Journal of Data Mining in Genomics & Proteomics最新文献

英文中文

Mammalian Glutamyl Aminopeptidase Genes (ENPEP) and Proteins: Comparative Studies of a Major Contributor to Arterial Hypertension. 哺乳动物谷氨酰氨基肽酶基因（ENPEP）和蛋白质：动脉高血压主要诱因的比较研究。

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2017-01-01 Epub Date: 2017-06-13 DOI: 10.4172/2153-0602.1000211

Roger S Holmes, Kimberly D Spradling-Reeves, Laura A Cox

Glutamyl aminopeptidase (ENPEP) is a member of the M1 family of endopeptidases which are mammalian type II integral membrane zinc-containing endopeptidases. ENPEP is involved in the catabolic pathway of the renin-angiotensin system forming angiotensin III, which participates in blood pressure regulation and blood vessel formation. Comparative ENPEP amino acid sequences and structures and ENPEP gene locations were examined using data from several mammalian genome projects. Mammalian ENPEP sequences shared 71-98% identities. Five N-glycosylation sites were conserved for all mammalian ENPEP proteins examined although 9-18 sites were observed, in each case. Sequence alignments, key amino acid residues and predicted secondary and tertiary structures were also studied, including transmembrane and cytoplasmic sequences and active site residues. Highest levels of human ENPEP expression were observed in the terminal ileum of the small intestine and in the kidney cortex. Mammalian ENPEP genes contained 20 coding exons. The human ENPEP gene promoter and first coding exon contained a CpG island (CpG27) and at least 6 transcription factor binding sites, whereas the 3'-UTR region contained 7 miRNA target sites, which may contribute to the regulation of ENPEP gene expression in tissues of the body. Phylogenetic analyses examined the relationships of mammalian ENPEP genes and proteins, including primate, other eutherian, marsupial and monotreme sources, using chicken ENPEP as a primordial sequence for comparative purposes.

谷氨酰氨肽酶（ENPEP）是哺乳动物内肽酶 M1 家族的成员，属于哺乳动物 II 型整膜含锌内肽酶。ENPEP 参与肾素-血管紧张素系统的分解代谢途径，形成血管紧张素 III，参与血压调节和血管形成。利用几个哺乳动物基因组项目的数据，研究了ENPEP氨基酸序列和结构的比较以及ENPEP基因的位置。哺乳动物的ENPEP序列具有71-98%的相同性。在所研究的所有哺乳动物ENPEP蛋白中，5个N-糖基化位点是保守的，尽管在每种情况下都观察到9-18个位点。此外，还研究了序列比对、关键氨基酸残基以及预测的二级和三级结构，包括跨膜序列、胞质序列和活性位点残基。在小肠末端回肠和肾皮质中观察到了最高水平的人类ENPEP表达。哺乳动物的ENPEP基因包含20个编码外显子。人类ENPEP基因启动子和第一个编码外显子含有一个CpG岛（CpG27）和至少6个转录因子结合位点，而3'-UTR区域含有7个miRNA靶位点，这些位点可能有助于调控ENPEP基因在身体组织中的表达。系统发育分析研究了哺乳动物ENPEP基因和蛋白质的关系，包括灵长类、其他有蹄类、有袋类和单脊类动物，并以鸡的ENPEP基因作为原始序列进行比较。

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引用次数: 0

Significances of OMV and Extracellular Vesicle Proteomics OMV和细胞外囊泡蛋白质组学的意义

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2017-01-01 DOI: 10.4172/2153-0602.1000208

V. Tiwari

Outer Membrane Vesicle (OMV) proteome has been involved into the pathogenesis of diseases and resistance of microorganisms against a number of antibiotics, mechanism of action of probiotics and host-pathogen interaction etc. We have enlightened the role played by extracellular vesicles proteomics in the pathogenesis of different diseases related to human. Isolation succeeded by purification of ample amount of OMV from biological samples, is one of the most important steps for further proteome related analysis. With the development of both labelled and label-free methods used in proteomics, significant progress has been made in previous years in membrane proteomics. Hence, it is important to review the biological significance of proteins found in the OMV fractions using membrane proteomics approach. We have also explained methods used for isolation, purification and quantification of OMV. In the present review, it can be concluded that proteomic study of outer membrane and extracellular vesicles has now gained priority for the detailed study of disease pathogenesis, drug resistance, vaccine development, cell signalling etc.

外膜囊泡(OMV)蛋白质组学在疾病的发病机制、微生物对多种抗生素的耐药性、益生菌的作用机制和宿主与病原体的相互作用等方面具有重要的研究意义。揭示了细胞外囊泡蛋白质组学在人类不同疾病发病机制中的作用。从生物样品中分离纯化大量的OMV是进一步进行蛋白质组相关分析的最重要步骤之一。随着膜蛋白质组学中标记和无标记方法的发展，近年来膜蛋白质组学研究取得了重大进展。因此，利用膜蛋白质组学方法来研究OMV组分中蛋白质的生物学意义是很重要的。我们还解释了OMV的分离、纯化和定量方法。目前，外膜和细胞外囊泡的蛋白质组学研究对疾病发病机制、耐药性、疫苗研制、细胞信号转导等方面的详细研究具有重要意义。

引用次数: 3

Quick Reliable Exploration of the PDB Universe Seeks a New Template Search Algorithm 快速可靠地探索PDB宇宙寻求一种新的模板搜索算法

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2016-10-31 DOI: 10.4172/2153-0602.1000206

Sunil Nahata, Ashish Runthala

Near-native protein structure prediction through Template Based Modelling (TBM) has been a major realistic goal of structural biology for several years. The TBM algorithms require the best-set of templates for a target protein sequence to maximally cover it and construct its correct topology. However, the accuracy of such prediction algorithms suffers from the algorithmic and logical problems of our template search measures which fail to quickly screen reliable structures for a target sequence. In this study, we employ the culled PDB95 dataset of 41,967 templates to predict the CASP10 target T0752 models for assessing the efficiency of the usually employ search engines PSI-BLAST and HHPred. Our analysis presents a detailed study in order to open new vistas for improving the accuracy of TBM prediction methodologies. It reveals weaknesses of most popular template search measures and thereby briefly provides a significant insight into the qualities of a foreseen template search algorithm to illustrate the need for a more reliable template search algorithm.

近年来，基于模板建模(TBM)的近天然蛋白结构预测一直是结构生物学研究的主要目标。TBM算法需要目标蛋白序列的最佳模板集，以最大限度地覆盖它并构建其正确的拓扑结构。然而，这种预测算法的准确性受到我们的模板搜索措施的算法和逻辑问题的影响，这些问题无法快速筛选目标序列的可靠结构。在本研究中，我们使用筛选的PDB95数据集41,967个模板来预测CASP10目标T0752模型，以评估通常使用的搜索引擎PSI-BLAST和HHPred的效率。我们的分析提出了一项详细的研究，以便为提高TBM预测方法的准确性开辟新的前景。它揭示了最流行的模板搜索方法的弱点，从而简要地提供了对可预见模板搜索算法的质量的重要见解，以说明需要更可靠的模板搜索算法。

引用次数: 2

Comparative and Evolutionary Studies of Mitochondrial and CytoplasmicPyrophosphatase (PPA) Genes and Proteins 线粒体和细胞质焦磷酸酶(PPA)基因和蛋白的比较和进化研究

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2016-10-30 DOI: 10.4172/2153-0602.1000205

R. Holmes, Kimberly D. Spradling-Reeves, L. Cox

Inorganic pyrophosphatase (PPA; PPase) (EC: 3.6.1.1) is a member of the diphosphatase enzyme family which functions as a diphosphate hydrolase within the cytoplasm (PPA1) and mitochondria (PPA2) of vertebrate tissues. PPA1 and PPA2 amino acid sequences and structures and PPA-like gene locations were examined using bioinformatic data from several genome projects. Sequence alignments and key conserved amino acid residues were also studied (human PPA2 residues identified): the mitochondrial signal peptide (1-31); and active site residues responsible for Mg2+ binding (164Asp, 169Asp and 201Asp), substrate binding (127Arg) and serving as the proton donor site (138Tyr). Predicted 2D and 3D structures were identified for vertebrate PPA1 and PPA2 using the reported yeast PPA1 structure (PDB: 1E9G). Vertebrate PPA1 and PPA2 genes usually contained 11 or 12 coding exons, respectively, with an extended exon 1 and an additional exon 3 observed for vertebrate PPA2 genes. Transcription factor binding sites and CpG104 were identified within the human PPA2 gene promoter; and MiR-590 for the PPA2 3’UTR. Phylogenetic analyses suggested that an ancestral invertebrate PPA gene underwent a gene duplication event to form 2 separate lines of vertebrate gene evolution: PPA1 and PPA2.

无机焦磷酸酶;PPase (EC: 3.6.1.1)是二磷酸酶家族的一员，在脊椎动物组织的细胞质(PPA1)和线粒体(PPA2)中起二磷酸水解酶的作用。利用多个基因组计划的生物信息学数据，对PPA1和PPA2氨基酸序列和结构以及ppa样基因的位置进行了检测。序列比对和关键保守氨基酸残基也进行了研究(人类PPA2残基鉴定):线粒体信号肽(1-31);以及负责Mg2+结合(164Asp, 169Asp和201Asp)，底物结合(127Arg)和作为质子供体位点(138Tyr)的活性位点残基。利用已报道的酵母PPA1结构(PDB: 1E9G)确定了脊椎动物PPA1和PPA2的预测二维和三维结构。脊椎动物PPA1和PPA2基因通常分别包含11或12个编码外显子，其中脊椎动物PPA2基因的外显子1和外显子3延长。在人PPA2基因启动子中鉴定了转录因子结合位点和CpG104;MiR-590用于PPA2 3'UTR。系统发育分析表明，祖先无脊椎动物PPA基因经历了基因复制事件，形成了2个独立的脊椎动物基因进化系:PPA1和PPA2。

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引用次数: 1

Genetic Predictive Scores in Heart Failure: Possibilities and Expectations 心力衰竭的遗传预测评分:可能性和期望

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2016-10-14 DOI: 10.4172/2153-0602.1000E127

Alex, er E. Berezin

Heart failure (HF) remains a major health problem worldwide. Currently used HF risk prediction scores based on clinical findings, echocardiography features, biomarkers cannot propose an individualized approach to risk stratification, whereas there is variability in predictive value of different scores amongst patients with various HF phenotypes. The editorial commentary is devoted the role of the genetic risk prediction scores in the predisposition of HF development and assay in the HF medical care response. The brand new risk scores reflecting variabilities in genetic and epigenetic features in HF development are discussed also

心力衰竭(HF)仍然是世界范围内的一个主要健康问题。目前使用的基于临床表现、超声心动图特征、生物标志物的HF风险预测评分不能提出一种个体化的风险分层方法，而在不同HF表型的患者中，不同评分的预测价值存在差异。社论评论致力于遗传风险预测评分在心衰发展易感性中的作用，以及在心衰医疗反应中的测定。还讨论了反映心衰发展中遗传和表观遗传特征变异的全新风险评分

引用次数: 4

Proteomics: An Indispensable Tool for Novel Biomarker Identification in Melanoma 蛋白质组学:黑色素瘤新生物标志物鉴定不可或缺的工具

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2016-07-25 DOI: 10.4172/2153-0602.1000204

P. Mittal, Manish Jain

Melanoma is a prevalent disease with a high mortality rate. The advent of proteomics has enabled the identification of various prognostic and diagnostic melanoma biomarkers, fulfilling a vital need. The development of various protein fractionation and analysis tools has advanced the role of proteomics in analyzing complex protein samples obtained from melanoma patients. Proteomics is also being utilized to help guide drug design and the development of treatment algorithms. Ultimately, proteomics-based methodologies have proven to be paramount to the success of research being done on melanoma and the drugs used for treatment. These techniques will continue to shed light on the mechanisms of action driving therapeutic efficacy and toxicity, in hopes of extending survival and improving patient outcomes and quality of life.

黑色素瘤是一种死亡率很高的流行疾病。蛋白质组学的出现使各种预后和诊断黑色素瘤生物标志物的鉴定成为可能，满足了至关重要的需求。各种蛋白质分离和分析工具的发展促进了蛋白质组学在分析黑色素瘤患者复杂蛋白质样本中的作用。蛋白质组学也被用来帮助指导药物设计和治疗算法的发展。最终，基于蛋白质组学的方法已被证明对黑色素瘤研究的成功和用于治疗的药物至关重要。这些技术将继续阐明驱动治疗疗效和毒性的作用机制，以期延长生存期，改善患者的预后和生活质量。

引用次数: 9

Insights into PPR Gene Family in Cajanus Cajan and Other Legume Species Cajanus Cajan和其他豆科植物PPR基因家族的研究

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2016-07-18 DOI: 10.4172/2153-0602.1000203

P. Kaur, M. Verma, Pavan K. Chaduvula, S. Saxena, Nikita Baliyan, Alim Junaid, A. Mahato, N. Singh, K. Gaikwad

PPR proteins comprises of several hundred members among land plants and govern a fascinating array of functions in organeller genomes that ranges from participation in stabilization of organeller transcripts, RNA editing to fertility restoration of CMS lines. Despite the availability of genome sequences of several legume species, comprehensive cataloguing of members of PPR gene family has not been carried out. In the current study, we identified 523, 830, 534, 816, 441 and 677 PPR proteins in Cajanus, Glycine, Phaseolus, Medicago, Vigna and Cicer genomes, respectively and their complete in silico categorization was undertaken to classify them into various sub-classes and their localization prediction. Chromosomal coordinates of 271 Cajanus PPR genes were predicted and their homologues were identified in 5 other legumes revealing extensive genome conservation. PPR genes of all 6 legume species were further probed to identify restorer of fertility-like PPRs (RFLs) on the basis of protein clustering and followed by homology searches to already known Rf-PPR genes. Seventy RFL PPR genes (P sub-class) were identified and were scrutinized by phylogenetic analysis which revealed extended similarity and common features shared by these RFLs across the species. Some of these RFL PPRs were present as small clusters in Glycine, Phaseolus, Vigna and Cicer genomes. This study has generated a knowledge base about PPR gene family in legumes and opens several avenues for future investigations into their molecular functions, evolutionary relationships and their potential in identifying markers to enable cloning of Rf genes.

在陆地植物中，PPR蛋白由数百个成员组成，并在细胞器基因组中控制着一系列迷人的功能，从参与细胞器转录物的稳定，RNA编辑到CMS系的育性恢复。尽管已有几种豆科植物的基因组序列，但尚未对小反刍兽疫基因家族成员进行全面编目。本研究在Cajanus、Glycine、Phaseolus、Medicago、Vigna和Cicer基因组中分别鉴定出523个、830个、534个、816个、441个和677个PPR蛋白，并对其进行完整的计算机分类，将其划分为不同的亚类并进行定位预测。预测了271个Cajanus PPR基因的染色体坐标，并在其他5种豆科植物中鉴定了同源基因，揭示了广泛的基因组保守性。对6种豆科植物的PPR基因进行了进一步的检测，在蛋白质聚类的基础上，确定了可育性样PPR (RFLs)的恢复者，并与已知的Rf-PPR基因进行了同源性搜索。共鉴定了70个RFL PPR基因(P亚类)，并进行了系统发育分析，揭示了这些RFL在整个物种中具有扩展的相似性和共同特征。部分RFL片段以小簇形式存在于甘氨酸(Glycine)、菜豆(Phaseolus)、葡萄(Vigna)和茜草(Cicer)基因组中。本研究建立了豆科植物小反刍兽疫基因家族的知识基础，为进一步研究其分子功能、进化关系及其在克隆小反刍兽疫基因标记方面的潜力开辟了若干途径。

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引用次数: 5

Genomics and Proteomics Studies of Zolpidem, Necopidem, Alpidem, Saripidem, Miroprofen, Zolimidine, Olprinone and Abafungin as Antitumor, Peptide Antibiotics, Antiviral and Central Nervous System (CNS) Drugs 唑吡坦、Necopidem、Alpidem、Saripidem、Miroprofen、Zolimidine、Olprinone和Abafungin抗肿瘤、多肽抗生素、抗病毒和中枢神经系统(CNS)药物的基因组学和蛋白质组学研究

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2016-07-06 DOI: 10.4172/2153-0602.1000E125

A. Heidari

Zolpidem, Necopidem, Alpidem, Saripidem, Miroprofen, Zolimidine, Olprinone and Abafungin (Figure 1) have severed as rich sources of variety of medicinal, pharmaceutical, anti-tumor, antibiotics and antiviral drugs (Figure 2) and biological properties [1-18]. These compounds represent an important class of Nitrogen, Oxygen, Phosphorus and Sulfur heterocyclic and they constitute useful intermediates in organic synthesis [19-39]. Zolpidem, Necopidem, Alpidem, Saripidem, Miroprofen, Zolimidine, Olprinone and Abafungin have proven to be very versatile reagents for heterocyclization and many diverse products can be prepared from the addition of these compounds to Nitrogen, Oxygen, Phosphorus and Sulfur containing compounds.

唑吡坦、Necopidem、Alpidem、Saripidem、Miroprofen、Zolimidine、Olprinone和Abafungin(图1)已成为多种药用、制药、抗肿瘤、抗生素和抗病毒药物(图2)和生物学特性的丰富来源[1-18]。这些化合物是一类重要的氮、氧、磷和硫杂环化合物，它们是有机合成中有用的中间体[19-39]。唑吡坦、Necopidem、Alpidem、Saripidem、Miroprofen、Zolimidine、Olprinone和Abafungin已被证明是非常通用的杂环化试剂，并且可以将这些化合物添加到含氮、氧、磷和硫的化合物中制备许多不同的产品。

引用次数: 108

Epigenetic Modifications the Development of Different Heart Failure Phenotypes 不同心力衰竭表型的表观遗传修饰

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2016-06-27 DOI: 10.4172/2153-0602.1000202

Alex, er E. Berezin

Heart failure (HF) remains a leading cause of death in patient population with known cardiovascular disease. Within last two decades there are evidences regarding decline to determine newel cases with HF with reduced ejection fraction (HFrEF) in developed countries, whereas the frequency of newly-diagnosed HF with preserved ejection fraction (HFpEF) exhibits dramatically rise. Epigenetic modification is considered a modification of the non- DNA sequences related heritable changes in gene expression of target cells. Epigenetic modifications affect several molecular mechanisms, i.e., DNA methylation and deactylation, ATP-dependent chromatin remodeling, histone modifications, and microRNA regulation. The short commentary is clarified the implication of epigenetic modifications in development of different HF phenotypes.

心衰(HF)仍然是已知心血管疾病患者死亡的主要原因。在过去的二十年里，有证据表明，在发达国家，新诊断的HF伴射血分数降低(HFrEF)的病例有所减少，而伴射血分数保持(HFpEF)的新诊断频率却显著上升。表观遗传修饰被认为是对靶细胞基因表达中与遗传变化相关的非DNA序列的修饰。表观遗传修饰影响多种分子机制，即DNA甲基化和去乙酰化，atp依赖性染色质重塑，组蛋白修饰和microRNA调节。这篇简短的评论澄清了表观遗传修饰在不同HF表型发育中的意义。

引用次数: 4

Decrypting the Treasures of Regulatory Non-coding RNAs in Highthroughput Era 在高通量时代解密调控非编码rna的宝藏

Journal of Data Mining in Genomics & Proteomics

Pub Date : 2016-06-27 DOI: 10.4172/2153-0602.1000E124

Bibekan, Mallick

引用次数: 0

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