Analytical biochemistry最新文献

Phylogenetic analysis of prevalent Mycobacterium species in Northeastern Iran based on hsp65 and tuf genes. 基于hsp65和tuf基因的伊朗东北部流行分枝杆菌的系统发育分析。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-14 DOI: 10.1016/j.ab.2025.115904

Roghayeh Mohammadzadeh, Nafiseh Izadi, Mojtaba Sankian, Mohammad Javad Najafzadeh, Hadi Farsiani

{"title":"Phylogenetic analysis of prevalent Mycobacterium species in Northeastern Iran based on hsp65 and tuf genes.","authors":"Roghayeh Mohammadzadeh, Nafiseh Izadi, Mojtaba Sankian, Mohammad Javad Najafzadeh, Hadi Farsiani","doi":"10.1016/j.ab.2025.115904","DOIUrl":"https://doi.org/10.1016/j.ab.2025.115904","url":null,"abstract":"<p><p>Phylogenetic analysis of Mycobacterium species can provide valuable insights into their evolutionary relationships and help to identify species and strains. In this study, two genetic markers, including the heat shock protein 65 (hsp65) gene and the elongation factor (EF)-Tu (tuf) gene were used for phylogenetic analysis of Mycobacterium species. Clinical samples were collected from patients suspected of tuberculosis. Bacterial isolates were obtained from sputum samples and cultured on Löwenstein-Jensen medium. Thirty Mycobacterium isolates (acid-fast +, culture +), were included in our study. After DNA extraction, hsp65 (441 bp) and tuf (741 bp) genes were PCR-amplified and sequenced. The Neighbor-Joining method was employed to infer the evolutionary history of the isolates and the analyses were conducted with MEGA X software. The phylogenetic trees were validated using bootstrap analysis with 1,000 replicates. Bootstrap values above 70% considered indicative of well support for the branches. The phylogenetic trees revealed the overall natural relationships among Mycobacterium species. Our results demonstrated that the tuf gene provides superior resolution for identifying distinct mycobacterial species, closely aligning its phylogenetic profile with the hsp65 gene. However, neither of the markers was effective in distinguishing members of the Mycobacterium tuberculosis complex (MTBC). This study highlights the high discriminatory power of the tuf gene, recommending its use as a primary genomic marker for phylogenetic analysis.</p>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":" ","pages":"115904"},"PeriodicalIF":2.6,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085691","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

Influence of experimental conditions on the adsorption of disease biomarker proteins to InP/ZnS quantum dots 实验条件对InP/ZnS量子点吸附疾病标志物蛋白的影响

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-12 DOI: 10.1016/j.ab.2025.115903

Nathaniel A. Gomez, Daniel Blumel, Davies Dueñas, Bronson Young, Matt Hazel, Ming Yu

{"title":"Influence of experimental conditions on the adsorption of disease biomarker proteins to InP/ZnS quantum dots","authors":"Nathaniel A. Gomez, Daniel Blumel, Davies Dueñas, Bronson Young, Matt Hazel, Ming Yu","doi":"10.1016/j.ab.2025.115903","DOIUrl":"10.1016/j.ab.2025.115903","url":null,"abstract":"<div><div>The spontaneous formation of quantum dot (QD)-protein assemblies in the physiological environment exhibits challenges or benefits for nanomedicine applications. In this study, we investigated the QD-protein assemblies spontaneously formed with the greener water soluble InP/ZnS–COOH QDs and isolated disease biomarker proteins under various environmental conditions, including QDs size, solution pH, incubation time, ionic strength, different salts, as well as the lowest concentrations of the proteins that started the formation of detectable assemblies. It was shown that higher ionic strength or valence charge disrupted the assembly's formation. The basic pH 8.5 facilitated the formation to a greater extent than the pH 7.4 did. The heat shock protein 90-alpha (HSP90α) adsorbed on QDs surface more readily than cytochrome C (CytoC) and lysozyme (Lyz) in the basic environment. Among the three-sized QDs compared, the medium-sized QDs were the most effective in promoting the assemblies' formation. The detectable assemblies started at as low as 0.4 ng/mL of CytoC, 1.0 ng/mL of HSP90α, or 1.8 ng/mL of Lyz, respectively. The findings add insights into how the biomarker proteins interacted with the QDs under different environmental conditions, which promotes the understanding of QD-protein assemblies' collaborative behaviors when they facilitate bioimaging and biomedicine applications.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"704 ","pages":"Article 115903"},"PeriodicalIF":2.6,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144069344","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

AFP-MCDF: Multi and cross-dimensional feature fusion methods for antifreeze protein prediction AFP-MCDF：用于抗冻蛋白预测的多维和跨维特征融合方法

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-08 DOI: 10.1016/j.ab.2025.115881

Jinfeng Li, Fan Zhang, Zhenguo Wen, Chun Fang

{"title":"AFP-MCDF: Multi and cross-dimensional feature fusion methods for antifreeze protein prediction","authors":"Jinfeng Li, Fan Zhang, Zhenguo Wen, Chun Fang","doi":"10.1016/j.ab.2025.115881","DOIUrl":"10.1016/j.ab.2025.115881","url":null,"abstract":"<div><div>Antifreeze proteins can effectively inhibit the formation of ice crystals and enhance cell survival in low-temperature environments. They protect the texture prolong the shelf life of food and maintain cell and tissue integrity in medical treatments, thereby improving the success rate of surgery and transplantation. Accurate prediction of Antifreeze proteins is important to advance these fields. Traditional wet-experiment methods, while providing reliable validation results, are usually time-consuming and costly. And existing computational methods still have room for improvement in predicting performance. In this study, a novel antifreeze protein prediction method, AFP-MCDF, is proposed. The AFP-MCDF method first extracts one- and two-dimensional feature representations of Antifreeze protein sequences using the pre-trained protein language models ProtBERT and ESM-2. Subsequently, these features are fused multidimensionally via BiLSTM and TextCNN to capture long-term dependencies and local features. Finally, the method predicts the frost resistance of Antifreeze protein sequences by cross-dimensional fusion and linear mapping from N to 2 dimensions. Experimental results show that AFP-MCDF performs well in the antifreeze protein prediction task, outperforming traditional computational methods and reaching the current state-of-the-art.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"704 ","pages":"Article 115881"},"PeriodicalIF":2.6,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143935882","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

Univariate versus multivariate approaches for resolving the overlapped spectra of azelastine hydrochloride and mometasone furoate 单变量与多变量方法分析盐酸氮唑elastine和糠酸莫米松的重叠光谱。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-08 DOI: 10.1016/j.ab.2025.115902

Alaa Reda , Hawa Khalil , Eman A. Bahgat , Michael Gamal Fawzy

{"title":"Univariate versus multivariate approaches for resolving the overlapped spectra of azelastine hydrochloride and mometasone furoate","authors":"Alaa Reda , Hawa Khalil , Eman A. Bahgat , Michael Gamal Fawzy","doi":"10.1016/j.ab.2025.115902","DOIUrl":"10.1016/j.ab.2025.115902","url":null,"abstract":"<div><div>Azelastine hydrochloride (AZE) and Mometasone furoate (MOM) combination is used to treat allergic rhinitis' symptoms. The aim of this work is to qualitatively and quantitatively analyze both medications using univariate and multivariate spectrophotometric techniques in a comparative study. Regarding univariate approaches; AZE was quantified by direct measurement at 291 nm within (5–60 μg/mL) concentration range. While, MOM was assayed by absorption correction (AC) approach at 250 nm within the range of (2–18 μg/mL). The LOD values for AZE and MOM were (0.79 μg/mL) and (0.21 μg/mL), respectively. Classical least squares (CLS), partial least squares (PLS), principal component regression (PCR), multivariate curve resolution-alternating least squares (MCR-ALS) and artificial neural networks (ANN) were the applied multivariate chemometric models. The proposed methods were utilized for analyzing the binary mixture in laboratory-synthetic mixtures and pharmaceutical preparation with correlation coefficients values ≥ 0.9996. No statistically significant variation was found between the applied methods and the reported HPLC one. The methods’ sustainability was assessed using blue applicability grade index (BAGI) and Red-Green-Blue 12 (RGB12) metrics. The obtained findings revealed that the suggested methodologies are safer option than the published HPLC technique for the conventional pharmaceutical analysis of the studied medications.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"704 ","pages":"Article 115902"},"PeriodicalIF":2.6,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958939","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

Absolute quantitation of neopterin as an endogenous pharmacodynamic Biomarker: The successful method development, validation, and use of a surrogate matrix for clinical sample analysis 新蝶呤作为内源性药效学生物标志物的绝对定量：成功的方法开发、验证和临床样品分析替代基质的使用

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-07 DOI: 10.1016/j.ab.2025.115893

Ryan De Palma, Murali Matta, Jeffry Florian, Vikram Patel, Rodney Rouse

{"title":"Absolute quantitation of neopterin as an endogenous pharmacodynamic Biomarker: The successful method development, validation, and use of a surrogate matrix for clinical sample analysis","authors":"Ryan De Palma, Murali Matta, Jeffry Florian, Vikram Patel, Rodney Rouse","doi":"10.1016/j.ab.2025.115893","DOIUrl":"10.1016/j.ab.2025.115893","url":null,"abstract":"<div><div>Biomarkers are playing an increasing role in the drug discovery and drug development process. Molecular biomarkers pose a bioanalytical challenge due to their low concentrations and endogenous presence. Inaccurate quantitation could lead to biased study results. Surrogate analyte and surrogate matrix approaches can be used to overcome the lack of a blank matrix and provide accurate quantitation. However, the suitability of the surrogate analyte or matrix must be established during method validation. Here we describe the development and validation of a surrogate matrix approach for the absolute quantitation of neopterin as a PD biomarker for use in an FDA-sponsored clinical study (NCT04183491). Matrix suitability was established through parallelism, precision and accuracy, and internal standard response. Parallelism experiments showed FBS, and serum had identical slopes 0.0145. Additionally, the difference in the X-intercepts was able to accurately predict the amount of endogenous neopterin (1.0 ng/mL). Inter-day accuracy across four surrogate QC levels ranged from 92.08 to 109.06 % while precision ranged from 3.36 to 16.00 %. Inter-day accuracy for the QCs in study matrix ranged from 96.81 to 108.86 % and precision ranged from 4.13 to 6.01 %. The internal standard response in FBS was only 6.9 % different from serum. Additionally, there was no matrix effect, injection carryover, or cross-analyte interference observed. The method was then qualified for automated sample processing.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"704 ","pages":"Article 115893"},"PeriodicalIF":2.6,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143935884","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

Identifying transglutaminase substrate glutaminyls using dansylcadaverine

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-07 DOI: 10.1016/j.ab.2025.115888

Thomas M. Jeitner , Pradeep K. Singh , Juan Azcona , Chad W. Euler , James M. Kelly

引用次数: 0

Double alkylation with maleimide-PEG-biotin: An enrichment method for cysteine redox states 马来酰亚胺-聚乙二醇-生物素双烷基化：半胱氨酸氧化还原态的富集方法

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-06 DOI: 10.1016/j.ab.2025.115892

Jung Mi Lim , Rodney L. Levine

引用次数: 0

Polyaniline-graphene oxide (PANI/GO)-grafted paper-based nanosensor for the detection of Helicobacter pylori 聚苯胺-氧化石墨烯接枝纸基幽门螺杆菌检测传感器

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-05 DOI: 10.1016/j.ab.2025.115891

Rachna Poria , Desmond Lutomia , Ankur Kaushal , Selva Kumar Ramasamy , Shagun Gupta

{"title":"Polyaniline-graphene oxide (PANI/GO)-grafted paper-based nanosensor for the detection of Helicobacter pylori","authors":"Rachna Poria , Desmond Lutomia , Ankur Kaushal , Selva Kumar Ramasamy , Shagun Gupta","doi":"10.1016/j.ab.2025.115891","DOIUrl":"10.1016/j.ab.2025.115891","url":null,"abstract":"<div><div>A polyaniline-graphene oxide (PANI-GO) nanocomposite-grafted DNA biosensor for detecting <em>Helicobacter pylori</em>-specific toxins, oncoprotein cytotoxin-associated gene A (<em>CagA</em>), has been reported. The nanocomposite was fabricated on Screen printed paper electrode (SPPE) and modified with a 5′NH<sub>2</sub>-labelled single-stranded DNA (ssDNA) probe specific to the <em>CagA</em> gene via an EDC/NHS cross-linker. Under optimized electrochemical experimental conditions, CV and DPV were used to analyse the performance of the developed biosensor. A linear dynamic range for <em>H. pylori</em> ssDNA was established between 0.00001 ng/μl and 0.1 ng/μl, with correlation coefficients of R<sup>2</sup> = 0.9813 for the CV and R<sup>2</sup> = 0.9343 for the DPV. The sensitivities of the developed sensor in the CV studies were 50.261 μA μL/ng∙mm<sup>2</sup> and 66.5 μA μL/ng∙mm<sup>2</sup> in the DPV studies. CV demonstrated an LOD of 0.0026 ng/μL, whereas the LOD of the DPV studies was 0.001 ng/μL. The developed sensor was validated using different concentrations of <em>H. pylori</em> ssDNA spiked in human stool samples. The results highlight the potential of the developed biosensor to detect and quantify <em>H. pylori</em> genomic DNA in a sensitive and reliable manner to aid in clinical diagnostics and pathogen detection applications.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"704 ","pages":"Article 115891"},"PeriodicalIF":2.6,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143923103","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 beginners guide to SELEX and DNA aptamers SELEX和DNA适体的初学者指南

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-02 DOI: 10.1016/j.ab.2025.115890

Cameron Stephens, Nina M. Goodey, Ueli Gubler

{"title":"A beginners guide to SELEX and DNA aptamers","authors":"Cameron Stephens, Nina M. Goodey, Ueli Gubler","doi":"10.1016/j.ab.2025.115890","DOIUrl":"10.1016/j.ab.2025.115890","url":null,"abstract":"<div><div>SELEX stands for \"Systematic Evolution of Ligands by Exponential Enrichment.” It is an <em>in vitro,</em> iterative, PCR-based, target-specific selection strategy used to generate single-stranded DNA (ssDNA) aptamers that bind a target of interest. Properly selected aptamers bind their targets with high affinity and specificity and have utility in a multitude of detection assays. They are thus similar to antibodies but have the advantage of being more stable and cheaper to produce. The SELEX process encompasses several steps, some of which are critical to the successful isolation of an aptamer. Careful analysis and optimization of the SELEX process are thus important. This review summarizes our own experience when we, as complete novices, were setting up the SELEX system in our lab. It is thus meant to give some general and practical but concise pointers for anyone interested in initiating their own SELEX experiments. As such, the review covers key elements of the SELEX process, including library design, target selection and immobilization strategies, aptamer binding conditions, partitioning techniques, and PCR optimization. We also discuss common pitfalls such as by-product formation and single-stranded DNA recovery challenges, along with practical strategies to overcome them. Emerging trends and post-SELEX considerations, such as sequencing, structure prediction, and chemical modifications, are included to guide beginners through every stage of aptamer development.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"703 ","pages":"Article 115890"},"PeriodicalIF":2.6,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912286","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

Inhibition of DNA glycoxidation by mannitol and Pyridoxamine: Implications for DNA-antibody development in diabetes and diabetic retinopathy 甘露醇和吡哆胺对DNA糖氧化的抑制作用：对糖尿病和糖尿病视网膜病变中DNA抗体发展的影响

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-02 DOI: 10.1016/j.ab.2025.115886

Rihab Akasha , Uzma Shahab , Ramendra Pati Pandey , Saif Khan , Paridhi Puri , Zeeshan Rafi , Sultan Alouffi , Saheem Ahmad

{"title":"Inhibition of DNA glycoxidation by mannitol and Pyridoxamine: Implications for DNA-antibody development in diabetes and diabetic retinopathy","authors":"Rihab Akasha , Uzma Shahab , Ramendra Pati Pandey , Saif Khan , Paridhi Puri , Zeeshan Rafi , Sultan Alouffi , Saheem Ahmad","doi":"10.1016/j.ab.2025.115886","DOIUrl":"10.1016/j.ab.2025.115886","url":null,"abstract":"<div><div>Chronic exposure to reactive carbonyl species such as glyoxal and methylglyoxal, along with hydroxyl radicals (<sup>•</sup>OH), leads to glycative and oxidative damage, contributing to insulin resistance and diabetic complications. Pyridoxamine (PM) is known to counteract these effects, but its potential synergy with mannitol (MN), a hydroxyl radical scavenger, remains unexplored. This study investigates the combined efficacy of MN and PM in preventing glycation and oxidative damage in vitro.</div><div>Calf thymus DNA was subjected to glycation using 10 mM glyoxal, oxidation via the Fenton reaction, and sequential glycoxidation (glycation followed by oxidation). The inhibitory effects of MN, PM, and their combination were assessed using NBT reduction for early glycation, GK-ribose for AGEs, TBARS for hydroxyl radicals, and spectroscopic analyses for AGEs formation. A clinical study also examined autoantibody prevalence in diabetes and diabetic retinopathy (DR).</div><div>Results showed that glycoxidated DNA exhibited structural alterations, with MN and PM individually reducing ketoamine content. Their combination further enhanced glycation and glycoxidation inhibition. Additionally, MN-PM co-administration synergistically reduced AGEs and hydroxyl radicals. Autoantibody levels were elevated in diabetes and DR. These findings suggest PM-MN co-administration as a promising strategy to mitigate diabetic complications.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"703 ","pages":"Article 115886"},"PeriodicalIF":2.6,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912297","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