Pub Date : 2024-05-01DOI: 10.1016/j.ab.2024.115548
Heyuan Zou , Huili Lai , Wenru Wu , Ruiying Cheng , Yaru Lu , Xiaoqi Peng
Oviductus Ranae is the dried oviduct from Rana dybowskii, a forest frog species with medicinal, tonic, and cosmetic properties. Due to the high price and resource shortage, counterfeit varieties of Oviductus Ranae often appear in the market. However, traditional identification methods cannot accurately differentiate between Oviductus Ranae and its adulterants. In this study, a rapid molecular identification method has been established. The method involves extracting genomic DNA in just 30 s using filter paper purification, species-specific rapid polymerase chain reaction (PCR) amplification, and finally, fluorescence detection of the products. It can accurately identify Oviductus Ranae and its three common adulterants in about 30 min, making the process simple, fast, and highly specific.
{"title":"Rapid molecular identification of Rana dybowskii by species-specific primers","authors":"Heyuan Zou , Huili Lai , Wenru Wu , Ruiying Cheng , Yaru Lu , Xiaoqi Peng","doi":"10.1016/j.ab.2024.115548","DOIUrl":"10.1016/j.ab.2024.115548","url":null,"abstract":"<div><p>Oviductus Ranae is the dried oviduct from <em>Rana dybowskii</em>, a forest frog species with medicinal, tonic, and cosmetic properties. Due to the high price and resource shortage, counterfeit varieties of Oviductus Ranae often appear in the market. However, traditional identification methods cannot accurately differentiate between Oviductus Ranae and its adulterants. In this study, a rapid molecular identification method has been established. The method involves extracting genomic DNA in just 30 s using filter paper purification, species-specific rapid polymerase chain reaction (PCR) amplification, and finally, fluorescence detection of the products. It can accurately identify Oviductus Ranae and its three common adulterants in about 30 min, making the process simple, fast, and highly specific.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140848485","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}
Pub Date : 2024-04-26DOI: 10.1016/j.ab.2024.115550
Jun Hu , Zhe Li , Bing Rao , Maha A. Thafar , Muhammad Arif
Interactions between proteins are ubiquitous in a wide variety of biological processes. Accurately identifying the protein-protein interaction (PPI) is of significant importance for understanding the mechanisms of protein functions and facilitating drug discovery. Although the wet-lab technological methods are the best way to identify PPI, their major constraints are their time-consuming nature, high cost, and labor-intensiveness. Hence, lots of efforts have been made towards developing computational methods to improve the performance of PPI prediction. In this study, we propose a novel hybrid computational method (called KSGPPI) that aims at improving the prediction performance of PPI via extracting the discriminative information from protein sequences and interaction networks. The KSGPPI model comprises two feature extraction modules. In the first feature extraction module, a large protein language model, ESM-2, is employed to exploit the global complex patterns concealed within protein sequences. Subsequently, feature representations are further extracted through CKSAAP, and a two-dimensional convolutional neural network (CNN) is utilized to capture local information. In the second feature extraction module, the query protein acquires its similar protein from the STRING database via the sequence alignment tool NW-align and then captures the graph embedding feature for the query protein in the protein interaction network of the similar protein using the algorithm of Node2vec. Finally, the features of these two feature extraction modules are efficiently fused; the fused features are then fed into the multilayer perceptron to predict PPI. The results of five-fold cross-validation on the used benchmarked datasets demonstrate that KSGPPI achieves an average prediction accuracy of 88.96 %. Additionally, the average Matthews correlation coefficient value (0.781) of KSGPPI is significantly higher than that of those state-of-the-art PPI prediction methods. The standalone package of KSGPPI is freely downloaded at https://github.com/rickleezhe/KSGPPI.
蛋白质之间的相互作用在各种生物过程中无处不在。准确鉴定蛋白质-蛋白质相互作用(PPI)对于了解蛋白质功能机制和促进药物发现具有重要意义。虽然湿实验室技术方法是鉴定 PPI 的最佳途径,但其主要限制因素是耗时长、成本高和劳动强度大。因此,人们一直在努力开发计算方法,以提高 PPI 预测的性能。在本研究中,我们提出了一种新型混合计算方法(称为 KSGPPI),旨在通过提取蛋白质序列和相互作用网络中的判别信息来提高 PPI 的预测性能。KSGPPI 模型包括两个特征提取模块。在第一个特征提取模块中,采用了大型蛋白质语言模型ESM-2,以利用隐藏在蛋白质序列中的全局复杂模式。随后,通过 CKSAAP 进一步提取特征表征,并利用二维卷积神经网络(CNN)捕捉局部信息。在第二个特征提取模块中,查询蛋白质通过序列比对工具 NW-align 从 STRING 数据库中获取其相似蛋白质,然后利用 Node2vec 算法在相似蛋白质的蛋白质相互作用网络中捕捉查询蛋白质的图嵌入特征。最后,将这两个特征提取模块的特征进行有效融合;然后将融合后的特征输入全连接神经网络,以预测 PPI。在所使用的基准数据集上进行的五倍交叉验证结果表明,KSGPPI 的平均预测准确率达到了 88.96%。此外,KSGPPI 的平均马修斯相关系数值(0.781)明显高于最先进的 PPI 预测方法。KSGPPI 的独立软件包可从 https://github.com/rickleezhe/KSGPPI 免费下载。
{"title":"Improving protein-protein interaction prediction using protein language model and protein network features","authors":"Jun Hu , Zhe Li , Bing Rao , Maha A. Thafar , Muhammad Arif","doi":"10.1016/j.ab.2024.115550","DOIUrl":"10.1016/j.ab.2024.115550","url":null,"abstract":"<div><p>Interactions between proteins are ubiquitous in a wide variety of biological processes. Accurately identifying the protein-protein interaction (PPI) is of significant importance for understanding the mechanisms of protein functions and facilitating drug discovery. Although the wet-lab technological methods are the best way to identify PPI, their major constraints are their time-consuming nature, high cost, and labor-intensiveness. Hence, lots of efforts have been made towards developing computational methods to improve the performance of PPI prediction. In this study, we propose a novel hybrid computational method (called KSGPPI) that aims at improving the prediction performance of PPI via extracting the discriminative information from protein sequences and interaction networks. The KSGPPI model comprises two feature extraction modules. In the first feature extraction module, a large protein language model, ESM-2, is employed to exploit the global complex patterns concealed within protein sequences. Subsequently, feature representations are further extracted through CKSAAP, and a two-dimensional convolutional neural network (CNN) is utilized to capture local information. In the second feature extraction module, the query protein acquires its similar protein from the STRING database via the sequence alignment tool NW-align and then captures the graph embedding feature for the query protein in the protein interaction network of the similar protein using the algorithm of Node2vec. Finally, the features of these two feature extraction modules are efficiently fused; the fused features are then fed into the multilayer perceptron to predict PPI. The results of five-fold cross-validation on the used benchmarked datasets demonstrate that KSGPPI achieves an average prediction accuracy of 88.96 %. Additionally, the average Matthews correlation coefficient value (0.781) of KSGPPI is significantly higher than that of those state-of-the-art PPI prediction methods. The standalone package of KSGPPI is freely downloaded at <span>https://github.com/rickleezhe/KSGPPI</span><svg><path></path></svg>.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140853741","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}
Pub Date : 2024-04-26DOI: 10.1016/j.ab.2024.115549
Ahmed H. Abdelazim , Saleh l. Alaqel , Atiah H. Almalki , Adnan Alharbi , Majed A. Algarni , Maram H. Abduljabbar , Mohamed H. Abdelazim
Ionic microenvironment of the nasal secretions especially calcium ions play essential role in the olfactory transmission. However, there is a critical need to determine the free calcium levels in healthy people's nasal secretions in contrast to those of patients with olfactory impairment. A selective spectrofluorometric method was created to quantify nasal calcium levels utilizing its quenching ability to the fluorescence of the functionalized carbon quantum dots. The surface of carbon quantum dots was functionalized with calcium ionophore A23187 and ion association complex, calcium phosphotungstate, to improve the selectively to quantify calcium ions. The functionalized carbon quantum dots exhibited a concentration-dependent fluorescence quenching upon interaction with calcium ions. Different factors influencing the quenching process were done to provide efficient analytical process. The new method, demonstrated accurate calcium determination over the concentration range of 200–4000 ng/mL. The suggested technique was used to measure the calcium in the nasal secretions of both healthy people and patients with olfactory impairment. The findings revealed significantly higher calcium levels in the patient with olfactory dysfunction (healthy vs. patient; 735 ± 20 ng/mL vs. 2987 ± 37 ng/mL, p < 0.05).
鼻腔分泌物中的离子微环境,尤其是钙离子在嗅觉传导中起着至关重要的作用。然而,与嗅觉障碍患者相比,健康人鼻腔分泌物中的游离钙水平亟待确定。利用功能化碳量子点对荧光的淬灭能力,创建了一种选择性光谱荧光测定法来量化鼻腔中的钙含量。为了提高钙离子定量的选择性,在碳量子点表面添加了钙离子载体 A23187 和离子结合复合物磷钨酸钙。功能化的碳量子点在与钙离子相互作用时表现出浓度依赖性荧光淬灭。为了提供高效的分析过程,对影响淬灭过程的不同因素进行了研究。新方法可在 200-4000 纳克/毫升的浓度范围内准确测定钙离子。所建议的技术被用于测量健康人和嗅觉障碍患者鼻腔分泌物中的钙。结果显示,嗅觉障碍患者的钙含量明显更高(健康人与患者;735±20 ng/mL 与 2987±37 ng/mL, p
{"title":"Spectrofluorometric determination of calcium in the human nasal secretions investigating the association with olfactory function","authors":"Ahmed H. Abdelazim , Saleh l. Alaqel , Atiah H. Almalki , Adnan Alharbi , Majed A. Algarni , Maram H. Abduljabbar , Mohamed H. Abdelazim","doi":"10.1016/j.ab.2024.115549","DOIUrl":"10.1016/j.ab.2024.115549","url":null,"abstract":"<div><p>Ionic microenvironment of the nasal secretions especially calcium ions play essential role in the olfactory transmission. However, there is a critical need to determine the free calcium levels in healthy people's nasal secretions in contrast to those of patients with olfactory impairment. A selective spectrofluorometric method was created to quantify nasal calcium levels utilizing its quenching ability to the fluorescence of the functionalized carbon quantum dots. The surface of carbon quantum dots was functionalized with calcium ionophore A23187 and ion association complex, calcium phosphotungstate, to improve the selectively to quantify calcium ions. The functionalized carbon quantum dots exhibited a concentration-dependent fluorescence quenching upon interaction with calcium ions. Different factors influencing the quenching process were done to provide efficient analytical process. The new method, demonstrated accurate calcium determination over the concentration range of 200–4000 ng/mL. The suggested technique was used to measure the calcium in the nasal secretions of both healthy people and patients with olfactory impairment. The findings revealed significantly higher calcium levels in the patient with olfactory dysfunction (healthy vs. patient; 735 ± 20 ng/mL vs. 2987 ± 37 ng/mL, <em>p</em> < 0.05).</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140851215","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}
Pub Date : 2024-04-25DOI: 10.1016/j.ab.2024.115546
Farwa Arshad, Saeed Ahmed, Aqsa Amjad, Muhammad Kabir
Diabetes is a chronic disease that is characterized by high blood sugar levels and can have several harmful outcomes. Hyperglycemia, which is defined by persistently elevated blood sugar, is one of the primary concerns. People can improve their overall well-being and get optimal health outcomes by prioritizing diabetes control. Although the use of experimental approaches in diabetes treatment is cost-effective, it necessitates the development of many strategies for evaluating the efficacy of therapies. Researchers can quickly create new strategies for managing diabetes and get vital insights by enabling virtual screening with computational tools and procedures. In this study, we suggest a predictor named STADIP (STacking-based predictor for AntiDiabetic Peptides), a new method to predict antidiabetic peptides (ADPs) utilizing a stacked-based ensemble approach. It uses 12 different feature encodings and seven machine-learning techniques to construct 84 baseline models. The impacts of various baseline models on ADP prediction were then thoroughly examined. A two-step feature selection method, eXtreme Gradient Boosting with Sequential Forward Selection (XGB-SFS), was employed to determine the optimal number, out of 84 PFs to enhance predictive performance. Subsequently, utilizing the meta-predictor approach, 45 selected PFs were integrated into an XGB classifier to formulate the final hybrid model. The proposed method demonstrated superior predictive capabilities compared to constituent baseline models, as evidenced by evaluations on both cross-validation and independent tests. During extensive independent testing, STADIP achieved promising performance with accuracy and mathew's correlation coefficient of 0.954 and 0.877, respectively. It is anticipated that it will be useful tool in helping the scientific community to identify new antidiabetic proteins.
{"title":"An explainable stacking-based approach for accelerating the prediction of antidiabetic peptides","authors":"Farwa Arshad, Saeed Ahmed, Aqsa Amjad, Muhammad Kabir","doi":"10.1016/j.ab.2024.115546","DOIUrl":"10.1016/j.ab.2024.115546","url":null,"abstract":"<div><p>Diabetes is a chronic disease that is characterized by high blood sugar levels and can have several harmful outcomes. Hyperglycemia, which is defined by persistently elevated blood sugar, is one of the primary concerns. People can improve their overall well-being and get optimal health outcomes by prioritizing diabetes control. Although the use of experimental approaches in diabetes treatment is cost-effective, it necessitates the development of many strategies for evaluating the efficacy of therapies. Researchers can quickly create new strategies for managing diabetes and get vital insights by enabling virtual screening with computational tools and procedures. In this study, we suggest a predictor named <strong><em>STADIP</em></strong> (<strong><em>ST</em></strong>acking-based predictor for <strong><em>A</em></strong>nti<strong><em>Di</em></strong>abetic <strong>P</strong>eptides), a new method to predict antidiabetic peptides (ADPs) utilizing a stacked-based ensemble approach. It uses 12 different feature encodings and seven machine-learning techniques to construct 84 baseline models. The impacts of various baseline models on ADP prediction were then thoroughly examined. A two-step feature selection method, eXtreme Gradient Boosting with Sequential Forward Selection (XGB-SFS), was employed to determine the optimal number, out of 84 PFs to enhance predictive performance. Subsequently, utilizing the meta-predictor approach, 45 selected PFs were integrated into an XGB classifier to formulate the final hybrid model. The proposed method demonstrated superior predictive capabilities compared to constituent baseline models, as evidenced by evaluations on both cross-validation and independent tests. During extensive independent testing, <em><strong>STADIP</strong></em> achieved promising performance with accuracy and mathew's correlation coefficient of 0.954 and 0.877, respectively. It is anticipated that it will be useful tool in helping the scientific community to identify new antidiabetic proteins.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140758028","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}
Pub Date : 2024-04-25DOI: 10.1016/j.ab.2024.115547
Hongli Wang , Daoli Wang , Yehong Xu
MicroRNAs (miRNAs) can serve as biomarkers for early-diagnosis, therapy, and postoperative care of cervical cancer. Sensitive and reliable quantification of miRNA remains a huge challenge due to its low expressing levels and background interference. Herein, we propose a novel exonuclease-III (Exo–III)–propelled DNAzyme cascade for sensitive and high-efficient miRNA analysis. This method involves the engineering of compact DNAzyme hairpin probes, including the H1 probe and H2 probe. The H1 probe is designed with exposed analyte recognition subunits that can specifically recognize target miRNA. This recognition triggers two processes: Exo-iii-assisted target regeneration and successive substrate cleavage catalyzed by DNAzyme. The unique character of Exo-III that catalyzes removal of mononucleotides from the blunt or recessed 3′-OH termini of dsDNA confers the approach with a minimal background signal. The multiple signal cycles provided an abundant signal amplification and consequently, the method exhibited a low limit of detection of 3.12 fM, and a better specificity over several homologous miRNAs. In summary, this powerful Exo-III driven DNAzyme cascaded system offers broader and more adaptable methods for comprehending the activities of miRNA in various biological occurrences.
微RNA(miRNA)可作为宫颈癌早期诊断、治疗和术后护理的生物标志物。由于 miRNA 的低表达水平和背景干扰,对其进行灵敏可靠的定量分析仍是一项巨大的挑战。在此,我们提出了一种新型的外切核酸酶 III(Exo-III)推进 DNA 酶级联,用于灵敏高效的 miRNA 分析。这种方法涉及设计紧凑的 DNA 酶发夹探针,包括 H1 探针和 H2 探针。H1 探针设计有暴露的分析物识别亚基,可特异性识别目标 miRNA。这种识别会触发两个过程:Exo-iii- 辅助靶再生和 DNA 酶催化的连续底物裂解。Exo-III 催化从 dsDNA 的钝端或凹陷的 3′-OH 端去除单核苷酸,这一独特特性使该方法的背景信号极低。多重信号循环提供了丰富的信号放大,因此,该方法的检测限低至 3.12 fM,对几种同源 miRNA 具有更好的特异性。总之,这种功能强大的 Exo-III 驱动 DNA 酶级联系统为了解 miRNA 在各种生物现象中的活性提供了更广泛、更灵活的方法。
{"title":"Exonuclease-iii -propelled DNAzyme cascade for sensitive and reliable cervical cancer related miRNA analysis","authors":"Hongli Wang , Daoli Wang , Yehong Xu","doi":"10.1016/j.ab.2024.115547","DOIUrl":"10.1016/j.ab.2024.115547","url":null,"abstract":"<div><p>MicroRNAs (miRNAs) can serve as biomarkers for early-diagnosis, therapy, and postoperative care of cervical cancer. Sensitive and reliable quantification of miRNA remains a huge challenge due to its low expressing levels and background interference. Herein, we propose a novel exonuclease-III (Exo–III)–propelled DNAzyme cascade for sensitive and high-efficient miRNA analysis. This method involves the engineering of compact DNAzyme hairpin probes, including the H1 probe and H2 probe. The H1 probe is designed with exposed analyte recognition subunits that can specifically recognize target miRNA. This recognition triggers two processes: Exo-iii-assisted target regeneration and successive substrate cleavage catalyzed by DNAzyme. The unique character of Exo-III that catalyzes removal of mononucleotides from the blunt or recessed 3′-OH termini of dsDNA confers the approach with a minimal background signal. The multiple signal cycles provided an abundant signal amplification and consequently, the method exhibited a low limit of detection of 3.12 fM, and a better specificity over several homologous miRNAs. In summary, this powerful Exo-III driven DNAzyme cascaded system offers broader and more adaptable methods for comprehending the activities of miRNA in various biological occurrences.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140762056","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}
Accurately predicting RNA-protein binding sites is essential to gain a deeper comprehension of the protein-RNA interactions and their regulatory mechanisms, which are fundamental in gene expression and regulation. However, conventional biological approaches to detect these sites are often costly and time-consuming. In contrast, computational methods for predicting RNA protein binding sites are both cost-effective and expeditious. This review synthesizes already existing computational methods, summarizing commonly used databases for predicting RNA protein binding sites. In addition, applications and innovations of computational methods using traditional machine learning and deep learning for RNA protein binding site prediction during 2018–2023 are presented. These methods cover a wide range of aspects such as effective database utilization, feature selection and encoding, innovative classification algorithms, and evaluation strategies. Exploring the limitations of existing computational methods, this paper delves into the potential directions for future development. DeepRKE, RDense, and DeepDW all employ convolutional neural networks and long and short-term memory networks to construct prediction models, yet their algorithm design and feature encoding differ, resulting in diverse prediction performances.
{"title":"Research progress on prediction of RNA-protein binding sites in the past five years","authors":"Yun Zuo , Huixian Chen , Lele Yang, Ruoyan Chen, Xiaoyao Zhang, Zhaohong Deng","doi":"10.1016/j.ab.2024.115535","DOIUrl":"10.1016/j.ab.2024.115535","url":null,"abstract":"<div><p>Accurately predicting RNA-protein binding sites is essential to gain a deeper comprehension of the protein-RNA interactions and their regulatory mechanisms, which are fundamental in gene expression and regulation. However, conventional biological approaches to detect these sites are often costly and time-consuming. In contrast, computational methods for predicting RNA protein binding sites are both cost-effective and expeditious. This review synthesizes already existing computational methods, summarizing commonly used databases for predicting RNA protein binding sites. In addition, applications and innovations of computational methods using traditional machine learning and deep learning for RNA protein binding site prediction during 2018–2023 are presented. These methods cover a wide range of aspects such as effective database utilization, feature selection and encoding, innovative classification algorithms, and evaluation strategies. Exploring the limitations of existing computational methods, this paper delves into the potential directions for future development. DeepRKE, RDense, and DeepDW all employ convolutional neural networks and long and short-term memory networks to construct prediction models, yet their algorithm design and feature encoding differ, resulting in diverse prediction performances.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140785825","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}
Pub Date : 2024-04-19DOI: 10.1016/j.ab.2024.115533
Arne Schön , Young Do Kwon , Michael F. Bender , Ernesto Freire
For irreversible denaturation transitions such as those exhibited by monoclonal antibodies, differential scanning calorimetry provides the denaturation temperature, Tm, the rate of denaturation at Tm, and the activation energy at Tm. These three quantities are essential but not sufficient for an accurate extrapolation of the rate of denaturation to temperatures of 25 °C and below. We have observed that the activation energy is not constant but temperature dependent due to the existence of an activation heat capacity, Cp,a. It is shown in this paper that a model that incorporates Cp,a is able to account for previous observations like, for example, that increasing the Tm does not always improve the stability at low temperatures; that some antibodies exhibit lower stabilities at 5 °C than at 25 °C; or that low temperature stabilities do not follow the rank order derived from Tm values. Most importantly, the activation heat capacity model is able to reproduce time dependent stabilities measured by size exclusion chromatography at low temperatures.
对于单克隆抗体等不可逆变性转换,差示扫描量热法可提供变性温度 Tm、Tm 时的变性速率和 Tm 时的活化能。这三个量对于准确推断变性率在 25 °C 及以下的温度是必不可少的,但还不够。我们注意到,由于活化热容量 Cp,a 的存在,活化能并非恒定不变,而是与温度有关。本文表明,包含 Cp,a 的模型能够解释之前的观察结果,例如,提高 Tm 值并不总能提高低温稳定性;一些抗体在 5 °C 时的稳定性低于 25 °C 时;或者低温稳定性并不遵循从 Tm 值得出的排名顺序。最重要的是,活化热容量模型能够再现尺寸排阻色谱法在低温下测得的随时间变化的稳定性。
{"title":"Extrapolating differential scanning calorimetry data for monoclonal antibodies to low temperatures","authors":"Arne Schön , Young Do Kwon , Michael F. Bender , Ernesto Freire","doi":"10.1016/j.ab.2024.115533","DOIUrl":"https://doi.org/10.1016/j.ab.2024.115533","url":null,"abstract":"<div><p>For irreversible denaturation transitions such as those exhibited by monoclonal antibodies, differential scanning calorimetry provides the denaturation temperature, T<sub>m</sub>, the rate of denaturation at T<sub>m</sub>, and the activation energy at T<sub>m</sub>. These three quantities are essential but not sufficient for an accurate extrapolation of the rate of denaturation to temperatures of 25 °C and below. We have observed that the activation energy is not constant but temperature dependent due to the existence of an activation heat capacity, C<sub>p,a</sub>. It is shown in this paper that a model that incorporates C<sub>p,a</sub> is able to account for previous observations like, for example, that increasing the T<sub>m</sub> does not always improve the stability at low temperatures; that some antibodies exhibit lower stabilities at 5 °C than at 25 °C; or that low temperature stabilities do not follow the rank order derived from T<sub>m</sub> values. Most importantly, the activation heat capacity model is able to reproduce time dependent stabilities measured by size exclusion chromatography at low temperatures.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140637850","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}
Pub Date : 2024-04-16DOI: 10.1016/j.ab.2024.115543
E.S. Cunha , E. Mazepa , M. Batista , F.K. Marchini , G.R. Martinez
Cancer development and progression are intimately related with post-translational protein modifications, e.g., highly reactive thiol moiety of cysteines enables structural rearrangements resulting in redox biological switches. In this context, redox proteomics techniques, such as 2D redox DIGE, biotin switch assay and OxIcat are fundamental tools to identify and quantify redox-sensitive proteins and to understand redox mechanisms behind thiol modifications. Given the great variability in redox proteomics protocols, problems including decreased resolution of peptides and low protein amounts even after enrichment steps may occur. Considering the biological importance of thiol's oxidation in melanoma, we adapted the biotin-switch assay technique for melanoma cells in order to overcome the limitations and improve coverage of detected proteins.
{"title":"Redox proteomics in melanoma cells: An optimized protocol","authors":"E.S. Cunha , E. Mazepa , M. Batista , F.K. Marchini , G.R. Martinez","doi":"10.1016/j.ab.2024.115543","DOIUrl":"https://doi.org/10.1016/j.ab.2024.115543","url":null,"abstract":"<div><p>Cancer development and progression are intimately related with post-translational protein modifications, e.g., highly reactive thiol moiety of cysteines enables structural rearrangements resulting in redox biological switches. In this context, redox proteomics techniques, such as 2D redox DIGE, biotin switch assay and OxIcat are fundamental tools to identify and quantify redox-sensitive proteins and to understand redox mechanisms behind thiol modifications. Given the great variability in redox proteomics protocols, problems including decreased resolution of peptides and low protein amounts even after enrichment steps may occur. Considering the biological importance of thiol's oxidation in melanoma, we adapted the biotin-switch assay technique for melanoma cells in order to overcome the limitations and improve coverage of detected proteins.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140621911","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}
Pub Date : 2024-04-16DOI: 10.1016/j.ab.2024.115526
Ying Wang , Ke Li , Weijian Shen , Xingxu Huang , Lina Wu
The imperative for the point-of-care testing of methamphetamine and cocaine in drug abuse prevention necessitates innovative solutions. To address this need, we have introduced a multi-channel wearable sensor harnessing CRISPR/Cas12a system. A CRISPR/Cas12a based system, integrated with aptamers specific to methamphetamine and cocaine, has been engineered. These aptamers function as signal-mediated intermediaries, converting methamphetamine and cocaine into nucleic acid signals, subsequently generating single-stranded DNA to activate the Cas12 protein. Additionally, we have integrated a microfluidic system and magnetic separation technology into the CRISPR system, enabling rapid and precise detection of cocaine and methamphetamine. The proposed sensing platform demonstrated exceptional sensitivity, achieving a detection limit as low as 0.1 ng/mL. This sensor is expected to be used for on-site drug detection in the future.
{"title":"Point-of-care testing of methamphetamine and cocaine utilizing wearable sensors","authors":"Ying Wang , Ke Li , Weijian Shen , Xingxu Huang , Lina Wu","doi":"10.1016/j.ab.2024.115526","DOIUrl":"https://doi.org/10.1016/j.ab.2024.115526","url":null,"abstract":"<div><p>The imperative for the point-of-care testing of methamphetamine and cocaine in drug abuse prevention necessitates innovative solutions. To address this need, we have introduced a multi-channel wearable sensor harnessing CRISPR/Cas12a system. A CRISPR/Cas12a based system, integrated with aptamers specific to methamphetamine and cocaine, has been engineered. These aptamers function as signal-mediated intermediaries, converting methamphetamine and cocaine into nucleic acid signals, subsequently generating single-stranded DNA to activate the Cas12 protein. Additionally, we have integrated a microfluidic system and magnetic separation technology into the CRISPR system, enabling rapid and precise detection of cocaine and methamphetamine. The proposed sensing platform demonstrated exceptional sensitivity, achieving a detection limit as low as 0.1 ng/mL. This sensor is expected to be used for on-site drug detection in the future.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140647118","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}
Pub Date : 2024-04-14DOI: 10.1016/j.ab.2024.115534
Xiaomei Zhao , Qiong Qu , Ying Zhang , Peiyuan Zhao , Xinbo Zhang , Yingying Tang , Xuan Lei , Xuan Wei , Xiao Song
Xing 9 Ling tablet candy (X9LTC) effectively treats alcoholic liver disease (ALD), but its potential mechanism and molecular targets remain unstudied. We aimed to address this gap using network pharmacology. Furthermore, high-performance liquid chromatography (HPLC) and database analysis revealed a total of 35 active ingredients and 311 corresponding potential targets of X9LTC. Protein interaction analysis revealed PTGS2, JUN, and FOS as its core targets. Enrichment analysis indicated that chemical carcinogenesis-receptor activation, IL-17 and TNF signaling pathway were enriched by multiple core targets, which might be the main pathway of action. Further molecular docking validation showed that the core targets had good binding activities with the identified compounds. Animal experiments showed that X9LTC could reduce the high expression of ALT, AST and TG in the serum of ALD mice, alleviate the lesions in liver tissues, and reverse the high expression of PTGS2, JUN, and FOS proteins in the liver tissues. In this study, we established a method for the determination of X9LTC content for the first time, and predicted its active ingredient and mechanism of action in treating ALD, providing theoretical basis for further research.
{"title":"Mechanism of Xing 9 ling tablet candy for alcoholic liver disease based on network pharmacology","authors":"Xiaomei Zhao , Qiong Qu , Ying Zhang , Peiyuan Zhao , Xinbo Zhang , Yingying Tang , Xuan Lei , Xuan Wei , Xiao Song","doi":"10.1016/j.ab.2024.115534","DOIUrl":"https://doi.org/10.1016/j.ab.2024.115534","url":null,"abstract":"<div><p>Xing 9 Ling tablet candy (X9LTC) effectively treats alcoholic liver disease (ALD), but its potential mechanism and molecular targets remain unstudied. We aimed to address this gap using network pharmacology. Furthermore, high-performance liquid chromatography (HPLC) and database analysis revealed a total of 35 active ingredients and 311 corresponding potential targets of X9LTC. Protein interaction analysis revealed PTGS2, JUN, and FOS as its core targets. Enrichment analysis indicated that chemical carcinogenesis-receptor activation, IL-17 and TNF signaling pathway were enriched by multiple core targets, which might be the main pathway of action. Further molecular docking validation showed that the core targets had good binding activities with the identified compounds. Animal experiments showed that X9LTC could reduce the high expression of ALT, AST and TG in the serum of ALD mice, alleviate the lesions in liver tissues, and reverse the high expression of PTGS2, JUN, and FOS proteins in the liver tissues. In this study, we established a method for the determination of X9LTC content for the first time, and predicted its active ingredient and mechanism of action in treating ALD, providing theoretical basis for further research.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140619042","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}