32 results on '"Osamu, Nishimura"'
Search Results
2. Control of Synaptic Levels of Nicotinic Acetylcholine Receptor by the Sequestering Subunit Dα5 and Secreted Scaffold Protein Hig.
- Author
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Minoru Nakayama, Osamu Nishimura, Yuhi Nishimura, Miwa Kitaichi, Shigehiro Kuraku, Masaki Sone, and Chihiro Hama
- Abstract
The presentation of nicotinic acetylcholine receptors (nAChRs) on synaptic membranes is crucial for generating cholinergic circuits, some of which are associated with memory function and neurodegenerative disorders. Although the physiology and structure of nAChR, a cation channel comprising five subunits, have been extensively studied, little is known about how the receptor levels in interneuronal synapses are determined and which nAChR subunits participate in the regulatory process in cooperation with synaptic cleft matrices and intracellular proteins. By a genetic screen of Drosophila, we identified mutations in the nAChR subunit Da5 gene as suppressors that restored the mutant phenotypes of hig, which encodes a secretory matrix protein localized to cholinergic synaptic clefts in the brain. Only the loss of function of Da5 among the 10 nAChR subunits suppressed hig mutant phenotypes in both male and female flies. Da5 behaved as a lethal factor when Hig was defective; loss of Da5 in hig mutants rescued lethality, upregulating Da6 synaptic levels. By contrast, levels of Da5, Da6, and Da7 subunits were all reduced in hig mutants. These three subunits have distinct properties for interaction with Hig or trafficking, as confirmed by chimeric subunit experiments. Notably, the chimeric Da5 protein, which has the extracellular sequences that display no positive interaction with Hig, exhibited abnormal distribution and lethality even in the presence of Hig. We propose that the sequestering subunit Da5 functions by reducing synaptic levels of nAChR through internalization, and this process is blocked by Hig, which tethers Da5 to the synaptic cleft matrix. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
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3. A formula on Stirling numbers of the second kind and its application to the unstable K-theory of stunted complex projective spaces.
- Author
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Osamu Nishimura
- Subjects
K-theory ,PROJECTIVE spaces ,ALGEBRAIC topology ,BERNOULLI numbers ,ISOMORPHISM (Mathematics) - Abstract
A formula on Stirling numbers of the second kind S(n, k) is proved. As a corollary, for odd n and even k, it is shown that k!S(n, k) is a positive multiple of the greatest common divisor of j!S(n, j) for k + 1 ≤ j ≤ n. Also, as an application to algebraic topology, some isomorphisms of unstable K¹-groups of stunted complex projective spaces are deduced. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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4. Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish.
- Author
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Kabir, Ahammad, Ieda, Risa, Sho Hosoya, Daigaku Fujikawa, Kazufumi Atsumi, Shota Tajima, Aoi Nozawa, Takashi Koyama, Shotaro Hirase, Osamu Nakamura, Mitsutaka Kadota, Osamu Nishimura, Shigehiro Kuraku, Yasukazu Nakamura, Hisato Kobayashi, Atsushi Toyoda, Satoshi Tasumi, and Kiyoshi Kikuchi
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SEX chromosomes ,PUFFERS (Fish) ,SEX determination ,CHROMOSOMES ,LOCUS (Genetics) - Abstract
Recent studies have revealed a surprising diversity of sex chromosomes in vertebrates. However, the detailed mechanism of their turnover is still elusive. To understand this process, it is necessary to compare closely related species in terms of sex-determining genes and the chromosomes harboring them. Here, we explored the genus Takifugu,in which one strong candidate sex-determining gene, Amhr2, has been identified. To trace the processes involved in transitions in the sex-determination system in this genus, we studied 12 species and found that while the Amhr2 locus likely determines sex in the majority of Takifugu species, three species have acquired sex-determining loci at different chromosomal locations. Nevertheless, the generation of genome assemblies for the three species revealed that they share a portion of the male-specific supergene that contains a candidate sex-determining gene, GsdfY, along with genes that potentially play a role in male fitness. The shared supergene spans ~100 kb and is flanked by two duplicated regions characterized by CACTA transposable elements. These results suggest that the shared supergene has taken over the role of sex-determining locus from Amhr2 in lineages leading to the three species, and repeated translocations of the supergene underlie the turnover of sex chromosomes in these lineages. These ?ndings highlight the underestimated role of a mobile supergene in the turnover of sex chromosomes in vertebrates. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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5. Hydrodynamic-Driven Changes in the Source and Composition of Sedimentary Organic Matter via Grain Size Distribution in Shallow Lakes.
- Author
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Xiaoguang Xu, Ruijie Shi, Chengxu Lv, Huazu Liu, Wei Yang, Shenhua Qian, Megumu Fujibayashi, Yue Zhi, Guoxiang Wang, Munehiro Nomura, Osamu Nishimura, and Wei Li
- Subjects
ORGANIC compounds ,PARTICLE size distribution ,HYDRODYNAMICS ,PEARSON correlation (Statistics) ,VELOCITY - Abstract
Sediment organic matter (SOM) differs in composition and function in different size fractions in relation to material and energy flows. The hydrodynamic effects on a lake's autochthonous (terrestrial plants) and allochthonous (microalgae, aquatic plants, and bacteria) inputs and transformation, and the components of SOM are still far from clear. To elucidate the SOM composition as driven by the hydrodynamic conditions associated with sedimentary grain size, we performed an ecosystem-level investigation in the shallow lake Izunuma, Japan, measuring source-specific fatty acids and the current velocity. High organic matter concentrations occurred in the finer fractions. Bacteria were dominant in the <32 μm fraction, microalgae were mainly present in the <32 and 63–125 μm fractions, aquatic plants appeared to be evenly distributed in all size fractions, and terrestrial plants mainly comprised the >125 μm fraction. Although the linear correlation between current velocity and sedimentary total organic carbon (TOC) was not statistically significant, the relationship between current velocity frequency and sedimentary TOC was significant. The highest Pearson coefficient occurred at a current velocity of 6 cm/s in sand. The relationship between allochthonous inputs and current velocity frequency was similar to that of TOC. Autochthonous organics had the greatest coefficient with two peaks at 4.5 and 8 cm/s. The threshold for sand resuspension varied with organic sources, while this phenomenon was absent in cohesive mud. Hydrodynamic forces affected the grain size of sediments and drove the gradient distribution of the SOM sources, which should be considered when managing freshwater lakes in light of future climate change. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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6. Developmental hourglass and heterochronic shifts in fin and limb development.
- Author
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Koh Onimaru, Kaori Tatsumi, Chiharu Tanegashima, Mitsutaka Kadota, Osamu Nishimura, and Shigehiro Kuraku
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- 2021
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7. Regularized regression analysis for the prediction of virus inactivation efficiency by chloramine disinfection.
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Syun-suke Kadoya, Osamu Nishimura, Hiroyuki Kato, and Daisuke Sano
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- 2020
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8. Plasma membrane expression of ZNF185 is a prognostic factor in pancreatic ductal carcinoma.
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Daisuke Furukawa, Tsuyoshi Chijiwa, Masahiro Matsuyama, Masaya Mukai, Ei-Ichi Matsuo, Osamu Nishimura, Kenji Kawai, Hiroshi Suemizu, Toshio Nakagohri, Soji Ozawa, Kazuaki Shimada, Nobuyoshi Hiraoka, and Masato Nakamura
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CELL membranes ,DUCTAL carcinoma ,METASTASIS ,MULTIVARIATE analysis ,CANCER cells ,PHYSIOLOGY ,DIAGNOSIS ,THERAPEUTICS - Abstract
Pancreatic ductal carcinoma (PDC) is one of the major causes of cancer-associated mortality globally due to its high potential for distant metastasis. To understand hematogenous metastasis, the molecular expression profiles of weak metastatic PDC cell subline BxPC-3 and highly liver-metastatic cell subline LM-BxPC-3 were compared, and zinc finger protein 185 (ZNF185) was identified as a molecule that is upregulated in LM-BxPC-3 cells. The aim of the present study was to evaluate the clinicopathological significance of ZNF185 in PDC. Using immunohistochemistry, ZNF185 expression was investigated in 182 patients with PDC, in association with numerous clinicopathological variables. The expression profile of ZNF185 was also characterized using xenograft models. In contrast to parent BxPC-3 cells in subcutaneous transplanted tumor foci, which only expressed ZNF185 on their plasma membrane (m)ZNF185, LM-BxPC-3 cells in liver-metastatic foci that were formed subsequent to transplantation all expressed cytoplasmic (c)ZNF185. Additionally, 51% of the cells at the periphery of the tumor foci expressed mZNF185. Expression of cZNF185, and of mZNF185 and cZNF185 combined was identified in 93 and 39% of clinical patients with PDC, respectively. Patients with mZNF185-negative and -positive PDC exhibited a median survival time of 30.2 months and 21.3 months, respectively. Multivariate analysis indicated that the expression of mZNF185 is closely associated with a shorter overall survival time. Increased marked venous invasion was more prevalent in patients who were mZNF185-positive, as compared with patients who were mZNF185-negative. These data suggest that the expression of mZNF185 is an independent and unfavorable prognosticator in patients with PDC. The results suggested that the amount and subcellular location of ZNF185 are correlated with the position of the cancer cells expressing it within the nests. Additionally, the subcellular location of ZNF185 may be important to its biological function. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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9. Differences in the removal mechanisms of Undaria pinnatifida and Phragmites australis as biomaterials for lead removal.
- Author
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Paula Cecilia Soto-Rios, Kazunori Nakano, Marco Leon-Romero, Yoshio Aikawa, Shigeyuki Arai, and Osamu Nishimura
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LEAD ,UNDARIA pinnatifida ,PHRAGMITES australis ,BIOMATERIALS ,PERMEABLE reactive barriers ,SPECIATION analysis - Abstract
This study offers the opportunity to utilize Undaria pinnatifida and Phragmites australis to remove lead from water in permeable reactive barrier (PRB) technology. Its efficacy was tested using batch experiments and PRB column systems. From the batch experiment results, a higher adsorption capacity was observed for Undaria pinnatifida. Nevertheless, Phragmites australis in the column system efficiently removed lead and the breakthrough occurred at the same time for both biomaterials. To dissipate this difference, a sequential extraction for metal speciation analysis was used for both columns. The results have shown that each biomaterial has a dominant mechanism. Phragmites australis removed lead by physical adsorption, whereas Undaria pinnatifida showed a higher tendency to bind lead due to organic matter, primary and secondary minerals. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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10. Influence of Milk on Aroma Release and Aroma Perception during Consumption of Coffee Beverages.
- Author
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Takafumi ITOBE, Osamu NISHIMURA, and Kenji KUMAZAWA
- Abstract
The aim of this study was to investigate the influence of milk on the aroma release and aroma perception of coffee. The amounts of in-mouth odorants exhaled through the nostrils during the consumption of black coffee and milk coffee were compared using the Retronasal Flavor Impression Screening System (R-FISS) by 3 trained panelists. As a result, it was found that the amounts of most in-mouth odorants including the potent odorants in brewed coffee did not significantly differ between the black coffee and milk coffee. However, the amounts of furfuryl methyl sulfide (FMS), difurylmethane, and furfuryl pyrrole exhaled through the nostrils during the consumption of milk coffee were significantly lower than those of the black coffee regardless of the panelist. It has been previously indicated that FMS could result from the methylation of 2-furfurylthioI (FFT), one of the most important potent odorants in brewed coffee. Based on these results, FFT and FMS were added to milk coffee so that the amount of FMS exhaled through the nostrils was about the same as that of black coffee, resulting in improved intensity of the coffee-like aroma quality for the milk coffee. The present results suggested that the significantly decreased intensity of the coffee-like aroma quality might result from decreased aroma release of a few odorants, including FFT, by the addition of milk to the coffee. Moreover, it was inferred that the difference in aroma release of FFT would have an especially significant impact on the perception of coffee-like aroma quality between the black coffee and milk coffee. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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11. INFLUENCE OF A NON-DIPOLE MAGNETIC FIELD ON THE PEAK ENERGIES OF CYCLOTRON ABSORPTION LINES.
- Author
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OSAMU NISHIMURA
- Subjects
MAGNETIC fields ,CYCLOTRONS ,NEUTRON stars ,PULSARS ,ASTRONOMY - Published
- 2007
12. EFFECT OF WAVE-INDUCED CURRENT ON ALGAL COMMUNITY DEVELOPMENT ON ARTIFICIAL REEFS.
- Author
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KIMIHITO INOUE, HITOSHI TANAKA, OSAMU NISHIMURA, and SATOSHI BABA
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ARTIFICIAL reef design & construction ,COASTAL ecology ,SHORE protection ,ALGAL communities ,OCEAN waves - Published
- 2002
13. gVolante for standardizing completeness assessment of genome and transcriptome assemblies.
- Author
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Osamu Nishimura, Yuichiro Hara, and Shigehiro Kuraku
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GENOMICS ,NUCLEOTIDE sequencing ,MACHINE learning ,DATA analysis ,BIOINFORMATICS - Abstract
Motivation: Along with the increasing accessibility to comprehensive sequence information, such as whole genomes and transcriptomes, the demand for assessing their quality has been multiplied. To this end, metrics based on sequence lengths, such as N50, have become a standard, but they only evaluate one aspect of assembly quality. Conversely, analyzing the coverage of pre-selected reference protein-coding genes provides essential content-based quality assessment, but the currently available pipelines for this purpose, CEGMA and BUSCO, do not have a user-friendly interface to serve as a uniform environment for assembly completeness assessment. Results: Here, we introduce a brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section. Completeness assessments performed on gVolante report scores based on not just the coverage of reference genes but also on sequence lengths (e.g. N50 scaffold length), allowing quality control in multiple aspects. Using gVolante, one can compare the quality of original assemblies between their multiple versions (obtained through program choice and parameter tweaking, for example) and evaluate them in comparison to the scores of public resources found in the database section. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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14. Antidepressant-Like Effects of 3-(3,4-dihydroxyphenyl)lactic Acid Isolated from Lavender (Lavandula angustifolia) Flowers in Mice.
- Author
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Toshio UENO, Yoko MATSUI, Hideki MASUDA, Osamu NISHIMURA, Makoto TOGAWA, Katsuya SAKUMA, and Hidehiko YOKOGOSHI
- Abstract
In the present study, we clarified the antidepressant-like constituents in an aqueous extract of lavender (Lavandula angustifolia) flowers. The antidepressant-like effects of the lavender extract (LE) and four fractions from the extract (Fr. 1-4) were evaluated using the forced swimming test (FST) in mice. Oral administration of the LE or Frs. 1, 3, and 4 significantly reduced immobility in the FST, whereas Fr. 2 had no significant effects. High-performance liquid chromatography using an authentic standard clearly showed that Fr. 3 contained a large amount of the known antidepressant-like substance rosmarinic acid (RA). Moreover, 3-(3,4-dihydroxyphenyl)lactic acid (DLA) was identified in Fr.1 as a new constituent for L. angustifoli. Oral administration of DLA (150 and 300mg/kg) and of RA (37.5 mg/kg) significantly reduced immobility time in the FST. These results suggest that RA and DLA may participate in the antidepressant-like effects of the LE in mice. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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15. Lead removal efficiency using biosorbents as alternative materials for permeable reactive barriers.
- Author
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Soto-Rios, Paula Cecilia, Kazunori Nakano, Megumu Fujibayashi, Leon-Romero, Marco, and Osamu Nishimura
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LEAD removal (Water purification) ,PERMEABLE reactive barriers ,UNDARIA pinnatifida ,PHRAGMITES australis ,ADSORPTION capacity ,LANGMUIR isotherms - Abstract
As alternative materials for heavy metal removal, this study investigated biosorbents to determine their suitability for permeable reactive barriers. The lead removal efficiencies of brown seaweed (Undaria pinnatifida) and reed (Phragmites australis) were determined under different conditions (batch and column system). The experimental results for these biomaterials fitted the Langmuir isotherm with high correlation values. It was verified that the influence of temperature on affinity was higher than that on adsorption capacity. While the lead removal efficiency of U. pinnatifida was higher than of P. australis in the batch experiments, lead removal efficiency decreased for both materials at approximately the same time in the column experiments. This indicates that the dominance of the chemical and physical adsorption mechanisms could result in differences in these systems. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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16. Availability of Detection Frequency Method Using Three-Port Gas Chromatography-Olfactometry for Rapid Comparison of Whole Milk Powders.
- Author
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Noriaki KOBAYASHI and Osamu NISHIMURA
- Abstract
The purpose of this study was to investigate the common components and characteristic compounds of whole milk powders (WMPs) produced in three different regions of Asia and Oceania. The volatile components were isolated from seven WMPs produced in Japan, New Zealand, and China. Forty-one aroma-active compounds were detected in these volatile components using gas chromatography-olfactometry by the detection frequency method. The binary data converted from the detection frequency values was applied to the principal component analysis (PCA) and hierarchical cluster analysis (HCA). The HCA result showed three clusters corresponding to the production regions. Based on the PCA, approximately 70% of the total variance of WMPs was explained by the PCI and PC2 scores. The PCI scores can be used to examine the property of WMPs based on the aroma of dairy products and the PC2 scores indicated the property of the production region based on the scattering plot of each WMP. Based on the PC2 loading values of aroma-active compounds, it was revealed that, depending on the production region, the difference between the whole aromas of different WMPs was caused not by the characteristic compound, but by the balance of aroma impact compounds that commonly occur in WMPs. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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17. Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals.
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Masahiro Uesaka, Osamu Nishimura, Yasuhiro Go, Kinichi Nakashima, Kiyokazu Agata, and Takuya Imamura
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GENETIC regulation ,NON-coding RNA ,MESSENGER RNA ,GENOMES ,GENE expression ,CHIMPANZEES - Abstract
Background The majority of non-coding RNAs (ncRNAs) involved in mRNA metabolism in mammals have been believed to downregulate the corresponding mRNA expression level in a pre- or post-transcriptional manner by forming short or long ncRNA-mRNA duplex structures. Information on non-duplex-forming long ncRNAs is now also rapidly accumulating. To examine the directional properties of transcription at the whole-genome level, we performed directional RNA-seq analysis of mouse and chimpanzee tissue samples. Results We found that there is only about 1% of the genome where both the top and bottom strands are utilized for transcription, suggesting that RNA-RNA duplexes are not abundantly formed. Focusing on transcription start sites (TSSs) of protein-coding genes revealed that a significant fraction of them contain switching-points that separate antisense- and sense-biased transcription, suggesting that head-to-head transcription is more prevalent than previously thought. More than 90% of head-to-head type promoters contain CpG islands. Moreover, CCG and CGG repeats are significantly enriched in the upstream regions and downstream regions, respectively, of TSSs located in head-to-head type promoters. Genes with tissuespecific promoter-associated ncRNAs (pancRNAs) show a positive correlation between the expression of their pancRNA and mRNA, which is in accord with the proposed role of pancRNA in facultative gene activation, whereas genes with constitutive expression generally lack pancRNAs. Conclusions We propose that single-stranded ncRNA resulting from head-to-head transcription at GC-rich sequences regulates tissue-specific gene expression. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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18. Utilization of Food Sources Before and After the Tsunami in Nuttallia olivacea at Gamo Lagoon, Japan.
- Author
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Woo-Seok Shin and Osamu Nishimura
- Subjects
FATTY acids ,INVERTEBRATES ,DINOFLAGELLATES ,ORGANIC compounds ,TSUNAMIS -- Environmental aspects - Abstract
This study was conducted June 2011 at Gamo Lagoon, after tsunami of March 2011, to estimate food sources and utilization. The results show that the tsunami affected the sediment properties by changing the physical environmental alterations. The fatty acids of the gut content of Nuttallia olivacea mostly comprised the same organic matter found in the sediment. Fatty acids in the tissues showed mainly diatoms, bacteria, and dinoflagellates. That is, most of the food sources (i.e., diatoms, bacteria, dinoflagellates, macroalgae, and terrestrial organic matter) probably pass through the digestive system unharmed; however, terrestrial organic matter, which is refractory to biochemical degradation, indicated a different assimilation trend between the gut content and the tissue. This result suggests that input of labile organic matter from the sediment may control selective metabolism in N. olivacea. From these results, although the physical environment of sediment characteristics by tsunami changed, the food utilization of N. olivacea suggested a better assimilation of selected components from the gut content, irrespective of physical alteration. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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19. Effects of Carvacrol and Volatile Fraction of Winter Savory (Satureja montana L.) on Body Temperature in Humans Who Experience Cold Sensitivity.
- Author
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Hideki MASUDA, Noriyuki MORI, Yoko MATSUI, Keiko TSUKIYAMA, Osamu NISHIMURA, Shunsuke TAKEUCHI, Yuko TERADA, Tatsuo WATANABE, and Tomonori NADAMOTO
- Abstract
Ingestion of winter savory extract has been reported to inhibit the decrease in peripheral body temperature in people who experience cold sensitivity. However, the active ingredients underlying this effect are not known. We sought to elucidate the effects of the volatile components of winter savory on body temperature. Carvacrol (the main volatile component and a transient receptor potential channel ankyrin 1 (TRPA1) agonist in winter savory) increased core body temperature, but did not inhibit the decrease in peripheral body temperature after ingestion. In addition, the volatile fraction of winter savory (which contained various components in addition to carvacrol) induced not only an increase in core body temperature, but also inhibited the decrease in peripheral body temperature. These results suggest that the volatile components in winter savory may be effective for alleviating cold sensitivity, and that carvacrol is one of the active ingredients in winter savory. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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20. aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
- Author
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Shigehiro Kuraku, Zmasek, Christian M., Osamu Nishimura, and Kazutaka Katoh
- Published
- 2013
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21. Key Aroma Compounds in Roasted In-shell Peanuts.
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Shu KANEKO, Ririka SAKAI, Kenji KUMAZAWA, Manabu USUKI, and Osamu NISHIMURA
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FOOD aroma ,PEANUT genetics ,PEANUT varieties ,FURANONES ,METHOXY compounds ,PYRAZINE derivatives - Abstract
The authors focus on aroma compounds present in roasted in-shell peanuts. They inform that an aroma extract dilution analysis of the aroma concentrates in peanuts has revealed a total of 43 key aroma compounds including 2-isobutyl-3-methoxypyrazine, 4-hydroxy-2,5-dimethyl-3(2H)-furanone and 3,5-dimethyl-2-ethylpyrazine. They mention that sensory experiments have revealed that fresh peanuts have roasty, popcorn-like and nutty notes.
- Published
- 2013
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22. Genome Features of "Dark-Fly", a Drosophila Line Reared Long-Term in a Dark Environment.
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Minako Izutsu, Jun Zhou, Yuzo Sugiyama, Osamu Nishimura, Tomoyuki Aizu, Atsushi Toyoda, Asao Fujiyama, Kiyokazu Agata, and Naoyuki Fuse
- Subjects
DROSOPHILA melanogaster ,GENOMES ,SINGLE nucleotide polymorphisms ,MORPHOLOGY ,AMINO acid sequence ,GENETIC mutation - Abstract
Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed ''Dark-fly'', which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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23. Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC3 profiling in snake.
- Author
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Kazumi Matsubara, Shigehiro Kuraku, Hiroshi Tarui, Osamu Nishimura, Chizuko Nishida, Kiyokazu Agata, Yoshinori Kumazawa, and Yoichi Matsuda
- Subjects
ANTISENSE DNA ,TURTLES ,FLUORESCENCE microscopy ,CHROMOSOME abnormalities ,IN situ hybridization - Abstract
Background: Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm lizards and snakes). Karyotypes of these sauropsidan groups generally consist of macrochromosomes and microchromosomes. In chicken, microchromosomes exhibit a higher GC-content than macrochromosomes. To examine the pattern of intra-genomic GC heterogeneity in lepidosaurian genomes, we constructed a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 183 cDNA clones by fluorescence in situ hybridization, and examined the correlation between the GC-content of exonic third codon positions (GC
3 ) of the genes and the size of chromosomes on which the genes were localized. Results: Although GC3 distribution of snake genes was relatively homogeneous compared with those of the other amniotes, microchromosomal genes showed significantly higher GC3 than macrochromosomal genes as in chicken. Our snake cytogenetic map also identified several conserved segments between the snake macrochromosomes and the chicken microchromosomes. Cross-species comparisons revealed that GC3 of most snake orthologs in such macrochromosomal segments were GC-poor (GC3 < 50%) whereas those of chicken orthologs in microchromosomes were relatively GC-rich (GC3 ≥ 50%). Conclusion: Our results suggest that the chromosome size-dependent GC heterogeneity had already occurred before the lepidosaur-archosaur split, 275 million years ago. This character was probably present in the common ancestor of lepidosaurs and but lost in the lineage leading to Anolis during the diversification of lepidosaurs. We also identified several genes whose GC-content might have been influenced by the size of the chromosomes on which they were harbored over the course of sauropsid evolution. [ABSTRACT FROM AUTHOR]- Published
- 2012
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24. A method for N-terminal de novosequencing of Nα-blocked proteins by mass spectrometry.
- Author
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Chihiro Nakajima, Hiroki Kuyama, Takashi Nakazawa, Osamu Nishimura, and Susumu Tsunasawa
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MASS spectrometry ,PROTEIN analysis ,PEPTIDES ,ACETYLATION ,PHOSPHORYLASES ,OREXINS ,CALMODULIN ,DERIVATIZATION - Abstract
A method for de novosequencing of Nα-blocked proteins by mass spectrometry (MS) is presented. The approach consists of enzymatic digestion of Nα-blocked protein, recovery of N-terminal peptide by depletion of non-N-terminal peptides from the digest pool, and selective derivatization of a C-terminal α-carboxyl group of isolated N-terminal peptide. The C-terminal α-carboxyl group of the N-terminal peptide was selectively derivatized with 3-aminopropyl-tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-propylamine), according to oxazolone chemistry. The reagent TMPP-propylamine was designed to facilitate sequence analysis with MALDI-MS by mass- and charge-tagging. All of the identities and N-terminal sequences of two Nα-acetylated proteins (rabbit phosphorylase b and bovine calmodulin) and human orexin A, which has pyroglutamic acid at the N-terminus, were successfully analyzed by allowing for the y-type ions almost exclusively. [ABSTRACT FROM AUTHOR]
- Published
- 2010
25. Characterization of the mod 3 cohomology of $E_7$.
- Author
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Akira Kono, James P. Lin, and Osamu Nishimura
- Subjects
OPERATIONS (Algebraic topology) ,HOMOTOPY theory ,LIE groups - Abstract
It is shown that the mod 3 cohomology of a homotopy associative mod 3 $H$-space which is rationally equivalent to the Lie group $E_7$ and which has integral 3-torsion is isomorphic to that of $E_7$ as a Hopf algebra over the mod 3 Steenrod algebra. [ABSTRACT FROM AUTHOR]
- Published
- 2003
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26. CHARACTERIZATION OF THE MOD 3 COHOMOLOGY OF THE COMPACT, CONNECTED, SIMPLE, EXCEPTIONAL LIE GROUPS OF RANK 6.
- Author
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AKIRA KONO and OSAMU NISHIMURA
- Subjects
HOMOLOGICAL algebra ,HOMOTOPY theory ,LIE algebras ,HOMOTOPY groups ,HOMOTOPY equivalences ,GROUP theory ,LINEAR algebra - Abstract
It is shown that the mod $3$ cohomology of a $1$-connected, homotopy associative mod $3$ $H$-space that is rationally equivalent to the Lie group $E_6$ is isomorphic to that of $E_6$ as an algebra. Moreover, it is shown that the mod $3$ cohomology of a nilpotent, homotopy-associative mod $3$ $H$-space that is rationally equivalent to $E_6$, and whose fundamental group localized at $3$ is non-trivial, is isomorphic to that of the Lie group $\Ad E_6$ as a Hopf algebra over the mod $3$ Steenrod algebra. It is also shown that the mod $3$ cohomology of the universal cover of such an $H$-space is isomorphic to that of $E_6$ as a Hopf algebra over the mod $3$ Steenrod algebra. [ABSTRACT FROM AUTHOR]
- Published
- 2003
- Full Text
- View/download PDF
27. A congenital anterior diaphragmatic hernia with massive pericardial effusion requiring neither emergency pericardiocentesis nor operation. A case report and review of the literature.
- Author
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Ikeda1, Kazushige, Isamu Hokuto, Keisuke Tokieda, Osamu Nishimura, Hitoshi Ishimoto, and Yasuhide Morikawa
- Published
- 2002
28. Spectral and Timing Analysis of the Accretion-powered Pulsar 4U 1626–67 Observed with Suzaku and NuSTAR.
- Author
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Wataru B. Iwakiri, Katja Pottschmidt, Sebastian Falkner, Paul B. Hemphill, Felix Fürst, Osamu Nishimura, Fritz-Walter Schwarm, Michael T. Wolff, Diana M. Marcu-Cheatham, Deepto Chakrabarty, John A. Tomsick, Colleen A. Wilson-Hodge, Matthias Bissinger Kühnel, Yukikatsu Terada, Teruaki Enoto, and Jörn Wilms
- Subjects
ACCRETION (Astrophysics) ,PULSARS ,RAY tracing ,MAGNETIC fields ,RADIATION ,CYCLOTRONS ,TELESCOPES - Abstract
We present an analysis of the spectral shape and pulse profile of the accretion-powered pulsar 4U 1626−67 observed with Suzaku and Nuclear Spectroscopic Telescope Array (NuSTAR) during a spin-up state. The pulsar, which experienced a torque reversal to spin-up in 2008, has a spin period of ∼7.7 s. Comparing the phase-averaged spectra obtained with Suzaku in 2010 and with NuSTAR in 2015, we find that the spectral shape changed between the two observations: the 3–10 keV flux increased by ∼5%, while the 30–60 keV flux decreased significantly by ∼35%. Phase-averaged and phase-resolved spectral analysis shows that the continuum spectrum observed by NuSTAR is well described by an empirical negative and positive power law times exponential continuum with an added broad Gaussian emission component around the spectral peak at ∼20 keV. Taken together with the observed value obtained from the Fermi/gamma-ray burst monitor data, we conclude that the spectral change between the Suzaku and NuSTAR observations was likely caused by an increase in the accretion rate. We also report the possible detection of asymmetry in the profile of the fundamental cyclotron line. Furthermore, we present a study of the energy-resolved pulse profiles using a new relativistic ray tracing code, where we perform a simultaneous fit to the pulse profiles assuming a two-column geometry with a mixed pencil- and fan-beam emission pattern. The resulting pulse profile decompositions enable us to obtain geometrical parameters of accretion columns (inclination, azimuthal and polar angles) and a fiducial set of beam patterns. This information is important to validate the theoretical predictions from radiation transfer in a strong magnetic field. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
29. PROPERTIES OF CYCLOTRON LINES IN A LINE-FORMING REGION INJECTED BY AN ANISOTROPIC CONTINUUM IN ACCRETING X-RAY PULSARS.
- Author
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Osamu Nishimura
- Subjects
STELLAR atmospheres ,CYCLOTRON radiation ,ANISOTROPY ,X-ray astronomy ,PULSARS ,MAGNETIC fields ,NEUTRON stars ,GEOMETRY - Abstract
I examine the characteristics of profiles of cyclotron lines formed by the superposition of a number of lines formed at a number of altitudes in line-forming regions illuminated by anisotropic injections in an accretion column, which formed around the polar cap of Roche-lobe-type accretion-powered X-ray pulsars. In the present paper, I consider the line-forming region near the walls of a cylindrical geometry illuminated from the inside of the cylinder. I also examine how the direction of the peak of a beam pattern affects the profiles of cyclotron lines. I found that the width and depth of the line in a phase-averaged spectrum provide information concerning the direction of a beam. I demonstrate that the cyclotron line has a pure absorption in the phase-averaged spectrum regardless of the height of the cylinder, which is expected to change with luminosity. On the other hand, in phase-resolved spectra, an emission-like feature can be formed in the phase with lower intensity in a short cylinder, which is expected at erg s
−1 , while a pure absorption feature tends to appear in all phases due to the superposition of a large number of lines in a tall cylinder, which is expected at erg s−1 . [ABSTRACT FROM AUTHOR]- Published
- 2015
- Full Text
- View/download PDF
30. The role of rapid mixing condition on picophytoplankton floc growth.
- Author
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Tugrul Selami Aktas, Megumu Fujibayashi, Fumihiko Takeda, Chikako Maruo, and Osamu Nishimura
- Subjects
PHYTOPLANKTON ,COAGULATION ,COAGULANTS ,POLYALUMINUM chloride ,TURBIDITY - Abstract
This work aims to evaluate the effect of different velocity gradient and rapid mixing time on floc properties of picophytoplankton, using polyaluminum chloride (PACl) and polysilicatoiron (PSI) as coagulant. The growth, breakage, and re-growth of flocs were followed by a particle size analyzer in order to investigate the underlying mechanisms. Three different zones were found to be depending on G value in coagulation process. At low G value (G< 200 s
-1 ), the aggregation dominated over breakup. At mean Gvalues (G= 250 s-1 for Synechococcus sp.-PSI flocs and G= 546 s-1 for kaolin-PSI flocs; G= 200 s-1 for Synechococcus sp.- PACl flocs and G= 390 s-1 for kaolin-PACl flocs) flocs formation wAS maximized, producing the largest flocs. For large G values (G> 250 s-1 for Synechococcus sp.-PSI flocs and G> 546 s-1 for kaolin-PSI flocs; G>200 Synechococcus sp.-PACl flocs and G> 390 s-1 for kaolin-PACl flocs), breakup dominated over floc formation. Broken flocs did not fully re-grow after breakage; however, the re-growth rate of Synechococcus sp. flocs was larger than that of kaolin flocs, probably as a result of the surface properties of Synechococcus sp. The rapid mixing time of 60 and 90 s led to maximum floc formation Synechococcus sp. and kaolin systems, respectively. [ABSTRACT FROM AUTHOR]- Published
- 2014
- Full Text
- View/download PDF
31. Influence of velocity gradient and rapid mixing time on flocs formed by polysilica iron (PSI) and polyaluminum chloride (PACl).
- Author
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Tugrul Selami Aktas, Megumu Fujibayashi, Chikako Maruo, Munehiro Nomura, and Osamu Nishimura
- Subjects
SILICA ,ALUMINUM chloride ,SUPEROXIDES - Abstract
The aim of this investigation was to evaluate the effect of different velocity gradient and rapid mixing time on coagulation and floc properties, using polysilica iron (PSI) and polyaluminum chloride (PACl) with different rapid mixing speeds and times. The growth, breakage, and re-growth of flocs were monitored by a particle-size analyzer during the rapid mixing, in order to determine the underlying mechanisms. For PSI and PACl, three different zones were found to depending on the G value in the coagulation process. At low G values (G<546s
-1 for PSI flocs and G<390 s-1 for PACl flocs), the aggregation dominated over breakup. At mean G values (G = 546 s-1 for PSI flocs and G = 390s-1 for PACl flocs), floc formation was maximized with the largest flocs produced at the lowest residual turbidity. For large G values (G>546s-1 for PSI flocs and G > 390 s-1 for PACl flocs), breakup dominated over floc formation. Broken flocs did not fully re-grow after breakage, probably as a result of a change in the floc surface properties arising from the rupture of bonds within the hydroxide precipitate. A rapid mixing time of 60 s led to maximum floc formation. In addition, PSI flocs were more durable to high than PACl. [ABSTRACT FROM AUTHOR]- Published
- 2013
- Full Text
- View/download PDF
32. Comparison of four kinds of coagulants for the removal of picophytoplankton.
- Author
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Aktas, Tugrul Selami, Fumihiko Takeda, Chikako Maruo, Megumu Fujibayashi, and Osamu Nishimura
- Subjects
COAGULATION (Water purification) ,ALUM removal (Water treatment plant residuals) ,DRINKING water purification ,FERRIC chloride ,ZETA potential - Abstract
The purpose of this study was to investigate the efficiency of the coagulation process for the removal of picophytoplankton from drinking water and, in addition, to investigate the performance of simple coagulants such as alum and ferric chloride, and polymer coagulants such as PAC and PSI, in picophytoplankton removal. Two simple coagulants such as alum (Al
2 (SO4 )3 ·16H2 O) and ferric chloride (FeCl3 ·6H2 O) and two polymer coagulants such as poly-silicate iron (PSI) and poly-aluminum chloride (PAC) were used in both raw water including picophytoplankton and synthetic water samples prepared by Synechococcus sp. Analyses included a picophytoplankton count, an assessment of the turbidity, dissolved organic carbon, UV254 , and zeta potential and the settling time measurements. The removal efficiency of picophytoplankton during the coagulation-flocculation-sedimentation process was determined using simple and polymer coagulants. Water samples with lower coagulation pH had better picophytoplankton removal in coagulation-flocculation-sedimentation. The results indicate that even low coagulant doses of PSI in both raw water and artificial water performs better than the other three types of coagulants in terms of picophytoplankton, turbidity, UV254 , and DOC removal. [ABSTRACT FROM AUTHOR]- Published
- 2013
- Full Text
- View/download PDF
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