Analytical biochemistry最新文献_第10页

Application and performance enhancement of FAIMS spectral data for deep learning analysis using generative adversarial network reinforcement 利用生成式对抗网络强化 FAIMS 光谱数据在深度学习分析中的应用和性能提升。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-20 DOI: 10.1016/j.ab.2024.115627

Ruilong Zhang, Xiaoxia Du, Hua Li

{"title":"Application and performance enhancement of FAIMS spectral data for deep learning analysis using generative adversarial network reinforcement","authors":"Ruilong Zhang, Xiaoxia Du, Hua Li","doi":"10.1016/j.ab.2024.115627","DOIUrl":"10.1016/j.ab.2024.115627","url":null,"abstract":"<div><p>When using High-field asymmetric ion mobility spectrometry (FAIMS) to process complex mixtures for deep learning analysis, there is a problem of poor recognition performance due to the lack of high-quality data and low sample diversity. In this paper, a Generative Adversarial Network (GAN) method is introduced to simulate and generate highly realistic and diverse spectral for expanding the dataset using real mixture spectral data of 15 classes collected by FAIMS. The mixed datasets were put into VGG and ResNeXt for testing respectively, and the experimental results proved that the best recognition effect was achieved when the ratio of real data to generated data was 1:4: where accuracy improved by 24.19 % and 6.43 %; precision improved by 23.71 % and 6.97 %; recall improved by 21.08 % and 7.09 %; and F1-score improved by 24.50 % and 8.23 %. The above results strongly demonstrate that GAN can effectively expand the data volume and increase the sample diversity without increasing the additional experimental cost, which significantly enhances the experimental effect of FAIMS spectral for the analysis of complex mixtures.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"694 ","pages":"Article 115627"},"PeriodicalIF":2.6,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733364","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

Development of TaqMan-based real-time PCR based on ψ gene for quantitative detection of CAR-T cells 开发基于 ψ 基因的 TaqMan 实时 PCR，用于 CAR-T 细胞的定量检测。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-18 DOI: 10.1016/j.ab.2024.115626

Han Hu , Yining Cheng , Jinjin Cao , Yujie Guo , Haixiao Duan , Yuling Jin , Lingfang Zhang , Yang Wang , Binlei Liu

{"title":"Development of TaqMan-based real-time PCR based on ψ gene for quantitative detection of CAR-T cells","authors":"Han Hu , Yining Cheng , Jinjin Cao , Yujie Guo , Haixiao Duan , Yuling Jin , Lingfang Zhang , Yang Wang , Binlei Liu","doi":"10.1016/j.ab.2024.115626","DOIUrl":"10.1016/j.ab.2024.115626","url":null,"abstract":"<div><p>Chimeric-antigen-receptor-T (CAR-T) have heralded a paradigm shift in the landscape of cancer immunotherapy. Retrovirus-mediated gene transfer serves to deliver the specific CAR expressing cassette into T cells across a spectrum of basic research and clinical contests in cancer therapy. However, it is necessary to devise a precise and validated quantitative methodology tailored to the diverse CAR constructs. In the investigation, a TaqMan real-time qPCR method was developed, utilizing primers targeting ψ gene sequence. This method offers a swift, sensitive, reproducible, and accurate tool for evaluating retroviral copy numbers at the integrated DNA level. Importantly, the established qPCR exhibits no cross-reactivity with non-transduced T cells or tissues. The regression equation characterizing TaqMan real-time PCR dynamics is y = −3.3841x + 41.402 (<em>R</em><sup>2</sup> = 0.999), showing an amplification efficiency of 97.47 %. Notably, the established qPCR method achieves a minimum detection of 43.1 copies/μL. Furthermore, both intra- and inter-group discrepancies remain below 4 %, underscoring the good repeatability of the established method. Our <em>in vitro</em> and <em>in vivo</em> results also support its sensitivity, specificity, and stability. Consequently, this method offers researchers with a cost-effective tool to quantify CAR copies both <em>in vitro</em> and <em>in vivo</em>.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"694 ","pages":"Article 115626"},"PeriodicalIF":2.6,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733365","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

Targeted analysis of organic acids with GC-MS/MS: Challenges and prospects 利用 GC-MS/MS 对有机酸进行目标分析：挑战与前景。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-18 DOI: 10.1016/j.ab.2024.115620

Jeremie Zander Lindeque

引用次数: 0

Nitro fatty acids: A comprehensive review on analytical methods and levels in health and disease 硝基脂肪酸：关于健康和疾病中的分析方法和水平的全面综述。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-17 DOI: 10.1016/j.ab.2024.115624

Yasmin Elshoura , Magy Herz , Mohamed Z. Gad , Rasha Hanafi

{"title":"Nitro fatty acids: A comprehensive review on analytical methods and levels in health and disease","authors":"Yasmin Elshoura , Magy Herz , Mohamed Z. Gad , Rasha Hanafi","doi":"10.1016/j.ab.2024.115624","DOIUrl":"10.1016/j.ab.2024.115624","url":null,"abstract":"<div><p>Nitro fatty acids (NO<sub>2</sub>–FAs) are biologically active compounds produced from the reaction of unsaturated fatty acids with reactive nitrogen species (RNS). Due to their electrophilic nature, these endogenously produced metabolites can react with nucleophilic targets, producing a spectrum of modulatory and protective effects. Determination of NO<sub>2</sub>–FAs in biological samples is challenging due to their low nanomolar to picomolar endogenous concentrations, indistinct metabolism, and distribution in many tissues and biofluids. Several attempts have been made to develop precise, standardized, and efficient methodologies for assessing physiological and pathophysiological processes to overcome the difficulties associated with their measurement. This review discusses those approaches utilizing liquid chromatography tandem mass spectrometry (LC‒MS/MS) and gas chromatography tandem mass spectrometry (GC‒MS/MS) for the quantification of NO<sub>2</sub>–FAs, in addition to a summary of their laboratory synthesis and extraction from biological samples. Clinical associations with different pathological conditions, including hyperlipidaemia, cardiac ischemia and herpes simplex type 2 viral infection (HSV-2), are also discussed.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"694 ","pages":"Article 115624"},"PeriodicalIF":2.6,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141726801","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

Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening 通过差异表达基因分析和硅学筛选鉴定急性淋巴细胞白血病耐药性的潜在抑制剂

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-16 DOI: 10.1016/j.ab.2024.115619

Başak Özay , Ezgi Yağmur Tükel , Gizem Ayna Duran , Yağmur Kiraz

{"title":"Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening","authors":"Başak Özay , Ezgi Yağmur Tükel , Gizem Ayna Duran , Yağmur Kiraz","doi":"10.1016/j.ab.2024.115619","DOIUrl":"10.1016/j.ab.2024.115619","url":null,"abstract":"<div><p>Acute lymphoblastic leukemia (ALL) is a disease of lymphocyte origin predominantly diagnosed in children. While its 5-year survival rate is high, resistance to chemotherapy drugs is still an obstacle. Our aim is to determine differentially expressed genes (DEGs) related to Asparaginase, Daunorubicin, Prednisolone, and Vincristine resistance and identify potential inhibitors via docking. Three datasets were accessed from the Gene Expression Omnibus database; GSE635, GSE19143, and GSE22529. The microarray data was analyzed using R4.2.0 and Bioconductor packages, and pathway and protein-protein interaction analysis were performed. We identified 1294 upregulated DEGs, with 12 genes consistently upregulated in all four resistant groups. KEGG analysis revealed an association with the PI3K-Akt pathway. Among DEGs, 33 hub genes including MDM2 and USP7 were pinpointed. Within common genes, CLDN9 and HS3ST3A1 were subjected to molecular docking against 3556 molecules. Following ADMET analysis, three drugs emerged as potential inhibitors: Flunarizine, Talniflumate, and Eltrombopag. Molecular dynamics analysis for HS3ST3A1 indicated all candidates had the potential to overcome drug resistance, Eltrombopag displaying particularly promising results. This study promotes a further understanding of drug resistance in ALL, introducing novel genes for consideration in diagnostic screening. It also presents potential inhibitor candidates to tackle drug resistance through repurposing.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"694 ","pages":"Article 115619"},"PeriodicalIF":2.6,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141637487","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

Spectroscopic, electrochemical, and molecular docking studies of the interaction between the antihistamine drug desloratadine and dsDNA 抗组胺药物地氯雷他定与 dsDNA 之间相互作用的光谱、电化学和分子对接研究

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-16 DOI: 10.1016/j.ab.2024.115622

Mehmetcan Bilkay , Cigdem Kanbes-Dindar , Burcin Bozal-Palabiyik , Gokcen Eren , Hayriye Eda Satana Kara , Bengi Uslu

{"title":"Spectroscopic, electrochemical, and molecular docking studies of the interaction between the antihistamine drug desloratadine and dsDNA","authors":"Mehmetcan Bilkay , Cigdem Kanbes-Dindar , Burcin Bozal-Palabiyik , Gokcen Eren , Hayriye Eda Satana Kara , Bengi Uslu","doi":"10.1016/j.ab.2024.115622","DOIUrl":"10.1016/j.ab.2024.115622","url":null,"abstract":"<div><p>Through the utilization of fluorescence spectroscopy, electrochemical, and molecular docking methods, this research investigates the interaction between the antihistamine drug desloratadine and calf thymus double-stranded DNA (ct-dsDNA). Deoxyguanosine (dGuo) and deoxyadenosine (dAdo) oxidation signals were diminished by incubation with varying concentrations of desloratadine, as determined by differential pulse voltammetry (DPV). This change was ascribed to desloratadine's binding mechanism to ct-dsDNA. The binding constant (K<sub>b</sub>) between desloratadine and ct-dsDNA was determined to be 2.2 × 10<sup>5</sup> M<sup>−1</sup> throughout electrochemical experiments. In order to further develop our comprehension of the interaction mechanism between desloratadine and ct-dsDNA, a series of spectroscopic experiments and molecular docking simulations were conducted. The K<sub>b</sub> value was found to be 8.85 × 10<sup>4</sup> M<sup>−1</sup> at a temperature of 25 °C by the use of fluorescence spectroscopic techniques. In summary, the utilization of electrochemical and spectroscopic techniques, alongside molecular docking investigations, has led to the prediction that desloratadine has the capability to interact with ct-dsDNA by groove binding.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"694 ","pages":"Article 115622"},"PeriodicalIF":2.6,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141691917","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

Single-round QuikChange PCR for engineering multiple site-directed mutations in plasmid DNA 单轮 QuikChange PCR，用于在质粒 DNA 中设计多个定点定向突变。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-15 DOI: 10.1016/j.ab.2024.115621

Yunxiang Li , Mileina Pinones , Alexis Breeland , Peilin Jiang

{"title":"Single-round QuikChange PCR for engineering multiple site-directed mutations in plasmid DNA","authors":"Yunxiang Li , Mileina Pinones , Alexis Breeland , Peilin Jiang","doi":"10.1016/j.ab.2024.115621","DOIUrl":"10.1016/j.ab.2024.115621","url":null,"abstract":"<div><p>Mutational study is a cornerstone methodology in biochemistry and genetics, and many mutagenesis strategies have been invented to promote the efficiency of gene engineering. In this study, we developed a simple and timesaving approach to integrate simultaneous mutagenesis at discrete sites. By using plasmid as a template and compatible oligonucleotide primers per the QuikChange strategy, our method was able to introduce multiple nucleotide insertions, deletions and replacements in one round of polymerase chain reaction. The longest insertion and deletion were achieved with 28 bp and 16 bp mismatch respectively. For minor nucleotide replacements (mismatch no more than 4 bp), mutations were achieved at up to 4 discrete locations. Usually, a successful clone with all desired mutations was found by screening 5 colonies. Clones with a subset of mutations may be stocked into the library of mutants or used as templates in the next rounds of mutagenic PCR to accomplish the entire construction project. This method can be applied to build up a combinatory library of mutants through saturation mutagenesis at multiple sites. It is promising to facilitate the research of protein biochemistry, forward genetics and synthetic biology.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"694 ","pages":"Article 115621"},"PeriodicalIF":2.6,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632419","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

Using absorbance detection for hs-SV-AUC characterization of adeno-associated virus 利用吸光检测法鉴定腺联体病毒的 hs-SV-AUC 特征。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-15 DOI: 10.1016/j.ab.2024.115617

Nicholas R. Larson , George M. Bou-Assaf , Thomas M. Laue , Steven A. Berkowitz

引用次数: 0

Experimental study on the detection of Gastrodia elata by enzymatic recombinase amplification and immunochromatography 利用酶重组酶等温扩增和免疫层析技术检测 G.elata。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-14 DOI: 10.1016/j.ab.2024.115618

Qiuhe Ma , Tao Li , Yue Liu , Jinjun Chai , Ziqiang Xu , Ang Liu , Yuhe Ma , Mingcheng Li , Yongmei Qu , Lijun Gao

{"title":"Experimental study on the detection of Gastrodia elata by enzymatic recombinase amplification and immunochromatography","authors":"Qiuhe Ma , Tao Li , Yue Liu , Jinjun Chai , Ziqiang Xu , Ang Liu , Yuhe Ma , Mingcheng Li , Yongmei Qu , Lijun Gao","doi":"10.1016/j.ab.2024.115618","DOIUrl":"10.1016/j.ab.2024.115618","url":null,"abstract":"<div><h3>Objective</h3><p>The objective of this research is to develop two methodologies, Enzymatic recombinase amplification (ERA) and Polymerase Chain Reaction (PCR) coupled with Lateral Flow Dipstick (LFD), for the swift authentication of <em>Gastrodia elata</em>.</p></div><div><h3>Methodology</h3><p>Primers and nfo probes for the ERA of <em>Gastrodia elata</em> were developed based on the ITS2 genome sequences of <em>Gastrodia elata</em> and its counterfeits. Specific primers for the PCR analysis of <em>Gastrodia elata</em> were generated using the NCBI (National Center for Biotechnology Information) online platform. Through experimental validation, the optimal reaction system and conditions for both methodologies were established, and their efficacy was assessed.</p></div><div><h3>Results</h3><p>The methodologies developed herein are applicable for the targeted analysis of the medicinal species, <em>Gastrodia elata</em>. The sensitivity of the ERA-LFD detection method matched that of the conventional PCR-LFD approach, recorded at 1 ng μL<sup>−1</sup>. Consistency was observed in the results across three replicates of visualization test strips for both techniques. Upon evaluation, both the PCR-LFD and ERA-LFD methods demonstrated a total compliance rate of 100 %.</p></div><div><h3>Conclusion</h3><p>The ERA-LFD and PCR-LFD methods facilitate reduced detection times and offer visual results. These techniques are particularly effective for on-site detection and quality control in the authentication of <em>Gastrodia elata</em> within traditional Chinese medicine markets and at the primary level of healthcare provision.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"694 ","pages":"Article 115618"},"PeriodicalIF":2.6,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141619075","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

Paper based analytical devices for ions determination in nasal secretions demonstrating association with olfactory function 用于测定鼻腔分泌物中离子含量的纸质分析装置，证明与嗅觉功能有关。

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2024-07-11 DOI: 10.1016/j.ab.2024.115614

Ahmed H. Abdelazim , Mohamed H. Abdelazim , Majed A. Algarni , Fahad T. Alsulami , Reem M. Alnemari , Adnan Alharbi , Maram H. Abduljabbar , Atiah H. Almalki

{"title":"Paper based analytical devices for ions determination in nasal secretions demonstrating association with olfactory function","authors":"Ahmed H. Abdelazim , Mohamed H. Abdelazim , Majed A. Algarni , Fahad T. Alsulami , Reem M. Alnemari , Adnan Alharbi , Maram H. Abduljabbar , Atiah H. Almalki","doi":"10.1016/j.ab.2024.115614","DOIUrl":"10.1016/j.ab.2024.115614","url":null,"abstract":"<div><p>Nasal ions environment plays a crucial role in maintaining nasal physiology and supports olfactory transmission. Addressing the limited research on nasal ion levels and their association with olfactory function, paper-based sensors were developed for determination of sodium, potassium, calcium and chloride in the nasal mucus of healthy volunteers and patients with olfactory dysfunction. Multi-walled carbon nanotubes and carbon quantum dots from beetroot were incorporated into paper substrate where sensors were designed with ion association complexes for sodium, potassium, calcium and chloride enhancing the recognition sensing capabilities. The sensors composition was optimized, including ion-exchange materials and plasticizers, to enhance sensitivity and selectivity. The performance of the sensors is evaluated based on Nernstian slope, dynamic range, detection limit and response time. Selectivity of the sensors was tested and the results demonstrated high selectivity for the target ions. The sensors were successfully determined sodium, potassium, calcium and chloride levels in nasal mucus of healthy volunteers and patients with olfactory dysfunction. The results revealed elevated calcium levels in patients with olfactory dysfunction, highlighting associated diagnostic implications. This suggests that the proposed sensors could serve as a diagnostic tool for olfactory evaluation, particularly in resource-constrained settings where access to advanced diagnostic tools is limited.</p></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"694 ","pages":"Article 115614"},"PeriodicalIF":2.6,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141598160","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