhu , Jingyan Ge

{"title":"A site-specific fluorogenic probe for protein disulfide isomerase A1","authors":"Yuli Zhuang , Danqi Hong , Wenjie Lang , Yinyan Xuan , Liquan Zhu , Jingyan Ge","doi":"10.1016/j.ab.2025.115851","DOIUrl":"10.1016/j.ab.2025.115851","url":null,"abstract":"<div><h3>Background</h3><div>Protein disulfide isomerase A1 (PDIA1) is essential for catalyzing disulfide bond isomerization, ensuring proper protein folding, and maintaining cellular homeostasis. Dysregulation of PDIA1 function is implicated in various diseases, emphasizing the need for tools to study its activity dynamically and specifically. Despite this need, current methods lack the sensitivity and robustness required for reliable detection of PDIA1 activity.(57)</div></div><div><h3>Results</h3><div>We synthesized a series of vinyl sulfone-based fluorescent probes capable of covalently binding to thiol groups, triggering fluorescence activation. Among these, the probe <strong>LS</strong> exhibited outstanding performance, achieving a ∼18-fold fluorescence intensity increase upon binding to PDIA1. <strong>LS</strong> showed high specificity for PDIA1 by selectively targeting the cysteine residue at position 397 in its active site. The probe demonstrated rapid fluorescence activation with significant intensity enhancement within a short time. Furthermore, <strong>LS</strong> featured consistent excitation and emission wavelengths, making it ideal for fluorescence-based detection. (84)</div></div><div><h3>Significance</h3><div>The strong targeting ability, rapid response, and stability of <strong>LS</strong> provide a powerful platform for real-time, dynamic monitoring of PDIA1 activity. This probe holds significant promise for exploring PDIA1's roles in physiological and pathological processes and advancing research in PDIA1-associated diseases using vinyl sulfone-based fluorescent probes.(46)</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115851"},"PeriodicalIF":2.6,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143705929","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