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}
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}
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}
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}
Yanwen Qi , Jiayu Zheng , Yingqiu Xie , Amr Amin , Bing Qiao , Chao Shi , Yong Li , Cuiping Ma
{"title":"Streptomycin-modified magnetic beads enable robust DNA extraction across diverse lysis conditions","authors":"Yanwen Qi , Jiayu Zheng , Yingqiu Xie , Amr Amin , Bing Qiao , Chao Shi , Yong Li , Cuiping Ma","doi":"10.1016/j.ab.2025.115836","DOIUrl":"10.1016/j.ab.2025.115836","url":null,"abstract":"<div><div>Here, we describe the applicability of a variety of functionalized magnetic beads (MBs) for DNA extraction under different lysis conditions. Various MBs, including hydroxyl, carboxylic, amino, chitosan-modified, and streptomycin-modified MBs (MBs-STR), were compared based on their extracted DNA quantity and quality. The results presented that the MBs exhibited different DNA adsorption capacities under specific conditions. Notably, MBs-STR maintained stable DNA adsorption capacity upon different conditions through a non-intercalative binding mechanism between STR and DNA minor groove. This discovery advances antibiotic-based DNA extraction strategies, offering a flexible, efficient alternative for biomedical applications while enriching the toolkit for nucleic acid isolation.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115836"},"PeriodicalIF":2.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143577092","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}
{"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}
Samira Nekooei , Mehrorang Ghaedi , Mohammad Reza Baezzat , Javad Tashkhourian , Mika Sillanpää
{"title":"Electrochemical aptasensor for determination of testosterone using an aptamer-nanogold-metal-organic framework-ionic liquid modified carbon paste electrode","authors":"Samira Nekooei , Mehrorang Ghaedi , Mohammad Reza Baezzat , Javad Tashkhourian , Mika Sillanpää","doi":"10.1016/j.ab.2025.115827","DOIUrl":"10.1016/j.ab.2025.115827","url":null,"abstract":"<div><div>The present study is based on the design and construction of a selective label-free electrochemical aptasensor for testosterone (TST) detection in real samples. A carbon paste electrode modified with gold nanoparticles and metal-organic framework-ionic liquid (AuNPs/Fe<sub>3</sub>O<sub>4</sub>–NH<sub>2</sub>@Cu-ILCPE) was used to covalently immobilize the TST aptamer (TST-apt). The AuNPs/Fe<sub>3</sub>O<sub>4</sub>–NH<sub>2</sub>@Cu-ILCPE represents a distinguished ability for enhancement of electrochemical peak current, which may emerge from the aptamer on the electrode surface. Initially, the dependency of signals to variables like the aptamer concentration, aptamer immobilization time, AuNPs electrodeposion time, and aptamer reaction time was investigated and optimized. Under the optimized conditions, the proposed aptasensor has two linear ranges over 1.0–50.0 nM and 50.1–1000.0 nM with a limit of detection of 0.31 nM, and a limit of quantification of 0.99 nM. The aptasensor was also applicable to detecting TST in urine samples with satisfactory recoveries of 97.2–103.8 %.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115827"},"PeriodicalIF":2.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565829","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}
Teresa Kwok, She Lin Chan, Niusheng Xu, Tiemin Huang, Tao Bo
{"title":"Advancing protein heterogeneity analysis: Nano-flow pressure mobilization for precise icIEF fractionation and online MS detection","authors":"Teresa Kwok, She Lin Chan, Niusheng Xu, Tiemin Huang, Tao Bo","doi":"10.1016/j.ab.2025.115825","DOIUrl":"10.1016/j.ab.2025.115825","url":null,"abstract":"<div><div>This study addresses the challenges of high-resolution protein charge variant fractionation and efficient online mass spectrometry (MS) detection in imaged capillary isoelectric focusing (icIEF)-based workflows. icIEF often faces limitations in efficiency, peak integrity, and detection sensitivity due to diffusion and uncontrolled mobilization. To overcome these, we developed a novel icIEF fractionation framework that integrates nano-flow pressure mobilization with the capillary diameter transformation technique (CDTT). Using a model system with a 320 μm ID separation channel and a 50 μm ID transfer capillary, we investigated the electrophoretic and nano-flow transport mechanisms influencing fractionation efficiency. The impact of these innovations on peak area, height, and width for charge proteoforms was assessed, showing improvements in precision. These insights were applied to a 200 μm ID separation channel system, resulting in enhanced separation efficiency and icIEF-MS sensitivity. This study offers a scalable, high-precision solution for charge heterogeneity analysis in biopharmaceutical development and regulatory applications.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"701 ","pages":"Article 115825"},"PeriodicalIF":2.6,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143534345","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}
Hong Xu , Yiran Hua , Haiqin Li , Jianhua Wang , Gaohong Liu , Xiaochun Li
{"title":"Smartphone-based colorimetric correction analysis system for long-term urine monitoring of chronic kidney disease","authors":"Hong Xu , Yiran Hua , Haiqin Li , Jianhua Wang , Gaohong Liu , Xiaochun Li","doi":"10.1016/j.ab.2025.115824","DOIUrl":"10.1016/j.ab.2025.115824","url":null,"abstract":"<div><div>The chronic kidney disease (CKD) poses a serious threat to human health. Long-term monitoring of urine is important in the management of CKD. Currently, the accuracy and stability of smartphone-based colorimetric analysis of urine indicators are limited due to the impact of different image-taking conditions on captured digital images of urine test strips. Herein, an attachment-free colorimetric correction analysis system (CCAS for short), consisting of a self-designed urine test strip array and an Android application integrated with an image calibration algorithm, were proposed for quantitative analysis of nine urine indicators. With this system the impact of image-taking conditions on captured digital image were largely corrected, and thus the accuracy and stability for digital image colorimetric analysis of urine test strip were improved. The limits of detection of creatinine, nitrite, urinary calcium, microalbumin, bilirubin, protein, pH, haemoglobin, and glucose were 1.607 mmol/L, 1.232 μmol/L, 0.297 mmol/L, 11.116 mg/L, 1.155 μmol/L, 0.042 g/L, 0.044, 0.058 mg/L, and 0.122 mmol/L, respectively. The accuracy of CCAS was validated by analyzing artificial urine samples and 143 clinical urine samples. As an accurate, low-cost and reliable system, CCAS addresses specific needs for patients to monitor their urine whenever and wherever possible with only their own smartphone.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115824"},"PeriodicalIF":2.6,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536547","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}
Nairo Brilhante-da-Silva , Sibele Andrade Roberto , Nidiane Dantas Reis Prado , Laura Rosilene Soares-de-Souza , Anna Carolina Machado Marinho , Carla Freire Celedonio Fernandes , Soraya dos Santos Pereira
{"title":"Diagnostic platforms for snakebite: Current approaches and challenges in medically important species","authors":"Nairo Brilhante-da-Silva , Sibele Andrade Roberto , Nidiane Dantas Reis Prado , Laura Rosilene Soares-de-Souza , Anna Carolina Machado Marinho , Carla Freire Celedonio Fernandes , Soraya dos Santos Pereira","doi":"10.1016/j.ab.2025.115823","DOIUrl":"10.1016/j.ab.2025.115823","url":null,"abstract":"<div><div>Diagnosing snakebite envenoming is a critical aspect of managing this life-threatening condition. Achieving the impacts and clinical applications of the diagnosis of snakebites is important to help clarify the challenges faced in identifying venomous snakebites and implementing effective treatment strategies. The complexity of the envenomation requires a comprehensive diagnostic approach, considering both clinical symptoms and laboratory findings. Despite advances in diagnostic technologies, the lack of standardized tools represents a significant obstacle to obtaining accurate and timely assessments. This paper analyzes the state-of-the-art snakebite diagnosis, emphasizing the need for methodologies for differential diagnosis of snakebites. Furthermore, it investigates the far-reaching consequences of late or incorrect diagnoses, emphasizing their role in the potential development of serious morbidity and even mortality. The discussion extends to the global health burden caused by snakebite envenoming, emphasizing the importance of personalized diagnostic methods in regions with diverse snake species. Furthermore, the review explores recent advances in the global scale diagnosis of snakebite venom. The clinical applications of these innovations are explored, highlighting their potential to revolutionize snakebite management in resource-limited settings. By addressing the multifaceted challenges in snakebite diagnosis, this summary contributes to ongoing efforts to mitigate the global impact of snakebite envenoming by highlighting the critical need for collaborative research, standardization, and accessibility of diagnostic tools.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"702 ","pages":"Article 115823"},"PeriodicalIF":2.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531177","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}