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  • 1
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    Cooperative action of APJ and α1A-adrenergic receptor in vascular smooth muscle cells induces vasoconstriction (2019)
    Oxford University Press
    Details
    Publication Date: 2019-09-03
    Description: The apelin receptor (APJ), a receptor for apelin and elabela/apela, induces vasodilation and vasoconstriction in blood vessels. However, the prolonged effects of increased APJ-mediated signalling, involving vasoconstriction, in smooth muscle cells have not been fully characterized. Here, we investigated the vasoactive effects of APJ gain of function under the control of the smooth muscle actin (SMA) gene promoter in mice. Transgenic overexpression of APJ (SMA-APJ) conferred sensitivity to blood pressure and vascular contraction induced by apelin administration in vivo. Interestingly, ex vivo experiments showed that apelin markedly increased the vasoconstriction of isolated aorta induced by noradrenaline (NA), an agonist for α- and β-adrenergic receptors, or phenylephrine, a specific agonist for α1-adrenergic receptor (α1-AR). In addition, intracellular calcium influx was augmented by apelin with NA in HEK293T cells expressing APJ and α1A-AR. To examine the cooperative action of APJ and α1A-AR in the regulation of vasoconstriction, we developed α1A-AR deficient mice using a genome-editing technique, and then established SMA-APJ/α1A-AR-KO mice. In the latter mouse line, aortic vasoconstriction induced by a specific agonist for α1A-AR, A-61603, were significantly less than in SMA-APJ mice. These results suggest that the APJ-enhanced response requires α1A-AR to contract vessels coordinately.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of Japanese Biochemical Society.
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  • 2
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    From birth to death of protoplanetary discs: modelling their formation, evolution and dispersal (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: The formation, evolution and dispersal processes of protoplanetary discs are investigated and the disc lifetime is estimated. The gravitational collapse of a pre-stellar core forms both a central star and a protoplanetary disc. The central star grows by accretion from the disc and irradiation by the central star heats up the disc and generates a thermal wind, which results in the disc's dispersal. Using the one-dimensional diffusion equation, we calculate the evolution of protoplanetary discs numerically. To calculate the disc evolution from formation to dispersal, we add source and sink terms that represent gas accretion from pre-stellar cores and photoevaporation, respectively. We find that the disc lifetimes of typical pre-stellar cores are around 2–4 million years (Myr). A pre-stellar core with high angular momentum forms a larger disc with a long lifetime, while a disc around an X-ray-luminous star has a short lifetime. Integrating disc lifetimes under various masses and angular velocities of pre-stellar cores and X-ray luminosities of young stellar objects, we obtain the disc fraction at a given stellar age and mean lifetime of the disc. Our model indicates that the mean lifetime of a protoplanetary disc is 3.7 Myr, which is consistent with the observational estimate from young stellar clusters. We also find that the dispersion of X-ray luminosity is needed to reproduce the observed disc fraction.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Structure and function of human histone H3.Y nucleosome (2016)
    Oxford University Press
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    Publication Date: 2016-07-28
    Description: Histone H3.Y is a primate-specific, distant H3 variant. It is evolutionarily derived from H3.3, and may function in transcription regulation. However, the mechanism by which H3.Y regulates transcription has not been elucidated. In the present study, we determined the crystal structure of the H3.Y nucleosome, and found that many H3.Y-specific residues are located on the entry/exit sites of the nucleosome. Biochemical analyses revealed that the DNA ends of the H3.Y nucleosome were more flexible than those of the H3.3 nucleosome, although the H3.Y nucleosome was stable in vitro and in vivo . Interestingly, the linker histone H1, which compacts nucleosomal DNA, appears to bind to the H3.Y nucleosome less efficiently, as compared to the H3.3 nucleosome. These characteristics of the H3.Y nucleosome are also conserved in the H3.Y/H3.3 heterotypic nucleosome, which may be the predominant form in cells. In human cells, H3.Y preferentially accumulated around transcription start sites (TSSs). Taken together, H3.Y-containing nucleosomes around transcription start sites may form relaxed chromatin that allows transcription factor access, to regulate the transcription status of specific genes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data (2015)
    Oxford University Press
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    Publication Date: 2015-05-12
    Description: Motivation: Sequence-variation analysis is conventionally performed on mapping results that are highly redundant and occasionally contain undesirable heuristic biases. A straightforward approach to single-nucleotide polymorphism (SNP) analysis, using the Burrows–Wheeler transform (BWT) of short-read data, is proposed. Results: The BWT makes it possible to simultaneously process collections of read fragments of the same sequences; accordingly, SNPs were found from the BWT much faster than from the mapping results. It took only a few minutes to find SNPs from the BWT (with a supplementary data, fragment depth of coverage [FDC]) using a desktop workstation in the case of human exome or transcriptome sequencing data and 20 min using a dual-CPU server in the case of human genome sequencing data. The SNPs found with the proposed method almost agreed with those found by a time-consuming state-of-the-art tool, except for the cases in which the use of fragments of reads led to sensitivity loss or sequencing depth was not sufficient. These exceptions were predictable in advance on the basis of minimum length for uniqueness (MLU) and FDC defined on the reference genome. Moreover, BWT and FDC were computed in less time than it took to get the mapping results, provided that the data were large enough. Availability and implementation: A proof-of-concept binary code for a Linux platform is available on request to the corresponding author. Contact: kouichi.kimura.hh@hitachi.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Common polymorphisms in WNT10A affect tooth morphology as well as hair shape (2015)
    Oxford University Press
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    Publication Date: 2015-04-04
    Description: Hair and teeth are appendages of ectodermal origin, and there are common molecular backgrounds involved in their formation. To date, it has been revealed that a non-synonymous polymorphism in EDAR has effects on the morphological variation in both hair and teeth. Previous association studies have confirmed that single-nucleotide polymorphisms (SNPs) in/near THADA , FRAS1 , WNT10A , NAF1 and FGFR2 are associated with hair morphology. In this study, we thus examined whether these SNPs are also associated with dental characteristics. We measured metric dental traits including crown size and also evaluated non-metric dental traits using plaster casts obtained from subjects (272 Japanese and 226 Koreans). DNA samples were prepared from the subjects and genotyped for the hair morphology-associated SNPs. We observed a significant association of crown size with an SNP in WNT10A (rs7349332), but not with SNPs in other genes. Therefore, we further examined four SNPs within and around WNT10A , among which rs10177996 had the strongest association with dental traits. World distribution of the derived allele in rs10177996, which is associated with larger teeth, showed that Eurasians have a higher allele frequency than Africans. Together with previous studies on hair morphology, this study demonstrated that common variations in WNT10A have pleiotropic effects on the morphology of ectodermal appendages.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Characterisation of novel RUNX2 mutation with alanine tract expansion from Japanese cleidocranial dysplasia patient (2015)
    Oxford University Press
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    Publication Date: 2015-12-31
    Description: Cleidocranial dysplasia (CCD; MIM 119600) is an autosomal dominant skeletal dysplasia characterised by hypopalstic and/or aplastic clavicles, midface hypoplasia, absent or delayed closure of cranial sutures, moderately short stature, delayed eruption of permanent dentition and supernumerary teeth. The molecular pathogenesis can be explained in about two-thirds of CCD patients by haploinsufficiency of the RUNX2 gene. In our current study, we identified a novel and rare variant of the RUNX2 gene (c.181_189dupGCGGCGGCT) in a Japanese patient with phenotypic features of CCD. The insertion led an alanine tripeptide expansion (+3Ala) in the polyalanine tract. To date, a RUNX2 variant with alanine decapeptide expansion (+10Ala) is the only example of a causative variant of RUNX2 with polyalanine tract expansion to be reported, whilst RUNX2 (+1Ala) has been isolated from the healthy population. Thus, precise analyses of the RUNX2 (+3Ala) variant were needed to clarify whether the tripeptide expanded RUNX2 is a second disease-causing mutant with alanine tract expansion. We therefore investigated the biochemical properties of the mutant RUNX2 (+3Ala), which contains 20 alanine residues in the polyalanine tract. When transfected in COS7 cells, RUNX2 (+3Ala) formed intracellular ubiquitinated aggregates after 24h, and exerted a dominant negative effect in vitro . At 24h after gene transfection, whereas slight reduction was observed in RUNX2 (+10Ala), all of these mutants significantly activated osteoblast-specific element-2, a cis-acting sequence in the promoter of the RUNX2 target gene osteocalcin. The aggregation growth of RUNX2 (+3Ala) was clearly lower and slower than that of RUNX2 (+10Ala). Furthermore, we investigated several other RUNX2 variants with various alanine tract lengths, and found that the threshold for aggregation may be RUNX2 (+3Ala). We conclude that RUNX2 (+3Ala) is the cause of CCD in our current case, and that the accumulation of intracellular aggregates in vitro is related to the length of the alanine tract.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30 (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-09
    Description: Pho Pop5 and Pho Rpp30 in the hyperthermophilic archaeon Pyrococcus horikoshii , homologues of human ribonuclease P (RNase P) proteins hPop5 and Rpp30, respectively, fold into a heterotetramer [ Pho Rpp30–( Pho Pop5) 2 – Pho Rpp30], which plays a crucial role in the activation of RNase P RNA ( Pho pRNA). Here, we examined the functional implication of Pho Pop5 and Pho Rpp30 in the tetramer. Surface plasmon resonance (SPR) analysis revealed that the tetramer strongly interacts with an oligonucleotide including the nucleotide sequence of a stem-loop SL3 in Pho pRNA. In contrast, Pho Pop5 had markedly reduced affinity to SL3, whereas Pho Rpp30 had little affinity to SL3. SPR studies of Pho Pop5 mutants further revealed that the C-terminal helix (α4) in Pho Pop5 functions as a molecular recognition element for SL3. Moreover, gel filtration indicated that Pho Rpp30 exists as a monomer, whereas Pho Pop5 is an oligomer in solution, suggesting that Pho Rpp30 assists Pho Pop5 in attaining a functionally active conformation by shielding hydrophobic surfaces of Pho Pop5. These results, together with available data, allow us to generate a structural and mechanistic model for the Pho pRNA activation by Pho Pop5 and Pho Rpp30, in which the two C-terminal helices (α4) of Pho Pop5 in the tetramer whose formation is assisted by Pho Rpp30 act as binding elements and bridge SL3 and SL16 in Pho pRNA.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 8
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    Model-Based Verification of Hypotheses on the Origin of Modern Japanese Revisited by Bayesian Inference Based on Genome-Wide SNP Data (2015)
    Oxford University Press
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    Publication Date: 2015-05-30
    Description: Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are assumed to have originated in southeast Asia and lived in the Japanese archipelago greater than 10,000 years ago, admixed with an agricultural people known as Yayoi, whom were migrants from the East Asian continent 2,000–3,000 years ago. Meanwhile, some anthropologists propose that rather, morphological differences between the Jomon and Yayoi people can be explained by microevolution following the lifestyle change. To resolve this controversy, we compared three demographic models by approximate Bayesian computation using genome-wide single nucleotide polymorphism (gwSNP) data from the Ainu people who are thought to be direct descendants of indigenous Jomon. If we assume Chinese people sampled in Beijing from HapMap have the same ancestry as Yayoi, then the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively. Furthermore, our data provide strong support for a model in which the Jomon lineages had population structure diversified in local areas before the admixture event. Initial divergence between the Jomon and Yayoi ancestries was dated to late Pleistocene, followed by the divergence of Jomon lineages at early Holocene. These results suggest gwSNP data provides a detailed picture of the complex hybridization model for Japanese population history.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    RlmCD-mediated U747 methylation promotes efficient G748 methylation by methyltransferase RlmAII in 23S rRNA in Streptococcus pneumoniae; interplay between two rRNA methylations responsible for telithromycin susceptibility (2015)
    Oxford University Press
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    Publication Date: 2015-10-15
    Description: Adenine at position 752 in a loop of helix 35 from positions 745 to 752 in domain II of 23S rRNA is involved in binding to the ribosome of telithromycin (TEL), a member of ketolides. Methylation of guanine at position 748 by the intrinsic methyltransferase RlmA II enhances binding of telithromycin (TEL) to A752 in Streptococcus pneumoniae . We have found that another intrinsic methylation of the adjacent uridine at position 747 enhances G748 methylation by RlmA II , rendering TEL susceptibility. U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae . Inactivation of RlmCD reduced N1-methylated level of G748 by RlmA II in vivo , leading to TEL resistance when the nucleotide A2058, located in domain V of 23S rRNA, was dimethylated by the dimethyltransferase Erm(B). In vitro methylation of rRNA showed that RlmA II activity was significantly enhanced by RlmCD-mediated pre-methylation of 23S rRNA. These results suggest that RlmCD-mediated U747 methylation promotes efficient G748 methylation by RlmA II , thereby facilitating TEL binding to the ribosome.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle (2015)
    Oxford University Press
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    Publication Date: 2015-01-24
    Description: Lineage potential is triggered by lineage-specific transcription factors in association with changes in the chromatin structure. Histone H3.3 variant is thought to play an important role in the regulation of lineage-specific genes. To elucidate the function of H3.3 in myogenic differentiation, we forced the expression of GFP-H3.1 to alter the balance between H3.1 and H3.3 in mouse C2C12 cells that could be differentiated into myotubes. GFP-H3.1 replaced H3.3 in the regulatory regions of skeletal muscle (SKM) genes and induced a decrease of H3K4 trimethylation (H3K4me3) and increase of H3K27 trimethylation (H3K27me3). Similar results were obtained by H3.3 knockdown. In contrast, MyoD-dependent H3.3 incorporation into SKM genes in fibroblasts induced an increase of H3K4me3 and H3K27me3. In mouse embryos, a bivalent modification of H3K4me3 and H3K27me3 was formed on H3.3-incorporated SKM genes before embryonic skeletal muscle differentiation. These results suggest that lineage potential is established through a selective incorporation of specific H3 variants that governs the balance of histone modifications.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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