Analytical biochemistry最新文献

英文中文

In-gel refolding allows fluorescence detection of fully denatured GFPs after SDS-PAGE

IF 2.6 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Analytical biochemistry

Pub Date : 2025-04-05 DOI: 10.1016/j.ab.2025.115861

Misa Shiratori , Rio Tsuyuki , Miwako Asanuma , Saki Kawabata , Hiromasa Yoshioka , Kenji Ohgane

Green fluorescent proteins (GFPs) have been widely used as fusion tags, especially to visualize subcellular localization and dynamics of the fused partner proteins. Also, GFPs serve as fluorescent tags in size-exclusion chromatography and native-PAGE, facilitating the evaluation of expression levels and quality of the expressed fusion proteins. However, the fluorescent detection of GFPs is generally incompatible with denaturing SDS-polyacrylamide gel electrophoresis (PAGE), where the samples are heat-denatured before loading. Accordingly, detecting GFP-fused proteins after SDS-PAGE usually relies on western blotting with anti-GFP antibodies. To enable in-gel fluorescence detection of SDS-PAGE-separated GFPs, some protocols employ mild denaturing conditions to keep the GFPs intact. However, such mild denaturation sometimes results in partial denaturation of the proteins and irregular electrophoretic mobility that is not proportional to their molecular weights. Here, we demonstrate that the fully denatured GFPs can be refolded within the gel by cyclodextrin-mediated removal of SDS in the presence of 20 % methanol, enabling the in-gel fluorescence detection of the GFP-fused proteins. The protocol is compatible with subsequent total protein staining and western blotting. Although future studies are needed to clarify the scope and generality, the technique developed here would provide a simple, time- and cost-effective alternative to the immunodetection of GFPs.

{"title":"In-gel refolding allows fluorescence detection of fully denatured GFPs after SDS-PAGE","authors":"Misa Shiratori , Rio Tsuyuki , Miwako Asanuma , Saki Kawabata , Hiromasa Yoshioka , Kenji Ohgane","doi":"10.1016/j.ab.2025.115861","DOIUrl":"10.1016/j.ab.2025.115861","url":null,"abstract":"<div><div>Green fluorescent proteins (GFPs) have been widely used as fusion tags, especially to visualize subcellular localization and dynamics of the fused partner proteins. Also, GFPs serve as fluorescent tags in size-exclusion chromatography and native-PAGE, facilitating the evaluation of expression levels and quality of the expressed fusion proteins. However, the fluorescent detection of GFPs is generally incompatible with denaturing SDS-polyacrylamide gel electrophoresis (PAGE), where the samples are heat-denatured before loading. Accordingly, detecting GFP-fused proteins after SDS-PAGE usually relies on western blotting with anti-GFP antibodies. To enable in-gel fluorescence detection of SDS-PAGE-separated GFPs, some protocols employ mild denaturing conditions to keep the GFPs intact. However, such mild denaturation sometimes results in partial denaturation of the proteins and irregular electrophoretic mobility that is not proportional to their molecular weights. Here, we demonstrate that the fully denatured GFPs can be refolded within the gel by cyclodextrin-mediated removal of SDS in the presence of 20 % methanol, enabling the in-gel fluorescence detection of the GFP-fused proteins. The protocol is compatible with subsequent total protein staining and western blotting. Although future studies are needed to clarify the scope and generality, the technique developed here would provide a simple, time- and cost-effective alternative to the immunodetection of GFPs.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115861"},"PeriodicalIF":2.6,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143800049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of Radioligand Binding Assays for REV-ERBα and REV-ERBβ.

IF 2.6 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Analytical biochemistry

Pub Date : 2025-04-04 DOI: 10.1016/j.ab.2025.115858

Thomas Koelblen, Elise P Burris, Thomas P Burris

REV-ERBα and REV-ERBβ are atypical nuclear receptors that function as ligand-dependent repressors of transcription. They play critical roles in the regulation of the circadian rhythm, inflammation, and metabolism. The natural ligand for the REV-ERBs is heme, and synthetic ligands (both agonists and antagonists) have been designed and utilized to probe the potential clinical utility of targeting REV-ERBs for drug development. Although biochemical assays that can detect REV-ERB ligands have been developed based on protein-protein interactions, no classical fluorescent- or radioligand-binding assay has yet been developed that directly detects ligand binding. Here, we describe the development of the first radioligand binding assay (RLBA) using scintillation proximity assay (SPA) technology for both REV-ERBα and REV-ERBβ using labeled STL1267, a potent REV-ERBα/β agonist we recently described. ³H-STL1267 displayed saturable binding to the ligand binding domains of both REV-ERBα and REV-ERBβ with equilibrium dissociation constants (K_ds) of 392 nM and 202 nM, respectively. In competition radioligand binding assays, we used unlabeled STL1267 or the well-characterized first-generation REV-ERB agonist SR9009 as competitors to ³H-STL1267 binding. STL1267 displayed K_is for REV-ERBα and REV-ERBβ of 253±30 nM and 98±14 nM, respectively. As expected, SR9009 displayed considerably lower potency than STL1267, with a K_i of 692±209 nM for REV-ERBα and 2546±127 nM for REV-ERBβ. Although developing an RLBA has been challenging due to the lack of high-affinity ligands that can be used as probes, our results demonstrate the feasibility of such an assay for both receptors, providing a robust assay with utility for ligand/drug discovery.

{"title":"Development of Radioligand Binding Assays for REV-ERBα and REV-ERBβ.","authors":"Thomas Koelblen, Elise P Burris, Thomas P Burris","doi":"10.1016/j.ab.2025.115858","DOIUrl":"https://doi.org/10.1016/j.ab.2025.115858","url":null,"abstract":"<p><p>REV-ERBα and REV-ERBβ are atypical nuclear receptors that function as ligand-dependent repressors of transcription. They play critical roles in the regulation of the circadian rhythm, inflammation, and metabolism. The natural ligand for the REV-ERBs is heme, and synthetic ligands (both agonists and antagonists) have been designed and utilized to probe the potential clinical utility of targeting REV-ERBs for drug development. Although biochemical assays that can detect REV-ERB ligands have been developed based on protein-protein interactions, no classical fluorescent- or radioligand-binding assay has yet been developed that directly detects ligand binding. Here, we describe the development of the first radioligand binding assay (RLBA) using scintillation proximity assay (SPA) technology for both REV-ERBα and REV-ERBβ using labeled STL1267, a potent REV-ERBα/β agonist we recently described. <sup>3</sup>H-STL1267 displayed saturable binding to the ligand binding domains of both REV-ERBα and REV-ERBβ with equilibrium dissociation constants (K<sub>d</sub>s) of 392 nM and 202 nM, respectively. In competition radioligand binding assays, we used unlabeled STL1267 or the well-characterized first-generation REV-ERB agonist SR9009 as competitors to <sup>3</sup>H-STL1267 binding. STL1267 displayed K<sub>i</sub>s for REV-ERBα and REV-ERBβ of 253±30 nM and 98±14 nM, respectively. As expected, SR9009 displayed considerably lower potency than STL1267, with a K<sub>i</sub> of 692±209 nM for REV-ERBα and 2546±127 nM for REV-ERBβ. Although developing an RLBA has been challenging due to the lack of high-affinity ligands that can be used as probes, our results demonstrate the feasibility of such an assay for both receptors, providing a robust assay with utility for ligand/drug discovery.</p>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":" ","pages":"115858"},"PeriodicalIF":2.6,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794462","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

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

IF 2.6 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

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

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.

针对 SARS-CoV-2 受体结合域（RBD）或尖峰的中和抗体（NAbs）在阻止病毒进入宿主细胞方面发挥着重要作用，检测其水平对于评估疫苗接种后或 SARS-CoV-2 感染恢复后的体液保护性免疫反应至关重要。在这里，我们比较了四种病毒中和试验在不同样本类型中测量中和抗体的性能。我们使用代病毒中和试验（SVNT）、伪病毒中和试验（PVNT）、传统病毒中和试验（CVNT）和一步或两步抑制流式细胞术病毒中和试验（IFVNT）分析了 25 份使用不同疫苗平台免疫的小鼠或家兔血清样本和 11 份小鼠抗 RBD 单克隆抗体（MAbs）。所有四种病毒中和检测方法都显示出明显的相关性，但 PVNT 和 CVNT 的检测限（LoD）明显低于其他两种检测方法。总之，我们的研究结果表明，所有四种 VNT 检测方法都能得出有效而准确的结果，可用于确定 SARS-CoV-2 中和单克隆抗体和多克隆抗体的水平。

{"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":"10.1016/j.ab.2025.115860","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 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 Q2 BIOCHEMICAL RESEARCH METHODS

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

O⁶-methylguanine-DNA methyltransferase (MGMT) promoter methylation is a crucial biomarker in glioblastoma (GBM) that influences response to temozolomide. Traditional detection methods, such as gene sequencing, are time-consuming and limited to postoperative analysis. This study explores the use of terahertz time-domain spectroscopy (THz-TDS) combined with machine learning to predict MGMT methylation status intraoperatively. By analyzing 180 GBM tissue samples, a Random Forest model was developed, achieving an AUC of 0.862. The findings suggest that THz spectroscopy offers a rapid, intraoperative alternative to traditional MGMT methylation detection methods, potentially enhancing surgical decision-making and personalized treatment strategies in GBM.

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 Q2 BIOCHEMICAL RESEARCH METHODS

Analytical biochemistry

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

Baha Öndeş, Deniz Aktaş Uygun

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.

{"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 Q2 BIOCHEMICAL RESEARCH METHODS

Analytical biochemistry

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

Qingxi Wu, Hongxuan Zhang, Li Fu, Li Jia

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@Cu²⁺). 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 o-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.

{"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 Q2 BIOCHEMICAL RESEARCH METHODS

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

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.

{"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 Q2 BIOCHEMICAL RESEARCH METHODS

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

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.

{"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 Q2 BIOCHEMICAL RESEARCH METHODS

Analytical biochemistry

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

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

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.

{"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 Q2 BIOCHEMICAL RESEARCH METHODS

Analytical biochemistry

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

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

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 Pseudomonas aeruginosa (P. aeruginosa) 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 P. aeruginosa to facilitate the early identification of home-acquired pneumonia. However, it is difficult to isolate and simultaneously quantify P. aeruginosa 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 P. aeruginosa. 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 P. aeruginosa, rendering it a viable instrument for identifying home-acquired pneumonia caused by P. aeruginosa and facilitating the early management of P. aeruginosa infections in the emergency department.

{"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

下一页尾页

类型

全部化学•材料生命科学医学物理工程技术环境•农林材料科学地球科学法学管理学化学环境科学与生态学计算机科学教育学经济学农林科学人文科学生物学数学物理与天体物理心理学综合性期刊其他工业工程理学历史学农学文学信息工程

数据库

全部 ACS Publications Elsevier ieeexplore Springer The Royal Society of Chemistry Wiley

期刊

Analytical biochemistry

全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.

﹀