Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-11-08DOI: 10.1016/j.ab.2025.116009
Anna Makovska , Erik Walinda , Ryo Aoyama , Minsoo Kim , Daichi Morimoto
{"title":"A minimal slow dialysis method for refolding inclusion body proteins: Structural application to NEDD8 and its Q40E mutant","authors":"Anna Makovska , Erik Walinda , Ryo Aoyama , Minsoo Kim , Daichi Morimoto","doi":"10.1016/j.ab.2025.116009","DOIUrl":"10.1016/j.ab.2025.116009","url":null,"abstract":"<div><div>NEDD8, a ubiquitin-like modifier essential for cullin-RING ligase regulation, is difficult to refold from <em>Escherichia coli</em> inclusion bodies due to aggregation during denaturant removal. Conventional refolding methods such as rapid dilution, one-step dialysis, and stepwise dialysis often produce poorly soluble proteins, limiting structural and functional analyses. To overcome this, we developed a simplified slow dialysis system using a single peristaltic pump to generate a gradual urea gradient over 96 h, enabling efficient refolding of NEDD8 under gentle conditions. Both wild-type and Q40E-mutant NEDD8, which mimics the bacteria-mediated deamidation observed during infection, refolded successfully into monomeric protein, as confirmed by size-exclusion chromatography. NMR spectra showed folded protein that matched reference assignments, demonstrating suitability for atomic level structural analysis. The method also enabled recovery of previously insoluble ISG15 mutants, highlighting its broad applicability for structural studies of diverse challenging proteins.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116009"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145487379","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-11-03DOI: 10.1016/j.ab.2025.116005
Mingxian Lu , Taigang Liu
{"title":"AHAPC: Multi-source feature fusion and ensemble learning for multiclass extremophilic protein prediction","authors":"Mingxian Lu , Taigang Liu","doi":"10.1016/j.ab.2025.116005","DOIUrl":"10.1016/j.ab.2025.116005","url":null,"abstract":"<div><div>Acidophilic, alkaliphilic, and halophilic proteins function under extreme conditions and hold great industrial value. However, their experimental identification is time-consuming and costly. Here, we introduce AHAPC, a unified computational framework for multiclass classification of extremophilic proteins. First, we construct a new benchmark dataset, TriExtrem, by combining three rigorously curated datasets. Then, we extracted two types of protein features, i.e., embeddings from pretrained protein language models (PLMs) and hand-crafted embeddings which include evolutionary descriptors derived from position-specific scoring matrix (PSSM), and sequence features, followed by the feature fusion and selection. Finally, convolutional neural network (CNN), gated recurrent unit (GRU), and bidirectional long short-term memory (BiLSTM) were used for three binary classification tasks respectively, while a multi-branch BiLSTM was adopted for the multiclass setting. Comprehensive evaluation and visualized analysis demonstrate that AHAPC achieves strong performance and provides interpretable predictions, facilitating reliable discovery of extremophilic proteins.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116005"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145450530","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-10-31DOI: 10.1016/j.ab.2025.116006
Guangxin Yuan , Meng Xia , Ya Li , Honglei Tian , Jianyu Zhu , Yanshuang Wang
{"title":"A high-throughout PCR test strip method for the rapid identification of four placentas","authors":"Guangxin Yuan , Meng Xia , Ya Li , Honglei Tian , Jianyu Zhu , Yanshuang Wang","doi":"10.1016/j.ab.2025.116006","DOIUrl":"10.1016/j.ab.2025.116006","url":null,"abstract":"<div><div>Deer placenta and Placenta Hominis are valued traditional Chinese medicines often adulterated with cheaper pig or cow placenta. Current identification methods frequently lack the throughput, speed, or simplicity for effective field monitoring. This study aimed to develop a high-throughput, rapid method to simultaneously identify deer, human, pig, and cow placenta. The approach involved screening a rapid genomic DNA extraction protocol and designing specific primers for the mitochondrial <em>cytochrome b</em> gene of each species, with primers labeled with FAM and Biotin. Following the optimization of PCR amplification conditions, results were visually detected using immunocolloidal gold test strips. The method was rigorously evaluated for its specificity, reproducibility, sensitivity, and stability. The results showed that the extracted DNA was of satisfactory concentration, purity, and integrity. Under optimized conditions (59 °C annealing temperature, 20 cycles), authentic samples for all four placenta types produced two distinct red bands on the test strips, while adulterated and blank controls showed only one control band. Agarose gel electrophoresis confirmed specific amplification for each target with no cross-reactivity. The method demonstrated strong specificity, excellent reproducibility and stability, and a high sensitivity of 0.01 ng μL<sup>−1</sup>, surpassing conventional electrophoresis. In conclusion, this PCR-based test strip method enables the visual, simultaneous authentication of the four placenta types in a single test, making it highly suitable for on-site rapid monitoring and quality control.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116006"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145429918","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-11-13DOI: 10.1016/j.ab.2025.116011
Rithwik Pradeep , Alexander Zhdanov , Evin Allen
{"title":"Comparative analysis of common potency assays for assessing human TNF-alpha neutralising antibodies","authors":"Rithwik Pradeep , Alexander Zhdanov , Evin Allen","doi":"10.1016/j.ab.2025.116011","DOIUrl":"10.1016/j.ab.2025.116011","url":null,"abstract":"<div><div>Tumour necrosis factor-alpha (TNF-α) plays a central role in inflammation and autoimmune pathology, making it a key therapeutic target. This study systematically evaluated the performance of monoclonal anti-human TNF-α antibodies derived from hybridoma cells—originally developed during early TNF research—using two widely adopted in vitro potency assays: a cytotoxicity-based assay in L929 fibroblasts and an NF-κB reporter assay in HEK293 Blue cells. Antibody performance was assessed in terms of neutralisation efficiency, signal reproducibility, and assay sensitivity. While both assays yielded comparable IC<sub>50</sub> values (1.98 for L929 and 1.34 for HEK293 Blue), they differed in dynamic range, sensitivity, and biological relevance. The HEK293 Blue assay provided rapid, robust, and high-throughput-compatible detection of early TNF-α signalling events, with minimal background and superior reproducibility. In contrast, the L929 assay offered physiologically relevant insights into the later consequences of TNF-α signalling, such as apoptosis and metabolic disruption. ATP quantification using the CellTiter-Glo® assay proved to be a practical and sensitive method for viability assessment, though alternative metabolic and membrane integrity assays may complement interpretation. Overall, our findings highlight the complementary strengths of these assay platforms and support a dual-assay approach for comprehensive evaluation of anti-TNF-α antibodies.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116011"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145530424","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-11-04DOI: 10.1016/j.ab.2025.116007
Wenxia Zhang , Guimei Wang , Zhenyu Wang , Guoqi Zhou , Hanliang Jiang
{"title":"The role of tyrosine metabolism-associated genes in predicting lung adenocarcinoma prognosis and their clinical relevance","authors":"Wenxia Zhang , Guimei Wang , Zhenyu Wang , Guoqi Zhou , Hanliang Jiang","doi":"10.1016/j.ab.2025.116007","DOIUrl":"10.1016/j.ab.2025.116007","url":null,"abstract":"<div><h3>Background</h3><div>Tyrosine metabolism (TM) plays an important role in the progression of cancer, but its role in lung adenocarcinoma (LUAD) is still unclear. This study aims to construct TM-related prognostic features for LUAD.</div></div><div><h3>Methods</h3><div>Transcriptomes and clinical data of LUAD were collected from public databases. A TM-related risk score (TMRS) model was constructed using 42 TM-related genes (TMRGs). The prognostic value of the model was comprehensively analyzed through survival analysis, enrichment analysis, immune assessment, and drug sensitivity prediction. The expression of key genes was also verified in LUAD cell lines and patient PBMCs.</div></div><div><h3>Results</h3><div>A 14-gene prognostic model (TMRS) was constructed. TMRS was an independent prognostic factor for LUAD. The low TMRS group has a more active immune microenvironment and may be more sensitive to immunotherapy. Patients with high TMRS may be more sensitive to various chemotherapy drugs. The model genes were specifically expressed in different cell types, suggesting that they may be involved in metabolic reprogramming and tumor progression.</div></div><div><h3>Conclusion</h3><div>This study establishes a foundation for personalized risk assessment and treatment decisions in LUAD, highlighting the prognostic significance of TM.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116007"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145457608","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-10-14DOI: 10.1016/j.ab.2025.115993
Shweta Mishra , Ashlesha J. Chauhan , Jayaveersinh Mahida
{"title":"Exploring biosensors: Distinctive features and emerging applications","authors":"Shweta Mishra , Ashlesha J. Chauhan , Jayaveersinh Mahida","doi":"10.1016/j.ab.2025.115993","DOIUrl":"10.1016/j.ab.2025.115993","url":null,"abstract":"<div><div>Biosensors have become essential analytical tools that integrate biological recognition elements with physical transducers to detect specific analytes with remarkable sensitivity. This review delves into the applications of biosensors in healthcare, environmental monitoring, and other fields. Notable advancements include nanotechnology-enhanced biosensors, wearable devices, and point-of-care systems, all of which are characterized by miniaturization and multiplexing capabilities. In healthcare, biosensors facilitate disease diagnosis and continuous monitoring, whereas in environmental applications, they aid in pollutant detection. In analytical technology, biosensors merge biological recognition with physical transduction, offering unparalleled sensitivity in biological and environmental systems. This review examines the characteristics and applications of biosensors in various fields. They support disease diagnosis and health surveillance in healthcare and enable real-time pollutant monitoring for environmental protection purposes. Recent advances have incorporated nanotechnology to enhance performance through miniaturization and label-free detection. Wearable biosensors have revolutionized point-of-care diagnostics by providing real-time health data outside clinical settings. The integration of artificial intelligence and microfluidics has led to the development of more adaptive biosensing platforms. Despite challenges such as biological component stability and nonspecific binding, innovations in materials science offer potential solutions. The convergence of expertise positions biosensors as vital instruments for improving health outcomes and ensuring environmental sustainability, thereby transforming diagnostics and ecological preservation.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 115993"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306919","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-11-19DOI: 10.1016/j.ab.2025.116013
Hadyn Duncan , Elisabeth Domingo-Contreras , Sotirios Athanasiou , Rosario Fernandez-Godino , Francisco Castillo , Ana Camacho
{"title":"Affinity-based selection of anti-Feline Leukaemia Virus p27 monoclonal antibodies for efficient lateral flow assay development","authors":"Hadyn Duncan , Elisabeth Domingo-Contreras , Sotirios Athanasiou , Rosario Fernandez-Godino , Francisco Castillo , Ana Camacho","doi":"10.1016/j.ab.2025.116013","DOIUrl":"10.1016/j.ab.2025.116013","url":null,"abstract":"<div><div>Traditional diagnostic methods like RT-PCR and proviral DNA PCR have limitations, underscoring the need for swift, sensitive alternatives such as lateral flow immunoassays (LFIA). Yet, efficiently identifying monoclonal antibody (mAb) pairs for robust ternary antigen-antibody interactions remains a universal bottleneck, as conventional ELISA screening is costly and may not accurately reflect native binding. Here, we combined ELISA with Spectral Shift Technology (SST) to minimise reagent use and comprehensively profile anti-FeLV p27 mAbs. This orthogonal approach enabled rapid selection of two low nanomolar mAbs with different epitope targets that form a ternary complex, which translates into a sensitive detection of the FeLV p27 in a LFIA prototype. Our screening methodology supports resource-efficient LFIA development for FeLV and extends to other significant animal and human pathogens like Monkeypox or <em>Helicobacter pylori</em>, improving diagnostics and quality control.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116013"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145562491","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-11-05DOI: 10.1016/j.ab.2025.116008
Thomas Olsen , Amany Elshorbagy , Jay E. Johnson , Sailendra N. Nichenametla , Zhen Dong , Kumar Sambamurti , John P. Richie Jr. , Kathrine J. Vinknes
{"title":"Sulfur amino acids, metabolic health and beyond: Recent advances, translational implications, and future research considerations","authors":"Thomas Olsen , Amany Elshorbagy , Jay E. Johnson , Sailendra N. Nichenametla , Zhen Dong , Kumar Sambamurti , John P. Richie Jr. , Kathrine J. Vinknes","doi":"10.1016/j.ab.2025.116008","DOIUrl":"10.1016/j.ab.2025.116008","url":null,"abstract":"<div><div>Dietary restriction of the sulfur amino acids methionine and cysteine (sulfur amino acid restriction [SAAR]) is a well-established paradigm for delaying disease onset and the aging process in several experimental models. <em>In vivo</em>, SAAR's anti-aging effects appear to be mediated by decreased growth hormone/insulin-like growth factor-1 (GH/IGF-1) signaling, along with improvement in insulin sensitivity and overall metabolic health. SAAR-fed animals also exhibit reduced regional and total adiposity, as well as oxidative stress and inflammation. Recent experimental studies suggest that SAAR improves cognition, induces significant changes in gut microbiome composition, and that its benefits may depend on the age at which the intervention begins. In humans, observational studies have shown that higher plasma total cysteine levels are positively correlated with adiposity, insulin resistance, and an increased incidence of diabetes. Likewise, high dietary methionine and cysteine intake has been linked to increased risk of cardiovascular disease and diabetes-related mortality. Human dietary intervention studies have only been partly successful in translating the benefits of SAAR, and practical challenges for implementation remain to be addressed. This review summarizes recent advances in the SAAR field and discusses its translational potential for promoting metabolic health and reducing the risk of age-related diseases.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116008"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145470385","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-10-29DOI: 10.1016/j.ab.2025.116002
Katelyn M. Brown , Dianne I. Greenfield , George S. Bullerjahn
{"title":"A novel sandwich hybridization assay method and probe sets for cyanobacterial harmful algal bloom detection","authors":"Katelyn M. Brown , Dianne I. Greenfield , George S. Bullerjahn","doi":"10.1016/j.ab.2025.116002","DOIUrl":"10.1016/j.ab.2025.116002","url":null,"abstract":"<div><div>A novel, rapid (2.5 h) sandwich hybridization assay (SHA) method for the detection of harmful cyanobacterial genera has been developed based on oligonucleotide hybridization to genus-specific sequences within the 16S ribosomal RNA. Unlike previously-developed 96-well plate SHA formats, this modification does not involve a robotic processor to maneuver reagents across the plate. Rather, it requires manual pipetting each reagent sequentially into the same well and washing the 96-well plate between each addition, thereby increasing sample throughput. Another key difference is the colorimetric reporter molecule. Yet, it enables specific detection of <em>Planktothrix, Raphidiopsis</em> and the <em>Anabaena-Dolichospermum-Aphanizomenon</em> (ADA) clade of the Nostocales. As these are the most common planktonic bloom-forming cyanobacteria, the method can be used to assess potential threats posed by these taxa, specifically cyanotoxins that are associated with particular bloom-forming taxa. The assays detected target groups and standard curves were created from cultured cyanobacteria biomass. Here, the SHA method, calibration, and the field performance of the assay on cyanobacterial bloom biomass is described. Linear standard curves were established for each assay, with a <em>Planktothrix</em> and <em>Raphidiopsis</em> quantification range of 10–500 mm<sup>3</sup> L<sup>−1</sup> 100 μL homogenate<sup>−1</sup> and a range of 50–500 mm<sup>3</sup> L<sup>−1</sup> 100 μL homogenate<sup>−1</sup> for the ADA clade assay. In environmental samples from three Ohio waterbodies, the assays detected the target genus in a mixed cyanobacterial community. This new SHA protocol will be highly beneficial to both management and research communities because it considerably broadens the capability to rapidly detect multiple cyanobacterial genera that cause persistent toxic blooms.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116002"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145414889","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}
Analytical biochemistryPub Date : 2026-02-01Epub Date: 2025-11-17DOI: 10.1016/j.ab.2025.116012
Rania A. Hussien
{"title":"Corrigendum to“Development of a green polymer-based sensor for enhanced iron detection in diverse biological, food and environmental matrices” [Analyt. Biochem. 705 (2025) 115927]","authors":"Rania A. Hussien","doi":"10.1016/j.ab.2025.116012","DOIUrl":"10.1016/j.ab.2025.116012","url":null,"abstract":"","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"709 ","pages":"Article 116012"},"PeriodicalIF":2.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145538562","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}