ELECTROPHORESIS最新文献_第8页

Investigation of sample handling steps for accurate heparan sulphate disaccharide analysis using HPLC-MS. 利用 HPLC-MS 对硫酸肝素二糖进行精确分析的样品处理步骤研究。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-21 DOI: 10.1002/elps.202400091

Domonkos Pál, Gábor Tóth, Lilla Turiák

{"title":"Investigation of sample handling steps for accurate heparan sulphate disaccharide analysis using HPLC-MS.","authors":"Domonkos Pál, Gábor Tóth, Lilla Turiák","doi":"10.1002/elps.202400091","DOIUrl":"https://doi.org/10.1002/elps.202400091","url":null,"abstract":"Heparan sulphates (HSs), a specific class of glycosaminoglycans (GAGs), are important participants of cellular signalling. Analytical characterization of GAGs requires a complex sample preparation workflow. Although a detailed stability and recovery study is available for the chondroitin sulphate GAG class, the literature concerning HS is incomplete in this regard. Therefore, our aim was to systematically investigate various parameters that could potentially influence the stability and recovery of HS samples when performing disaccharide analysis using high-performance liquid chromatography-mass spectrometry. First, effects concerning vacuum evaporation and freezing were investigated. Next, the storage stability of the HS disaccharides was analysed under several conditions such as temperature, pH, digestion buffers, injection solvents and storage vessels. We have identified several critical parameters influencing the stability and recovery of HS disaccharides. We concluded that major sample loss is expected when Tris-HCl is used as digestion buffer, followed by vacuum evaporation at elevated temperatures, or samples are stored under alkaline conditions. Following the practical considerations of this paper can contribute to increasing the reliability of future analytical measurements.","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A semen-specific deoxyribonucleic acid methylation model for epigenetic age estimation and its robustness under environmental challenges 用于表观遗传年龄估计的精液特异性脱氧核糖核酸甲基化模型及其在环境挑战下的稳健性。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-20 DOI: 10.1002/elps.202400054

Sena Er, Zehra Abik, Gokhan Ersoy, Gonul Filoglu, Hamdi Ozkara, Ozlem Bulbul

{"title":"A semen-specific deoxyribonucleic acid methylation model for epigenetic age estimation and its robustness under environmental challenges","authors":"Sena Er, Zehra Abik, Gokhan Ersoy, Gonul Filoglu, Hamdi Ozkara, Ozlem Bulbul","doi":"10.1002/elps.202400054","DOIUrl":"10.1002/elps.202400054","url":null,"abstract":"In forensic investigations, semen samples are a common form of biological evidence, especially in cases involving sexual assault. Therefore, accurately estimating the age of an individual is crucial in criminal cases. This study presents a novel age estimation model based on semen-specific CpG methylation patterns. A multiplex panel was developed, consisting of 12 CpG sites (PARP14, C5orf25, cg23488376, MXRA5, PFKFB3, DLL1, NOX4, cg12837463, TTC7B, KCNA7, NKX2-1, and SYNE4), which exhibit strong correlations with age. Additionally, this study investigates the resilience of these methylation markers under simulated environmental challenges. We collected ejaculate samples from a diverse cohort of 115 male individuals, aged 20–71 years, who underwent deoxyribonucleic acid extraction and bisulfite conversion. Methylation levels of the selected CpG sites were assessed using a SNaPshot assay, which revealed significant correlations with chronological age. We developed and validated two robust age estimation models through stepwise and enter regression analyses, achieving reliable accuracy with mean absolute errors ranging from 3.81 to 4.1 years. Additionally, the study also investigated the robustness of semen stains under diverse environmental conditions, including fabric type, washing, hematin exposure, and UV-C light. The selected methylation markers demonstrated remarkable resilience despite the challenges posed by washing procedures and environmental exposure, confirming their potential for age estimation in forensic genetics. This research presents successful age estimation models, emphasizing the strong correlations between methylation levels and chronological age. The proposed methodology's accuracy is affirmed through model validation on an independent test set, while also highlighting the resilience of semen stains on fabrics under varying storage and washing conditions.","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 19-20","pages":"1820-1833"},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/elps.202400054","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Feasibility study of a single-primer extension-based microhaplotype NGS system. 基于单引物延伸的微单体型 NGS 系统的可行性研究。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-20 DOI: 10.1002/elps.202400012

Qiang Zhu, Panyin Shu, Haoyu Wang, Yifan Wei, Yuting Wang, Yufang Wang, Ji Zhang

{"title":"Feasibility study of a single-primer extension-based microhaplotype NGS system.","authors":"Qiang Zhu, Panyin Shu, Haoyu Wang, Yifan Wei, Yuting Wang, Yufang Wang, Ji Zhang","doi":"10.1002/elps.202400012","DOIUrl":"https://doi.org/10.1002/elps.202400012","url":null,"abstract":"DNA degradation has been a thorny problem in forensic science. Shortening the amplicon length of the genetic markers improves the analysis of degraded DNA effectively. Microhaplotype (MH) has been proposed as a potential genetic marker that can be used for degraded DNA analysis. In the present study, a 146-plex MH-next-generation sequencing (NGS) system with an average Ae of 6.876 was constructed. Unlike other MH studies, a single-primer extension (SPE)-based NGS library preparation method was used to improve the detection of MH markers for degraded DNA. SPE employs a locus-specific and universal primer to amplify target fragments, reducing the necessity for complete fragment sequences. SPE might effectively mitigate the impact of degradation on amplification. However, SPE produces amplicons of varying lengths, posing challenges in allele calling for SPE-NGS data. To address this issue, this study proposed a flexible allele-calling strategy to improve amplicon detection. In addition, this study evaluated the forensic efficacy of the system using 12 low-template samples (from 1 ng to 7.8 pg), 10 mock-degraded DNA with various degrees of degradation, and 8 forensic casework samples. When the template is as low as 7.8 pg, our system can accurately detect at least 37 loci and achieves a random match probability (RMP) of 10-30 using the complete allele-calling strategy. Eighty-two loci can be detected, and RMP can reach 10-54 using a flexible allele-calling strategy. After 150 min of 98°C treatment, 36 loci can still be detected, and an RMP of 10-5 can be obtained using the flexible allele-calling strategy. Furthermore, the number of single nucleotide polymorphism detected at different DNA amounts and degradation levels suggests that the SPE method combined with a flexible allele-calling strategy is effective.","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Food profiling goes green: Sustainable analysis strategies for food authentication. 食品分析走向绿色：食品认证的可持续分析策略。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-14 DOI: 10.1002/elps.202400098

Marina Creydt, Markus Fischer

引用次数: 0

Performance optimization of a DLD microfluidic device for separating deformable CTCs 用于分离可变形 CTC 的 DLD 微流体设备的性能优化。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-14 DOI: 10.1002/elps.202400136

Roya Mohammadali, Morteza Bayareh, Afshin Ahmadi Nadooshan

{"title":"Performance optimization of a DLD microfluidic device for separating deformable CTCs","authors":"Roya Mohammadali, Morteza Bayareh, Afshin Ahmadi Nadooshan","doi":"10.1002/elps.202400136","DOIUrl":"10.1002/elps.202400136","url":null,"abstract":"Deterministic lateral displacement (DLD) microfluidic devices work based on the streamlines created by an array of micro-posts. The configuration of pillars alters the isolation efficiency of these devices. The present paper optimizes the performance of a DLD device for isolating deformable circulating tumor cells. The input variables include cell diameter (d), Young's modulus (<math>\u0000 <semantics>\u0000 <msub>\u0000 <mi>E</mi>\u0000 <mi>s</mi>\u0000 </msub>\u0000 <annotation>${E}_s$</annotation>\u0000 </semantics></math>), Reynolds number (Re), and tan θ, where θ is the tilted angle of micro-posts. The output, which is the response of the system, is DLD. The numerical simulation results are employed to optimize the device using the response surface method, leading to the proposition of a correlation to estimate DLD as a function of input variables. It is demonstrated that the maximum and minimum impacts on cell lateral displacement correspond to <math>\u0000 <semantics>\u0000 <msub>\u0000 <mi>E</mi>\u0000 <mi>s</mi>\u0000 </msub>\u0000 <annotation>${E}_s$</annotation>\u0000 </semantics></math> and Re, respectively.","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 19-20","pages":"1775-1784"},"PeriodicalIF":3.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Label-free detection of ConA-induced T-lymphocyte activation at single-cell level by microfluidics. 利用微流体技术在单细胞水平对 ConA 诱导的 T 淋巴细胞活化进行无标记检测。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-09 DOI: 10.1002/elps.202400060

Yameng Liu, Xiaohu Wang, Yuxia Lan

{"title":"Label-free detection of ConA-induced T-lymphocyte activation at single-cell level by microfluidics.","authors":"Yameng Liu, Xiaohu Wang, Yuxia Lan","doi":"10.1002/elps.202400060","DOIUrl":"https://doi.org/10.1002/elps.202400060","url":null,"abstract":"Lymphocyte activation is critical in regulating immune responses. The resulting T-cell proliferation has been implicated in the pathogenesis of a variety of autoimmune diseases, such as SLE and rheumatoid arthritis. ConA (concanavalin A)-induced activation has been widely used in the T lymphocytes model of immune-mediated liver injury, autoimmune hepatitis, and so on. In those works, it usually requires fluorescent labeling or cell staining to confirm whether the cells are transformed successfully after medicine treatment to figure out efficacy/pharmacology. The detection preparation steps are time-consuming and have limitations for further proteomic/genomic identifications. Here, a label-free microfluidic method is established to detect lymphocyte activation degree. The lymphocyte and ConA-activated lymphocyte were investigated by a microfluidic device. According to where single cells in the sample were captured in the designed channel, lymphocyte and ConA-activated samples are differentiated and characterized by population electric field factors, 2.08 × 104 and 2.21 × 104 V/m, respectively. Furthermore, salidroside, a herbal medicine that was documented to promote the transformation, was used to treat lymphocyte cells, and the treated cell population is detected to be 2.67 × 104 V/m. The characterization indicates an increasing trend with the activation degree. The result maintains a high consistency with traditional staining methods with transformed cells of 15.8%, 28.8%, and 48.3% in each cell population. Dielectrophoresis is promising to work as a tool for detecting lymphocyte transformation and medical efficacy detection.","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Comparative analysis of SNaPshot and massively parallel sequencing for body fluid–specific DNA methylation markers 体液特异性 DNA 甲基化标记的 SNaPshot 和大规模平行测序比较分析。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-09 DOI: 10.1002/elps.202400037

Bo Min Kim, Sang Un Park, Hwan Young Lee

{"title":"Comparative analysis of SNaPshot and massively parallel sequencing for body fluid–specific DNA methylation markers","authors":"Bo Min Kim, Sang Un Park, Hwan Young Lee","doi":"10.1002/elps.202400037","DOIUrl":"10.1002/elps.202400037","url":null,"abstract":"The identification of tissue-specific differentially methylated regions has significantly contributed to the field of forensic genetics, particularly in body fluid identification crucial for linking evidence to crimes. Among the various approaches to analyzing DNA methylation, the SNaPshot assay has been popularly studied in numerous researches. However, there is a growing interest in exploring alternative methods such as the use of massively parallel sequencing (MPS), which can process a large number of samples simultaneously. This study compares SNaPshot and MPS multiplex assays using nine cytosine-phosphate-guanine markers for body fluid identification. As a result of analyzing 112 samples, including blood, saliva, vaginal fluid, menstrual blood, and semen, both methods demonstrated high sensitivity and specificity, indicating their reliability in forensic investigations. A total of 92.0% samples were correctly identified by both methods. Although both methods accurately identified all blood, saliva, and semen samples, some vaginal fluid samples showed unexpected methylation signals at nontarget loci in addition to the target loci. In the case of menstrual blood samples, due to their complexity, independent typing criteria were applied, and successful menstrual blood typing was possible, whereas a few samples showed profiles similar to vaginal fluid. The MPS method worked better in vaginal fluid samples, and the SNaPshot method performed better in menstrual blood samples. This study offers valuable insights into body fluid identification based on the characteristics of the SNaPshot and MPS methods, which may help in more efficient forensic applications.","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 19-20","pages":"1805-1819"},"PeriodicalIF":3.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/elps.202400037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A brief history and future directions of dielectrophoretic filtration: A review. 介质电泳过滤的简史和未来方向：综述。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-09 DOI: 10.1002/elps.202400116

Mary Clare O'Donnell, Mariia Kepper, Georg R Pesch

引用次数: 0

Short-term impact of vitamin K2 supplementation on biochemical parameters and lipoprotein fractions. 维生素 K2 补充剂对生化指标和脂蛋白组分的短期影响。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-02 DOI: 10.1002/elps.202400058

Milos Barna, Katerina Dunovska, Jana Cepova, Julia Werle, Richard Prusa, Geir Bjørklud, Pavel Melichercik, Rene Kizek, Eva Klapkova

{"title":"Short-term impact of vitamin K2 supplementation on biochemical parameters and lipoprotein fractions.","authors":"Milos Barna, Katerina Dunovska, Jana Cepova, Julia Werle, Richard Prusa, Geir Bjørklud, Pavel Melichercik, Rene Kizek, Eva Klapkova","doi":"10.1002/elps.202400058","DOIUrl":"https://doi.org/10.1002/elps.202400058","url":null,"abstract":"This study explored the short-term effects of vitamin K2 (VK2) supplementation on biochemical parameters (vitamin D, vitamin E, vitamin A, alkaline phosphatase, calcium, phosphorus (P), magnesium, metallothionein, triglycerides, cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL), and lipoprotein fractions (albumin, HDL, very low-density lipoprotein (VLDL), LDL, and chylomicrons). A short-term experiment (24 h, six probands) was performed to track changes in VK2 levels after a single-dose intake (360 µg/day). Liquid chromatography-tandem mass spectrometry was used to monitor vitamin K levels (menaquinone-4 (MK-4), menaquinone-7 (MK-7), and vitamin K1 [VK1]) with a limit of detection of 1.9 pg/mL for VK1 and 3.8 pg/mL for the two forms of VK2. Results showed that MK-7 levels significantly increased within 2-6 h post-administration and then gradually declined. MK-4 levels were initially low, showing a slight increase, whereas VK1 levels rose initially and then decreased. Biochemical analyses indicated no significant changes in sodium, chloride, potassium, calcium, magnesium, albumin, or total protein levels. A transient increase in P was observed, peaking at 12 h before returning to baseline. Agarose gel electrophoresis of lipoprotein fractions revealed distinct chylomicron bands and variations in VLDL and HDL mobility, influenced by dietary lipids and VK2 supplementation. These findings suggest effective absorption and metabolism of MK-7 with potential implications for bone metabolism and cardiovascular health.","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Proper application of DNA dyes in agarose gel electrophoresis 在琼脂糖凝胶电泳中正确使用 DNA 染料。

IF 3 3区生物学

ELECTROPHORESIS Pub Date : 2024-08-02 DOI: 10.1002/elps.202400082

Ling-Jin Tuo, Teng Zhang, Guo-Qing Chen, Yuan Liu, Cheng Zhao, Shi-Wen Jiang

{"title":"Proper application of DNA dyes in agarose gel electrophoresis","authors":"Ling-Jin Tuo, Teng Zhang, Guo-Qing Chen, Yuan Liu, Cheng Zhao, Shi-Wen Jiang","doi":"10.1002/elps.202400082","DOIUrl":"10.1002/elps.202400082","url":null,"abstract":"Various dyes are used to visualize DNA bands in agarose gel electrophoresis (AGE) by the methods of pre- or post-staining. The DNA dye user's guides generally state that the binding of the dye to DNA will affect DNA mobility in electrophoresis, thus recommending post-staining for accurate measurement of DNA size. However, many AGE performers prefer pre-staining procedures for reasons such as convenience, real-time observation of DNA bands, and/or the use of a minimal amount of dye. The detrimental effect of the dye on DNA mobility and the associated risk for inaccurate measurement of DNA size are often overlooked by AGE performers. Here we quantitatively determine the impact on DNA migration imposed by frequently used dyes, including GelRed, ethidium bromide (EB), and Gold View. It was observed that pre-staining with GelRed and EB significantly slowed down DNA migration to cause as much as 39.1% overestimation on the size of sample DNA, whereas Gold View had little effect. The slowdown of DNA migration increased with dye concentration until it plateaued when the dye concentration reached a saturated level. Thus, to take advantage of pre-staining, saturated levels of DNA dyes should always be applied for both DNA samples and DNA markers to ensure a fair comparison of DNA sizes. In addition, GelRed and EB display much higher sensitivity than Gold View in the detection of DNA bands in post-staining. The saturated concentrations, cost considerations, and other useful features of these frequently used dyes are summarized for the information of AGE performers.","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 19-20","pages":"1796-1804"},"PeriodicalIF":3.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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