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Epigenetics Evolution and Replacement Histones: Evolutionary Changesat Drosophila H2AvD 表观遗传学、进化和替代组蛋白:果蝇H2AvD的进化变化
Journal of Data Mining in Genomics & Proteomics Pub Date : 2017-01-01 DOI: 10.4172/2153-0602.1000207
Y. Matsuo
{"title":"Epigenetics Evolution and Replacement Histones: Evolutionary Changesat Drosophila H2AvD","authors":"Y. Matsuo","doi":"10.4172/2153-0602.1000207","DOIUrl":"https://doi.org/10.4172/2153-0602.1000207","url":null,"abstract":"The evolutionary changes in the Drosophila H2A and H2AvD genes, which encode histones, were analyzed using the sequences of 12 Drosophila sp. for understanding the evolution of histone replacement and epigenetics. The Ball gene, coding for a histone threonine kinase, was located head-to-head with the H2AvD gene in seven Drosophila sp. A strongly conserved DNA sequence was also found in the region upstream of the H2AvD gene; this sequence is most likely a transcriptional signal, because the sequence was also conserved in four other Drosophila sp. that did not have an upstream Ball gene. The SPARC gene, coding for a calcium-binding domain, was located tail-to-tail in the region downstream of the H2AvD gene in 11 Drosophila sp. studied. A moderately conserved DNA sequence was found in the H2AvD gene region at the splicing site in the first intron. Different codon usages for the H2A and H2AvD genes were found for 11 of 17 amino acids, and codon usages characteristic of replacement histones (H2AvD, H4r, H3.3A and H3.3B) were found for amino acids. Codon usage was considerably different at several histone modification sites in the H2A gene. These results suggested that unlike the H3.3 and H4r genes, not only post-transcriptional control, but also transcriptional control played a role in the H2AvD gene. In addition to post-transcriptional controls, such as splicing and translation, the development of a control system for transcription must have occurred during the evolution of histone replacement and epigenetic systems.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"95 8 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87684457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
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
{"title":"Significances of OMV and Extracellular Vesicle Proteomics","authors":"V. Tiwari","doi":"10.4172/2153-0602.1000208","DOIUrl":"https://doi.org/10.4172/2153-0602.1000208","url":null,"abstract":"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.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"13 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74492010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Quick Reliable Exploration of the PDB Universe Seeks a New Template Search Algorithm","authors":"Sunil Nahata, Ashish Runthala","doi":"10.4172/2153-0602.1000206","DOIUrl":"https://doi.org/10.4172/2153-0602.1000206","url":null,"abstract":"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.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"52 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2016-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84696566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Comparative and Evolutionary Studies of Mitochondrial and CytoplasmicPyrophosphatase (PPA) Genes and Proteins","authors":"R. Holmes, Kimberly D. Spradling-Reeves, L. Cox","doi":"10.4172/2153-0602.1000205","DOIUrl":"https://doi.org/10.4172/2153-0602.1000205","url":null,"abstract":"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.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"19 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2016-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75695416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Genetic Predictive Scores in Heart Failure: Possibilities and Expectations","authors":"Alex, er E. Berezin","doi":"10.4172/2153-0602.1000E127","DOIUrl":"https://doi.org/10.4172/2153-0602.1000E127","url":null,"abstract":"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","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"78 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2016-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76085221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Proteomics: An Indispensable Tool for Novel Biomarker Identification in Melanoma","authors":"P. Mittal, Manish Jain","doi":"10.4172/2153-0602.1000204","DOIUrl":"https://doi.org/10.4172/2153-0602.1000204","url":null,"abstract":"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.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"44 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2016-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90833354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Insights into PPR Gene Family in Cajanus Cajan and Other Legume Species","authors":"P. Kaur, M. Verma, Pavan K. Chaduvula, S. Saxena, Nikita Baliyan, Alim Junaid, A. Mahato, N. Singh, K. Gaikwad","doi":"10.4172/2153-0602.1000203","DOIUrl":"https://doi.org/10.4172/2153-0602.1000203","url":null,"abstract":"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.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"50 1","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2016-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73620254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"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","authors":"A. Heidari","doi":"10.4172/2153-0602.1000E125","DOIUrl":"https://doi.org/10.4172/2153-0602.1000E125","url":null,"abstract":"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.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"14 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2016-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82412373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Epigenetic Modifications the Development of Different Heart Failure Phenotypes","authors":"Alex, er E. Berezin","doi":"10.4172/2153-0602.1000202","DOIUrl":"https://doi.org/10.4172/2153-0602.1000202","url":null,"abstract":"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.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"7 1","pages":"1-3"},"PeriodicalIF":0.0,"publicationDate":"2016-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84139708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Decrypting the Treasures of Regulatory Non-coding RNAs in Highthroughput Era","authors":"Bibekan, Mallick","doi":"10.4172/2153-0602.1000E124","DOIUrl":"https://doi.org/10.4172/2153-0602.1000E124","url":null,"abstract":"","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"8 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2016-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73317368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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