Analytical biochemistry最新文献

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An indole-oxadiazole-derived fluorescent probe for the detection of the human serum albumin level in thoracic surgery 一种用于胸外科手术中检测人血清白蛋白水平的吲哚-恶二唑衍生荧光探针。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-22 DOI: 10.1016/j.ab.2026.116090
Hanzhang Sun , Guanglei Zuo , Yueming Wu , Yangyong Lou , Jiang Feng , Yulong Zheng
{"title":"An indole-oxadiazole-derived fluorescent probe for the detection of the human serum albumin level in thoracic surgery","authors":"Hanzhang Sun ,&nbsp;Guanglei Zuo ,&nbsp;Yueming Wu ,&nbsp;Yangyong Lou ,&nbsp;Jiang Feng ,&nbsp;Yulong Zheng","doi":"10.1016/j.ab.2026.116090","DOIUrl":"10.1016/j.ab.2026.116090","url":null,"abstract":"<div><div>In this work, the fluorescent probe <strong>InOx-HSA</strong> was developed from an indole-oxadiazole derivative for the detection of the HSA level in thoracic surgery. The probe reported a ratio fluorescence response from 405 nm to 505 nm under the excitation at 310 nm. <strong>InOx-HSA</strong> occupied the binding site of phenylbutazone in HSA and generated the fluorescence enhancement via Förster resonance energy transfer/twisted intramolecular charge transfer mechanisms. The response between <strong>InOx-HSA</strong> and HSA completed within 30 min. The probe-HSA complex kept stable within the range of 7.0-9.0. The ratio response was in a dosage-dependent manner with the limit of detection as 0.0002 mg/mL. <strong>InOx-HSA</strong> exhibited high specificity and low cytotoxicity. The site-binding strategy was confirmed by the drug competition, trypsin digestion, and protein denaturation by high temperature. <strong>InOx-HSA</strong> achieved visualizing HSA in living pulmonary cells, and revealed the ventilation-related consumption of HSA during the thoracic surgery.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116090"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147282090","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
Imidazole stabilizes NAD(P)H and improves reductase assays under challenging conditions 咪唑稳定NAD(P)H和改善还原酶在挑战性条件下的测定。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-28 DOI: 10.1016/j.ab.2026.116094
Shengkai Yin , Litao Wang , Xian'ai Shi , Guozeng Wang
{"title":"Imidazole stabilizes NAD(P)H and improves reductase assays under challenging conditions","authors":"Shengkai Yin ,&nbsp;Litao Wang ,&nbsp;Xian'ai Shi ,&nbsp;Guozeng Wang","doi":"10.1016/j.ab.2026.116094","DOIUrl":"10.1016/j.ab.2026.116094","url":null,"abstract":"<div><div>The reduced form of nicotinamide adenine dinucleotide (NAD(P)H) is prone to hydrolysis and ring-opening degradation under high-temperature and acidic conditions, resulting in a loss of reducing power and substantial inaccuracies in enzymatic assays. In this study, we systematically investigated the stabilizing effect of imidazole on NADH and NADPH under elevated temperature (30–60 °C) and acidic (pH 3–5) conditions, and further evaluated its applicability in reductase activity assays. Incubation experiments with varying imidazole concentrations (0–300 mM) demonstrated a pronounced concentration-dependent stabilization of NAD(P)H. Enzymatic assays revealed that imidazole enhanced the apparent activities of lactate dehydrogenase (LDH) and imine reductase (IRED) under both acidic and high-temperature conditions. Moreover, imidazole addition broadened the optimal pH and temperature range of these enzymes, markedly improving the accuracy and reproducibility of activity measurements. Collectively, these findings identify imidazole as an efficient stabilizing additive for NAD(P)H, enabling more reliable assessment of NAD(P)H-dependent reductase activities under high-temperature or acidic conditions.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116094"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147324467","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
Physiological role of gamma-glutamyl transpeptidase: Demise of the gamma-glutamyl cycle γ -谷氨酰转肽酶的生理作用:γ -谷氨酰循环的消亡。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-14 DOI: 10.1016/j.ab.2026.116087
Marie H. Hanigan
{"title":"Physiological role of gamma-glutamyl transpeptidase: Demise of the gamma-glutamyl cycle","authors":"Marie H. Hanigan","doi":"10.1016/j.ab.2026.116087","DOIUrl":"10.1016/j.ab.2026.116087","url":null,"abstract":"<div><div>Gamma-glutamyl transpeptidase (GGT) is an enzyme with a plethora of names and purported functions. The enzyme has long been identified with an amino acid transport system called the gamma-glutamyl cycle which was proposed in the 1970s. The foundation of this cycle held that GGT catalyzed a transpeptidation reaction and in the process transported an extracellular amino acid into the cell as a gamma-glutamyl amino acid. However, subsequent studies showed that under physiological conditions the enzyme is a hydrolase. It cleaves the gamma-glutamyl bond of glutathione, glutathione <em>S</em>-conjugates and other gamma-glutamyl compounds releasing glutamate. The release of glutamate from glutathione, renders the other product of the reaction, cysteinyl-glycine, susceptible to cleavage by cell surface dipeptidases. The development of the GGT-deficient mouse showed definitively that the primary role of GGT <em>in vivo</em> is cysteine homeostasis, not amino acid transport. GGT also plays a role in oxidative stress, drug metabolism, and inflammation. Despite numerous studies showing that the gamma-glutamyl cycle is incorrect, it nonetheless persists in the literature, in textbooks, and currently on the GGT Wikipedia page. Confusion regarding the physiological role of GGT can lead to misinterpretation of data and blunt progress in many important areas of investigation. This review focuses on the physiological functions of GGT and summarizes the data demonstrating the gamma-glutamyl cycle does not exist.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116087"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146200181","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 new paradigm in tuberculosis diagnostics: Biosensing advances for early detection of Mycobacterium tuberculosis 结核病诊断的新范式:结核分枝杆菌早期检测的生物传感进展。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-16 DOI: 10.1016/j.ab.2026.116088
Pooja Khandelwal, Neelam Yadav, Arzoo Saini, Neelam Singh Sangwan
{"title":"A new paradigm in tuberculosis diagnostics: Biosensing advances for early detection of Mycobacterium tuberculosis","authors":"Pooja Khandelwal,&nbsp;Neelam Yadav,&nbsp;Arzoo Saini,&nbsp;Neelam Singh Sangwan","doi":"10.1016/j.ab.2026.116088","DOIUrl":"10.1016/j.ab.2026.116088","url":null,"abstract":"<div><div>Tuberculosis (TB) remains one of the most serious and deadly infectious diseases worldwide. Despite being preventable and curable, it is responsible for increasing the annual fatality by millions. The situation is even more alarming in the developing nations, where TB ranked in the top 10 in terms of global mortality. <em>Mycobacterium tuberculosis</em> is the causal pathogen for tuberculosis. It is an extremely resilient bacterium that eludes the immunity of the host and prevails in latent forms. Several biomarkers, including antigens (CFP-10, ESAT-6), antibodies, and nucleic acids, have been identified for their rapid and accurate detection. Conventional screening approaches like culture, chest X-ray, sputum smear microscopy, and PCR-based assays are widely used. However, these approaches suffer from various shortcomings, <em>viz.,</em> less sensitivity, delayed diagnosis, potential false negatives, requirement of biosafety infrastructure, and skilled personnel. These diagnostic challenges are resolved by biosensors as they are quick, sensitive, and resource-efficient alternatives to conventional methods. This review comprehensively discusses the pathogenicity of TB as well as conventional approaches for its diagnosis. Further, we have also provided an in-depth analysis of recently reported biosensors for TB detection and critically evaluated their analytical performance.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116088"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146218505","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
Untargeted metabolomic and lipidomic profiling in a hyperuricemic rabbit model: a pilot study 高尿酸血症兔模型的非靶向代谢组学和脂质组学分析:一项初步研究。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-03 DOI: 10.1016/j.ab.2026.116072
Junyoung Ahn , Bo Young Hwang , Kyo Bin Kang , Nak-Hoon Son , Hyang-Ja Lee , Jongwon Oh , Mi-Young Kim , Sanghoo Lee , Mikyeong Lee , Kyoung-Ryul Lee , Sung Kweon Cho , Jeong-Ho Kim
{"title":"Untargeted metabolomic and lipidomic profiling in a hyperuricemic rabbit model: a pilot study","authors":"Junyoung Ahn ,&nbsp;Bo Young Hwang ,&nbsp;Kyo Bin Kang ,&nbsp;Nak-Hoon Son ,&nbsp;Hyang-Ja Lee ,&nbsp;Jongwon Oh ,&nbsp;Mi-Young Kim ,&nbsp;Sanghoo Lee ,&nbsp;Mikyeong Lee ,&nbsp;Kyoung-Ryul Lee ,&nbsp;Sung Kweon Cho ,&nbsp;Jeong-Ho Kim","doi":"10.1016/j.ab.2026.116072","DOIUrl":"10.1016/j.ab.2026.116072","url":null,"abstract":"<div><div>The incidence of hyperuricemia is rising globally; however, its molecular mechanisms and reliable progression biomarkers remain unclear. This study characterized temporal changes in serum metabolites and lipids in hyperuricemic rabbit models using untargeted metabolomic and lipidomic profiling with ultra-high-performance liquid chromatography–quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS/MS). Serum samples collected at baseline (0 h), 48 h, and 84 h (n = 3 per time point) were analyzed using both hydrophilic interaction chromatography (HILIC) and reversed-phase C18 columns to achieve broad metabolite and lipid coverage. HILIC analysis yielded 9813 peaks with 65 annotated compounds, whereas C18 analysis identified 7333 peaks with 122 annotated compounds across both positive and negative ion modes. Significant monotonic increases were observed in the normalized feature intensities of 4-aminohippuric acid, L-alanine, N-isobutyrylglycine, and uric acid, whereas the normalized feature intensity of inosine decreased relative to baseline. These metabolites satisfied two selection criteria, [|log<sub>2</sub>(fold change, FC)| ≥ 0.58, Nemenyi <em>p</em> &lt; 0.05] and variable importance in projection (VIP) &gt; 1.0 using orthogonal partial least squares-discriminant analysis (OPLS-DA). Among them, inosine and 4-aminohippuric acid, which showed a strong correlations with uric acid, emerged as the most exploratory candidate biomarkers for hyperuricemia progression. The C18-based lipidomic profiling identified the phosphatidylinositols, PI(16:0_20:4) and PI(18:1_18:2), as the only lipid species that met the two selection criteria. In particular, PI(16:0_20:4) was strongly correlate with uric acid. Collectively, our study reveals the metabolomic and lipidomic changes for hyperuricemia and suggests exploratory candidate biomarkers for its early detection and monitoring.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116072"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146123408","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
Electrochemical quantification of dopamine using a nanocomposite of silver nanoparticles-potassium modified graphitic carbon nitride (Ag/K-g-CN) 纳米银-钾修饰石墨化碳纳米复合材料(Ag/K-g-CN)对多巴胺的电化学定量研究。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-26 DOI: 10.1016/j.ab.2026.116091
Smriti Dogra , Saumya Dwivedi , Jaspreet Kaur Rajput , Jigyasa , Sareen
{"title":"Electrochemical quantification of dopamine using a nanocomposite of silver nanoparticles-potassium modified graphitic carbon nitride (Ag/K-g-CN)","authors":"Smriti Dogra ,&nbsp;Saumya Dwivedi ,&nbsp;Jaspreet Kaur Rajput ,&nbsp;Jigyasa ,&nbsp;Sareen","doi":"10.1016/j.ab.2026.116091","DOIUrl":"10.1016/j.ab.2026.116091","url":null,"abstract":"<div><div>Herein, a selective and sensitive electrochemical sensor based on silver nanoparticles–potassium modified graphitic carbon nitride (Ag/K-g-CN) was developed. The nanocomposite was synthesised via a combined thermal and solvothermal method for the dopamine (DA) detection. To create bulk CN, melamine was thermally polymerised at 550 °C. Subsequently, solvothermal-assisted exfoliation yielded g-CN nanosheets. Next, the porous g-CN was modified with KOH by grinding, dispersing it in an ethanol-water mixture, and calcined it at 300 °C to create K-modified g-CN. Ultrasonication was used to disperse Ag NPs evenly within K-g-CN, yielding a homogeneous Ag/K-g-CN nanocomposite. The Ag/K-g–CN–modified electrode exhibited significant electrochemical responses, demonstrating its successful attachment to the electrode surface. High-resolution transmission electron microscopy (HR-TEM), Fourier-transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD) were used to investigate the structural and morphological features. The sensor's performance was evaluated using linear sweep voltammetry (LSV) and cyclic voltammetry (CV), with a broad linear range of 0-500 μM, a low detection limit of 0.629 μM, and a sensitivity of 0.432 μA μM<sup>−1</sup> cm<sup>−2</sup> for DA. Practical application was demonstrated using spiked recovery studies in 100-fold diluted human serum samples, yielding recoveries of 99–100%, validating the reliability of the proposed sensor.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116091"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147321194","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
EnsemGlyPred: Intelligent prediction system for lysine glycation sites integrating deep semantic features and sequence information 集成深度语义特征和序列信息的赖氨酸糖基化位点智能预测系统
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-10 DOI: 10.1016/j.ab.2026.116077
Yun Zuo, Sifan Zhu
{"title":"EnsemGlyPred: Intelligent prediction system for lysine glycation sites integrating deep semantic features and sequence information","authors":"Yun Zuo,&nbsp;Sifan Zhu","doi":"10.1016/j.ab.2026.116077","DOIUrl":"10.1016/j.ab.2026.116077","url":null,"abstract":"<div><h3>Motivation</h3><div>Protein non-enzymatic glycation plays a crucial role in chronic diseases such as diabetes, atherosclerosis, and neurodegenerative diseases. Accurate identification of lysine glycation sites is essential for elucidating disease pathogenesis and developing diagnostic biomarkers. However, current computational methods face challenges in capturing complex contextual features, integrating multi-source heterogeneous features, and providing biological interpretability.</div></div><div><h3>Results</h3><div>This study proposes EnsemGlyPred, an intelligent prediction system integrating multi-dimensional features with weighted ensemble learning. We constructed a reliable benchmark dataset from the PLMD database after rigorous data processing. A multi-level feature extraction framework was designed, integrating AAC features (amino acid composition), PAAC features (incorporating sequence order), and deep semantic features from ProGen2. Three optimized base classifiers were constructed: AAC-based XGBoost, PAAC-based XGBoost, and ProGen2-based BiLSTM models, with scientifically allocated weights (0.33, 0.4, 0.27) for ensemble prediction.</div><div>Rigorous ten-fold cross-validation and independent testing demonstrated that the ensemble model significantly outperformed existing methods, particularly achieving significant improvement in recall metrics. Systematic ablation experiments confirmed the effectiveness of multi-feature fusion and weighted ensemble strategies. Feature importance analysis revealed the key regulatory role of amino acids in the lysine neighboring region and positively charged residues. t-SNE visualization demonstrated improved discriminative feature space distribution. This research provides a systematic methodological framework for computational prediction of protein post-translational modifications, offering reliable theoretical foundation and important guidance for related fields.</div></div><div><h3>Availability</h3><div>an intelligent online prediction platform (<span><span>http://www.ensemglypred.com</span><svg><path></path></svg></span>) has been developed to facilitate the efficient conduct of academic research. The predictive model EnsemGlyPred and associated datasets are available at: <span><span>https://github.com/pigyoo-1009/EnsemGlyPred</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116077"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146154283","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
Establishment of a homogeneous immunoassay for quantitative detection of total procollagen type 1 N-terminal propeptide 建立一种均相免疫法定量检测总前胶原1型n端前肽。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-18 DOI: 10.1016/j.ab.2026.116089
Shanshan Cheng , Yuanmin Sun , Xiaohui Yang , Hongwei Yang , Xiaoming Cui , Xue Li , Huiqiang Li , Yang Yu
{"title":"Establishment of a homogeneous immunoassay for quantitative detection of total procollagen type 1 N-terminal propeptide","authors":"Shanshan Cheng ,&nbsp;Yuanmin Sun ,&nbsp;Xiaohui Yang ,&nbsp;Hongwei Yang ,&nbsp;Xiaoming Cui ,&nbsp;Xue Li ,&nbsp;Huiqiang Li ,&nbsp;Yang Yu","doi":"10.1016/j.ab.2026.116089","DOIUrl":"10.1016/j.ab.2026.116089","url":null,"abstract":"<div><h3>Objective</h3><div>To establish a homogeneous immunoassay for quantitative detection of total procollagen type 1 n-terminal propeptide (P1NP) in human serum.</div></div><div><h3>Methods</h3><div>The assay was established after screening raw materials and optimizing the reaction conditions, and the performance of the assay was evaluated according to the clinical guidelines. Meanwhile, the detection results of the established assay were compared with those of the Roche electrochemiluminescence immunoassay.</div></div><div><h3>Results</h3><div>The coefficient of variation was 4.20 % ∼9.37 %, and the intermediate precision was 6.20 % ∼9.80 %. The limit of blank (LoB) was 1.14 ng/mL, and the limit of quantification (LoQ) was 3.83 ng/mL. The linear range was 5.88 ng/mL ∼1447.65 ng/mL. The correlation coefficient (<em>r</em>) between the results of the established total P1NP-LiCA and the Roche ECLIA was 0.8969.</div></div><div><h3>Conclusions</h3><div>A homogeneous quantitative immunoassay for total P1NP was developed, which could be used as a practical and cost-effective alternative for routine clinical use in assessing bone formation markers.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116089"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146257182","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
msCNN-PLM-FAD: Enhanced predicting FAD binding sites by using protein language representation combined with multiple separable windows convolutional neural networks msCNN-PLM-FAD:利用蛋白语言表示结合多可分离窗口卷积神经网络增强FAD结合位点预测。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-26 DOI: 10.1016/j.ab.2026.116092
Dinh-Quy Nguyen , Viet-Thanh Nguyen , Cam-Hong Ly , Yu-Yen Ou , Quang-Thai Ho
{"title":"msCNN-PLM-FAD: Enhanced predicting FAD binding sites by using protein language representation combined with multiple separable windows convolutional neural networks","authors":"Dinh-Quy Nguyen ,&nbsp;Viet-Thanh Nguyen ,&nbsp;Cam-Hong Ly ,&nbsp;Yu-Yen Ou ,&nbsp;Quang-Thai Ho","doi":"10.1016/j.ab.2026.116092","DOIUrl":"10.1016/j.ab.2026.116092","url":null,"abstract":"<div><div>The FAD binding sites classification problem is crucial because it is directly related to many diseases, such as flavoprotein-associated diseases, developmental disorders, digestive and lipid metabolism abnormalities, anemia, cancer, cardiovascular diseases, and neurological diseases. Researchers have conducted numerous studies to classify FAD binding sites, achieving varying levels of effectiveness. Nevertheless, significant potential for enhancement persists. Our study proposes msCNN-PLM-FAD, an innovative computational model predicting FAD binding sites in electron transport proteins using a sliding window feature extraction technique and pretrained protein language models (PLMs). Our approach combines a convolutional neural network-based window scanning technique able to capture various sequence features relevant to FAD binding sites with embeddings from the ESM PLM. Built on a dataset of 12,850 samples, the model outperformed previous studies, particularly in class-balance metrics, with an area under the curve (AUC) of 0.9614 and a Matthews correlation coefficient (MCC) of 0.7491, specificity of 0.9836, and accuracy of 0.9795, while maintaining a sensitivity of 0.8704. The results of this study demonstrate the potential to improve the accuracy of FAD binding site prediction, thereby promoting the development of drugs for diseases associated with FAD deficiency as well as therapeutic approaches that target bacterial FAD synthesis without affecting human health.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116092"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147321200","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
Deep learning assisted cell electrical signal analysis in impedance cytometry 深度学习辅助阻抗细胞术中的细胞电信号分析。
IF 2.5 4区 生物学
Analytical biochemistry Pub Date : 2026-06-01 Epub Date: 2026-02-26 DOI: 10.1016/j.ab.2026.116093
Houchen Zhou , Zheng Zhou , Longlong Wang , Wenlai Tang , Shijie Wei , Shu Zhu
{"title":"Deep learning assisted cell electrical signal analysis in impedance cytometry","authors":"Houchen Zhou ,&nbsp;Zheng Zhou ,&nbsp;Longlong Wang ,&nbsp;Wenlai Tang ,&nbsp;Shijie Wei ,&nbsp;Shu Zhu","doi":"10.1016/j.ab.2026.116093","DOIUrl":"10.1016/j.ab.2026.116093","url":null,"abstract":"<div><div>In this study, we developed BioFluxNet, a 1D CNN-based algorithm for automated analysis of raw electrical signals in impedance cytometry to directly classify cell types and quantify cell counts. The network comprises three functional blocks: a feature extraction module with five alternating convolutional, normalization, activation, and pooling layers; a classification block with a single linear layer; and a counting block incorporating two linear layers and an activation layer. Raw signal streams of particles and cells, collected from an impedance cytometry featuring a serpentine microchannel and four pairs of face-to-face electrodes, are stored as training and testing sets, and then used to train and test BioFluxNet. Results demonstrate that the well-trained network achieves robust classification of raw signal streams from diverse particles and cells (including blood and tumor cells), while simultaneously enabling accurate counting of particles or cells form corresponding signal streams. Compared to conventional signal processing methods, BioFluxNet eliminates many time-consuming signal processing steps, reduces manual intervention, and minimizes subjectivity of operators. The proposed deep learning framework offers a rapid, automated solution for electrical signal analysis in impedance cytometry, showcasing broad applicability in cell characterization and related biomedical fields.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"713 ","pages":"Article 116093"},"PeriodicalIF":2.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147321174","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
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