The open genomics journal最新文献

{"title":"Interferon -Inducible Protein 27 Computational Network Construction and Comparison between the Frontal Cortex of HIV Encephalitis (HIVE) and HIVE-Control Patients","authors":"Juxiang Huang, Lin Wang, Minghu Jiang, Xiguang Zheng","doi":"10.2174/1875693X01003010001","DOIUrl":"https://doi.org/10.2174/1875693X01003010001","url":null,"abstract":"Interferon � -inducible protein 27 (IFI27) computational network construction and analysis of frontal cortex of HIV encephalitis (HIVE) is very useful to identify novel markers and potential targets for prognosis and therapy. Based on integrated gene regulatory network infer (GRNInfer) method by linear programming and a decomposition procedure with analysis of the significant function cluster using Kappa statistics and fuzzy heuristic clustering from DAVID, we identified and constructed significant molecular IFI27 networks from 12 frontal cortex of HIVE-control patients and 16 HIVE in the same GEO Dataset GDS1726. Our integrative results reflected an IFI27 membrane module only in the up- stream of the frontal cortex of HIVE-control patients (BTN3A2, RASGRP3, ROR1 inhibition), and the frontal cortex of HIVE (DGKG, LY96 activation; RASGRP3 inhibition); IFI27 organelle only in the upstream of HIVE-control patients (CREB5, OAS1, PDCD4 activation), and HIVE (PDCD4 activation; ZC3HAV1, ZNF652 inhibition); IFI27 sequence variant only in the upstream of HIVE-control patients (ISG15_2, OAS1, TNFRSF11B activation; BTN3A2, LCAT, ROR1 inhibition), and HIVE (CFB, DGKG, LCAT, LY96 activation; ISG15_2, TNFRSF11B, ZC3HAV1 inhibition).","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"3 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2010-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123085","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}

{"title":"Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping.","authors":"Heinz-Ulrich G Weier, Karin M Greulich-Bode, Jenny Wu, Thomas Duell","doi":"10.2174/1875693X00902010015","DOIUrl":"10.2174/1875693X00902010015","url":null,"abstract":"<p><p>Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.</p>","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"2 ","pages":"15-23"},"PeriodicalIF":0.0,"publicationDate":"2009-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874907/pdf/nihms154287.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29016588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Proposed Solution to the Historic Puzzle of Chargaff's Second Parity Rule","authors":"K. Sorimachi","doi":"10.2174/1875693X00902010012","DOIUrl":"https://doi.org/10.2174/1875693X00902010012","url":null,"abstract":"Chargaff 's first parity rule for the contents of the four nucleotides in DNA is easily understood based on the double-stranded DNA structure. However, the second parity rule, based on similar nucleotide relationships in single- stranded DNA, has been a puzzle in molecular biology, because it is impossible to imagine how pairs of G and C, and A and T are formed in the single DNA strand. In the present study, Chargaff's second parity rule can be solved based on nu- cleotide contents and the correlation between the two strands in double-stranded DNA.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"2 1","pages":"12-14"},"PeriodicalIF":0.0,"publicationDate":"2009-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68123073","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}

{"title":"Gene Flow at the Crossroads of Humanity: mtDNA Sequence Diversity and Alu Insertion Polymorphism Frequencies in Uzbekistan","authors":"E. Devor, I. Abdurakhmonov, M. Zlojutro, M. P. Millis, Jessica J. Galbraith, M. Crawford, S. Shermatov, Z. Buriev, A. Abdukarimov","doi":"10.2174/1875693X00902010001","DOIUrl":"https://doi.org/10.2174/1875693X00902010001","url":null,"abstract":"Mitochondrial DNA (mtDNA) HVS-I region sequences were obtained from 47 unrelated individuals represent- ing 10 of 12 viloyats of Uzbekistan. In addition, frequencies for five Alu insertion polymorphisms were determined for the same 47 individuals. These data were used to assess the genetic position of Uzbekistan relative to other Central Asians and, more generally, to Eurasian groups. Results show that the Uzbek sample has an approximate balance of west Eura- sian (53.2%) and Asian (46.8%) mtDNA lineages, which is reflected by their intermediate position relative to other Eura- sian groups in MDS plots based on genetic distance matrices. The Uzbeks also exhibit high sequence diversity, a frag- mented median-joining network, and a low regionalST score, all of which suggests a high degree of gene flow from neighboring gene pools. This is consistent with Central Asia's history of repeated incursions by various nomadic peoples from the Asian steppe and the location of the well-traveled Silk Road within the present-day borders of Uzbekistan. In ad- dition, a star-like cluster within haplogroup H was identified in the Uzbek network, potentially representing a west Eura- sian genetic substratum of an earlier occupation by Caucasoid peoples.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"2 1","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2009-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68122071","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}

{"title":"Comparative Nucleotide Sequence of Encoding for Quaking Protein of Birds and Mammals~!2008-09-26~!2008-11-07~!2008-12-05~!","authors":"Tomoaki Murata, Y. Yamashiro, Tatsuya Kondo, A. Amimoto, M. Shirasu, M. Yasuda, N. Ito, Minako Hino, M. Nakaichi, S. Une, K. Itamoto, Y. Taura","doi":"10.2174/1875693X00801010044","DOIUrl":"https://doi.org/10.2174/1875693X00801010044","url":null,"abstract":"Partial nucleotide sequences of eight kinds of bird (common crane, gray pelican, goose, black swan, bewisk's swan, whooper swan, ostrich, and chicken) gene encoding quaking protein were analyzed. Variously sized bands were ob- served in all eight birds compared with the same sized band in mammals based on nested PCR results, and all sequence data showed a very high level of homology. Three bases (CD223(Ala)) in exon 6 of all eight bird species were defective compared with sequence data from the mouse, and both the existence and defect of 24 bases (CD211 ~ 219) in exon 6 of the eight birds were confirmed on complementary DNA sequence analysis. These findings suggest that birds generate specific alternative sequencing data, there are many alternative splicing variants, and the avian quaking gene may be a specific marker differentiating between birds and mammals. The mouse quaking I (qkI) gene, encoding a KH domain containing RNA-binding protein (1), was first isolated as a candidate gene for neurological mutation, quaking viable, and was known as a model for human leukodystrophy (2). Genes highly homologous to qkI have been found in various animal species from nematodes to humans (3-7), and muta- tions in these genes result in various developmental defects other than demyelination. It is therefore believed that mem- bers of the qkI gene family are essential for multiple biologi- cal processes. Herein, we report the isolation and sequence analysis of eight kinds of avian qk. Genomic DNA was isolated from whole blood cells of eight kinds of bird (common crane, gray pelican, goose, black swan, bewisk's swan, whooper swan, ostrich, and chicken) by the standard method. RNA was isolated from whole blood cells of these birds with Trizol LS reagent (Invi- trogen, USA). The ostrich was one-week-old and the others were adults, and none showed abnormality according to","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"1 1","pages":"44-46"},"PeriodicalIF":0.0,"publicationDate":"2008-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68122056","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}

{"title":"Universal Rules Governing Genome Evolution Expressed by Linear Formulas","authors":"K. Sorimachi, T. Okayasu","doi":"10.2174/1875693X00801010033","DOIUrl":"https://doi.org/10.2174/1875693X00801010033","url":null,"abstract":"Codon evolution is influenced by an organelle-specific bias existing within cellular compartments. The discov- ery of evidence that codon evolution is controlled by different factors among nuclei, mitochondria and chloroplasts, indi- cates the existence of biases based on what we term \"organelle biases\". In plant chloroplasts and mitochondria, nucleotide substitutions, based on the correlations among nucleotides, were governed by the linear formula, y = ax + b, where y and x represent nucleotide contents, and a and b are constants. In animal mitochondria, with respect to the correlations between each nucleotide, only the correlations between purines (A versus G) or pyrimidines (C versus T) were almost linear, while the other correlations between purine and pyrimidine (A or G versus T or C) were not. However, nucleotide substitutions, based on the correlations of the same nucleotide between complete single-strand DNA and its coding or non-coding re- gion, were always linear, y = ax + b, in any organelle. Linear correlations of the same nucleotide were also obtained be- tween coding and non-coding region DNAs. The present results clearly reveal evidence that genome evolution is governed by universal linear formulas, although different rules are apparently observed in the different organelle fields formed by nuclei, mitochondria and chloroplasts. This report quantitatively demonstrates the existence of factors controlling genome evolution that are expressed by linear formulas.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"1 1","pages":"33-43"},"PeriodicalIF":0.0,"publicationDate":"2008-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68121961","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}

{"title":"miRNA Profile of a Triassic Common Mammalian Ancestor and PremiRNA Evolution in the Three Mammalian Reproductive Lineages","authors":"E. Devor, A. S. Peek","doi":"10.2174/1875693X00801010022","DOIUrl":"https://doi.org/10.2174/1875693X00801010022","url":null,"abstract":"MicroRNAs (miRNAs) are major factors in the regulation of gene expression. Recent evolutionary studies of miRNAs indicate that important biological innovations, such as the advent of bilateral symmetry and placental reproduc- tion, are accompanied by bursts of miRNA creation which are subsequently conserved via purifying selection. The emer- gence of eutherian (placental) mammals followed by as much as fifty million years the appearance of the first true mam- mals in the late Triassic, some 230 million years ago. We have utilized microRNA inventories of eutherian, metatherian (marsupial), monotreme (platypus), and chicken genomes to assemble a minimal microRNA profile of the last common ancestor of all mammals consisting of 171 miRNAs. This profile suggests that the rise of placental reproduction launched a more than three-fold expansion of microRNAs. In addition to expansion of the microRNA repertoire, the conserved mi- croRNAs from five mammalian and one avian genome show evidence for conforming to a canonical phylogenetic history as well as dramatic deviations from the assumptions of molecular clock-like rates and the equality of substitution rates among lineages. We also show that many of these basal mammalian miRNAs are highly expressed in eutherian placenta thus creating an opportunity to gain insight on how microRNAs acquire new targets and new functions.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"1 1","pages":"22-32"},"PeriodicalIF":0.0,"publicationDate":"2008-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68121949","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}

{"title":"Molecular Genetic Etiology of Prostate Cancer","authors":"V. Pethe, B. Bapat","doi":"10.2174/1875693X00801010013","DOIUrl":"https://doi.org/10.2174/1875693X00801010013","url":null,"abstract":"Prostate Cancer (PCa) is the most frequently diagnosed non-skin cancer and second leading cause of cancer deaths after lung cancer in the western industrialized countries. It varies widely by geographic location and ethnicity. It is clinically heterogeneous, complex and indeed a multi-factorial disease. While the majority of PCa is sporadic, as much as up to 40% of the cases are associated with some form of genetic susceptibility. It is clear today that etiology of PCa involves several genetic loci with no single major gene accounting for a large proportion of susceptibility to the disease. In particular, allelic variations in four genes, namely RNASEL (1q25), MSR1 (8p22), ELAC2 (17p11) and EphB2 (1p36) have been shown to be associated with increased susceptibility to PCa. Also, tumors harboring mutations in these genes present with more aggressive clinical features and poor outcome. Recently, novel genetic alterations in prostate cancer patients have been identified – these include gene fusions involving the prostate-specific gene transmembrane protease, serine 2 (TMPRSS2) and members of the erythroblastosis virus E26 transforming sequence (ETS) family of transcription factors. This predominant molecular subtype is considered to be an early event in PCa, and emerging evidence demonstrates its potential in prostate cancer detection, stratification and treatment. In addition to gene fusions, there is compelling evidence demonstrating 8q24 region as a prostate cancer susceptibility locus and markers at this locus are statistically significantly associated with an increased PCa risk in different ethnic groups. Genotyping of SNPs / markers in a predefined 8q24 region as well as genome-wide association studies have implicated several polymorphisms ( rs7008482, rs1447295, rs16901979, rs698367) in this region as risk factors for PCa. In additions to genetic alterations, frequent epigenetic aberrations such as DNA hypermethylation of tumor suppressor genes has been observed in PCa affecting the expression and function of a battery of genes leading to tumorigenesis, tumor progression and metastasis. In this review, we highlight some of the recent advances in molecular genetic etiology of PCa including promising candidate hereditary PCa susceptibility genes, novel gene fusions in acquired PCa, 8q24 susceptibility locus, as well as examine current literature regarding epigenetic changes leading to prostate cancer development and progression.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"1 1","pages":"13-21"},"PeriodicalIF":0.0,"publicationDate":"2008-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68121841","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}

{"title":"Target Site Preferences of Subgroup C Rous Sarcoma Virus Integration into the Chicken DNA","authors":"M. Reinišová, A. Pavlícek, Petr Divina, J. Geryk, J. Plachy, J. Hejnar","doi":"10.2174/1875693X00801010006","DOIUrl":"https://doi.org/10.2174/1875693X00801010006","url":null,"abstract":"We sequenced unselected integration sites of subgroup C Rous sarcoma virus from infected chicken cells and mapped them on the chicken draft genome assembly. Our genome-wide analysis demonstrates the non-random character of subgroup C Rous sarcoma virus integration into genes, gene-rich regions and GC-rich regions. Within genes, there is no significant integration bias in favor of transcription start sites. Integration sites are underrepresented on microchromo- somes. These results may be important for the development of gene transfer vectors and gene therapy strategies based on avian sarcoma and leukosis viruses.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"1 1","pages":"6-12"},"PeriodicalIF":0.0,"publicationDate":"2008-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68121803","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}

{"title":"Effect of Endogamy and Consanguinity on the Development of Labial Venous Malformations in Area of Tlemcen (West Algeria)","authors":"B. Sari, M. Aribi, B. Saari","doi":"10.2174/1875693X00801010001","DOIUrl":"https://doi.org/10.2174/1875693X00801010001","url":null,"abstract":"Background: Vascular malformation is extremely rare, yet has a profound impact on quality of life, aesthetic and functional disorders. Aim: To show that endogamy and consanguinity may represent risk factors for labial venous malforma- tion (LVM) development. Materials and Methodology: Among the 18093 scrutinized families on a 20 years back period from marriage registers, five families with a child presenting LVM were recruited from two geographic areas, one highly endoga- mous (Nedroma), the other slightly endogamous (Maghnia). These families were recruited for a retrospective descriptive es- say at the Pathology and Oral Surgery Department of Tlemcen University Hospital Center (north-west of Algeria). Results: Four cases of LVM were from the Nedroma region, the fifth one from the Maghnia region. High consanguinity level was reg- istered in patient families from Nedroma. On the other hand, the blood group O frequency was slightly higher compared to that of the blood group non-O. Conclusions: The present study suggests that consanguinity could beget LVM and that endog- amy could increase its prevalence. The postulated association between this genetic disease and the OO genotype seems to be not confirmed. Therefore, it would be interesting to seek the SNP markers in this region.","PeriodicalId":89034,"journal":{"name":"The open genomics journal","volume":"1 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2008-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68121758","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}