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  • 1
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    New susceptibility variants to narcolepsy identified in HLA class II region (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-13
    Description: Narcolepsy, a sleep disorder characterized by excessive daytime sleepiness, cataplexy and rapid eye movement sleep abnormalities, is tightly associated with human leukocyte antigen HLA-DQB1*06:02. DQB1*06:02 is common in the general population (10–30%); therefore, additional genetic factors are needed for the development of narcolepsy. In the present study, HLA-DQB1 in 664 Japanese narcoleptic subjects and 3131 Japanese control subjects was examined to determine whether HLA-DQB1 alleles located in trans of DQB1*06:02 are associated with narcolepsy. The strongest association was with DQB1*06:01 ( P = 1.4 x 10 –10 , odds ratio, OR = 0.39), as reported in previous studies. Additional predisposing effects of DQB1*03:02 were also found ( P = 2.5 x 10 –9 , OR = 1.97). A comparison between DQB1*06:02 heterozygous cases and controls revealed dominant protective effects of DQB1*06:01 and DQB1*05:01 . In addition, a single-nucleotide polymorphism-based conditional analysis controlling for the effect of HLA-DQB1 was performed to determine whether there were other independent HLA associations outside of HLA-DQB1 . This analysis revealed associations at HLA-DPB1 in the HLA class II region (rs3117242, P = 4.1 x 10 –5 , OR = 2.45; DPB1*05:01 , P = 8.1 x 10 –3 , OR = 1.39). These results indicate that complex HLA class II associations contribute to the genetic predisposition to narcolepsy.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    In situ visualization of a glycoform of transferrin: localization of {alpha}2,6-sialylated transferrin in the liver (2015)
    Oxford University Press
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    Publication Date: 2015-03-28
    Description: We previously found that a lectin, Sambucus sieboldiana agglutinin (SSA), bound to α2,6-sialylated glycan epitopes on transferrin and inhibited anti-transferrin antibody binding to the antigen in ELISA (SSA inhibition). Here we report that SSA inhibition is applicable to immunohistochemistry, localizing α2,6-sialylated transferrin in the liver. Immunohistochemistry using anti-transferrin polyclonal antibody revealed that transferrin was detected in hepatocytes near interlobular veins. Addition of SSA lectin markedly attenuated the staining. Sialidase treatment of a liver section abolished SSA binding and concomitantly cancelled SSA inhibition, suggesting that SSA binding to glycan epitopes on the section was essential for the inhibition. To examine the importance of proximity between antigen epitopes and SSA-binding (glycosylation) sites, we prepared two anti-peptide antibodies against partial amino acid sequences of transferrin. One antibody (Tf-596Ab) is against a peptide sequence, Cys596-Ala614, which is proximal to N -glycosylation sites (Asn-432 and Asn-630). The other (Tf-120Ab) is against a peptide sequence, Val120-Cys137, distal to the sites. The staining signals of Tf-596Ab were reduced by the addition of SSA, whereas those of Tf-120Ab were reduced only a little. This result suggests that proximity of the antigen epitope to SSA binding sites is critical for SSA inhibition in immunohistochemistry.
    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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  • 3
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    A glycosynthase derived from an inverting chitinase with an extended binding cleft (2016)
    Oxford University Press
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    Publication Date: 2016-07-30
    Description: We created a glycosynthase from a GH19 chitinase from rye seeds (RSC-c), that has a long-extended binding cleft consisting of eight subsites; -4, -3, -2, -1, +1, +2, +3 and +4. When wild-type RSC-c was incubated with α-(GlcNAc) 3 -F [α-(GlcNAc) 3 fluoride], (GlcNAc) 3 and hydrogen fluoride were produced through the Hehre resynthesis–hydrolysis mechanism. Glu89, which acts as a catalytic base, and Ser120, which fixes a nucleophilic water molecule, were mutated to produce two single mutants, E89G and S120A, and a double mutant, E89G/S120A. E89G only produced a small amount of (GlcNAc) 7 from α-(GlcNAc) 3 -F in the presence of (GlcNAc) 4 . S120A, with the highest F – -releasing activity, produced a larger amount of (GlcNAc) 7 , a fraction of which was decomposed by its own residual hydrolytic activity. However, the double mutant E89G/S120A, of which the hydrolytic activity was completely abolished while its F – -releasing activity was only moderately affected, produced the largest amount of (GlcNAc) 7 from α-(GlcNAc) 3 -F and (GlcNAc) 4 without decomposition. We concluded that E89G/S120A was an efficient glycosynthase, that enabled the addition of a three-sugar unit.
    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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  • 4
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    Flexible phytoplankton functional type (FlexPFT) model: size-scaling of traits and optimal growth (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-20
    Description: Recent studies have analysed valuable compilations of data for the size-scaling of phytoplankton traits, but these cannot be employed directly in most large-scale modelling studies, which typically do not explicitly resolve the relevant trait values. Although some recent large-scale modelling studies resolve species composition and sorting within communities, most do not account for the observed flexible response of phytoplankton communities, such as the dynamic acclimation often observed in laboratory experiments. In order to derive a simple yet flexible model of phytoplankton growth that can be useful for a wide variety of ocean modelling applications, we combine two trade-offs, one for growth and the other for nutrient uptake, under the optimality assumption, i.e. that intracellular resources are dynamically allocated to maximize growth rate. This yields an explicit equation for growth as a function of nutrient concentration and daily averaged irradiance. We furthermore show how with this model effective Monod parameter values depend on both the underlying trait values and environmental conditions. We apply this new model to two contrasting time-series observation sites, including idealized simulations of size diversity. The flexible model responds differently compared with an inflexible control, suggesting that acclimation by individual species could impact models of plankton diversity.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences (2015)
    Oxford University Press
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    Publication Date: 2015-07-12
    Description: Recent advances in next-generation sequencing technologies have revealed that cellular functional RNAs are not always expressed as single entities with fixed terminal sequences but as multiple isoforms bearing complex heterogeneity in both length and terminal sequences, such as isomiRs, the isoforms of microRNAs. Unraveling the biogenesis and biological significance of heterogenetic RNA expression requires distinctive analysis of each RNA variant. Here, we report the development of dumbbell PCR (Db-PCR), an efficient and convenient method to distinctively quantify a specific individual small RNA variant. In Db-PCR, 5'- and 3'-stem–loop adapters are specifically hybridized and ligated to the 5'- and 3'-ends of target RNAs, respectively, by T4 RNA ligase 2 (Rnl2). The resultant ligation products with ‘dumbbell-like’ structures are subsequently quantified by TaqMan RT-PCR. We confirmed that high specificity of Rnl2 ligation and TaqMan RT-PCR toward target RNAs assured both 5'- and 3'-terminal sequences of target RNAs with single nucleotide resolution so that Db-PCR specifically detected target RNAs but not their corresponding terminal variants. Db-PCR had broad applicability for the quantification of various small RNAs in different cell types, and the results were consistent with those from other quantification method. Therefore, Db-PCR provides a much-needed simple method for analyzing RNA terminal heterogeneity.
    Keywords: Nucleic acid amplification, RNA characterisation and manipulation, Transcriptome Mapping - Monitoring Gene Expression
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Comparing the temporal colonization and microbial diversity of showerhead biofilms in Hawai'i and Colorado (2016)
    Oxford University Press
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    Publication Date: 2016-02-07
    Description: The household is a potential source of opportunistic pathogens to humans, a particularly critical issue for immunodeficient individuals. An important human–microbe interface is the biofilm that develops on showerhead surfaces. Once microbe-laden biofilms become aerosolized, they can potentially be inhaled into the lungs. Understanding how quickly a new showerhead becomes colonized would provide useful information to minimize exposure to potentially pathogenic environmental microbes. High school scientists sampled the inner surfaces of pre-existing and newly fitted showerheads monthly over a nine-month period and applied standard microbiologic culture techniques to qualitatively assess microbial growth. Water chemistry was also monitored using commercial test strips. Sampling was performed in households on Oahu, Hawai'i and Denver, Colorado, representing warm/humid and cold/arid environments, respectively. Pre-existing showerheads in Hawai'i showed more diverse microbial growth and significantly greater microbial numbers than a comparable showerhead from Colorado. New, chrome-plated or plastic showerheads in Hawai'i showed diverse and abundant growth one month after installment compared to new showerheads from Colorado. The pH, total chlorine and water hardness levels varied significantly between the Hawai'i and Colorado samples. Enthusiastic student and teacher participation allowed us to answer long-standing questions regarding the temporal colonization of microbial biofilms on pre-existing and new showerhead surfaces.
    Keywords: Professional Development
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Characterization of the dipeptide repeat protein in the molecular pathogenesis of c9FTD/ALS (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-26
    Description: The expansion of the GGGGCC hexanucleotide repeat in the non-coding region of the chromosome 9 open-reading frame 72 ( C9orf72 ) gene is the most common cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) (c9FTD/ALS). Recently, it was reported that an unconventional mechanism of repeat-associated non-ATG (RAN) translation arises from C9orf72 expansion. Sense and anti-sense transcripts of the expanded C9orf72 repeat, i.e. the dipeptide repeat protein (DRP) of glycine–alanine (poly-GA), glycine–proline (poly-GP), glycine–arginine (poly-GR), proline–arginine (poly-PR) and proline–alanine (poly-PA), are deposited in the brains of patients with c9FTD/ALS. However, the pathological significance of RAN-translated peptides remains unknown. We generated synthetic cDNAs encoding 100 repeats of DRP without a GGGGCC repeat and evaluated the effects of these proteins on cultured cells and cortical neurons in vivo. Our results revealed that the poly-GA protein formed highly aggregated ubiquitin/p62-positive inclusion bodies in neuronal cells. In contrast, the highly basic proteins poly-GR and PR also formed unique ubiquitin/p62-negative cytoplasmic inclusions, which co-localized with the components of RNA granules. The evaluation of cytotoxicity revealed that overexpressed poly-GA, poly-GP and poly-GR increased the substrates of the ubiquitin–proteasome system (UPS), including TDP-43, and enhanced the sensitivity to a proteasome inhibitor, indicating that these DRPs are cytotoxic, possibly via UPS dysfunction. The present data indicate that a gain-of-function mechanism of toxic DRPs possibly contributes to pathogenesis in c9FTD/ALS and that DRPs may serve as novel therapeutic targets in c9FTD/ALS.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Introduction of H-antigens into oligosaccharides and sugar chains of glycoproteins using highly efficient 1,2-{alpha}-L-fucosynthase (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-02
    Description: Fucα1-2 Gal linkages, or H-antigens, constitute histo-blood group antigens and are involved in various physiological processes. In addition, recent studies have shown that the H-antigen-containing glycans play an important role, not only in establishing harmonious relationship between gut microbes and the host, but also in preventing gut dysbiosis-related diseases. Therefore, development of an efficient method for introducing Fuc residue at Gal residue at the nonreducing end of glycans via α-(1-〉2) linkage is desired for research as well as medicinal purposes. In this study, we succeeded in derivatizing inverting 1,2-α- l -fucosidase (AfcA) into a highly efficient 1,2-α- l -fucosynthase. The synthase specifically synthesized H type 1-, type 2-, type 3- and type 4-chain-containing oligosaccharides with yields of 57–75% based on acceptor depletion. The synthase was also able to specifically introduce Fuc residues into Lewis a/x antigens to produce Lewis b/y antigens, with yields of 43% and 62%, respectively. In addition, the enzyme efficiently introduced H-antigens into sugar chains of porcine gastric mucins, as revealed by lectin blotting and mass spectroscopy analysis of the sugars. Detailed acceptor specificity analysis using various monosaccharides and oligosaccharides unraveled unique substrate recognition feature of this synthase at the subsite (+1), which can be explained by our previous X-ray crystallographic study of AfcA. These results show that the synthase developed in this study could serve as an alternative to other H-antigen synthesis methods involving α-1,2-fucosyltransferases and retaining α-fucosidase.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 9
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    Cell models lead to understanding of multi-cellular morphogenesis consisting of successive self-construction of cells (2015)
    Oxford University Press
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    Publication Date: 2015-02-26
    Description: Morphogenesis of multi-cellular organisms occurs through cell behaviours within a cell aggregate. Cell behaviours have been described using cell models involving equations of motion for cells. Cells in cell models construct shapes of the cell aggregate by themselves. Here, a history of cell models, the cell centre model and the vertex cell model, which we have constructed, are described. Furthermore, the application of these cell models is explained in detail. These cell models have been applied to transformation of cell aggregates to become spherical, formation of mammalian blastocysts and cell intercalation in elongating tissues. These are all elemental processes of morphogenesis and take place in succession during the whole developmental process. A chain of successive elemental processes leads to morphogenesis. Finally, we highlight that cell models are indispensable to understand the process whereby genes direct biological shapes.
    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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  • 10
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    Sodium phenobarbital-enhanced mutation frequency in the liver DNM of lacz transgenic mice treated with diethylnitrosamine (1997)
    Oxford University Press
    Details
    Publication Date: 1997-01-01
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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