Journal of Data Mining in Genomics & Proteomics最新文献_第4页

The Highest Mutation in mtDNA Hypervariable Region and Application of Biostatistics with Nucleotide Base X t-n in Determining the Identity of the Mutation through a Transition Intensity Matrix mtDNA高变区最高突变及其应用核苷酸碱基X - t-n生物统计学通过过渡强度矩阵确定突变的身份

Journal of Data Mining in Genomics & Proteomics Pub Date : 2018-01-01 DOI: 10.4172/2153-0602.1000213

Palit Eiy, Y. Ngili

{"title":"The Highest Mutation in mtDNA Hypervariable Region and Application of Biostatistics with Nucleotide Base X t-n in Determining the Identity of the Mutation through a Transition Intensity Matrix","authors":"Palit Eiy, Y. Ngili","doi":"10.4172/2153-0602.1000213","DOIUrl":"https://doi.org/10.4172/2153-0602.1000213","url":null,"abstract":"Human mitochondrial DNA (mtDNA) have been used intensively in the field of forensic identification of victims or suspects of crime through biological evidence. The number of mtDNA molecules in a single cell are in the tens of thousands which enable analysis of samples very little or damaged. Till now there is no standard method for identification using mtDNA in a mass disaster victims such as natural disasters, wars and accidents so that the identification process can not run fast. This study found C16.223t variants in mtDNA sequences that can be used to divide the database into two groups so as to accelerate the process of identification through a mathematical algorithm. This variant has the highest frequency (29.7%) of the 91 polymorphic human mtDNA HVS1 along the 300 nucleotide (16,024-16,324) derived from the NCBI database as much as 142 sequences. MtDNA sequences obtained from data collection Papuan human mtDNA groups that have been published in the NCBI. The next variant that can be used as a classifier in a row in the sequence is 16,311; 16,304; 16,189; and 16,270 with the identity (T→c). For a matrix Q is reversible so the matrix and could have the opposite diagonal. Thus the above equation can be solved by using the diagonal method that can be written: U³ = Uµ ×¨Uµ aµ1 . This equation could count the number of transitions and transversion substitution mutations that occur in a nucleotide sequence of mtDNA. With this grouping, the database can be reduced so as to accelerate the process of identification of samples. Expected method of grouping by the variant with the highest frequency can be developed in the codification database for forensic interest such as the police or the mtDNA database purposes of study anthropology and evolutionary biology.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"4 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86263010","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

Vertebrate Arylsulfatase K (ARSK): Comparative and Evolutionary Studies of the Lysosomal 2-Sulfoglucuronate Sulfatase 脊椎动物芳基硫酸酯酶K (ARSK):溶酶体2-硫脲酸酯硫酸酯酶的比较和进化研究

Journal of Data Mining in Genomics & Proteomics Pub Date : 2018-01-01 DOI: 10.4172/2153-0602.1000212

R. Holmes

引用次数: 0

Molecular Modeling and Simulation of Human Stomatin and Predictions for its Membrane Association 人类口蛋白的分子建模和模拟及其膜关联预测

Journal of Data Mining in Genomics & Proteomics Pub Date : 2018-01-01 DOI: 10.4172/2153-0602.1000216

Yosuke Kondo, H. Yokoyama, I. Matsui, S. Miyazaki

{"title":"Molecular Modeling and Simulation of Human Stomatin and Predictions for its Membrane Association","authors":"Yosuke Kondo, H. Yokoyama, I. Matsui, S. Miyazaki","doi":"10.4172/2153-0602.1000216","DOIUrl":"https://doi.org/10.4172/2153-0602.1000216","url":null,"abstract":"Stomatin is a membrane protein in human red blood cells. The crystal structure, in which the monomeric stomatin from the hyperthermophilic archaeon Pyrococcus horikoshii consists of the α/β domain and the C-terminal α-helical segment, forms a homo-trimer, and stomatin is organized into further high order homo-oligomeric complexes, comprising 9- to 12-mers. To better understand the molecular functions of stomatin, the hypothesis how human stomatin oligomerizes and is associated with cell membranes should be validated. Here, we report what conformations can be generated from the stomatin structure by estimating the flexibility of α-helical segments of human stomatin. And we also simulate how the oligomeric structure of human stomatin interacts with cell membranes. The results showed that the α-helical segments can make flexible movements; the α-helical segment and the α/β domain of the monomer can form a flat structure, and the α-helical segments of the trimer can approach lipid membranes. Based on the flat structure of human stomatin, we proposed a hypothetical oligomeric model to interact with the surface of cell membranes. The oligomeric model well explains the stomatin functions as a scaffolding protein to support the cell membrane.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"45 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81229264","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

Analysis and Mutation of Codon in rpoB and katG Genes and Bioinformatics Study of RIF Binding Model by RNA β Polymerase Subunit: Study in Tuberculosis Patients at Merauke General Hospital-Indonesia rpoB和katG基因密码子分析与突变及RNA β聚合酶亚基RIF结合模型的生物信息学研究——印度尼西亚Merauke总医院肺结核患者的研究

Journal of Data Mining in Genomics & Proteomics Pub Date : 2018-01-01 DOI: 10.4172/2153-0602.1000214

Kawulur Hsi, Y. Ngili

{"title":"Analysis and Mutation of Codon in rpoB and katG Genes and Bioinformatics Study of RIF Binding Model by RNA β Polymerase Subunit: Study in Tuberculosis Patients at Merauke General Hospital-Indonesia","authors":"Kawulur Hsi, Y. Ngili","doi":"10.4172/2153-0602.1000214","DOIUrl":"https://doi.org/10.4172/2153-0602.1000214","url":null,"abstract":"Treatment of TB patients is usually done by administering three types of antituberculosis drugs with the main options being Rifampin (RIF) and Isoniazid (INH), then accompanied by streptomycin or pyrazinamide. RIF resistance is attributable to the mutation of the rpoB gene, the gene that produces the RNA polymerase β-subunit, and the INH resistance is largely due to the mutation of the katG gene. The aim of this study was to obtain information on the association of MDR-TB with related genes, as well as information on the combination of Mycobacterium tuberculosis genotype in tuberculosis patients in Merauke. Here we reported that most of the MDRTB isolates are resistant to other antituberculosis drugs, and the mutation frequency of rpoB526 and rpoB531 (mutations that occur on both sides/this place almost always occur together) is almost the same but the katG315 mutation is present in only 16 isolates (the number of mutations that occur in katG315 is less than in rpoB526 and rpoB531). The presence of C1363A nucleotide changes in sensitive Mycobacterium tuberculosis of six antituberculosis drugs showed that not all rpoB mutations caused resistance. On the basis of this phenomenon, it can be proposed that the mechanism of formation of MDR-TB strains begins with a rpoB mutation followed by a mutation of katG. This study demonstrates that the mechanism of resistance to a drug that affects only one gene, such as rifampin that affects rpoB, is more easily controlled than antituberculous drugs affecting several genes, such as isoniazid which affects other genes besides katG.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"31 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83678759","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

Mitochondrial Genome Mutation Analysis: Indonesian Human mtG Comparation and Several GenBank Sequence Data on Gene Control and Encoding Regions 线粒体基因组突变分析:印度尼西亚人mtG比较和基因控制和编码区域的几个GenBank序列数据

Journal of Data Mining in Genomics & Proteomics Pub Date : 2018-01-01 DOI: 10.4172/2153-0602.1000215

Y. Ngili, J. Siallagan, Tanjung Rhr, Palit Eiy

{"title":"Mitochondrial Genome Mutation Analysis: Indonesian Human mtG Comparation and Several GenBank Sequence Data on Gene Control and Encoding Regions","authors":"Y. Ngili, J. Siallagan, Tanjung Rhr, Palit Eiy","doi":"10.4172/2153-0602.1000215","DOIUrl":"https://doi.org/10.4172/2153-0602.1000215","url":null,"abstract":"Comparative study of DNA mutations occurring in human mitochondrial genomes in Indonesian humans and its comparison with some ethnic worlds has been done. The purpose of this study was to analyze mutant variants in all the complete human genome mitochondrial areas by using G-repliant techniques for mitochondrial genomic amplification, the result of Indonesian human nucleotide sequencing was then compared against some individuals representing some ethnicities in the world. DNA samples were isolated from human tissue and then sequenced using 10 pairs of primers to amplify human mtG. The mtG sequence is aligned and compared with rCRS using the DNAstar program. The result of mutation analysis shows the presence of point mutation in some mtG region fragments with different mutation proportions. Most mutations outside the HVS1 and HVS2 D-loops are in the ATP6 region. The encoding region of ATP6 is the gene coding region of human mtG and shows a high mutation rate of CRS. This opens a new paradigm for mutation analysis on ATP6 areas other than the mtG D-loop. The ATP6 gene segment located at 8553-8902 can be selected for studies in population genetics, forensic medicine and bioethnoanthropology studies, in addition to the HVS1/HVS2 D-loop areas that have been used.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"3 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86846253","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

Organellar Proteomics: Tissue Specificity, Absolute Quantity, PosttranslationalModifications and Protein-Protein Interactions 器官蛋白质组学:组织特异性，绝对数量，翻译后修饰和蛋白质-蛋白质相互作用

Journal of Data Mining in Genomics & Proteomics Pub Date : 2017-03-24 DOI: 10.4172/2153-0602.1000E129

Moussa Ae, X. Chen

引用次数: 0

Insights into Genomic Variation within Salmonella enterica 肠道沙门氏菌基因组变异研究

Journal of Data Mining in Genomics & Proteomics Pub Date : 2017-03-23 DOI: 10.4172/2153-0602.1000E128

Serrano Pc, P. Lam, Hern, ez Ye, Nava Gm

{"title":"Insights into Genomic Variation within Salmonella enterica","authors":"Serrano Pc, P. Lam, Hern, ez Ye, Nava Gm","doi":"10.4172/2153-0602.1000E128","DOIUrl":"https://doi.org/10.4172/2153-0602.1000E128","url":null,"abstract":"Advances in molecular microbiology, comparative genomics and data mining have allowed us to uncover new insights into genome structure within bacterial species. To evolve, Bacteria gains and loses genes and other genomic sequences to adapt to specific ecological niches [1]. Thus, the intraspecies genomic variation found in numerous bacterial species has highlighted the need of analyzing genome composition to define bacterial species [1]. Fortunately, Whole-Genome Sequence Analysis (WGSA) has uncovered the dynamic nature of genomic plasticity and the consequent extensive genetic diversity in Bacteria [2]. Currently, microbiological research has been focused on WGSA within-species to identify molecular or virulence determinants. These studies could accelerate our understanding of bacterial pathogenesis and strains-specific traits of virulence; key factors in improving bacterial surveillance and development of antibacterial treatments or vaccines [3]. Herein, we investigate the genomic variation within Salmonella enterica as an example of the potential of comparative analysis of WGSA to uncover intraspecies variation. A total of 1,604 S. enterica whole genomes were analyzed. This dataset comprised 38 different serotypes (Table 1) retrieved from the Integrated Microbial Genomes (IMG) system [4]. Serotypes with at least 3 genomes available were used for bioinformatics analyses. Intraspecies traits of genomic variation were assessed for each of the selected serotypes. Briefly, it was found that the genome size S. enterica serotypes varies considerably; for example, serotype Muenchen, in average, possess the largest genome size (5.00 Mbp) whereas Paratyphi possess the smallest (4.59 Mbp). Unexpectedly, a high variation in the genome size was observed in each serotype (Figure 1 and Table 1).","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"22 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2017-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75595945","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

Concerted Evolution of the Replication-Dependent Histone Gene Family in Drosophila immigrans 移民果蝇复制依赖组蛋白基因家族的协同进化

Journal of Data Mining in Genomics & Proteomics Pub Date : 2017-01-05 DOI: 10.4172/2153-0602.1000210

N. Kakubayashi

引用次数: 1

Obesity and Female Fertility: The Bridging Role of Leptin 肥胖和女性生育能力:瘦素的桥梁作用

Journal of Data Mining in Genomics & Proteomics Pub Date : 2017-01-01 DOI: 10.4172/2153-0602.1000209

P. Karoutsos

引用次数: 2

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