A stacking-based approach for accurate prediction of antidiabetic peptides
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, XGB-RFE, was employed to determine the optimal number, m, of 84 PFs to enhance predictive performance. Subsequently, utilizing the meta-predictor approach, 45 selected PFs were integrated into...
Source: Analytical Biochemistry - April 26, 2024 Category: Biochemistry Authors: Farwa Arshad Saeed Ahmed Aqsa Amjad Muhammad Kabir Source Type: research
Exonuclease-iii -propelled DNAzyme cascade for sensitive and reliable cervical cancer related miRNA analysis
Anal Biochem. 2024 Apr 24:115547. doi: 10.1016/j.ab.2024.115547. Online ahead of print.ABSTRACTMicroRNAs (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 re...
Source: Analytical Biochemistry - April 26, 2024 Category: Biochemistry Authors: Hongli Wang Daoli Wang Yehong Xu Source Type: research
Research Progress on Prediction of RNA-protein Binding Sites in the Past Five Years
Anal Biochem. 2024 Apr 19:115535. doi: 10.1016/j.ab.2024.115535. Online ahead of print.ABSTRACTAccurately 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 f...
Source: Analytical Biochemistry - April 21, 2024 Category: Biochemistry Authors: Yun Zuo Huixian Chen Lele Yang Ruoyan Chen Xiaoyao Zhang Zhaohong Deng Source Type: research
Research Progress on Prediction of RNA-protein Binding Sites in the Past Five Years
Anal Biochem. 2024 Apr 19:115535. doi: 10.1016/j.ab.2024.115535. Online ahead of print.ABSTRACTAccurately 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 f...
Source: Analytical Biochemistry - April 21, 2024 Category: Biochemistry Authors: Yun Zuo Huixian Chen Lele Yang Ruoyan Chen Xiaoyao Zhang Zhaohong Deng Source Type: research
Research Progress on Prediction of RNA-protein Binding Sites in the Past Five Years
Anal Biochem. 2024 Apr 19:115535. doi: 10.1016/j.ab.2024.115535. Online ahead of print.ABSTRACTAccurately 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 f...
Source: Analytical Biochemistry - April 21, 2024 Category: Biochemistry Authors: Yun Zuo Huixian Chen Lele Yang Ruoyan Chen Xiaoyao Zhang Zhaohong Deng Source Type: research
Extrapolating Differential Scanning Calorimetry Data for Monoclonal Antibodies to Low Temperatures
Anal Biochem. 2024 Apr 18:115533. doi: 10.1016/j.ab.2024.115533. Online ahead of print.ABSTRACTFor 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 oC 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 ...
Source: Analytical Biochemistry - April 20, 2024 Category: Biochemistry Authors: Arne Sch ön Young Do Kwon Michael F Bender Ernesto Freire Source Type: research
Redox proteomics in melanoma cells: An optimized protocol
Anal Biochem. 2024 Apr 16;691:115543. doi: 10.1016/j.ab.2024.115543. Online ahead of print.ABSTRACTCancer 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 i...
Source: Analytical Biochemistry - April 18, 2024 Category: Biochemistry Authors: E S Cunha E Mazepa M Batista F K Marchini G R Martinez Source Type: research
Point-of-care testing of methamphetamine and cocaine utilizing wearable sensors
Anal Biochem. 2024 Apr 13:115526. doi: 10.1016/j.ab.2024.115526. Online ahead of print.ABSTRACTThe 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 acti...
Source: Analytical Biochemistry - April 15, 2024 Category: Biochemistry Authors: Ying Wang Ke Li Weijian Shen Xingxu Huang Lina Wu Source Type: research
Mechanism of Xing 9 ling tablet candy for alcoholic liver disease based on network pharmacology
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.PMID:38621605 | DOI:10.1016/j.ab.2024.115534 (Source: Analytical Biochemistry)
Source: Analytical Biochemistry - April 15, 2024 Category: Biochemistry Authors: Xiaomei Zhao Qiong Qu Ying Zhang Peiyuan Zhao Xinbo Zhang Yingying Tang Xuan Lei Xuan Wei Xiao Song Source Type: research
Point-of-care testing of methamphetamine and cocaine utilizing wearable sensors
Anal Biochem. 2024 Apr 13:115526. doi: 10.1016/j.ab.2024.115526. Online ahead of print.ABSTRACTThe 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 acti...
Source: Analytical Biochemistry - April 15, 2024 Category: Biochemistry Authors: Ying Wang Ke Li Weijian Shen Xingxu Huang Lina Wu Source Type: research
Mechanism of Xing 9 Ling tablet candy for alcoholic liver disease based on network pharmacology
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.PMID:38621605 | DOI:10.1016/j.ab.2024.115534 (Source: Analytical Biochemistry)
Source: Analytical Biochemistry - April 15, 2024 Category: Biochemistry Authors: Xiaomei Zhao Qiong Qu Ying Zhang Peiyuan Zhao Xinbo Zhang Yingying Tang Xuan Lei Xuan Wei Xiao Song Source Type: research
Point-of-care testing of methamphetamine and cocaine utilizing wearable sensors
Anal Biochem. 2024 Apr 13:115526. doi: 10.1016/j.ab.2024.115526. Online ahead of print.ABSTRACTThe 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 acti...
Source: Analytical Biochemistry - April 15, 2024 Category: Biochemistry Authors: Ying Wang Ke Li Weijian Shen Xingxu Huang Lina Wu Source Type: research
Mechanism of Xing 9 Ling tablet candy for alcoholic liver disease based on network pharmacology
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.PMID:38621605 | DOI:10.1016/j.ab.2024.115534 (Source: Analytical Biochemistry)
Source: Analytical Biochemistry - April 15, 2024 Category: Biochemistry Authors: Xiaomei Zhao Qiong Qu Ying Zhang Peiyuan Zhao Xinbo Zhang Yingying Tang Xuan Lei Xuan Wei Xiao Song Source Type: research
Point-of-care testing of methamphetamine and cocaine utilizing wearable sensors
Anal Biochem. 2024 Apr 13:115526. doi: 10.1016/j.ab.2024.115526. Online ahead of print.ABSTRACTThe 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 acti...
Source: Analytical Biochemistry - April 15, 2024 Category: Biochemistry Authors: Ying Wang Ke Li Weijian Shen Xingxu Huang Lina Wu Source Type: research
Mechanism of Xing 9 Ling tablet candy for alcoholic liver disease based on network pharmacology
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.PMID:38621605 | DOI:10.1016/j.ab.2024.115534 (Source: Analytical Biochemistry)
Source: Analytical Biochemistry - April 15, 2024 Category: Biochemistry Authors: Xiaomei Zhao Qiong Qu Ying Zhang Peiyuan Zhao Xinbo Zhang Yingying Tang Xuan Lei Xuan Wei Xiao Song Source Type: research
