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  • 1
    Publication Date: 2013-02-26
    Description: Human sialidase 2 (NEU2) is a cytoplasmic sialidase that degrades sialylglycoconjugates, including glycoproteins and gangliosides, via hydrolysis of terminal sialic acids to produce asialo-type molecules. Here, we first report the inhibitory effects of a series of synthetic sialyldendrimers comprising three types [Dumbbell(1)6- S -Neu5Ac 6 , Fan(0)3- S -Neu5Ac 3 and Ball(0)4- S -NeuAc 4 ] toward recombinant human NEU2 in vitro. Among them, Dumbbell(1)6- S -Neu5Ac 6 exhibited the most potent inhibitory activity (concentration causing 50% inhibition (IC 50 ), 0.4 ~ 0.5 mM). In addition, NeuSLac and NeuSCel carrying thiosialyltrisaccharide moieties exhibited more potent inhibitory effects than NeuSGal and NeuSGlc carrying thiosialyldisaccharides. Docking models composed of NEU2 and the thiosialyloligosaccharide suggested that the active pocket of NEU2 prefers the second galactose-β (Galβ) to the glucose-β (Glcβ) residue in the trisaccharide structure, there being a hydrogen bond between the 4-hydroxy group of the second Galβ and the side chain of the D46 residue of NEU2. The third Glcβ residues of NeuSLac and NeuSCel were also predicted to be stabilized by hydrogen bonds with the side chains of the R21, R304, D358 and Y359 residues of NEU2. NEU2 mutants (D358A and Y359A) exhibited reduced affinity for NeuSLac carrying thiosialyltrisaccharide moieties, suggesting the significant roles of D358 and Y359 residues in recognition of thiosialyltrisaccharide moieties of NeuSLac bound in the active pocket of NEU2. Thus, the present sialyldendrimers could be utilized not only as a new class of NEU2 inhibitors but also as molecular probes for evaluating the biological functions of NEU2, including the catalytic activity and mechanism as to natural substrates carrying sialyloligosaccharides.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 2
    Publication Date: 2014-01-11
    Description: The hallmark of Alzheimer's disease (AD) pathology is an accumulation of amyloid β (Aβ) and phosphorylated tau, which are encoded by the amyloid precursor protein (APP) and microtubule-associated protein tau ( MAPT ) genes, respectively. Less than 5% of all AD cases are familial in nature, i.e. caused by mutations in APP , PSEN1 or PSEN2 . Almost all mutations found in them are related to an overproduction of Aβ 1–42 , which is prone to aggregation. While these genes are mutation free, their function, or those of related genes, could be compromised in sporadic AD as well. In this study, pyrosequencing analysis of post-mortem brains revealed aberrant CpG methylation in APP , MAPT and GSK3B genes of the AD brain. These changes were further evaluated by a newly developed in vitro -specific DNA methylation system, which in turn highlighted an enhanced expression of APP and MAPT . Cell nucleus sorting of post-mortem brains revealed that the methylation changes of APP and MAPT occurred in both neuronal and non-neuronal cells, whereas GSK3B was abnormally methylated in non-neuronal cells. Further analysis revealed an association between abnormal APP CpG methylation and apolipoprotein E 4 allele ( APOE 4)-negative cases. The presence of a small number of highly methylated neurons among normal neurons contribute to the methylation difference in APP and MAPT CpGs, thus abnormally methylated cells could compromise the neural circuit and/or serve as ‘seed cells’ for abnormal protein propagation. Our results provide a link between familial AD genes and sporadic neuropathology, thus emphasizing an epigenetic pathomechanism for sporadic AD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 3
    Publication Date: 2014-09-30
    Description: This Comment was prompted by the substantial difference in weir catch estimates in the Gulf between (i) those reported by Al-Abdulrazzak and Pauly (2014. Managing fisheries from space: Google Earth improves estimates of distant fish catches. ICES Journal of Marine Science, 71(3), 450–454), who used Google Earth to count weir numbers, and (ii) those available from official national statistics provided by two major weir fishing countries (Bahrain and Iran). Satellite imageries, including Google Earth, are powerful tools for collecting data on visible structures when verified with adequate ground validation. However, an extension of their contribution to improving overall catch estimates is rather limited without having solid information on daily catch, which will substantially differ according to time and area, and fishing season lengths. It was noted that Al-Abdulrazzak and Pauly (2013) introduced positive biases through their interpretation of Google Earth images and data treatment. They included several assumptions, such as removing the impact of poor visibility, correcting grids of low resolutions, estimating number of unseen weirs, and applying daily catch rates higher than referenced observed values. The overall extent of such potential positive bias could be more than six times that which we considered reasonable. This Comment also corrects misconceptions about "FAO catch data", discusses other available national data, and introduces the existence of the Regional Commission for Fisheries (RECOFI), a mechanism for fisheries management in the Gulf region, and its recent activities to collect more complete catch and effort data separated by gear.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 4
    Publication Date: 2014-03-19
    Description: Motivation: Long expansions of short tandem repeats (STRs), i.e. DNA repeats of 2–6 nt, are associated with some genetic diseases. Cost-efficient high-throughput sequencing can quickly produce billions of short reads that would be useful for uncovering disease-associated STRs. However, enumerating STRs in short reads remains largely unexplored because of the difficulty in elucidating STRs much longer than 100 bp, the typical length of short reads. Results: We propose ab initio procedures for sensing and locating long STRs promptly by using the frequency distribution of all STRs and paired-end read information. We validated the reproducibility of this method using biological replicates and used it to locate an STR associated with a brain disease (SCA31). Subsequently, we sequenced this STR site in 11 SCA31 samples using SMRT TM sequencing (Pacific Biosciences), determined 2.3–3.1 kb sequences at nucleotide resolution and revealed that (TGGAA)- and (TAAAATAGAA)-repeat expansions determined the instability of the repeat expansions associated with SCA31. Our method could also identify common STRs, (AAAG)- and (AAAAG)-repeat expansions, which are remarkably expanded at four positions in an SCA31 sample. This is the first proposed method for rapidly finding disease-associated long STRs in personal genomes using hybrid sequencing of short and long reads. Availability and implementation: Our TRhist software is available at http://trhist.gi.k.u-tokyo.ac.jp/ . Contact: moris@cb.k.u-tokyo.ac.jp Supplementary information : Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 5
    Publication Date: 2013-10-29
    Description: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by progressive and selective loss of motor neurons. The discovery of mutations in the gene encoding an RNA-binding protein, TAR DNA-binding protein of 43 kD (TDP-43), in familial ALS, strongly implicated abnormalities in RNA processing in the pathogenesis of ALS, although the mechanisms whereby TDP-43 leads to neurodegeneration remain elusive. To clarify the mechanism of degeneration caused by TDP-43, we generated transgenic Drosophila melanogaster expressing a series of systematically modified human TDP-43 genes in the retinal photoreceptor neurons. Overexpression of wild-type TDP-43 resulted in vacuolar degeneration of the photoreceptor neurons associated with thinning of the retina, which was significantly exacerbated by mutations of TDP-43 linked to familial ALS or disrupting its nuclear localization signal (NLS). Remarkably, these degenerative phenotypes were completely normalized by addition of a mutation or deletion of the RNA recognition motif that abolishes the RNA binding ability of TDP-43. Altogether, our results suggest that RNA binding is key to the neurodegeneration caused by overexpression of TDP-43, and that abnormalities in RNA processing may be crucial to the pathogenesis of TDP-43 proteinopathy.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 6
    Publication Date: 2013-03-27
    Description: Mouse sialyltransferases are grouped into four families according to the type of carbohydrate linkage they synthesize: β-galactoside α2,3-sialyltransferases (ST3Gal-I–VI), β-galactoside α2,6-sialyltransferases (ST6Gal-I and ST6Gal-II), N -acetylgalactosamine α2,6-sialyltransferases (ST6GalNAc-I–VI) and α2,8-sialyltransferases (ST8Sia-I–VI). These sialyltransferases feature a type II transmembrane topology and contain highly conserved motifs termed sialylmotifs L, S, III and VS. Sialylmotifs L and S are involved in substrate binding, whereas sialylmotifs III and VS are involved in catalytic activity. In addition to the conventional sialylmotifs, family and subfamily specific sequence motifs have been proposed. In this study, we analyzed the properties and functions of sialylmotifs in characterizing the enzymatic activity of mouse ST8Sia-I and ST8Sia-VI, both of which are α2,8-sialyltransferases involved in the synthesis of either ganglioside GD3 or disialic acid structures on O -glycans, respectively. The ST8Sia-VI-based chimeric enzymes, whose sialylmotif L sequences were replaced with those of ST8Sia-I and ST8Sia-IV (polysialic acid synthetase), were still active toward O -glycans. However, ST8Sia-VI-based chimeric enzymes lost expression or activity when their sialylmotif L sequences were replaced with those of ST3Gal-I and ST6GalNAc-II, suggesting the existence of an ST8Sia family specific motif in the sialylmotif L. The ST8Sia-I- and ST8Sia-VI-based chimeric enzymes lost enzymatic activity when their sialylmotif S sequences were interchanged. Amino acid substitutions in the sialylmotif S of ST8Sia-I and ST8Sia-VI also affected the enzymatic activity in many cases, indicating the crucial and functional importance of the sialylmotif S in substrate binding, which determines the substrate specificity of sialyltransferase.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2016-10-04
    Description: Motivation: Determining the methylation state of regions with high copy numbers is challenging for second-generation sequencing, because the read length is insufficient to map reads uniquely, especially when repetitive regions are long and nearly identical to each other. Single-molecule real-time (SMRT) sequencing is a promising method for observing such regions, because it is not vulnerable to GC bias, it produces long read lengths, and its kinetic information is sensitive to DNA modifications. Results: We propose a novel linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read coverage of ~30-fold from an inbred strain medaka ( Oryzias latipes ), we observed that both the sensitivity and precision of our method on individual CpG sites were ~93.7%. We also observed a high correlation coefficient ( R = 0.884) between our method and bisulfite sequencing, and for 92.0% of CpG sites, methylation levels ranging over [0,1] were in concordance within an acceptable difference 0.25. Using this method, we characterized the landscape of the methylation status of repetitive elements, such as LINEs, in the human genome, thereby revealing the strong correlation between CpG density and hypomethylation and detecting hypomethylation hot spots of LTRs and LINEs. We uncovered the methylation states for nearly identical active transposons, two novel LINE insertions of identity ~99% and length 6050 base pairs (bp) in the human genome, and 16 Tol2 elements of identity 〉99.8% and length 4682 bp in the medaka genome. Availability and Implementation: AgIn ( Ag gregate on In tervals) is available at: https://github.com/hacone/AgIn Contact: ysuzuki@cb.k.u-tokyo.ac.jp or moris@cb.k.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2000-03-01
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 9
  • 10
    Publication Date: 2009-01-29
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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