ELECTROPHORESIS最新文献

{"title":"Forensic STR and SNP Genotyping of Formalin-Fixed Skeleton Samples With Illumina's ForenSeq System","authors":"Tingting Yang,&nbsp;Linlin Gao,&nbsp;Jiarong Zhang,&nbsp;Wei Xie,&nbsp;Wenjing Hu,&nbsp;Jiangwei Yan","doi":"10.1002/elps.202400056","DOIUrl":"10.1002/elps.202400056","url":null,"abstract":"<div>\u0000 \u0000 <p>Formalin fixatives are widely used in forensics to preserve tissues. However, extracting high-quality genomic DNA from formalin-fixed samples is challenging. Traditional short tandem repeat (STR) analysis using capillary electrophoresis (CE) for forensic DNA typing frequently results in failure. Massively parallel sequencing (MPS) can handle many samples and thousands of genetic markers, usually single-nucleotide polymorphisms (SNPs) and STRs, in a single test. Thus, it is useful for assessing highly deteriorated forensic evidence. Few studies have examined the effectiveness of STRs and SNPs genotyping of formalin-fixed skeletons using MPS. In this study, 55 skeletal samples from 5 individuals that were treated under different formalin fixation times (5–75 days) were examined and sequenced using the ForenSeq DNA Signature Prep Kit on the Illumina MiSeq FGX platform. The results showed that as the duration of formalin fixation increased, the detection rates of STRs and SNPs gradually decreased. After 75 days of fixation, the average detection rates for STRs and SNPs were 4% and 10%, respectively. The cumulative discrimination power (CDP) of individual identification SNPs (iiSNPs) was &gt;0.9999 on the 45th day. However, the CDP of STRs was 0.9930 on the 22nd day. Low detection rates were observed for six STRs (D1S1656, PentaE, D22S1045, PentaD, DX8378 and DX10103) and five SNPs (rs2920816, rs354439, rs1736442, rs338882 and rs1031825). In conclusion, DNA extracted from formalin-fixed skeletons decomposes rapidly over time, and MPS technology can be a useful tool for detecting forensic genetic markers in such samples.</p>\u0000 </div>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 21-22","pages":"2019-2027"},"PeriodicalIF":3.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460734","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}

{"title":"Epigenetic Age Estimation by Detecting DNA Methylation Status in Buccal Swabs","authors":"Zimeng Guan,&nbsp;Jiaqi Wang,&nbsp;Zidong Liu,&nbsp;Chengwen Yang,&nbsp;Xin Xu,&nbsp;Xinjie Wang,&nbsp;Gengqian Zhang","doi":"10.1002/elps.202400075","DOIUrl":"10.1002/elps.202400075","url":null,"abstract":"<div>\u0000 \u0000 <p>The analysis of DNA methylation (DNAm) levels at specific CpG sites represents one of the most promising molecular techniques for estimating an individual's age. To date, a considerable number of studies have reported the development of age prediction models on the basis of DNAm in body fluids, with only a few utilizing buccal swabs. The objective of this study was to identify age-dependent methylation CpG sites in three different genes (HOXC4, TRIM59, and ELOVL2) in buccal swab samples from the Chinese Han population. A total of 461 buccal swabs, with an age range of 0.4–80.8 years, were divided into a training set (<i>n</i> = 325) and a validation set (<i>n</i> = 136). Samples were analyzed by pyrosequencing in order to identify age-related genes with correlation coefficient. A random forest regression model was ultimately proposed, including eight CpGs in three genes, with a mean absolute error (MAE) of 2.119 years. The model performs independent validation set with an MAE of 4.391 years. Our findings illustrate that buccal swabs present a suitable alternative to biological traces for age prediction based on DNAm pattern using pyrosequencing and random forest regression, offering the additional advantage of being collected noninvasively.</p>\u0000 </div>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 21-22","pages":"2012-2018"},"PeriodicalIF":3.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460733","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}

{"title":"Simultaneous Genotyping of Three SNVs, rs5471, rs5472, and rs2000999 Involved in Serum Haptoglobin Levels by Fluorescent Probe-Based Melting Curve Analysis","authors":"Mikiko Soejima,&nbsp;Yoshiro Koda","doi":"10.1002/elps.202400172","DOIUrl":"10.1002/elps.202400172","url":null,"abstract":"<div>\u0000 \u0000 <p>Haptoglobin (Hp) is a hemoglobin-binding acute-phase serum protein. Several single nucleotide variations (SNVs) within the Hp gene (<i>HP</i>) or Hp-related protein gene (<i>HPR</i>), such as rs5471 (A &gt; C) and rs5472 (A &gt; G) in <i>HP</i> promoter region and rs2000999 (G &gt; A) in intron 2 of <i>HRP</i>, are suggested to correlate with the serum Hp levels. To determine these three SNVs simultaneously, a genotyping assay based on duplex dual-labeled fluorescent probes was developed. The method was then validated by analyzing genomic DNA from 121 Ghanaian and two Japanese subjects who had been previously genotyped for rs5471, rs5472, and rs2000999. Both rs5471 and rs5472 could be determined as haplotypes with a single FAM-labeled fluorescent probe, and rs2000999 could be genotyped with a HEX-labeled fluorescent probe. The results obtained with the present method were consistent with the previous results except for those of three Ghanaian subjects. All three subjects appear to have multiple HPR copy number variants characteristic of African populations, which may have led to incorrect results during previous genotyping. This method allows us to genotype these three SNVs in a relatively large number of samples, especially in African populations where rs5471 is uniquely distributed.</p>\u0000 </div>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 21-22","pages":"2028-2033"},"PeriodicalIF":3.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460737","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}

{"title":"Suspended Stir Bar Sorptive Extraction Based on Zr-MOF-Modified Cotton Thread for Enrichment and Detection of Three Trace Quinolones in Fish Tissue.","authors":"Jiao Long, Yan Gao, Kangjia Sheng, Tao Bao, Sicen Wang","doi":"10.1002/elps.202400096","DOIUrl":"https://doi.org/10.1002/elps.202400096","url":null,"abstract":"<p><p>In this study, an efficient and practical method was established to enrich and detect three trace quinolones in fish tissue. Low-cost and environment-friendly cotton threads were coated with PCN-224 using a simple one-pot hydrothermal method. The PCN-224-modified cotton threads (PCN-224@CTs) were characterized to ensure that the crystal was successfully fabricated on the surface of cotton threads. The prepared PCN-224@CTs were wrapped around steel needles to form suspended bars. Key factors of extraction and desorption were optimized, and analytical performance was tested. Suspended bar sorptive extraction coupled with ultra-performance liquid chromatography (UPLC) with a photodiode array detector was used to analyze the quinolones in fish tissue. The detection limits of quinolones were 0.26-1.15 ng/mL, and the recoveries were achieved in the range of 81.31%-115.81%, indicating a simple method with high sensitivity and satisfactory practicability of enriching, separating, and detecting trace quinolones was successfully established.</p>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460738","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}

{"title":"Offline Coupling of Hydrophobic Interaction Chromatography–Capillary Zone Electrophoresis for Monitoring Charge-Based Heterogeneity of Recombinant Monoclonal Antibodies","authors":"Deepika Sarin,&nbsp;Sunil Kumar,&nbsp;Anurag S. Rathore","doi":"10.1002/elps.202400158","DOIUrl":"10.1002/elps.202400158","url":null,"abstract":"<div>\u0000 \u0000 <p>A holistic understanding of the charge heterogeneity in monoclonal antibodies (mAbs) is paramount for ensuring acceptable product quality. Hence, biotherapeutic manufacturers are expected to thoroughly characterize their products via advanced analytical techniques. Recently, two-dimensional liquid chromatography (2DLC) methods have gained popularity for resolving complex charged species. Capillary electrophoresis (CE) is regarded as a sensitive and faster tool for charged species estimation in biotherapeutics. In this study, we aim to combine the separation power of chromatographic and electrophoretic tools (liquid chromatography [LC]–CE) so as to achieve maximum resolution of mAb charge variants. Hydrophobic interaction chromatography (HIC) has been used as the preferred LC mode with CE for achieving successful separation of both charge and hydrophobic variants for two of the mAbs (trastuzumab and rituximab). The standalone HIC and capillary zone electrophoresis (CZE) methods separated 4 hydrophobic variants and 7 charge variants for each mAb, whereas the 2DLC method separated 10 and 11 variants for mAbs A and B. On the other hand, the HIC–CZE–UV method resolved 29 variants in mAb A and 23 variants in mAb B. The reproducibility of the HIC–CZE–UV method was demonstrated by % change in values of retention time (RT) and peak area as &lt;5% (mAb A), &lt;3% (mAb B), and &lt;12% (for both mAbs), respectively. Thus, the utility of the proposed LC–CE method for characterization of mAb charge variants has been displayed.</p>\u0000 </div>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 21-22","pages":"1927-1938"},"PeriodicalIF":3.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460735","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}

{"title":"Development of the SupersonicIEF Method for High-Throughput Charge Variant Analysis","authors":"Will McElroy,&nbsp;Christopher D. Heger","doi":"10.1002/elps.202400117","DOIUrl":"10.1002/elps.202400117","url":null,"abstract":"<p>The analysis of biopharmaceuticals for charge variants occurs from early-stage samples through formulation and process-development optimization. Higher throughput methods allow increased analysis of these samples to facilitate greater understanding of the samples and to better optimize their production and formulation. To enable higher throughput charge variant analysis, a new, rapid platform imaged capillary isoelectric focusing (icIEF) method was optimized to be two to three times faster than standard methods.</p>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 21-22","pages":"1968-1975"},"PeriodicalIF":3.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/elps.202400117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460732","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}

{"title":"Enrichment of low-abundance osteopontin in bovine milk via reciprocating free-flow isoelectric focusing","authors":"Ke-Er Chen,&nbsp;Youli Tian,&nbsp;Yiren Cao,&nbsp;Zixian Yu,&nbsp;Qiang Zhang,&nbsp;Weiwen Liu,&nbsp;Yishu Xing,&nbsp;Chengxi Cao,&nbsp;Zhishen Mu,&nbsp;Xu Xu","doi":"10.1002/elps.202400071","DOIUrl":"10.1002/elps.202400071","url":null,"abstract":"<p>Osteopontin (OPN) in milk plays an important role in intestinal and brain development in early infancy, and great attention has been focused on OPN isolation to add extra OPN in infant formula. However, large-scale OPN isolation is limited by the low efficiency of sample pretreatment. Herein, we utilized preparative reciprocating free-flow isoelectric focusing (RFFIEF) to showcase the enrichment of low-abundance OPN in bovine milk, which contained an extremely high concentration of unwanted proteins. The reciprocating IEF format and the design of the multi-channel collector allowed us to enrich OPN in 1 L milk within 6 h. We removed 97.5% of unwanted proteins and obtained an enrichment factor of 11. Thus, our RFFIEF method can be applied to the preparative pretreatment of the large-scale milk sample and potentially improve the efficiency of downstream OPN purification.</p>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 21-22","pages":"1963-1967"},"PeriodicalIF":3.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380288","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}

{"title":"Determination of an Anti-Parasitic Active Pharmaceutical Ingredient in Wastewater Effluents Using Capillary Zone Electrophoresis","authors":"Emma O'Sullivan-Carroll,&nbsp;Anna Hogan,&nbsp;N. O'Mahoney,&nbsp;S. Howlett,&nbsp;C. Pyne,&nbsp;P. Downing,&nbsp;M. Lynch,&nbsp;Eric Moore","doi":"10.1002/elps.202400131","DOIUrl":"10.1002/elps.202400131","url":null,"abstract":"<p>Ireland has a successful pharmaceutical industry with over 100 pharmaceutical manufacturing sites across the island. Although this success has many benefits, the irreversible effects emissions from pharmaceutical manufacturing can have on the environment are a major drawback. Although known pollutants are regularly monitored with limits set out by the Environmental Protection Agency, one significant pollutant has been overlooked: pharmaceutical pollution. Detecting these pollutants and ensuring they are at a safe concentration for the environment is of utmost importance. In recent years, capillary electrophoresis is being recognised as a suitable alternative to high-performance liquid chromatography due to its many benefits such as faster analysis, water-based buffers and smaller sample volumes. In this paper, a capillary zone electrophoresis (CZE) method with a preconcentration step of solid-phase extraction was developed for an anti-parasitic active pharmaceutical ingredient (API) called ZB23. The API was successfully detected in a wastewater sample in less than 10 min using the CZE parameters of 25 mM borate buffer with a pH of 10.5, 15% MeOH, 10 kV voltage, 25 mbar for 5 s injection size, an Lt of 40 cm, an Ld of 31.5 cm and a detection wavelength of 214 nm.</p>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 21-22","pages":"1906-1914"},"PeriodicalIF":3.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/elps.202400131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380287","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}

{"title":"Online Isotope Analysis of Sulfur in Proteins via Capillary Electrophoresis Coupled With Multicollector ICP-MS (CE/MC-ICP-MS): A Proof of Concept Study.","authors":"Dariya Tukhmetova, Nicole Langhammer, Jochen Vogl, Björn Meermann","doi":"10.1002/elps.202400128","DOIUrl":"https://doi.org/10.1002/elps.202400128","url":null,"abstract":"<p><p>Isotope ratio analysis of sulfur in biological samples using inductively coupled plasma-mass spectrometry (ICP-MS) has gained significant interest for applications in quantitative proteomics. Advancements like coupling separation techniques with multicollector ICP-MS (MC-ICP-MS) enhance the throughput of species-specific sulfur isotope ratio measurements, fostering new avenues for studying sulfur metabolism in complex biological matrices. This proof-of-concept study investigates the feasibility of online CE/MC-ICP-MS for directly analyzing sulfur isotope ratios in proteins (albumin). Leveraging our previous work on the applicability of CE/ICP-MS for quantifying sulfur-containing biological molecules, we explore its potential for sulfur isotope analysis. Our results demonstrate that direct analysis of sulfur isotopes in albumin protein using online capillary electrophoresis MC-ICP-MS (CE/MC-ICP-MS) eliminates the need for laborious pretreatment steps, while yielding isotope ratios comparable to the reference values. Although initial precision can be improved through further system optimization and protein injection techniques, this approach paves the way for future analysis of mixtures of various biological compounds in, for example, clinical diagnosis studies.</p>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343834","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}

{"title":"Developmental Validation of the Microreader 23HS Plex ID System: A Novel Supplementary Non-CODIS STR Multiplex Assay for Forensic Application","authors":"Hui Li,&nbsp;He Ren,&nbsp;Fan Yang,&nbsp;Man Chen,&nbsp;Weifen Sun,&nbsp;Lei Jiang,&nbsp;Zhixiao Gao,&nbsp;Yacheng Liu,&nbsp;Xiling Liu","doi":"10.1002/elps.202400106","DOIUrl":"10.1002/elps.202400106","url":null,"abstract":"<div>\u0000 \u0000 <p>A novel supplementary non-CODIS STR multiplex assay designated as the “Microreader 23HS Plex ID System” was developed. The Microreader 23HS Plex ID System enables simultaneous profiling of 23 STR loci and the amelogenin locus. The majority of these loci are non-CODIS STRs (D4S2408, D9S2157, D20S161, D3S2459, D18S1364, D13S305, D1S2142, D19S400, D6S1017, D7S1517, D2S1776, D2S1360, D3S1744, D16S3391, D3S1545, D11S4463, D20S85, D1S549, D10S2325, D21S2055), with the exception of three CODIS STRs (D2S441, D12S391, and D22S1045). Followed the recommendations of Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese validation standards, a comprehensive set of validation studies were conducted, encompassing PCR conditions, stutter ratio and peak height balance, sensitivity, precision and accuracy, reproducibility, species specificity, inhibition, as well as mixture testing. The results demonstrated that the Microreader 23HS Plex ID System is a reliable and robust assay, with well-balanced peak heights, high precision and accuracy, species specificity, and resistance to common inhibitors. The sensitivity of the assay was determined to be 0.125 ng of template DNA. In mixture study, all minor alleles were detected in two-sample mixtures across various ratios (1:19, 1:9, 1:4, 3:7, 2:3, 1:1, 3:2, 4:1, 9:1, and 19:1). In population study, a total of 500 unrelated individuals of Han ethnicity from East China were genotyped. The allele frequencies and forensic population genetic parameters were calculated, with a cumulative random match probability of 7.757 × 10⁻²⁷, and a total power of discrimination exceeding 0.999,999,999,999,999,999,999,999,99. In conclusion, the Microreader 23HS Plex ID System shows promise as a valuable supplementary tool for forensic applications, particularly in addressing complex kinship testing and challenges posed by STR mutation.</p>\u0000 </div>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":"45 21-22","pages":"1976-1987"},"PeriodicalIF":3.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343831","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}