Analytical biochemistry最新文献_第3页

Molecularly imprinted polymers-ZnS quantum dots based composite sensor for optical detection of chlorogenic acid

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-14 DOI: 10.1016/j.ab.2025.115846

Himshweta , Neelam Verma , Nitu Trehan , Minni Singh

{"title":"Molecularly imprinted polymers-ZnS quantum dots based composite sensor for optical detection of chlorogenic acid","authors":"Himshweta , Neelam Verma , Nitu Trehan , Minni Singh","doi":"10.1016/j.ab.2025.115846","DOIUrl":"10.1016/j.ab.2025.115846","url":null,"abstract":"<div><div>Chlorogenic acid (CGA), a key phenolic acid found in coffee, fruits, vegetables, and herbs, has significant pharmacological activities, necessitating its accurate detection in complex matrices. In this study, an organic acrylate molecularly imprinted polymers-chitosan modified zinc sulphide quantum dots/polydopamine (MIPs-CS:ZnS QDs/PDA) based composite sensor for the detection of CGA has been designed. In MIPs shell, CGA served as template and 4-vinylpyridine and methacrylic acid as functional monomers, azobisisobutyronitrile acting as the initiator and ethylene glycol dimethacrylate as the cross-linker. Chitosan was incorporated to enhance the stability of ZnS QDs, while polydopamine was introduced during polymerization to improve adhesion and the selectivity of MIPs for CGA. Under ideal conditions, the composite sensor had shown a linear range of 0.02–11 μg/mL with detection limit of 8.9 × 10<sup>−3</sup> μg/mL. The composite sensor showed imprinting factor of 6.3, and response time of 12 min. The sensor demonstrated good selectivity towards CGA, in the presence of interfering agents. Composite sensor was successfully applied to detect CGA in plant extracts, coffee and fruit juices, with recovery ranges from 88.93 to 98.49 %. The MIPs-CS:ZnS QDs/PDA composite sensor offers a simple and robust approach for CGA detection in real samples without requiring pre-treatment.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115846"},"PeriodicalIF":2.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143632205","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

Sensitive electrochemiluminescent detection of hydroquinone using silver/luminol-functionalized carbon microspheres

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-12 DOI: 10.1016/j.ab.2025.115842

Hui Zhang, Ziqi Wang, Yahui Ji, Junfeng Li, Feifei Chen, Fangxin Du, Gen Liu

引用次数: 0

A simple, rapid, cost-effective and reliable molecular technique for early sex determination in Phoenix dactylifera

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-12 DOI: 10.1016/j.ab.2025.115843

Asmita Detroja, Jaykumar Koradiya, Munir Ibrahim, Avani Bhimani, Tirth Chetankumar Bhatt, Gaurav Sanghvi, Ashok Kumar Bishoyi

{"title":"A simple, rapid, cost-effective and reliable molecular technique for early sex determination in Phoenix dactylifera","authors":"Asmita Detroja, Jaykumar Koradiya, Munir Ibrahim, Avani Bhimani, Tirth Chetankumar Bhatt, Gaurav Sanghvi, Ashok Kumar Bishoyi","doi":"10.1016/j.ab.2025.115843","DOIUrl":"10.1016/j.ab.2025.115843","url":null,"abstract":"<div><div>The <em>Phoenix dactylifera</em> is an important horticultural cash crop in arid and semi-arid regions, known for its sweet, edible, nutritious fruit. Date palm is a diecious plant; females are commercially important to produce fruits, and males are required for pollination. Dates are easily segregated through seeds, then seed-raised plants revealed 50 % of each male and female plant. But a farmer needs a 95:5 ratio of female to male in the farming land. However, the gender of the plant can be identified four to five years after planting when it begins to flower, and there is no other method available for the identification of the gender. Hence, the present investigation focused on the development of techniques for the early sex determination of dates. Seventy-nine ISSR primers were used to analyze DNA from bulked female and male date palms. Among 79 markers, one marker, ISSR-49, has been selected and successfully validated in 105 female and 103 male date palm samples. The novel reliable biomarker (TG)8RC alone generates both female (400 bp) and male (600 bp) specific, unique amplicons. In conclusion, this investigation developed a simple, efficient, cost-effective technique that can discriminate the gender of date palms in a single PCR reaction within 5 h.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115843"},"PeriodicalIF":2.6,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630040","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

Colorimetric and fluorescent dual-modality assay for cell-free mitochondrial DNA copy number in saliva

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-11 DOI: 10.1016/j.ab.2025.115840

Jiaxu Wang, Zhengrong Lu, Zhanmin Liu, Qiming Chen

{"title":"Colorimetric and fluorescent dual-modality assay for cell-free mitochondrial DNA copy number in saliva","authors":"Jiaxu Wang, Zhengrong Lu, Zhanmin Liu, Qiming Chen","doi":"10.1016/j.ab.2025.115840","DOIUrl":"10.1016/j.ab.2025.115840","url":null,"abstract":"<div><div>Copy number of cell-free mitochondrial DNA (cf-mtDNA) has garnered significant attention as a biomarker for studying and diagnosing various diseases. However, Quantitative Real-time PCR (qPCR) and Droplet Digital PCR (ddPCR) assays for cf-mtDNA copy number detection require expensive equipment and high experiment conditions. In this study, a colorimetric and fluorescent dual-modality assay was developed for quantitative detection of cf-mtDNA copy number. With G-quadruplex (G4) sequence modified primers, the assay could quantitatively detect cf-mtDNA with spectrophotometry, RGB (Red, Green, Blue) visual method and fluorescence method, which made the application scenarios more diverse. The specificity of dual-mode method was better, and the detection limits of spectrophotometry, RGB visual method and fluorescence method were as low as 1.45 × 10<sup>−1</sup> copies/μL, 1.65 copies/μL and 1.58 × 10<sup>−1</sup> copies/μL, respectively. Compared with qPCR and ddPCR assays developed in previous studies, the dual-modality assay in this study had a lower detection limit. It was also independent of expensive qPCR and ddPCR equipment and the detection cost was low. Therefore, the colorimetric and fluorescent dual-modality assay represent a label-free and sensitive approach for assessing cf-mtDNA levels, offering promising implications for biomedical research and clinical diagnostics.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115840"},"PeriodicalIF":2.6,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143621459","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

Peptidomic and proteomic analysis of precision-cut lung slice supernatants

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-07 DOI: 10.1016/j.ab.2025.115837

Annika H. Hansen , Lasse G. Lorentzen , Diana J. Leeming , Jannie M.B. Sand , Per Hägglund , Michael J. Davies

{"title":"Peptidomic and proteomic analysis of precision-cut lung slice supernatants","authors":"Annika H. Hansen , Lasse G. Lorentzen , Diana J. Leeming , Jannie M.B. Sand , Per Hägglund , Michael J. Davies","doi":"10.1016/j.ab.2025.115837","DOIUrl":"10.1016/j.ab.2025.115837","url":null,"abstract":"<div><div>The precision-cut lung slice (PCLS) model is an <em>ex vivo</em> tissue system that has been used to model disease and examine the effects of exogenous compounds. Few studies have been carried out on the complement of proteins (proteome) and peptides (peptidome) secreted by PCLS and other tissue sections, during tissue culture, although such data are likely to provide critical information on the biology of tissue slices and the changes these undergo. In this study, a workflow was developed to examine the peptidome and proteome of PCLS supernatants using a modified single-pot, solid-phase-enhanced sample preparation (SP3) workflow. The performance of the SP3 workflow was evaluated in a head-to-head comparison against ultrafiltration by quantifying the recovery of synthetic peptide constructs. The SP3 workflow outperformed ultrafiltration in terms of recovery of small synthetic peptides regardless of the organic solvent used in SP3 (acetone or acetonitrile) and ultrafiltration molecular mass cut-off (2 or 10 kDa). The developed SP3 workflow provided robust data when analyzing PCLS supernatants across different conditions. The method allows, within a single workflow from individual samples, the identification of both large numbers of different native peptides (489) and also proteins (370) released from the tissue to the supernatants. This approach therefore has the capacity to provide both broad and in-depth peptidome and proteome data, with potential wide applicability to analyze the secretome of cultured tissue samples.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115837"},"PeriodicalIF":2.6,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584345","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

Quantification of MPT-64 within pleural fluid extracellular vesicles of tuberculous pleurisy patients by real-time immuno-PCR

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-07 DOI: 10.1016/j.ab.2025.115829

Promod K. Mehta , Aishwarya Soni , Bhawna Dahiya , Reetu Sheoran , Kiran Nehra , Mukesh Sharma

{"title":"Quantification of MPT-64 within pleural fluid extracellular vesicles of tuberculous pleurisy patients by real-time immuno-PCR","authors":"Promod K. Mehta , Aishwarya Soni , Bhawna Dahiya , Reetu Sheoran , Kiran Nehra , Mukesh Sharma","doi":"10.1016/j.ab.2025.115829","DOIUrl":"10.1016/j.ab.2025.115829","url":null,"abstract":"<div><div>Diagnosis of tuberculous (TB) pleurisy is an exigent task owing to atypical clinical presentations and low bacillary content in clinical samples. Hence, there is a crucial need to deliberate a quick and consistent diagnostic test. We recently quantified <em>Mycobacterium tuberculosis</em> (<em>Mtb</em>)-specific MPT-64 (Rv1980c) within pleural fluid extracellular vesicles (pEVs) of TB pleurisy patients by SYBR Green real-time immuno-PCR (RT-I-PCR) assay and compared its diagnostic efficacy with respective ELISA and GeneXpert assay. The size of pEVs of TB pleurisy patients ranged between 47.7 and 170.2 nm as evaluated by Nanoparticle tracking analysis and Transmission electron microscopy. Noticeably, a dynamic range (0.7 pg/mL-9.7 ng/mL) of <em>Mtb</em> MPT-64 was quantitatively detected within pEVs of TB pleurisy individuals by RT-I-PCR, albeit ELISA exhibited a thin range (2.5 ng/mL-11.2 ng/mL). Our RT-I-PCR demonstrated sensitivity of 80 % and 80.9 % in clinically suspected/probable (n = 35) and total (n = 42) TB pleurisy individuals, respectively, with 97.3 % specificity in 38 non-TB controls, against a composite reference standard. Concurrently, MPT-64 detection within pEVs of clinically suspected/probable TB pleurisy cases by ELISA and GeneXpert displayed substantially lower sensitivities (<em>p</em> < 0.05–0.01) than RT-I-PCR. After further improving the sensitivity and authenticating these RT-I-PCR results with a larger sample size, this assay may yield a promising diagnostic kit.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115829"},"PeriodicalIF":2.6,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584346","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

DHUpredET: A comparative computational approach for identification of dihydrouridine modification sites in RNA sequence

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-06 DOI: 10.1016/j.ab.2025.115828

Md Fahim Sultan , Tasmin Karim , Md Shazzad Hossain Shaon , Sayed Mehedi Azim , Iman Dehzangi , Mst Shapna Akter , Sobhy M. Ibrahim , Md Mamun Ali , Kawsar Ahmed , Francis M. Bui

{"title":"DHUpredET: A comparative computational approach for identification of dihydrouridine modification sites in RNA sequence","authors":"Md Fahim Sultan , Tasmin Karim , Md Shazzad Hossain Shaon , Sayed Mehedi Azim , Iman Dehzangi , Mst Shapna Akter , Sobhy M. Ibrahim , Md Mamun Ali , Kawsar Ahmed , Francis M. Bui","doi":"10.1016/j.ab.2025.115828","DOIUrl":"10.1016/j.ab.2025.115828","url":null,"abstract":"<div><div>Laboratory-based detection of D sites is laborious and expensive. In this study, we developed effective machine learning models employing efficient feature encoding methods to identify D sites. Initially, we explored various state-of-the-art feature encoding approaches and 30 machine learning techniques for each and selected the top eight models based on their independent testing and cross-validation outcomes. Finally, we developed DHUpredET using the extra tree classifier methods for predicting DHU sites. The DHUpredET model demonstrated balanced performance across all evaluation criteria, outperforming state-of-the-art models by 8 % and 14 % in terms of accuracy and sensitivity, respectively, on an independent test set. Further analysis revealed that the model achieved higher accuracy with position-specific two nucleotide (PS2) features, leading us to conclude that PS2 features are the best suited for the DHUpredET model. Therefore, our proposed model emerges as the most favorite choice for predicting D sites. In addition, we conducted an in-depth analysis of local features and identified a particularly significant attribute with a feature score of 0.035 for PS2_299 attributes. This tool holds immense promise as an advantageous instrument for accelerating the discovery of D modification sites, which contributes too many targeting therapeutic and understanding RNA structure.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115828"},"PeriodicalIF":2.6,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584343","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

Streptomycin-modified magnetic beads enable robust DNA extraction across diverse lysis conditions

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-05 DOI: 10.1016/j.ab.2025.115836

Yanwen Qi , Jiayu Zheng , Yingqiu Xie , Amr Amin , Bing Qiao , Chao Shi , Yong Li , Cuiping Ma

引用次数: 0

Ammonium bicarbonate buffer system for DNA hybridization and quantification by LC-ESI-MS/MS

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-05 DOI: 10.1016/j.ab.2025.115822

Zhuo Zhen Chen, Nan Cheng, Lloyd Johnson, Jaimie Dufresne, John G. Marshall

{"title":"Ammonium bicarbonate buffer system for DNA hybridization and quantification by LC-ESI-MS/MS","authors":"Zhuo Zhen Chen, Nan Cheng, Lloyd Johnson, Jaimie Dufresne, John G. Marshall","doi":"10.1016/j.ab.2025.115822","DOIUrl":"10.1016/j.ab.2025.115822","url":null,"abstract":"<div><div>High salt buffer may be used for the UV/VIS or radiometric based detection of trihybrid DNA but would contaminate the electrospray mass spectrometer. Colorimetric DNA hybridization assays with the substrate BCIP/NBT reacted with the alkaline phosphatase-streptavidin (APSA) enzyme conjugate that showed a linear range for HIV DNA from 1 pM to 100 pM DNA in presence of high salt concentrations. Ammonia bicarbonate (AMBIC) or ethanolamine resulted in strong DNA hybridization similar to NaCl but was compatible with specific and sensitive mass spectrometry. Linear and Gaussian analysis of HIV DNA with 10 % error was achieved across the pico Molar range from APSA amplification that converted the substrate AMP to adenosine for detection by monitoring the precursor ion at m/z 268 and plotting the fragment intensity at <em>m/z</em> 136 (<em>m/z</em> 268→ <em>m/z</em> 136) that was linear to 100 fM after log transformation. The novel observation that specific DNA hybridization in NaCl may be substituted with AMBIC permitted the direct analysis of a target DNA in femto molar to pico molar range by enzyme linked mass spectrometric assay (ELiMSA) using as little as 0.1 μL (100 nL) of sample reaction injected on column.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115822"},"PeriodicalIF":2.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584342","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

Glycosyltransferase enzymatic assays: Overview and comparative analysis

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-03-04 DOI: 10.1016/j.ab.2025.115826

Ghazal Khaled , Thierry Benvegnu , Khadija Amin , Sylvain Tranchimand , Hala Chamieh

{"title":"Glycosyltransferase enzymatic assays: Overview and comparative analysis","authors":"Ghazal Khaled , Thierry Benvegnu , Khadija Amin , Sylvain Tranchimand , Hala Chamieh","doi":"10.1016/j.ab.2025.115826","DOIUrl":"10.1016/j.ab.2025.115826","url":null,"abstract":"<div><div>Glycosyltransferases (GTs) are enzymes that catalyze the transfer of an activated sugar donor to a variety of acceptors including proteins, lipids, carbohydrates, and other small molecules. GTs participate in numerous cellular and physiological processes in both prokaryotic and eukaryotic cells. Those include prokaryotic cell wall biogenesis, eukaryotic post-translational protein modifications, extracellular matrix synthesis, cell signaling, biofilm formation and many others. As such, GTs are exploited as molecular therapeutical targets but also as synthetic tools for the development of polysaccharides and glycoconjugates. <em>In vitro</em> study of GTs activities is now essential to characterize the growing number of predicted GTs, available from sequenced genomes, in order to determine their specificities, their modes of action and their roles <em>in vivo</em>. However, characterization of glycosyltransferases <em>in vitro,</em> both on cellular extracts and on purified enzymes, faces significant challenges. Many methods are currently employed <em>i. e.</em> radiochemical techniques, spectrometric measurements, generally after coupling with∗ other reactions, and even more sophisticated strategies involving product separations by chromatography or/and electrophoresis, followed by detailed structural analysis by NMR or mass spectrometry. Here we overview the common methods deployed for the characterization of GTs. We highlight the challenges arising from these enzymes. The advantages and limitations of each of the presented techniques are also discussed.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115826"},"PeriodicalIF":2.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562353","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