Pub Date : 2018-01-01DOI: 10.4172/2153-0602.1000213
Palit Eiy, Y. Ngili
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 רUµ 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.
人类线粒体DNA (mtDNA)已被广泛应用于通过生物证据对被害人或犯罪嫌疑人进行法医鉴定。单个细胞中mtDNA分子的数量数以万计，这使得分析样品很少或损坏。目前，针对自然灾害、战争、事故等重大灾害受害者的mtDNA鉴定还没有统一的标准方法，导致鉴定过程无法快速进行。本研究在mtDNA序列中发现了C16.223t变异，可用于将数据库分为两组，从而通过数学算法加快鉴定过程。该变异在NCBI数据库中多达142个序列的300个核苷酸(16,024-16,324)沿线的91个多态人类mtDNA HVS1中频率最高(29.7%)。从已在NCBI上发表的巴布亚人MtDNA组数据收集中获得的MtDNA序列。下一个可以在序列的一行中用作分类器的变体是16,311;16304;16189;16270的恒等式为(T→c)。对于矩阵Q是可逆的所以矩阵和可以有相反的对角线。因此，上面的方程可以用对角线法求解，可以写成:U³= U μ רU μ a μ μ 1。这个方程可以计算mtDNA核苷酸序列中发生的转变和翻转取代突变的数量。通过这种分组，可以减少数据库，从而加快样本识别的过程。根据频率最高的变异进行分组的预期方法可以在法医学数据库(如警察)或mtDNA数据库(用于研究人类学和进化生物学)中开发。
{"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 רUµ 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}
Pub Date : 2018-01-01DOI: 10.4172/2153-0602.1000212
R. Holmes
Arylsulfatase K (ARSK) is one of 17 sulfatase gene family members encoded on the human genome for which a role has been recently identified as a lysosomal 2-sulfoglucuronate sulfatase. Vertebrate ARSK sequences shared 60-82% identity but only <27% identities with other arylsulfatase family members. Comparative enzyme structures were studied, including residues with predicted roles in forming N-glycosylation sites, Ca2+ binding and active site residues. Vertebrate ARSK genes usually contained 8 coding exons. A human ARSK gene promoter comprised CpG61 and multiple TFBS, which may be involved in signal transduction, transcription activation or regulating entry into cell division. Phylogenetic analyses examined evolutionary changes for the vertebrate ARSK and the invertebrate SUL1 genes. In summary, a major role for this enzyme as a 2-sulfoglucuronate sulfatase is supported which has been conserved throughout vertebrate evolution.
Arylsulfatase K (ARSK)是人类基因组编码的17个硫酸盐酶基因家族成员之一，其作用最近被确定为溶酶体2-硫脲酸盐硫酸盐酶。脊椎动物ARSK序列与其他芳基磺化酶家族成员具有60-82%的同源性，但同源性仅<27%。研究了比较酶的结构，包括在形成n -糖基化位点、Ca2+结合位点和活性位点残基中具有预测作用的残基。脊椎动物的ARSK基因通常包含8个编码外显子。人类ARSK基因启动子由CpG61和多个TFBS组成，可能参与信号转导、转录激活或调节进入细胞分裂。系统发育分析检查了脊椎动物ARSK和无脊椎动物SUL1基因的进化变化。总之，该酶作为2-硫脲酸盐硫酸酯酶的主要作用在整个脊椎动物进化过程中得到了支持。
{"title":"Vertebrate Arylsulfatase K (ARSK): Comparative and Evolutionary Studies of the Lysosomal 2-Sulfoglucuronate Sulfatase","authors":"R. Holmes","doi":"10.4172/2153-0602.1000212","DOIUrl":"https://doi.org/10.4172/2153-0602.1000212","url":null,"abstract":"Arylsulfatase K (ARSK) is one of 17 sulfatase gene family members encoded on the human genome for which a role has been recently identified as a lysosomal 2-sulfoglucuronate sulfatase. Vertebrate ARSK sequences shared 60-82% identity but only <27% identities with other arylsulfatase family members. Comparative enzyme structures were studied, including residues with predicted roles in forming N-glycosylation sites, Ca2+ binding and active site residues. Vertebrate ARSK genes usually contained 8 coding exons. A human ARSK gene promoter comprised CpG61 and multiple TFBS, which may be involved in signal transduction, transcription activation or regulating entry into cell division. Phylogenetic analyses examined evolutionary changes for the vertebrate ARSK and the invertebrate SUL1 genes. In summary, a major role for this enzyme as a 2-sulfoglucuronate sulfatase is supported which has been conserved throughout vertebrate evolution.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"34 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":"87986982","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}
Pub Date : 2018-01-01DOI: 10.4172/2153-0602.1000216
Yosuke Kondo, H. Yokoyama, I. Matsui, S. Miyazaki
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.
{"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}
Pub Date : 2018-01-01DOI: 10.4172/2153-0602.1000214
Kawulur Hsi, Y. Ngili
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.
{"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}
Pub Date : 2018-01-01DOI: 10.4172/2153-0602.1000215
Y. Ngili, J. Siallagan, Tanjung Rhr, Palit Eiy
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.
对印度尼西亚人线粒体基因组发生的DNA突变进行了比较研究，并与一些民族进行了比较。本研究的目的是利用g -复制技术进行线粒体基因组扩增，分析人类基因组所有线粒体区域的突变变异，并将印度尼西亚人核苷酸测序结果与世界上一些种族的一些个体进行比较。从人组织中分离DNA样本，用10对引物扩增人mtG序列，用DNAstar程序比对mtG序列并与rCRS进行比较。突变分析结果表明，不同突变比例的mtG区片段存在点突变。大多数HVS1和HVS2 d -环外的突变都在ATP6区。ATP6的编码区是人类mtG的基因编码区，CRS的突变率较高。这为mtG D-loop以外的ATP6区域的突变分析开辟了新的范式。位于8553-8902的ATP6基因片段除了已经使用的HVS1/HVS2 D-loop区域外，还可用于群体遗传学、法医学和生物民族人类学研究。
{"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}
Pub Date : 2017-03-24DOI: 10.4172/2153-0602.1000E129
Moussa Ae, X. Chen
Organellar proteomics combines subcellular fractionation and mass spectrometry-based protein identifications. In the past decades, organellar proteomic analysis has been carried out for virtually every subcellular compartment in mammalian cells and tissues [1-4]. While conventional biochemical and biophysical approaches study the structures and functions of individual proteins, mass spectrometrybased proteomic studies allow us to understand the entire proteome or sub proteome systematically by: (i) Identifying proteins present in each subcellular organelle; (ii) Quantifying their expression levels; and (iii) Characterizing their posttranslational modifications and proteinprotein interactions. All of the above determines the protein’s function and activity.
{"title":"Organellar Proteomics: Tissue Specificity, Absolute Quantity, PosttranslationalModifications and Protein-Protein Interactions","authors":"Moussa Ae, X. Chen","doi":"10.4172/2153-0602.1000E129","DOIUrl":"https://doi.org/10.4172/2153-0602.1000E129","url":null,"abstract":"Organellar proteomics combines subcellular fractionation and mass spectrometry-based protein identifications. In the past decades, organellar proteomic analysis has been carried out for virtually every subcellular compartment in mammalian cells and tissues [1-4]. While conventional biochemical and biophysical approaches study the structures and functions of individual proteins, mass spectrometrybased proteomic studies allow us to understand the entire proteome or sub proteome systematically by: (i) Identifying proteins present in each subcellular organelle; (ii) Quantifying their expression levels; and (iii) Characterizing their posttranslational modifications and proteinprotein interactions. All of the above determines the protein’s function and activity.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"115 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2017-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80854085","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}
Pub Date : 2017-03-23DOI: 10.4172/2153-0602.1000E128
Serrano Pc, P. Lam, Hern, ez Ye, Nava Gm
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).
{"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}
Pub Date : 2017-01-05DOI: 10.4172/2153-0602.1000210
N. Kakubayashi
The replication-dependent histone genes in Drosophila immigrans were analyzed for elucidating the evolutionary mechanism of the histone multigene family. A region of approximately 3.9 kb containing H2A-H2B-H1 genes was cloned. Six independent clones were sequenced and analyzed for nucleotide variability. The average nucleotide sequence identity in the region among repetitive copies was more than 99%, indicating that the histone multigene family in D. immigrans has evolved in a concerted fashion and with a similar level as in D. melanogaster. Amino acid variants were found at a low frequency. Analysis of the GC content at the 3rd codon position of histone genes revealed that a change in GC content, i.e., a decrease, observed in D. hydei and D. americana has occurred after the divergence of an ancestor of these two species from D. immigrans.
{"title":"Concerted Evolution of the Replication-Dependent Histone Gene Family in Drosophila immigrans","authors":"N. Kakubayashi","doi":"10.4172/2153-0602.1000210","DOIUrl":"https://doi.org/10.4172/2153-0602.1000210","url":null,"abstract":"The replication-dependent histone genes in Drosophila immigrans were analyzed for elucidating the evolutionary mechanism of the histone multigene family. A region of approximately 3.9 kb containing H2A-H2B-H1 genes was cloned. Six independent clones were sequenced and analyzed for nucleotide variability. The average nucleotide sequence identity in the region among repetitive copies was more than 99%, indicating that the histone multigene family in D. immigrans has evolved in a concerted fashion and with a similar level as in D. melanogaster. Amino acid variants were found at a low frequency. Analysis of the GC content at the 3rd codon position of histone genes revealed that a change in GC content, i.e., a decrease, observed in D. hydei and D. americana has occurred after the divergence of an ancestor of these two species from D. immigrans.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"69 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2017-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83326344","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}
Pub Date : 2017-01-01DOI: 10.4172/2153-0602.1000209
P. Karoutsos
Leptin secretion is a requirement in order for both of energy balance and reproductive capacity to be preserved. That is because leptin plays an important role in appetite regulation and balance of body weight. Leptin binds to leptin receptor in the cells of the hypothalamus. This stimulates an intracrine signalling pathway that drives downregulation of the receptors expression involved in appetite increase. It is clearly set that leptin impairs production of sex steroid hormones in granulosa cells. In addition, alterations noted in follicular fluid from obese women include increased androgen activity and decreased human chorionic gonadotropin levels by other studies. Likewise, adiponectin levels are inversely correlated with levels of insulin, which by inhibiting the production of hepatic sex hormone binding globulin, because increased levels of androgens. On meeting with the fertility problems that arise among these women, scientists must understand the pathophysiology of adipose signalling on reproductive function.
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Pub Date : 2017-01-01Epub Date: 2017-06-13DOI: 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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