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51.
Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics. 相似文献
52.
Yifan Xie Ning Qu Shaobin Lin Haojun Jiang Yanyan Zhang Xiuqing Zhang Hao Liang Fang Chen Xueling Ou 《Electrophoresis》2020,41(12):1095-1102
SNPs, combined with massively parallel sequencing technology, have proven applicability in noninvasive prenatal paternity testing (NIPPT) for singleton pregnancies in our previous research, using circulating cell-free DNA in maternal plasma. However, the feasibility of NIPPT in twin pregnancies has remained uncertain. As a pilot study, we developed a practical method to noninvasively determine the paternity of twin pregnancies by maternal plasma DNA sequencing based on a massively parallel sequencing platform. Blood samples were collected from 15 pregnant women (twin pregnancies at 9–18 weeks of gestation). Parental DNA and maternal plasma cell-free DNA were analyzed with custom-designed probes covering 5226 polymorphic SNP loci. A mathematical model for data interpretation was established, including the zygosity determination and paternity index calculations. Each plasma sample was independently tested against the alleged father and 90 unrelated males. As a result, the zygosity in each twin case was correctly determined, prior to paternity analysis. Further, the correct biological father was successfully identified, and the paternity of all 90 unrelated males was excluded in each case. Our study demonstrates that NIPPT can be performed for twin pregnancies. This finding may contribute to development in NIPPT and diagnosis of certain genetic diseases. 相似文献
53.
人肝癌细胞系HLE细胞表面抗原多肽的纳升电喷雾串联质谱从头测序分析 总被引:2,自引:0,他引:2
肿瘤细胞表面的抗原多肽能够被细胞毒T淋巴细胞特异性识别而引起免疫应答,因此有可能用于研制基于多肽的抗肿瘤疫苗。用弱酸将人肝癌细胞系HLE细胞表面抗原多肽和人正常肝细胞表面多肽洗脱后,经RP-HPLC分离,选择HLE细胞表面特异性多肽进行纳升电喷雾串联质谱(nanoESI-MS/MS)测序,共测定5个色谱峰中的20个多肽序列,分子量分布范围为1000~2000 Da。借助M asSeq软件分析出其中12个多肽的序列。经数据库查寻,其中的3个肽段分别来自钙调节蛋白、核蛋白S19和伴侣蛋白10。这些多肽的生物学功能及与肿瘤的关系值得深入研究。该研究表明nanoESI-MS/MS是测定微量混合多肽序列的最有效方法。 相似文献
54.
Pyrosequencing is a relatively recent method for sequencing short stretches of DNA. Because both Pyrosequencing and Sanger dideoxy sequencing were recently used to characterize and validate DNA molecular barcodes in a large yeast gene-deletion project, a meta-analysis of those data allow an excellent and timely opportunity for evaluating Pyrosequencing against the current gold standard, Sanger dideoxy sequencing. Starting with yeast genomic DNA, parallel PCR amplification methods were used to prepared 4747 short barcode-containing constructs from 6000 Saccharomyces cerevisiae gene-deletion strains. Pyrosequencing was optimized for average read lengths of 25-30 bases, which included in each case a 20-mer barcode sequence. Results were compared with sequence data obtained by the standard Sanger dideoxy chain termination method. In most cases, sequences obtained by Pyrosequencing and Sanger dideoxy sequencing were of comparable accuracy, and the overall rate of failure was similar. The DNA in the barcodes is derived from synthetic oligonucleotide sequences that were inserted into yeast-deletion-strain genomic DNA by homologous recombination and represents the most significant amount of DNA from a synthetic source that has been sequenced to date. Although more automation and quality control measures are needed, Pyrosequencing was shown to be a fast and convenient method for determining short stretches of DNA sequence. 相似文献
55.
In chemical and biochemical processes, steady‐state models are widely used for process assessment, control and optimisation. In these models, parameter adjustment requires data collected under nearly steady‐state conditions. Several approaches have been developed for steady‐state identification (SSID) in continuous processes, but no attempt has been made to adapt them to the singularities of batch processes. The main aim of this paper is to propose an automated method based on batch‐wise unfolding of the three‐way batch process data followed by a principal component analysis (Unfold‐PCA) in combination with the methodology of Brown and Rhinehart 2 for SSID. A second goal of this paper is to illustrate how by using Unfold‐PCA, process understanding can be gained from the batch‐to‐batch start‐ups and transitions data analysis. The potential of the proposed methodology is illustrated using historical data from a laboratory‐scale sequencing batch reactor (SBR) operated for enhanced biological phosphorus removal (EBPR). The results demonstrate that the proposed approach can be efficiently used to detect when the batches reach the steady‐state condition, to interpret the overall batch‐to‐batch process evolution and also to isolate the causes of changes between batches using contribution plots. Copyright © 2007 John Wiley & Sons, Ltd. 相似文献
56.
Summary: A novel combinatorial, high-throughput experimentation (HTE) setup has been developed, which allows for rapid mapping of the phase behavior of blends of homopolymers and block copolymers. The principle is based on the preparation of composition (ϕ)-temperature (T) gradient films. Linear ϕ gradients were obtained over a large composition range, as shown by FTIR microscopy. The applicability of this combinatorial approach was demonstrated by studying the phase behavior of a poly(styrene-co-acrylonitrile) (SAN)/poly(methyl methacrylate-co-ethyl acrylate) (PMMA-EA) blend with varying EA content and a poly(styrene-b-butadiene-b-methyl methacrylate) (SBM) triblock copolymer. 相似文献
57.
Lee M Lee Y Kang M Park H Seong Y Sung BJ Moon B Oh HB 《Journal of mass spectrometry : JMS》2011,46(8):830-839
The gas‐phase free radical initiated peptide sequencing (FRIPS) fragmentation behavior of o‐TEMPO‐Bz‐conjugated peptides with an intra‐ and intermolecular disulfide bond was investigated using MSn tandem mass spectrometry experiments. Investigated peptides included four peptides with an intramolecular cyclic disulfide bond, Bactenecin (RLC RIVVIRVC R), TGF‐α (C HSGYVGVRC ), MCH (DFDMLRC MLGRVFRPC WQY) and Adrenomedullin (16–31) (C RFGTC TVQKLAHQIY), and two peptides with an intermolecular disulfide bond. Collisional activation of the benzyl radical conjugated peptide cation, which was generated through the release of a TEMPO radical from o‐TEMPO‐Bz‐conjugated peptides upon initial collisional activation, produced a large number of peptide backbone fragments in which the S? S or C? S bond was readily cleaved. The observed peptide backbone fragments included a‐, c‐, x‐ or z‐types, which indicates that the radical‐driven peptide fragmentation mechanism plays an important role in TEMPO‐FRIPS mass spectrometry. FRIPS application of the linearly linked disulfide peptides further showed that the S? S or C? S bond was selectively and preferentially cleaved, followed by peptide backbone dissociations. In the FRIPS mass spectra, the loss of ?SH or ?SSH was also abundantly found. On the basis of these findings, FRIPS fragmentation pathways for peptides with a disulfide bond are proposed. For the cleavage of the S? S bond, the abstraction of a hydrogen atom at Cβ by the benzyl radical is proposed to be the initial radical abstraction/transfer reaction. On the other hand, H‐abstraction at Cα is suggested to lead to C? S bond cleavage, which yields [ion ± S] fragments or the loss of ?SH or ?SSH. Copyright © 2011 John Wiley & Sons, Ltd. 相似文献
58.
59.
Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry 下载免费PDF全文
Bartosz Setner Magdalena Rudowska Ewelina Klem Marek Cebrat Zbigniew Szewczuk 《Journal of mass spectrometry : JMS》2014,49(10):995-1001
Improving the sensitivity of detection and fragmentation of peptides to provide reliable sequencing of peptides is an important goal of mass spectrometric analysis. Peptides derivatized by bicyclic quaternary ammonium ionization tags: 1‐azabicyclo[2.2.2]octane (ABCO) or 1,4‐diazabicyclo[2.2.2]octane (DABCO), are characterized by an increased detection sensitivity in electrospray ionization mass spectrometry (ESI‐MS) and longer retention times on the reverse‐phase (RP) chromatography columns. The improvement of the detection limit was observed even for peptides dissolved in 10 mM NaCl. Collision‐induced dissociation tandem mass spectrometry of quaternary ammonium salts derivatives of peptides showed dominant a‐ and b‐type ions, allowing facile sequencing of peptides. The bicyclic ionization tags are stable in collision‐induced dissociation experiments, and the resulted fragmentation pattern is not significantly influenced by either acidic or basic amino acid residues in the peptide sequence. Obtained results indicate the general usefulness of the bicyclic quaternary ammonium ionization tags for ESI‐MS/MS sequencing of peptides. Copyright © 2014 John Wiley & Sons, Ltd. 相似文献
60.
Jinny Claire Lee Hye Yun Kim Sejin Lee Jisu Shin Hyunjin Vincent Kim Kyeonghwan Kim Seungyeop Baek Donghee Lee Hanna Jeon DaWon Kim Seung‐Hoon Yang Gyoonhee Han Keunwan Park Jaeho Choi Jinwoo Park Jason A. Moss Kim D. Janda YoungSoo Kim 《Angewandte Chemie (International ed. in English)》2020,59(28):11491-11500
Amyloid‐β (Aβ) oligomers are implicated in Alzheimer disease (AD). However, their unstable nature and heterogeneous state disrupts elucidation of their explicit role in AD progression, impeding the development of tools targeting soluble Aβ oligomers. Herein parallel and anti‐parallel variants of Aβ(1–40) dimers were designed and synthesized, and their pathogenic properties in AD models characterized. Anti‐parallel dimers induced cognitive impairments with increased amyloidogenesis and cytotoxicity, and this dimer was then used in a screening platform. Through screening, two FDA‐approved drugs, Oxytetracycline and Sunitinib, were identified to dissociate Aβ oligomers and plaques to monomers in 5XFAD transgenic mice. In addition, fluorescent Astrophloxine was shown to detect aggregated Aβ in brain tissue and cerebrospinal fluid samples of AD mice. This screening platform provides a stable and homogeneous environment for observing Aβ interactions with dimer‐specific molecules. 相似文献