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  • 1
    Electronic Resource
    Electronic Resource
    Hatch date-dependent differences in early growth and development recorded in the otolith microstructure of Trachurus japonicus (2005)
    Oxford, UK; Malden, USA : Blackwell Science Ltd
    Journal of fish biology 66 (2005), S. 0 
    Details
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Otolith microstructure of 308 juvenile jack mackerel Trachurus japonicus sampled in the southern Sea of Japan between June and September 2002 were examined by light microscopy. Hatch-date distribution indicated a protracted spawning season from 16 January to 30 May 2002. The first secondary primordium (SP) was formed at ages 19–54 days, with a mean ± s.d. of 30·4 ± 6·1. The number of SP in an otolith ranged from two to 15, with a mean of 6·1 ± 1·7. Age of the first SP formation, number of SP and increment width varied with hatch date. In general, late-hatched fish were younger when the first SP formed, and had a higher number of SP and wider increments, than early-hatched fish. As increment width is a linear function of somatic growth and formation of the first SP is associated with metamorphosis in jack mackerel, these variations in otolith microstructure indicated that rates of growth (as inferred from wider increments) and development (as inferred by younger age of first SP formation) were higher in late-hatched fish relative to early-hatched fish. Higher temperature experienced by late-hatched fish during early life stages may contribute critically to their higher growth and development rates compared to early-hatched fish.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.0022-1112.2005.00764.x
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  • 2
    Electronic Resource
    Electronic Resource
    Growth and morphological development of sagittal otoliths of larval and early juvenile Trachurus japonicus (2005)
    Oxford, UK; Malden, USA : Blackwell Science Ltd
    Journal of fish biology 66 (2005), S. 0 
    Details
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The daily periodicity of growth increment formation in sagittal otoliths of jack mackerel Trachurus japonicus was validated by marking otoliths with alizarin complexone (ALC). Analysis of otoliths of known-age juveniles confirmed that the first increment formed on day 3 after hatching, and was associated with first feeding. A total of 198 specimens, ranging from 2·6 to 49·2 mm in body length (notochord length or standard length) and from 7 to 78 days in age, were collected in the East China Sea and Tosa Bay, and used to examine the association between otolith morphological development and ontogenetic development. The relationship between body length (L) and otolith radius (R) was significantly described by the linear function L = 2·65 + 0·0425R(n = 198, r2 = 0·99, P 〈 0·001), indicating that somatic growth history can be reconstructed from otolith growth patterns. The otolith was primarily spherical in the preflexion larval stage, and became elongated with notochord flexion. The first secondary primordium formed at c. 25 days, during the middle postflexion stage, and was associated with metamorphosis. By c. 42 days the sagittal otolith was adult-like in morphology, with the primary growth zone enclosed by the marginal growth zone, except in the anterior rostrum area. Thus age, growth and developmental stages were recorded in sagittal otoliths during the larval and early juvenile stages of jack mackerel.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.0022-1112.2005.00717.x
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  • 3
    Electronic Resource
    Electronic Resource
    Validation of daily otolith increment formation in the larval myctophid fish Diaphus slender-type spp. (2005)
    Oxford, UK; Malden, USA : Blackwell Science Ltd
    Journal of fish biology 67 (2005), S. 0 
    Details
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The marginal increment growth in sagittal otoliths of the myctophid larvae Diaphus slender-type spp. collected in the north-eastern East China Sea was examined based on specimens collected at different times of the day. The calcification of the incremental zone began after midnight and took place throughout the day, and the discontinuous zone was formed only around midnight. These results indicate that otolith increments are formed daily.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.0022-1112.2005.00824.x
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  • 4
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    Subnuclear re-localization of SOX10 and p54NRB correlates with a unique neurological phenotype associated with SOX10 missense mutations (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-07
    Description: SOX10 is a transcription factor with well-known functions in neural crest and oligodendrocyte development. Mutations in SOX10 were first associated with Waardenburg–Hirschsprung disease (WS4; deafness, pigmentation defects and intestinal aganglionosis). However, variable phenotypes that extend beyond the WS4 definition are now reported. The neurological phenotypes associated with some truncating mutations are suggested to be the result of escape from the nonsense-mediated mRNA decay pathway; but, to date, no mechanism has been suggested for missense mutations, of which approximately 20 have now been reported, with about half of the latter shown to be redistributed to nuclear bodies of undetermined nature and function in vitro . Here, we report that p54NRB, which plays a crucial role in the regulation of gene expression during many cellular processes including differentiation, interacts synergistically with SOX10 to regulate several target genes. Interestingly, this paraspeckle protein, as well as two other members of the Drosophila behavior human splicing (DBHS) protein family, co-localize with SOX10 mutants in nuclear bodies, suggesting the possible paraspeckle nature of these foci or re-localization of the DBHS members to other subnuclear compartments. Remarkably, the co-transfection of wild-type and mutant SOX10 constructs led to the sequestration of wild-type protein in mutant-induced foci. In contrast to mutants presenting with additional cytoplasmic re-localization, those exclusively found in the nucleus alter synergistic activity between SOX10 and p54NRB. We propose that such a dominant negative effect may contribute to or be at the origin of the unique progressive and severe neurological phenotype observed in affected patients.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Effect of nitric oxide on VnfA, a transcriptional activator of VFe-nitrogenase in Azotobacter vinelandii (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-29
    Description: The transcriptional activator, VnfA, is necessary for the expression of the structural genes encoding vanadium-dependent nitrogenase in Azotobacter vinelandii . We have previously reported that VnfA harbours a Fe-S cluster as a prosthetic group, presumably a 3Fe-4S type, which is vital for the transcriptionally active VnfA. A plausible effector molecule is a reactive oxygen species (ROS), which disassembles the Fe-S cluster switching the active VnfA to become fully inactive. This finding prompted us to investigate the effect of nitric oxide (NO), another physiologically important radical species on the VnfA activity. Unlike ROS, the VnfA activity was moderately inhibited and converged to 70% of the maximum by NO irrespective of its concentration. The Fe-S cluster of VnfA was found to react with NO to form a dinitrosyl–iron complex, either in the dimeric or monomeric form, dependent on the relative stoichiometry of NO to the Fe-S cluster. The VnfA species harbouring the dinitrosyl–iron complexes in each form exhibited 50% ATPase activity compared to the active VnfA. The findings of this study would open an argument about a biological effect of NO on nitrogenase in light of its transcriptional regulatory system.
    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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  • 6
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    Structural basis of Cu, Zn-superoxide dismutase amyloid fibril formation involves interaction of multiple peptide core regions (2016)
    Oxford University Press
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    Publication Date: 2016-01-26
    Description: Cu, Zn-superoxide dismutase (SOD1), an enzyme implicated in the progression of familial amyotrophic lateral sclerosis (fALS), forms amyloid fibrils under certain experimental conditions. As part of our efforts to understand ALS pathogenesis, in this study we found that reduction of the intramolecular disulfide bond destabilized the tertiary structure of metal free wild-type SOD1 and greatly enhanced fibril formation in vitro . We also identified fibril core peptides that are resistant to protease digestion by using mass spectroscopy and Edman degradation analyses. Three regions dispersed throughout the sequence were detected as fibril core sequences of SOD1. Interestingly, by using three synthetic peptides that correspond to these identified regions, we determined that each region was capable of fibril formation, either alone or in a mixture containing multiple peptides. It was also revealed that by reducing the disulfide bond and causing a decrease in the structural stability, the amyloid fibril formation of a familial mutant SOD1 G93A was accelerated even under physiological conditions. These results demonstrate that by destabilizing the structure of SOD1 by removing metal ions and breaking the intramolecular disulfide bridge, multiple fibril-forming core regions are exposed, which then interact with each another and form amyloid fibrils under physiological conditions.
    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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  • 7
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    Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-24
    Description: Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus ( Tt ) and Geobacillus kaustophilus ( Gk ) were determined. For Tt PurM, the maximum resolution was 2.2 Å and the space group was P 2 1 2 1 2 with four dimers in an asymmetric unit. For Gk PurM, the maximum resolution was 2.2 Å and the space group was P 2 1 2 1 2 with one monomer in asymmetric unit. The biological unit is dimer for both Tt PurM and Gk PurM and the dimer structures were similar to previously determined structures of PurM in general. For Tt PurM, ~50 residues at the amino terminal were disordered in the crystal structure whereas, for Gk PurM, the corresponding region covered the ATP-binding site forming an α helix in part, suggesting that the N-terminal region of PurM changes its conformation upon binding of ligands. FGAM binding site was predicted by the docking simulation followed by the MD simulation based on the SO 4 2– binding site found in the crystal structure of Tt PurM.
    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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    Critical roles of the mitochondrial complex II in oocyst formation of rodent malaria parasite Plasmodium berghei (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-29
    Description: It is generally accepted that the mitochondria play central roles in energy production of most eukaryotes. In contrast, it has been thought that Plasmodium spp., the causative agent of malaria, rely mainly on cytosolic glycolysis but not mitochondrial oxidative phosphorylation for energy production during blood stages. However, Plasmodium spp. possesses all genes necessary for the tricarboxylic acid (TCA) cycle and most of the genes for electron transport chain (ETC) enzymes. Therefore, it remains elusive whether oxidative phosphorylation is essential for the parasite survival. To elucidate the role of TCA metabolism and ETC in malaria parasites, we deleted the gene for flavoprotein (Fp) subunit, Pbsdha , one of four components of complex II, a catalytic subunit for succinate dehydrogenase activity. The Pbsdha(-) parasite grew normally at blood stages in mouse. In contrast, ookinete formation of Pbsdha(-) parasites in the mosquito stage was severely impaired. Finally, Pbsdha(-) ookinetes failed in oocyst formation, leading to complete malaria transmission blockade. These results suggest that malaria parasite may switch the energy metabolism from glycolysis to oxidative phosphorylation to adapt to the insect vector where glucose is not readily available for ATP production.
    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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  • 9
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    Growth and photosynthetic traits of hybrid larch F1 (Larix gmelinii var. japonica x L. kaempferi) under elevated CO2 concentration with low nutrient availability (2011)
    Oxford University Press
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    Publication Date: 2011-11-24
    Description: The hybrid larch F 1 ( Larix gmelinii var. japonica x Larix kaempferi ) is considered one of the most important tree species not only for timber production but also as an afforestation material for severe conditions such as infertile soil. To predict the ability of hybrid larch F 1 as an afforestation material under potential climates in the future, it is important to understand the response of hybrid larch F 1 to elevated CO 2 concentration ([CO 2 ]) under low nutrient availability. Three-year-old seedlings of hybrid larch F 1 were grown under two different levels of [CO 2 ], 360 (ambient) and 720 µmol mol –1 (elevated), in combination with two different levels of nitrogen (N) supply (0 and 30 kg ha –1 ) for one growing season. Elevated [CO 2 ] reduced the maximum rates of carboxylation and electron transport in the needles. Net photosynthetic rates at growth [CO 2 ] (i.e., 360 and 720 µmol mol –1 for ambient and elevated treatment, respectively) did not differ between the two CO 2 treatments. Reductions in N content and N use efficiency to perform photosynthetic functions owing to the deficiency of nutrients other than N, such as P and K, and/or increase in cell wall mass were considered factors of photosynthetic down-regulation under elevated [CO 2 ], whereas stomatal closure little affected the photosynthetic down-regulation. Although we observed strong down-regulation of photosynthesis, the dry matter increase of hybrid larch F 1 seedlings was enhanced under elevated [CO 2 ]. This is mainly attributable to the increase in the amount of needles on increasing the number of sylleptic branches. These results suggest that elevated CO 2 may increase the growth of hybrid larch F 1 even under low nutrient availability, and that this increase may be regulated by changes in both crown architecture and needle photosynthesis, which is mainly affected not by stomatal limitation but by biochemical limitation.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 10
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    Evaluating the role of conserved amino acids in bacterial O-oligosaccharyltransferases by in vivo, in vitro and limited proteolysis assays (2013)
    Oxford University Press
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    Publication Date: 2013-12-07
    Description: Bacterial O -Oligosaccharyltransferases ( O -OTases) constitute a growing family of enzymes that catalyze the transfer of a glycan from a lipid carrier to protein acceptors. O -OTases are inner membrane proteins that display limited sequence similarity, except for the Wzy_C signature domain also present in a predicted periplasmic loop of the WaaL ligase, the enzyme responsible for transferring the O antigen to the lipid A core. The mechanism of O -OTase-dependent glycosylation is poorly understood. In this work, conserved amino acid residues in the O -OTases were replaced with alanine in PglL, the O -OTase of Neisseria meningitidis . The activity of wild-type PglL and its mutant derivatives were analyzed in vivo in engineered Escherichia coli cells, and in in vitro assays. We identified two additional sites of pilin glycosylated exclusively by PglL in E. coli . Both sites are modified with phosphoglycerol (PG) by different enzymes in Neisseria gonorrhoeae and Neisseria meningitidis . Limited proteolysis experiments revealed a conformational change that is triggered upon interaction of the C-terminal region of PglL with the lipid-linked oligosaccharide (LLO) substrate. These experiments showed that Q178 and Y405 are required for optimal function, whereas H349 is essential for activity and plays a critical role in the interaction with LLO. The equivalent His residue is also essential for WaaL activity, which suggests a common mechanism for both enzymes, and supports the hypothesis that O -glycosylation and lipopolysaccharide (LPS) synthesis are evolutionarily related. These results contribute to the elucidation of the mechanism of O -OTases, which are promising targets for novel antibiotics and present an enormous potential for glycoengineering novel vaccines and therapeutics.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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