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Glutaminase I and glutamine transaminase–ω-amidase pathways in colorectal cancer: Metabolic reprogramming and emerging therapeutic strategies 谷氨酰胺酶I和谷氨酰胺转氨酶ω-氨基酶途径在结直肠癌中的作用:代谢重编程和新的治疗策略。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-10 DOI: 10.1016/j.ab.2025.115989
Sarah F. Voor, Arthur J.L. Cooper, John T. Pinto
Colorectal cancer (CRC) cells exhibit a pronounced dependence on l-glutamine to support anabolic growth, redox balance, and mitochondrial metabolism, a phenomenon known as “glutamine addiction.” The canonical glutaminase I pathway is mediated by a liver type glutaminase isozyme (LGA; GLS1), a kidney type glutaminase isozyme (KGA; GLS2), and a shortened form (glutaminase C, GAC). GLS1 and GLS2 convert glutamine to glutamate and subsequently to α-ketoglutarate (α-KG) by glutamate dehydrogenase, fueling the TCA cycle. GLS1 inhibitors, such as CB-839 (Telaglenastat), are under clinical evaluation and shows promise in treatment of CRC, particularly in combination therapies. In addition to the canonical pathway, the glutamine transaminase–ω-amidase (GTωA) pathway, a noncanonical route involving transamination of glutamine to α-ketoglutaramate (KGM) by KYAT1/2 and subsequent hydrolysis by ω-amidase (NIT2), offers metabolic flexibility under hypoxic or nutrient-limited conditions. Preclinical studies suggest that GTωA may compensate for GLS1 inhibition, contributing to therapeutic resistance. This review explores the dual roles of glutamine metabolism in CRC, emphasizing the GTωA pathway as a potentially targetable metabolic route that may contribute to therapeutic resistance. While GLS1 inhibitors are under clinical evaluation, emerging evidence suggests that dual targeting of both pathways may enhance treatment efficacy by overcoming metabolic compensation. Understanding the regulatory mechanisms driving the “glutamine shift” between these pathways is critical for developing effective metabolic interventions in CRC.
结直肠癌(CRC)细胞明显依赖l -谷氨酰胺来支持合成代谢生长、氧化还原平衡和线粒体代谢,这种现象被称为“谷氨酰胺成瘾”。典型谷氨酰胺酶I途径由肝型谷氨酰胺酶同工酶(LGA; GLS1)、肾型谷氨酰胺酶同工酶(KGA; GLS2)和缩短形式(谷氨酰胺酶C, GAC)介导。GLS1和GLS2通过谷氨酸脱氢酶将谷氨酰胺转化为谷氨酸,随后转化为α-酮戊二酸(α-KG),促进TCA循环。GLS1抑制剂,如CB-839 (Telaglenastat),正在进行临床评估,并显示出治疗结直肠癌的希望,特别是在联合治疗中。除了典型途径外,谷氨酰胺转氨酶-ω-氨基酶(gt -ω-a)途径是一种非典型途径,涉及由KYAT1/2将谷氨酰胺转氨酶转化为α-酮戊二酸盐(KGM),随后被ω-氨基酶(NIT2)水解,在缺氧或营养受限条件下提供代谢灵活性。临床前研究表明,GTωA可能补偿GLS1抑制,有助于治疗耐药。这篇综述探讨了谷氨酰胺代谢在结直肠癌中的双重作用,强调GTωA途径可能是一个潜在的靶向代谢途径,可能有助于治疗耐药。虽然GLS1抑制剂仍处于临床评估阶段,但新出现的证据表明,双重靶向这两种途径可能通过克服代谢代偿来提高治疗效果。了解这些途径之间驱动“谷氨酰胺转移”的调节机制对于开发有效的CRC代谢干预措施至关重要。
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引用次数: 0
Understanding the mode of action of arsenic(III) on the fungus Neofusicoccum parvum: Target protein identification 了解砷(III)对新褐菌的作用模式:靶蛋白鉴定。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-08 DOI: 10.1016/j.ab.2025.115988
Andréa Engel , Florence Ferrari , Maude Meyer , Jean-Marc Strub , Martin Spichty , Christophe Bertsch , Christine Schaeffer-Reiss , Céline Tarnus , Sébastien Albrecht , Mary-Lorène Goddard
Before it was banned, sodium arsenite was the unique fungicide able to control fungi associated with grapevine trunk diseases. However, its mode of action has not been fully elucidated yet. This study focuses on the identification of arsenic(III)-binding proteins using an arsenic-based fluorescent probe and an arsenic-based affinity chromatography. To the best of our knowledge, this is the first comparative study of these techniques to demonstrate their complementarity. Mainly cysteine-rich proteins were identified, the majority of which are involved in the infection process, in particular in plant cell wall degradation, host-pathogen interaction, adhesion and pathogenicity. These proteins could therefore be relevant targets for the development of new ways of grapevine trunk disease control.
在被禁止之前,亚砷酸钠是一种独特的杀菌剂,能够控制与葡萄树干疾病相关的真菌。然而,其作用方式尚未完全阐明。本研究的重点是利用砷基荧光探针和砷基亲和色谱法鉴定砷(III)结合蛋白。据我们所知,这是第一次对这些技术进行比较研究,以证明它们的互补性。主要鉴定出富含半胱氨酸的蛋白质,其中大部分参与了感染过程,特别是在植物细胞壁降解、宿主-病原体相互作用、粘附和致病性方面。因此,这些蛋白质可能是开发葡萄树干疾病控制新方法的相关靶点。
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引用次数: 0
High-performance Sn/AuNP-based spectroscopic ellipsometric sensor for patulin 基于Sn/ aunp的展青霉素光谱椭偏传感器。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-03 DOI: 10.1016/j.ab.2025.115987
Zafer Üstündağ , Sinem Tunçer Çağlayan , Mustafa Oguzhan Caglayan
A label-free spectroscopic ellipsometric (SE) aptasensor was developed for ultra-sensitive patulin (PAT) detection on a tin (Sn) substrate modified via electrochemical grafting of a 4-mercaptobenzene diazonium-derived self-assembled monolayer. Cyclic voltammetry and high-resolution X-ray photoelectron spectroscopy confirmed uniform nanofilm formation, followed by citrate-reduced gold nanoparticle decoration and thiolated anti-PAT aptamer immobilization. Monitoring the ellipsometric phase shift (Δ) at 507 nm and 508 nm yielded linear responses over 0.01–1000 ng/mL PAT (R2 > 0.98) with limits of detection of 10.7 pg/mL and 9.5 pg/mL (3.3 σ), respectively. Isotherm fitting indicated pseudo-second-order binding (R2 = 1.00), consistent with surface-constrained, mass-transfer-limited interactions. Precision (%RSD <1.1 %) and accuracy (%RE within ±5 %) were validated in both buffer and spiked apple-juice samples (recoveries 98.9–103.2 %). This label-free SE approach combines a wide dynamic range and sub-10 pg/mL sensitivity with minimal sample preparation and no external labels.
在电化学接枝4-巯基苯重氮衍生自组装单层修饰的锡(Sn)衬底上,研制了一种用于超灵敏展青霉素(PAT)检测的无标记光谱椭偏(SE)适体传感器。循环伏安法和高分辨率x射线光电子能谱法证实了均匀的纳米膜形成,随后是柠檬酸还原金纳米颗粒装饰和硫代抗pat适配体固定。在507 nm和508 nm处监测椭偏相移(Δ),在0.01 ~ 1000 ng/mL PAT (R2 > 0.98)范围内产生线性响应,检出限分别为10.7 pg/mL和9.5 pg/mL (3.3 σ)。等温线拟合显示伪二阶结合(R2 = 1.00),符合表面约束的、传质受限的相互作用。精密度(%RSD < 1.1%)和准确度(%RE≤±5%)在缓冲液和加标苹果汁样品中均得到验证(回收率为98.9 ~ 103.2%)。这种无标签的SE方法结合了宽动态范围和低于10 pg/mL的灵敏度,最小的样品制备和无外部标签。
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引用次数: 0
An ultrasensitive electrochemical immunosensor constructed via Ag-GO-Nf nanocomposites for the detection of pefloxacin Ag-GO-Nf纳米复合材料构建的超灵敏培氟沙星电化学免疫传感器。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-03 DOI: 10.1016/j.ab.2025.115985
Jiaojiao Zhang , Yankai Liu , Enping Liu , Yajiao Li , Jingming Zhou , Yumei Chen , Hongliang Liu , Xifang Zhu , Aiping Wang
Pefloxacin (PEF), a third-generation quinolone antimicrobial drug, is widely used in fisheries and animal husbandry. However, overuse poses food safety hazards and serious threats to human health. In this study, a label-free electrochemical immunosensor based on Ag-GO-Nf nanocomposites was developed for the rapid detection of PEF. Although electrochemical immunoassays are well-established for quinolone detection, no specific method has been reported for PEF. We synthesized silver nanoparticle/graphene oxide/Nafion nanocomposites (Ag-GO-Nf) via in situ reduction, where the synergistic effect of GO (high conductivity) and AgNPs (redox-active) significantly enhanced electron transfer efficiency. The nanocomposites were characterised by UV–Vis, XRD, SEM, and TEM, while electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) were employed to monitor the stepwise immunosensor assembly. Key experimental parameters were optimized systematically. The developed sensor exhibited a wide linear range (0.50–100 ng/mL), an ultra-low limit of detection (0.27 ng/mL, S/N = 3), and high specificity toward structural analogs. Practical assays in spiked pork and milk samples yielded recoveries of 97.0–100.4 %, while the current signal retained 90.77 % of its initial value after 28 days, demonstrating excellent long-term stability. This work provides a robust technical strategy for rapid, sensitive, and efficient PEF detection.
佩氟沙星(PEF)是第三代喹诺酮类抗菌药物,广泛用于渔业和畜牧业。然而,过量使用会对食品安全造成危害,并严重威胁人体健康。本研究开发了一种基于Ag-GO-Nf纳米复合材料的无标记电化学免疫传感器,用于PEF的快速检测。虽然电化学免疫测定法已被广泛应用于喹诺酮类药物的检测,但目前尚无针对PEF的特异性方法报道。我们通过原位还原合成了银纳米颗粒/氧化石墨烯/纳米复合材料(Ag-GO-Nf),其中GO(高导电性)和AgNPs(氧化还原活性)的协同效应显著提高了电子传递效率。采用UV-Vis、XRD、SEM和TEM对复合材料进行了表征,并用电化学阻抗谱(EIS)和循环伏安法(CV)对免疫传感器组装过程进行了监测。对关键实验参数进行了系统优化。该传感器具有宽线性范围(0.50 ~ 100 ng/mL)、超低检出限(0.27 ng/mL, S/N = 3)和对结构类似物的高特异性。在加标猪肉和牛奶样品中进行实际测定,回收率为97.0-100.4%,而当前信号在28天后仍保持其初始值的90.77%,表现出优异的长期稳定性。这项工作为快速、灵敏和高效的PEF检测提供了一个强大的技术策略。
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引用次数: 0
Highly sensitive luciferase-based assay with red fluorescent protein expression for accurate quantitative monitoring and real-time visualization of cell invasion 高灵敏度荧光素酶为基础的实验与红色荧光蛋白表达准确定量监测和实时可视化的细胞入侵。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-27 DOI: 10.1016/j.ab.2025.115986
Michael Lyngbæk Christensen , Tove Kirkegaard , Ismail Gögenur , Frederik Diness , Jesper Thorvald Troelsen , Stine Bull Jessen

Background

Traditional migration and invasion assays like scratch, Transwell, and Boyden chamber are widely used but have disadvantages such as being time-consuming, lacking real-time monitoring, and relying on endpoint measurements. We addressed these limitations by developing a novel fluorescent and luciferase-based invasion assay.

Materials and methods

Three stable cell lines co-expressing the red fluorescent protein dTomato, and secreting luciferase were generated based on Caco-2, MDA-MB-231 and HEK293T cells. Transwell chamber membranes were coated with Matrigel for invasion assay, onto which the modified cells were seeded. To simulate non-invasive and invasive conditions, chambers were incubated for 48 h in FBS-free or FBS-supplemented medium. Following incubation, the Matrigel along with non-invasive cells were removed, and the chambers washed before being transferred into fresh media for 24 h allowing the cells to secrete luciferase. Luciferase activity was measured and compared to traditional cell counting invasion assay, with further confirmations through Z-stacking and microscopic fluorescent imaging.

Results

Our results demonstrated that luciferase activity accurately correlates with cell count. Applying luciferase efficiently quantifies variation in cell invasion with higher sensitivity, hence improving detection of low-level invasion as compared to cell counting techniques based on nuclear staining. The expression of the fluorescent dTomato protein proved ideal for real-time visualization of invading cells.

Conclusion

Overall, using luciferase and dTomato co-expressing cells for invasion assay showed reliable and accurate measurements of variations in cell invasion patterns. Introducing these cells reduced time-consuming steps, improved sensitivity, and endpoints measurements, while being capable of real-time visualization, providing advantages over traditional methods.
背景:传统的迁移和侵袭试验(如scratch、Transwell和Boyden chamber)被广泛使用,但存在耗时、缺乏实时监测、依赖于终点测量等缺点。我们通过开发一种新的荧光和荧光素酶为基础的入侵试验来解决这些局限性。材料与方法:以Caco-2、MDA-MB-231和HEK293T细胞为基础,制备了3株共表达红色荧光蛋白dTomato并分泌荧光素酶的稳定细胞系。在Transwell室膜上涂上一层Matrigel进行侵袭试验,并将修饰的细胞播种在其上。为了模拟无创和有创条件,实验室在不含fbs或添加fbs的培养基中孵育48小时。孵育后,除去基质和非侵入性细胞,清洗室,然后将细胞转移到新鲜培养基中24小时,使细胞分泌荧光素酶。测量荧光素酶活性,并与传统的细胞计数侵袭试验进行比较,并通过z堆叠和显微荧光成像进一步证实。结果:荧光素酶活性与细胞计数有准确的相关性。应用荧光素酶以更高的灵敏度有效地量化细胞侵袭的变化,因此与基于核染色的细胞计数技术相比,提高了对低水平侵袭的检测。荧光dTomato蛋白的表达被证明是实时可视化入侵细胞的理想选择。结论:总体而言,利用荧光素酶和dTomato共表达细胞进行侵袭实验,可以可靠、准确地测量细胞侵袭模式的变化。引入这些单元减少了耗时的步骤,提高了灵敏度和端点测量,同时能够实时可视化,与传统方法相比具有优势。
{"title":"Highly sensitive luciferase-based assay with red fluorescent protein expression for accurate quantitative monitoring and real-time visualization of cell invasion","authors":"Michael Lyngbæk Christensen ,&nbsp;Tove Kirkegaard ,&nbsp;Ismail Gögenur ,&nbsp;Frederik Diness ,&nbsp;Jesper Thorvald Troelsen ,&nbsp;Stine Bull Jessen","doi":"10.1016/j.ab.2025.115986","DOIUrl":"10.1016/j.ab.2025.115986","url":null,"abstract":"<div><h3>Background</h3><div>Traditional migration and invasion assays like scratch, Transwell, and Boyden chamber are widely used but have disadvantages such as being time-consuming, lacking real-time monitoring, and relying on endpoint measurements. We addressed these limitations by developing a novel fluorescent and luciferase-based invasion assay.</div></div><div><h3>Materials and methods</h3><div>Three stable cell lines co-expressing the red fluorescent protein dTomato, and secreting luciferase were generated based on Caco-2, MDA-MB-231 and HEK293T cells. Transwell chamber membranes were coated with Matrigel for invasion assay, onto which the modified cells were seeded. To simulate non-invasive and invasive conditions, chambers were incubated for 48 h in FBS-free or FBS-supplemented medium. Following incubation, the Matrigel along with non-invasive cells were removed, and the chambers washed before being transferred into fresh media for 24 h allowing the cells to secrete luciferase. Luciferase activity was measured and compared to traditional cell counting invasion assay, with further confirmations through Z-stacking and microscopic fluorescent imaging.</div></div><div><h3>Results</h3><div>Our results demonstrated that luciferase activity accurately correlates with cell count. Applying luciferase efficiently quantifies variation in cell invasion with higher sensitivity, hence improving detection of low-level invasion as compared to cell counting techniques based on nuclear staining. The expression of the fluorescent dTomato protein proved ideal for real-time visualization of invading cells.</div></div><div><h3>Conclusion</h3><div>Overall, using luciferase and dTomato co-expressing cells for invasion assay showed reliable and accurate measurements of variations in cell invasion patterns. Introducing these cells reduced time-consuming steps, improved sensitivity, and endpoints measurements, while being capable of real-time visualization, providing advantages over traditional methods.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"708 ","pages":"Article 115986"},"PeriodicalIF":2.5,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190684","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
Heterodimeric aptamer improves the limit of detection of sandwich ELASA and dot blot assay 异二聚体提高了夹心ELASA和斑点印迹法的检出限。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-25 DOI: 10.1016/j.ab.2025.115984
Tzi Shien Yeoh, Marimuthu Citartan
Heterodimerization, which is an amalgamation of discrete aptamers into a single functional module is a viable strategy to augment the binding strength of aptamers. In this study, we sought to derive several heterodimeric aptamers using the discrete aptamers, LepDapt-2a and LepDapt-5a prior to their binding evaluation against the target LipL32. We further integrated heterodimeric aptamer LepDapt-H1b as a detection aptamer into aptamer-based sandwich ELASA and dot blot assay for the detection of Leptospira, attaining a LOD of 4 and 10 CFU/mL for both assays, respectively, which are better compared to our previous study. Additionally, the LOQ acquired for sandwich ELASA assay was 11 CFU/mL. We have proven that heterodimerization has improved the performance of sandwich ELASA and dot blot assay, suggesting them to be applicable for the diagnostics of leptospirosis.
异二聚化是将离散的适体合并成一个单一的功能模块,是增强适体结合强度的一种可行策略。在这项研究中,我们试图在LepDapt-2a和LepDapt-5a与目标LipL32结合评估之前,使用离散的适体推导出几种异二聚体适体。我们进一步将LepDapt-H1b作为检测适配体整合到基于适配体的三明治式ELASA法和点印迹法中检测钩端螺旋体,两种检测方法的LOD分别为4和10 CFU/mL,与我们之前的研究相比有更好的提高。此外,夹心ELASA法获得的定量限为11 CFU/mL。我们已经证明,异源二聚化提高了夹心ELASA和斑点印迹法的性能,表明它们适用于钩端螺旋体病的诊断。
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引用次数: 0
H-ferritin nanocages: refined strategy for optimized protein production and purification h -铁蛋白纳米笼:优化蛋白质生产和纯化的精制策略。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-25 DOI: 10.1016/j.ab.2025.115983
Arianna Bonizzi, Marta Sevieri, Leopoldo Sitia, Raffaele Allevi, Francesca Gorgoglione, Ilaria Tagliolini, Beatrice Bignami, Serena Mazzucchelli
H-ferritin (HFn) nanocages are promising tools in biomedical applications, yet producing sufficient injectable quantities remains challenging. To optimize production, we compared two lysis methods and purification protocols, focusing on the ClearColi BL21(DE3) strain, which features a modified lipopolysaccharide that avoids triggering endotoxin responses in humans. Our findings show that omitting protease inhibitors during lysis and using 20 mM Tris-HCl pH 8.0 buffer with Q-Sepharose resin significantly enhances protein yield. Importantly, these adjustments do not compromise encapsulation efficiency or cytotoxicity, offering a more efficient and cost-effective strategy for obtaining pure, stable HFn suitable for therapeutic use.
h -铁蛋白(HFn)纳米笼在生物医学应用中是很有前途的工具,但生产足够的可注射量仍然具有挑战性。为了优化生产,我们比较了两种裂解方法和纯化方案,重点研究了ClearColi BL21(DE3)菌株,该菌株具有修饰的脂多糖,可避免引发人体内毒素反应。我们的研究结果表明,在裂解过程中省略蛋白酶抑制剂,并使用20 mM Tris-HCl pH 8.0缓冲液和Q-Sepharose树脂显著提高了蛋白质产量。重要的是,这些调整不会影响包封效率或细胞毒性,为获得适合治疗用途的纯净、稳定的HFn提供了更有效和更具成本效益的策略。
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引用次数: 0
StackAPP: Advancing autophagy protein identification with ensemble learning 利用集成学习推进自噬蛋白鉴定。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-18 DOI: 10.1016/j.ab.2025.115981
Munem Shahriar Shoyshob , Kusay Faisal Al-Tabatabaie , Lway Faisal Abdulrazak , Md. Ashikur Rahman , Md. Mamun Ali , Sobhy M. Ibrahim , Kawsar Ahmed , Francis M. Bui , Mohammad Ali Moni
Autophagy is an important cell process that may be critical for various physiological activities as well as maintenance of the cellular bioenergetic and metabolic homeostasis. Identifying the proteins involved in autophagy is essential for understanding autophagy pathways and developing treatments for autophagy-related disorders. This work introduces an innovative approach to the prediction of autophagy proteins that involves the integration of stacking classifiers with the feature fusion of Amphiphilic Pseudo Amino Acid Composition and Amino Acid Composition. Initially, protein sequences are used to extract Amphiphilic Pseudo Amino Acid Composition and Amino Acid Composition features. The complementary data collected by Amphiphilic Pseudo Amino Acid Composition and Amino Acid Composition are then integrated using a feature fusion technique. Stacking classifiers combines multiple base classifiers to improve predictive performance, using the fused features as input. The proposed method proves its efficacy in the identification of autophagy proteins by achieving an impressive accuracy of 0.9606 and the Matthews correlation coefficient (MCC) of 0.9241 on the independent test. Further, our methodology is better than the standard methods in terms of predictive accuracy, as evidenced through comparative analysis. Overall, the current study provides a realistic model for the prediction of autophagy proteins with prospects for use in the protein prediction field as well as the field of bioinformatics and biomedical to enhance future research directions.
自噬是一个重要的细胞过程,它可能对各种生理活动以及维持细胞的生物能量和代谢稳态至关重要。确定参与自噬的蛋白质对于理解自噬途径和开发自噬相关疾病的治疗方法至关重要。这项工作引入了一种预测自噬蛋白的创新方法,该方法涉及将堆叠分类器与两亲性伪氨基酸组成和氨基酸组成的特征融合。最初,蛋白质序列用于提取两亲性伪氨基酸组成和氨基酸组成特征。然后使用特征融合技术对两亲性伪氨基酸组成和氨基酸组成收集的互补数据进行整合。叠加分类器结合多个基分类器,使用融合的特征作为输入来提高预测性能。该方法鉴定自噬蛋白的准确性达到0.9606,独立检测的Matthews相关系数(MCC)达到0.9241,证明了该方法的有效性。此外,通过对比分析,我们的方法在预测准确性方面优于标准方法。总的来说,本研究为自噬蛋白的预测提供了一个现实的模型,在蛋白质预测领域以及生物信息学和生物医学领域都有应用前景,以加强未来的研究方向。
{"title":"StackAPP: Advancing autophagy protein identification with ensemble learning","authors":"Munem Shahriar Shoyshob ,&nbsp;Kusay Faisal Al-Tabatabaie ,&nbsp;Lway Faisal Abdulrazak ,&nbsp;Md. Ashikur Rahman ,&nbsp;Md. Mamun Ali ,&nbsp;Sobhy M. Ibrahim ,&nbsp;Kawsar Ahmed ,&nbsp;Francis M. Bui ,&nbsp;Mohammad Ali Moni","doi":"10.1016/j.ab.2025.115981","DOIUrl":"10.1016/j.ab.2025.115981","url":null,"abstract":"<div><div>Autophagy is an important cell process that may be critical for various physiological activities as well as maintenance of the cellular bioenergetic and metabolic homeostasis. Identifying the proteins involved in autophagy is essential for understanding autophagy pathways and developing treatments for autophagy-related disorders. This work introduces an innovative approach to the prediction of autophagy proteins that involves the integration of stacking classifiers with the feature fusion of Amphiphilic Pseudo Amino Acid Composition and Amino Acid Composition. Initially, protein sequences are used to extract Amphiphilic Pseudo Amino Acid Composition and Amino Acid Composition features. The complementary data collected by Amphiphilic Pseudo Amino Acid Composition and Amino Acid Composition are then integrated using a feature fusion technique. Stacking classifiers combines multiple base classifiers to improve predictive performance, using the fused features as input. The proposed method proves its efficacy in the identification of autophagy proteins by achieving an impressive accuracy of 0.9606 and the Matthews correlation coefficient (MCC) of 0.9241 on the independent test. Further, our methodology is better than the standard methods in terms of predictive accuracy, as evidenced through comparative analysis. Overall, the current study provides a realistic model for the prediction of autophagy proteins with prospects for use in the protein prediction field as well as the field of bioinformatics and biomedical to enhance future research directions.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"708 ","pages":"Article 115981"},"PeriodicalIF":2.5,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102569","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
High-throughput protein A chromatography platform for accurate antibody quantification in IV admixtures 高通量蛋白A层析平台用于IV外加剂中抗体的准确定量。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-18 DOI: 10.1016/j.ab.2025.115982
Tse-Hong Chen, Xiaoyang Liu, Shao-Chun Wang, Mohammed Shameem, Kenneth S. Graham
Antibodies hold significant therapeutic potential, but accurate quantification of them in complex intravenous (IV) admixtures is critical for ensuring therapeutic efficacy and patient safety. Traditional reversed-phase liquid chromatography (RPLC) often faces challenges in resolving antibodies from non-product related impurities within IV matrices. This study first evaluates the specificity of Protein A (ProA) affinity chromatography for quantifying bispecific antibodies (BsAbs) in IV matrices. The method leverages the selective binding of ProA to the antibody Fc region to achieve clear separation of antibodies from potential interference, including human serum albumin (HSA), and extractables and leachables (E&L) from contact materials, enabling accurate quantification down to 0.1 μg/mL. The fit-for-purpose method qualification secondly demonstrates linearity, accuracy, and precision across the tested concentration ranges. The ProA method achieves rapid and complete separation in 5 min without sample preparation, significantly enhancing throughput. This platform capability is further demonstrated by its successful application to five different BsAbs in this study. These findings highlight the ProA method as a reliable, efficient, and specific approach for accurately quantifying antibodies in the presence of challenging IV admixture matrices, supporting the development and administration of low-dose antibody therapies.
抗体具有重要的治疗潜力,但在复杂的静脉(IV)混合物中准确定量抗体对于确保治疗效果和患者安全至关重要。传统的反相液相色谱(RPLC)在从IV基质中的非产品相关杂质中分离抗体时经常面临挑战。本研究首先评估了蛋白A (ProA)亲和层析法定量IV基质中双特异性抗体(BsAbs)的特异性。该方法利用ProA与抗体Fc区的选择性结合,实现了抗体与潜在干扰物的清晰分离,包括人血清白蛋白(HSA)、可提取物和可浸出物(E&L),可精确定量至0.1 μg/mL。适合用途的方法鉴定其次证明了在测试浓度范围内的线性、准确性和精密度。ProA方法在5分钟内实现快速、完全的分离,无需样品制备,显著提高了通量。在本研究中,该平台在五个不同的bsab上的成功应用进一步证明了该平台的能力。这些发现强调了ProA方法是一种可靠、高效和特异性的方法,可准确定量具有挑战性的IV外加剂基质中存在的抗体,支持低剂量抗体疗法的开发和管理。
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引用次数: 0
Real-time electrochemical detection of Ascorbic acid in mouse brain homogenate using SCN-wrapped Co@NiO Nanosensor scn包覆Co@NiO纳米传感器实时电化学检测小鼠脑匀浆中抗坏血酸。
IF 2.5 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-17 DOI: 10.1016/j.ab.2025.115980
Shahid Habib Ansari , Sana Amjad , Tehreem Ul Wara , Sehrish Hanif , Ali Raza , Hafiza Khushbakht Hussain , Naeem Akhtar , Mohibullah Shah , Imran Imran , Sonam Javaid Khan , Bushra Yaqub , Samra Rasheed
Oxidative stress, a major key factor to neurological disorders such as Parkinson's, Alzheimer's, and Huntington's disease. Ascorbic acid (AA), a vital brain antioxidant, protects neurons by scavenging reactive oxygen species, and its fluctuations can damage neuronal function. Therefore, precise monitoring of AA in humans is critical for early diagnosis and disease management. However, despite significant advancements in noble metal-free nanocomposite based electrochemical sensors, precise detection remains challenging due to low physiological concentrations and interference from coexisting biomolecules, which limit sensor sensitivity, selectivity, and real-time applicability. To address these limitations herein, we synthesized cobalt-doped nickel oxide (Co@NiO), wrapped with thiourea, and dopamine (SCN- wrapped Co@NiO) for selective and sensitive detection of AA. The SCN groups provide abundant binding sites through hydrogen-bonding interactions with AA, thereby enhancing selectivity, while the Co@NiO nanostructure catalytically facilitates AA oxidation, significantly improving sensitivity and enabling efficient sensing efficacy against interfering species. The findings demonstrated that the fabricated material exhibits excellent sensitivity (0.1837 μA/nM/cm2), a wide linear range (5nM–20μM), and low detection limit (12.72 nM). Furthermore, the designed electrode has shown excellent selectivity towards AA even in presence of various interfering species, highlighting its potential in real-time analysis for practical applications.
氧化应激是帕金森氏症、阿尔茨海默氏症和亨廷顿氏症等神经系统疾病的主要关键因素。抗坏血酸(AA)是一种重要的大脑抗氧化剂,通过清除活性氧来保护神经元,其波动会损害神经元功能。因此,精确监测人类AA对早期诊断和疾病管理至关重要。然而,尽管基于无贵金属纳米复合材料的电化学传感器取得了重大进展,但由于低生理浓度和共存生物分子的干扰,精确检测仍然具有挑战性,这限制了传感器的灵敏度、选择性和实时适用性。为了解决这些限制,我们合成了用硫脲包裹的钴掺杂氧化镍(Co@NiO)和多巴胺(SCN包裹Co@NiO),用于选择性和敏感地检测AA。SCN基团通过与AA的氢键相互作用提供了丰富的结合位点,从而提高了选择性,而Co@NiO纳米结构催化促进AA氧化,显著提高了灵敏度,实现了对干扰物种的高效传感效果。结果表明,该材料具有良好的灵敏度(0.1837 μA/nM/cm2)、较宽的线性范围(5nM-20μM)和较低的检出限(12.72 nM)。此外,所设计的电极即使在各种干扰物质存在的情况下也对AA表现出良好的选择性,突出了其在实际应用中的实时分析潜力。
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Analytical biochemistry
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