Next generation, sequencing & applications最新文献

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Hispanic and Catholic, or Hispanic-Catholic? Racialized Religious Identity for Self-Identified “Hispanic” Students at a Predominantly White Institution 西班牙裔天主教徒，还是西班牙裔天主教徒?在一所以白人为主的大学里，自我认定的“西班牙裔”学生的种族化宗教身份

Next generation, sequencing & applications

Pub Date : 2019-01-01 DOI: 10.33011/next/5/1/1

C. Dalessandro

Drawing from in-depth interviews with undergraduates at a predominantly non-Hispanic white and secular university in the U.S., I investigate how those self-identified as both Hispanic and Catholic negotiate the identity statuses that classify them as minorities on their campus. While participants in this study who did not identify as Hispanic also did not make connections between religious affiliation and racial/ethnic group membership, most Hispanic undergraduates did make these connections. I found that self-identified Hispanic students used the meanings they attach to Catholic religious affiliation to help them also make sense of their racialized Hispanic identities in the university space. Despite coming from diverse geographic, social class, and cultural backgrounds, these students move toward creating a shared definition of what it means to be a racialized Hispanic person (or Latinx person with Spanish-speaking ancestors) in this particular collegiate context. I conclude with suggestions for future research.

通过对美国一所非西班牙裔白人和世俗大学的本科生进行深入访谈，我调查了那些自我认同为西班牙裔和天主教徒的人是如何在校园里协商将他们归类为少数民族的身份地位的。同时参与这项研究不确定西班牙也没有宗教信仰和种族/民族之间的联系会员,大多数拉美裔本科生做了这些联系。我发现，自认为是西班牙裔的学生利用天主教宗教信仰的含义，帮助他们在大学空间中理解自己被种族化的西班牙裔身份。尽管这些学生来自不同的地理位置、社会阶层和文化背景，但在这个特殊的大学背景下，这些学生正在努力创造一个共同的定义，即作为一个种族化的西班牙裔人(或祖先说西班牙语的拉丁裔人)意味着什么。最后，我对未来的研究提出了建议。

引用次数: 0

The Apostle Paul in Spinoza and Badiou 斯宾诺莎和巴迪欧的使徒保罗

Next generation, sequencing & applications

Pub Date : 2019-01-01 DOI: 10.33011/next/5/1/2

P. A. Rodríguez

This paper offers an analysis of the philosophical interpretations of the apostle Paul in Spinoza’s Tractatus Theologico-Politicus (1669) and Badiou's Saint Paul: La foundation de l'universalisme (1997). In addition, a brief description is offered on the difference between, on the one hand, the theological Paul, the Apostle of Faith, and, on the other hand, the historical Paul. Both Spinoza and Badiou offer complex philosophical readings of Paul that can be better understood when taking into consideration how they square with the image of Paul that has been constructed by the various theological traditions of Europe (i.e., the theological Paul), as well as the figure of Paul that is currently being reconstructed by historical-critical biblical scholarship (both New Perspective on Paul and postcolonial/empire-critical readings of Paul).

本文分析了斯宾诺莎的《神学政治论》(1669)和巴迪欧的《圣保罗:普遍主义的基础》(1997)中对使徒保罗的哲学解释。此外，简要描述了神学上的保罗，信仰的使徒，和历史上的保罗之间的区别。斯宾诺莎和巴迪欧都提供了对保罗的复杂哲学解读，当考虑到他们如何与欧洲各种神学传统(即神学上的保罗)所构建的保罗形象，以及目前由历史批判的圣经学者(保罗的新视角和后殖民/帝国批判的保罗解读)所重构的保罗形象相吻合时，可以更好地理解保罗。

引用次数: 0

The Violence of Nonviolence: Contextualizing the Movements of King and Gandhi 非暴力的暴力:金和甘地运动的背景

Next generation, sequencing & applications

Pub Date : 2019-01-01 DOI: 10.33011/next/5/1/4

Greg Mileski

King and Gandhi: two names that have come to be synonymous with nonviolence. And yet, the movements they led responded to and, in some cases with, significant violence. In a recent paper (2016), August H. Nimtz analyzes the role of violence in the movement of Dr. King, concluding that violence played a significant role in the success of the African-American Civil Rights Movement. Using Nimtz’s work as a starting point, this paper analyzes King’s movement and views, comparing definitions of “principled nonviolence” versus “pragmatic nonviolence.” From there, this paper analyzes the role of violence in the struggle for Indian independence from British colonialism and Gandhi’s own views on when, if ever, violence is appropriate. This paper concludes that, indeed, violence—that of sanctioned, state-sponsored violence and that of non-sanctioned actors—has had significant roles in both of these movements. In what way, then, could these movements be said to be nonviolent? Finally, this paper asks why there remains such an impetus to identify these movements, and their leaders, with “principled nonviolence.”

金和甘地:这两个名字已经成为非暴力的代名词。然而，他们领导的运动回应了，在某些情况下，严重的暴力。在最近的一篇论文(2016)中，August H. Nimtz分析了金博士运动中暴力的作用，得出结论认为暴力在非洲裔美国人民权运动的成功中发挥了重要作用。本文以尼姆兹的著作为出发点，分析了金的运动和观点，比较了“原则性非暴力”和“实用主义非暴力”的定义。在此基础上，本文分析了暴力在印度从英国殖民主义中独立的斗争中所起的作用，以及甘地自己对何时(如果有的话)使用暴力是适当的看法。本文的结论是，事实上，暴力——受制裁的、国家支持的暴力以及未受制裁的行为者的暴力——在这两种运动中都发挥了重要作用。那么，这些运动如何才能被称为非暴力的呢?最后，本文提出了一个问题，为什么仍然有这样一种动力将这些运动及其领导人与“有原则的非暴力”联系起来。

引用次数: 1

Genomics of Colorectal Cancer in African Americans. 非裔美国人结直肠癌基因组学研究。

Next generation, sequencing & applications

Pub Date : 2016-09-21 DOI: 10.4172/2469-9853.1000133

H. Brim, H. Ashktorab

Genome-wide studies are increasingly becoming a must, especially for complex diseases such as cancer where multiple genes and diverse molecular mechanisms are known to be involved in genes' function alteration. In this review, we report our latest genomic and epigenomic findings in African-American colorectal cancer patients. This population suffers a higher burden of the disease and most investigators in this field are looking for the underlying genetic and epigenetic targets that might be responsible for this disparity. We here report genome-wide copy number variations, single nucleotide mutations and DNA methylation findings that might be specific to this population.

全基因组研究日益成为一种必须，特别是对于癌症等复杂疾病，已知多个基因和多种分子机制参与基因功能改变。在这篇综述中，我们报告了我们在非裔美国人结直肠癌患者中最新的基因组和表观基因组学发现。这一人群承受着更高的疾病负担，该领域的大多数研究人员正在寻找可能导致这种差异的潜在遗传和表观遗传目标。我们在此报告全基因组拷贝数变异，单核苷酸突变和DNA甲基化的发现，可能是特定于这一群体。

引用次数: 14

Targeted Exome Sequencing Outcome Variations of Colorectal Tumors within and across Two Sequencing Platforms. 结直肠肿瘤的靶向外显子组测序结果在两个测序平台内和之间的差异。

Next generation, sequencing & applications

Pub Date : 2016-06-01 Epub Date: 2016-03-14 DOI: 10.4172/2469-9853.1000123

Hassan Ashktorab, Hamed Azimi, Michael L Nickerson, Sara Bass, Sudhir Varma, Hassan Brim

Background and aim: Next generation sequencing (NGS) has quickly the tool of choice for genome and exome data generation. The multitude of sequencing platforms as well as the variabilities within each platform need to be assessed. In this paper we used two platforms (ION TORRENT AND ILLUMINA) to assess single nucleotides variants in colorectal cancer (CRC) specimens.

Methods: CRC specimens (n = 13) collected from 6 CRC (cancer and matched normal) patients were used to establish the mutational profile using ION TORRENT AND ILLUMINA sequencing platforms. We analyzed a set of samples from Formalin Fixed Paraffin Embedded and FF (FF) samples on both platforms to assess the effect of sample nature (FFPE vs. FF) on sequencing outcome and to evaluate the similarity/differences of SNVs across the two platforms. In addition, duplicates of FF samples were sequenced on each platform to assess variability within platform.

Results: The comparison of FF replicates to each other gave a concordance of 77% (± 15.3%) in Ion Torrent and 70% (± 3.7%) in Illumina. FFPE vs. FF replicates gave a concordance of 40% (± 32%) in Ion Torrent and 49% (± 19%) in Illumina. For the cross platform concordance were FFPE compared to FF (Average of 75% (± 9.8%) for FFPE samples and 67% (± 32%) for FF and 70% (± 26.8%) overall average).

Conclusion: Our data show a significant variability within and across platforms. Also the number of detected variants depend on the nature of the specimen; FF vs. FFPE. Validation of NGS discovered mutations is a must to rule-out false positive mutants. This validation might either be performed through a second NGS platform or through Sanger sequencing.

背景与目的:下一代测序(NGS)是快速生成基因组和外显子组数据的首选工具。需要评估众多测序平台以及每个平台内的可变性。在本文中，我们使用两个平台(ION TORRENT和ILLUMINA)来评估结直肠癌(CRC)标本中的单核苷酸变异。方法:采用ION TORRENT和ILLUMINA测序平台，收集6例结直肠癌(癌和配对正常)患者的结直肠癌标本(n = 13)，建立突变谱。我们分析了两种平台上福尔马林固定石蜡包埋和FF (FF)样品的一组样品，以评估样品性质(FFPE vs. FF)对测序结果的影响，并评估两种平台上snv的相似性/差异性。此外，在每个平台上对FF样本的重复序列进行测序，以评估平台内的变异性。结果:在Ion Torrent和Illumina中，FF重复序列的一致性分别为77%(±15.3%)和70%(±3.7%)。在Ion Torrent和Illumina中，FFPE和FF重复的一致性分别为40%(±32%)和49%(±19%)。对于跨平台一致性，FFPE与FF比较(FFPE样本平均为75%(±9.8%)，FF样本平均为67%(±32%)，整体平均为70%(±26.8%))。结论:我们的数据显示了平台内部和平台之间的显著差异。此外，检测到的变异数量取决于标本的性质;FF vs. FFPE。为了排除假阳性突变，必须对NGS发现的突变进行验证。该验证可以通过第二个NGS平台进行，也可以通过Sanger测序进行。

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引用次数: 11

Accuracy of Next Generation Sequencing Platforms. 下一代测序平台的准确性。

Next generation, sequencing & applications

Pub Date : 2014-01-01 DOI: 10.4172/jngsa.1000106

Edward J Fox, Kate S Reid-Bayliss, Mary J Emond, Lawrence A Loeb

Next-generation DNA sequencing has revolutionized genomic studies and is driving the implementation of precision diagnostics. The ability of these technologies to disentangle sequence heterogeneity, however, is limited by their relatively high error rates. A Several single molecule barcoding strategies have been propose to reduce the overall error frequency. A Duplex Sequencing additionally exploits the fact that DNA is double-strand, with one strand reciprocally encoding the sequence information of its complement, and can eliminate nearly all sequencing errors by comparing the sequence of individually tagged amplicons derived from one strand of DNA with that of its complementary strand. This method reduces errors to fewer than one per ten million nucleotides sequenced.

下一代DNA测序已经彻底改变了基因组研究，并正在推动精确诊断的实施。然而，这些技术解开序列异质性的能力受到其相对较高的错误率的限制。已经提出了几种单分子条形码策略来降低总体错误频率。双工测序还利用了DNA是双链的事实，其中一条链相互编码其补体的序列信息，并且可以通过比较来自一条DNA链的单独标记的扩增子序列与其互补链的扩增子序列来消除几乎所有的测序错误。这种方法将误差降低到少于1 / 1000万个核苷酸测序。

引用次数: 221

Molecular Cloning, Modeling, and Characterization of Type 2 Metallothionein from Plantago ovata Forsk 车前草2型金属硫蛋白的分子克隆、建模及表征

Next generation, sequencing & applications

Pub Date : 2013-03-13 DOI: 10.1155/2013/756983

Amitava Moulick, Debashis Mukhopadhyay, Shonima Talapatra, Nirmalya Ghoshal, S. Raychaudhuri

Plantago ovata Forsk is a medicinally important plant. Metallothioneins are cysteine rich proteins involved in the detoxification of heavy metals. Molecular cloning and modeling of MT from P. ovata is not reported yet. The present investigation will describe the isolation, structure prediction, characterization, and expression under copper stress of type 2 metallothionein (MT2) from this species. The gene of the protein comprises three exons and two introns. The deduced protein sequence contains 81 amino acids with a calculated molecular weight of about 8.1 kDa and a theoretical pI value of 4.77. The transcript level of this protein was increased in response to copper stress. Homology modeling was used to construct a three-dimensional structure of P. ovata MT2. The 3D structure model of P. ovata MT2 will provide a significant clue for further structural and functional study of this protein.

车前草是一种重要的药用植物。金属硫蛋白是一种富含半胱氨酸的蛋白质，参与重金属的解毒。目前，尚没有关于卵黄芽孢杆菌的分子克隆和分子模型的报道。本文将介绍该物种2型金属硫蛋白(MT2)的分离、结构预测、表征及其在铜胁迫下的表达。该蛋白的基因由三个外显子和两个内含子组成。该蛋白序列包含81个氨基酸，计算分子量约为8.1 kDa，理论pI值为4.77。该蛋白的转录水平在铜胁迫下升高。利用同源性建模方法构建了卵形芽孢杆菌MT2的三维结构。卵形蛋白MT2的三维结构模型将为进一步研究该蛋白的结构和功能提供重要线索。

引用次数: 9

Identification of Prophages and Prophage Remnants within the Genome of Avibacterium paragallinarum Bacterium 副allinarum Avibacterium细菌基因组中原噬菌体和残体的鉴定

Next generation, sequencing & applications

Pub Date : 2012-12-18 DOI: 10.1155/2012/953609

Y. Roodt, R. Bragg, J. Albertyn

Bacterial whole genome sequencing has delivered an abundance of prophage sequences as a by-product and the analysis of these sequences revealed ways in which phages have affected the genome of their host bacteria in various bacterial species. The aim of this study was to identify the phage-related sequences in the draft assembly of the Avibacterium paragallinarum genome, the causative agent of infectious coryza in poultry. Whole genome assembly was not possible due to the presence of gaps and/or repeats existent on the ends of contigs. However, genome annotation revealed prophage and prophage remnant sequences present in this genome. From the results obtained, a complete Mu-like bacteriophage could be identified that was termed AvpmuC-2M. A complete sequence of HP2-like bacteriophage, named AvpC-2M-HP2, was also identified.

细菌全基因组测序已经提供了大量的前噬菌体序列作为副产品，这些序列的分析揭示了噬菌体在不同细菌物种中影响宿主细菌基因组的方式。本研究的目的是鉴定禽传染性鼻炎的病原体副鸡芽Avibacterium paragallinarum基因组草图组装中的噬菌体相关序列。全基因组组装是不可能的，因为在contigs的末端存在间隙和/或重复。然而，基因组注释显示该基因组中存在前噬菌体和前噬菌体残体序列。根据获得的结果，可以鉴定出一个完整的mu样噬菌体，命名为AvpmuC-2M。还鉴定了一个完整的hp2样噬菌体序列，命名为AvpC-2M-HP2。

引用次数: 8

Cost-Effective Paramagnetic Bead Technique for Purification of Cycle Sequencing Products 高性价比的顺磁珠循环测序产品纯化技术

Next generation, sequencing & applications

Pub Date : 2012-09-23 DOI: 10.1155/2012/767959

S. Mijatovic-Rustempasic, M. Frace, M. Bowen

The quality of sequencing results depends greatly upon the quality and purity of the template as well as the purity of the fluorescently labeled products generated by cycle sequencing. Numerous approaches have been used for purification of cycle sequencing products, including alcohol precipitation, affinity-based chromatography, size exclusion chromatography, commercially-available proprietary methods, and paramagnetic bead technology. In this paper, we describe an affordable paramagnetic technology method using BioMag Carboxyl beads. Compared to other well-established, proprietary methods for purification of cycle sequencing products, this method produced consistently good results, with a very low reagent cost and short procedure time.

测序结果的质量在很大程度上取决于模板的质量和纯度，以及循环测序产生的荧光标记产物的纯度。许多方法已被用于循环测序产品的纯化，包括醇沉淀、基于亲和的色谱、尺寸排除色谱、商业上可用的专有方法和顺磁珠技术。在本文中，我们描述了一种经济实惠的使用BioMag羧基珠的顺磁技术方法。与其他成熟的、专有的循环测序产品纯化方法相比，该方法具有非常低的试剂成本和较短的操作时间，始终产生良好的结果。

引用次数: 11

Molecular Cloning, Sequencing, and Characterization of a Putative Acetyl-CoA-C-acetyltransferase cDNA from a Highly Fragrant Orchid Hybrid Vanda Mimi Palmer 高香兰杂种Vanda Mimi Palmer乙酰辅酶a - c -乙酰转移酶cDNA的克隆、测序和鉴定

Next generation, sequencing & applications

Pub Date : 2012-06-19 DOI: 10.1155/2012/509034

Seow-Ling Teh, J. Abdullah, P. Namasivayam

Vanda Mimi Palmer, a hybrid of Vanda Tan Chay Yan and Vanda tessellata (Roxb.) Hk.f. ex G. Don, is cultivated as a potted ornamental plant mainly for its fragrance rather than its look. Plant acetyl-CoA-C-acetyltransferase (ACA) is involved in the condensation of two acetyl-CoAs to form acetoacetyl-CoA, which condenses with another acetyl-CoA to yield a crucial molecule, 3-hydroxyl-3-methylglutaryl-CoA, at the initial step of the mevalonate (MVA) pathway. An ACA gene from vandaceous orchid has never been reported. We describe the isolation and molecular characterization of an ACA-like gene from V. Mimi Palmer (designated as VMPACA) to facilitate a better understanding of the terpenoid biosynthesis pathway in orchids. The deduced VMPACA encodes a 376-amino-acid protein with a molecular weight of 39 kDa, which comprises an open reading frame of 1128 bp. It is flanked by 87 bp of 5′-untranslated region and 174 bp of 3′-untranslated region including a poly-A tail. Its protein sequence is 81% identical to other plant ACAs and contains a thiolase active site. The fluctuation expression pattern of VMPACA transcript by real-time RT-PCR showed that it is developmentally and temporally regulated with predominant expression in outer and lateral inner tepals compared to vegetative tissues.

Vanda Mimi Palmer, Vanda Tan Chay Yan和Vanda tessellata (Roxb.)的混血儿。Hk.f。唐是一种盆栽观赏植物，主要是因为它的香味而不是它的外观。植物乙酰辅酶a - c -乙酰转移酶(ACA)参与两个乙酰辅酶a缩合形成乙酰乙酰辅酶a，乙酰乙酰辅酶a与另一个乙酰辅酶a缩合产生关键分子3-羟基-3-甲基戊二酰辅酶a，这是甲羟酸(MVA)途径的初始步骤。从汪达兰中提取ACA基因从未被报道过。为了更好地了解兰科植物萜类化合物的生物合成途径，我们从V. Mimi Palmer中分离了一个类似aca的基因(称为VMPACA)并进行了分子表征。推导出的VMPACA编码一个376个氨基酸的蛋白，分子量为39 kDa，包含一个1128 bp的开放阅读框。它的两侧有87 bp的5 '非翻译区和174 bp的3 '非翻译区，包括poly-A尾。其蛋白质序列与其他植物ACAs相同81%，并含有硫酶活性位点。实时RT-PCR检测的VMPACA转录本的波动表达模式表明，与营养组织相比，VMPACA转录本受发育和时间调控，主要表达于外、外侧、内被片。

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