Genetic Techniques

遗传技术
  • 文章类型: Journal Article
    Long DNA and RNA reads from nanopore and PacBio technologies have many applications, but the raw reads have a substantial error rate. More accurate sequences can be obtained by merging multiple reads from overlapping parts of the same sequence. lamassemble aligns up to ∼1000 reads to each other, and makes a consensus sequence, which is often much more accurate than the raw reads. It is useful for studying a region of interest such as an expanded tandem repeat or other disease-causing mutation.
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  • 文章类型: Journal Article
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    文章类型: Journal Article
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  • 文章类型: Guideline
    大鼠长期以来一直是心血管研究的关键生理模型,大多数自交系先前已选择对各种心血管疾病(CVD)的易感性或抗性。这些CVD大鼠模型提供了生理相关背景,在该背景上,可以在更临床可翻译的实验环境中测试人CVD的候选者。然而,一个用于基因改造大鼠基因组以测试分子机制的多样化工具箱直到最近才出现。这里,我们对开发转基因CVD大鼠模型的几种策略进行了高水平的描述.
    The rat has long been a key physiological model for cardiovascular research, most of the inbred strains having been previously selected for susceptibility or resistance to various cardiovascular diseases (CVD). These CVD rat models offer a physiologically relevant background on which candidates of human CVD can be tested in a more clinically translatable experimental setting. However, a diverse toolbox for genetically modifying the rat genome to test molecular mechanisms has only recently become available. Here, we provide a high-level description of several strategies for developing genetically modified rat models of CVD.
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  • 文章类型: Consensus Development Conference
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  • 文章类型: Case Reports
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  • 文章类型: Journal Article
    流感病毒的快速进化通过多种遗传机制和选择压力发生在克隆和非克隆中。流感病毒的非克隆进化包括基因片段之间相对频繁的重排和较少报道的非同源RNA重组过程。片段内的同源RNA重组已被提出作为第三种这样的机制,但是迄今为止,在流感病毒中存在这一过程的证据既薄弱又有争议。由于同源重组尚未在实验室得到证实,支持证据,如果它存在,可能主要来自基因序列数据中观察到的系统发育不一致模式。这里,我们审查了与实验室程序和样品处理相关的必要标准,生物信息学分析,以及已知的流感病毒的生态学和进化需要满足,以确认同源重组事件发生在一组序列的历史。为了确定这些标准是否对重组分析有影响,我们收集了8307份公开可用的甲型流感片段全长序列,并将其分为通过美国国立卫生研究院流感基因组测序项目(IGSP)测序的序列和未测序的序列.由于样品处理和测序在IGSP中以非常高的标准执行,这些序列应该不太可能受到其他样品或实验室菌株的污染,因此不应表现出实验室产生的同源重组信号。我们的分析表明,IGSP数据集仅包含两个系统发育支持的单重组序列,没有重组进化枝。与此形成鲜明对比的是,非IGSP数据显示非常大量的潜在重组。我们得出的结论是,在非IGSP数据中存在假阳性信号比在IGSP数据中存在假阴性更可能。鉴于迄今为止的证据,同源重组似乎在甲型流感病毒的进化中几乎没有或根本没有作用。
    The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses.
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  • 文章类型: Journal Article
    Epithelial neuroendocrine tumors (NETs) have been the subject of much debate regarding their optimal classification. Although multiple systems of nomenclature, grading, and staging have been proposed, none has achieved universal acceptance. To help define the underlying common features of these classification systems and to identify the minimal pathology data that should be reported to ensure consistent clinical management and reproducibility of data from therapeutic trials, a multidisciplinary team of physicians interested in NETs was assembled. At a group meeting, the participants discussed a series of \"yes\" or \"no\" questions related to the pathology of NETs and the minimal data to be included in the reports. After discussion, anonymous votes were taken, using the Delphic principle that 80% agreement on a vote of either yes or no would define a consensus. Questions that failed to achieve a consensus were rephrased once or twice and discussed, and additional votes were taken. Of 108 questions, 91 were answerable either yes or no by more than 80% of the participants. There was agreement about the importance of proliferation rate for tumor grading, the landmarks to use for staging, the prognostic factors assessable by routine histology that should be reported, the potential for tumors to progress biologically with metastasis, and the current status of advanced immunohistochemical and molecular testing for treatment-related biomarkers. The lack of utility of a variety of immunohistochemical stains and pathologic findings was also agreed upon. A consensus could not be reached for the remaining 17 questions, which included both minor points related to extent of disease assessment and some major areas such as terminology, routine immunohistochemical staining for general neuroendocrine markers, use of Ki67 staining to assess proliferation, and the relationship of tumor grade to degree of differentiation. On the basis of the results of the Delphic voting, a minimum pathology data set was developed. Although there remains disagreement among experts about the specific classification system that should be used, there is agreement about the fundamental pathology data that should be reported. Examination of the areas of disagreement reveals significant opportunities for collaborative study to resolve unanswered questions.
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  • 文章类型: Consensus Development Conference
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    文章类型: English Abstract
    The need and development of clinical guidelines for the diagnosis and treatment of chronic periodontitis in Belgium has been previously described. The use of supplementary diagnostic tests in this field is widespread. The question is whether the existing scientific evidence justifies the routine use of these tests in the diagnosis of chronic periodontitis. A thorough search of the literature was conducted in reference to microbiological testing as well as genetic testing for periodontitis.
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