SR
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ABSTRACT:
PROVIDER: PRJEB12295 | ENA |
REPOSITORIES: ENA
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Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization
2008-10-09 | GSE13128 | GEO
Project description:Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification.
2013-05-09 | GSE46733 | GEO
Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization Comparative genomic analysis of 7 clinically prevalent P. gingivalis strains was performed, using whole genome microarrays based on the sequence of strain W83. Strain W83 was the reference strains and there were 6 test strains. Flip-dye replicates were performed.
2010-05-18 | E-GEOD-13128 | biostudies-arrayexpress
Project description:In March 2010, Orexigen(R) Therapeutics submitted a new drug application (NDA) for approval of naltrexone sustained release (SR)/bupropion SR (Contrave(R)) for the treatment of obesity in the US. The tablet contains naltrexone SR 32 mg and bupropion SR 360 mg. The drug has been tested in four randomized, double-blind, placebo-controlled, phase III trials and the co-primary endpoints were met in each case. This review discusses the key development milestones and clinical trial program to date.
| S-EPMC3586099 | biostudies-literature
Project description:The title compounds, strontium perchlorate trihydrate {di-?-aqua-aquadi-?-perchlorato-strontium, [Sr(ClO4)2(H2O)3] n }, strontium perchlorate tetra-hydrate {di-?-aqua-bis-(tri-aqua-diperchloratostrontium), [Sr2(ClO4)4(H2O)8]} and strontium perchlorate nona-hydrate {hepta-aqua-diperchloratostrontium dihydrate, [Sr(ClO4)2(H2O)7]·2H2O}, were crystallized at low temperatures according to the solid-liquid phase diagram. The structures of the tri- and tetra-hydrate consist of Sr(2+) cations coordinated by five water mol-ecules and four O atoms of four perchlorate tetra-hedra in a distorted tricapped trigonal-prismatic coordination mode. The asymmetric unit of the trihydrate contains two formula units. Two [SrO9] polyhedra in the trihydrate are connected by sharing water mol-ecules and thus forming chains parallel to [100]. In the tetra-hydrate, dimers of two [SrO9] polyhedra connected by two sharing water mol-ecules are formed. The structure of the nona-hydrate contains one Sr(2+) cation coordinated by seven water mol-ecules and by two O atoms of two perchlorate tetra-hedra (point group symmetry ..m), forming a tricapped trigonal prism (point group symmetry m2m). The structure contains additional non-coordinating water mol-ecules, which are located on twofold rotation axes. O-H?O hydrogen bonds between the water mol-ecules as donor and ClO4 tetra-hedra and water mol-ecules as acceptor groups lead to the formation of a three-dimensional network in each of the three structures.
| S-EPMC4257379 | biostudies-literature
Project description:The SR proteins, a group of abundant arginine/serine (RS)-rich proteins, are essential pre-mRNA splicing factors that are localized in the nucleus. The RS domain of these proteins serves as a nuclear localization signal. We found that RS domain-bearing proteins do not utilize any of the known nuclear import receptors and identified a novel nuclear import receptor specific for SR proteins. The SR protein import receptor, termed transportin-SR (TRN-SR), binds specifically and directly to the RS domains of ASF/SF2 and SC35 as well as several other SR proteins. The nuclear transport regulator RanGTP abolishes this interaction. Recombinant TRN-SR mediates nuclear import of RS domain- bearing proteins in vitro. TRN-SR has amino acid sequence similarity to several members of the importin beta/transportin family. These findings strongly suggest that TRN-SR is a nuclear import receptor for the SR protein family.
| S-EPMC2133142 | biostudies-literature
Project description:Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification. 9 Chinese indigenous pig, 4 commercial pigs and 1 wild pig were genotyped by PorcineSNP60 array (Illumina) for exploring the phylogeny relationships among them.
2013-05-09 | E-GEOD-46733 | biostudies-arrayexpress
Project description:Clonal diversity contributes to treatment resistance and cancer recurrence. Precise delineation of clonal substructure is essential to understand the resistance mechanism, however, bulk DNA sequencing cannot accurately resolve the complex clonal architectures. Here we report the single-cell DNA sequencing of 123 acute myeloid leukemia (AML) patients and provide cell-level evidence of co-occurrence and mutual exclusivity among driver mutations. Reconstruction of tumor phylogeny uncovers linear and branching clonal evolution patterns, with the latter involving functional convergence. Single-cell DNA sequencing of xenotransplanted samples reveales clonal diversity in leukemia initiating cell populations. Simultaneous single-cell profiling of mutations and cell surface proteins provides cellular genotype-phenotype associations. Analysis of longitudinal samples visualizes the behavior of each individual clone in response to therapy, illustrating the underlying evolutionary process of therapeutic resistance and disease recurrence. Together, these data portray clonal diversity, architecture, and evolution of AML, and highlight their clinical relevance in the era of precision medicine.
2020-09-08 | GSE156934 | GEO
Project description:In order to determine specifically the RNA-binding function of proteins involved in nuclear mRNP assembly, we first determined the amino acids involved in RNA-binding by RNPXL. We identified about 100 amino acids cross-linked to RNA in vivo in the nuclear mRNP components Npl3, Nab2, Tho1, Mex67-Mtr2 and the TREX complex. Second, we can now specifically elucidate the function of the RNA-binding activity of these proteins by mutation of the identified amino acids. Npl3 is an SR-like protein with functions in transcription elongation, splicing, 3’ end processing, mRNP assembly and nuclear mRNA export. The middle part of Npl3 consists of two RNA recognition motif (RRM) domains, RRM1 and RRM2, connected by an eight amino acid long flexible linker. In order to analyze the function of the RNA-binding activity of Npl3, we mutated several amino acids that cross-linked to RNA. We generated three npl3 mutants, one in the RRM1, one in the linker and a third in the RRM2 domain, and elucidated the functional consequences of these mutations. Interestingly, these three npl3 mutants show different phenotypes. Thus, abrogation of mRNA-binding in different regions of Npl3 has different functional outcomes. Furthermore, analysis of the npl3-Linker mutant revealed a novel function of Npl3. Npl3 functions in the transfer of nuclear mRNP components from the site of transcription onto the mRNA. Taken together, we identify the in vivo RNA-binding sites of nuclear mRNA-binding proteins involved in mRNP assembly and nuclear mRNA export. In addition, we show that abrogation of RNA-binding in different regions of the protein Npl3 has specific and surprisingly different functional consequences. Furthermore, we uncovered a novel function of Npl3 in nuclear mRNP assembly.
2022-11-26 | GSE160709 | GEO
Project description:LC-MS/MS dataset for marine sponges of disparate phylogeny collected from different geographical locations.
2022-04-12 | MSV000089245 | MassIVE