2,359 research outputs found
Flow-induced Alignment of Amyloid Protofilaments Revealed by Linear Dichroism
No full textThis research was originally published in the Journal of Biological Chemistry. Rumi Adachi, Kei-ichi Yamaguchi, Hisashi Yagi, Kazumasa Sakurai, Hironobu Naiki and Yuji Goto. Flow-induced Alignment of Amyloid Protofilaments Revealed by Linear Dichroism. J. Biol. Chem. 2007; 282, 8978-8983. © the American Society for Biochemistry and Molecular Biolog
sj-docx-1-tae-10.1177_20420188221099349 – Supplemental material for Perioperative glycemic status is linked to postoperative complications in non-intensive care unit patients with type-2 diabetes: a retrospective study
No full textSupplemental material, sj-docx-1-tae-10.1177_20420188221099349 for Perioperative glycemic status is linked to postoperative complications in non-intensive care unit patients with type-2 diabetes: a retrospective study by Takeshi Oba, Mototsugu Nagao, Shunsuke Kobayashi, Yuji Yamaguchi, Tomoko Nagamine, Kyoko Tanimura-Inagaki, Izumi Fukuda and Hitoshi Sugihara in Therapeutic Advances in Endocrinology and Metabolism</p
Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis
No full textPHYTOCHROME INTERACTING FACTOR 3-LIKE5 (PIL5) is a basic helix-loop-helix transcription factor that inhibits seed germination by regulating the expression of gibberellin (GA)- and abscisic acid (ABA)-related genes either directly or indirectly. It is not yet known, however, whether PIL5 regulates seed germination solely through GA and ABA. Here, we used Chromatin immunoprecipitation-chip (ChIP-chip) analysis to identify 748 novel PIL5 binding sites in the Arabidopsis thaliana genome. Consistent with the molecular function of PIL5 as a transcription regulator, most of the identified binding sites are located in gene promoter regions. Binding site analysis shows that PIL5 binds to its target sites mainly through the G-box motif in vivo. Microarray analysis reveals that phytochromes regulate a large number of genes mainly through PIL5 during seed germination. Comparison between the ChIP-chip and microarray data indicates that PIL5 regulates 166 genes by directly binding to their promoters. Many of the identified genes encode transcription regulators involved in hormone signaling, while some encode enzymes involved in cell wall modification. Interestingly, PIL5 directly regulates many transcription regulators of hormone signaling and indirectly regulates many genes involved in hormone metabolism. Taken together, our data indicate that PIL5 inhibits seed germination not just through GA and ABA, but also by coordinating hormone signals and modulating cell wall properties in imbibed seeds
Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis
No full textAngiosperm seeds integrate various environmental signals, such as water availability and light conditions, to make a proper decision to germinate. Once the optimal conditions are sensed, gibberellin (GA) is synthesized, triggering germination. Among environmental signals, light conditions are perceived by phytochromes. However, it is not well understood how phytochromes regulate GA biosynthesis. Here we investigated whether phytochromes regulate GA biosynthesis through PIL5, a phytochrome-interacting bHLH protein, in Arabidopsis. We found that pil5 seed germination was inhibited by paclobutrazol, the ga1 mutation was epistatic to the pil5 mutation, and the inhibitory effect of PIL5 overexpression on seed germination could be rescued by exogenous GA, collectively indicating that PIL5 regulates seed germination negatively through GA. Expression analysis revealed that PIL5 repressed the expression of GA biosynthetic genes (GA3ox1 and GA3ox2), and activated the expression of a GA catabolic gene (GA2ox) in both PHYA- and PHYB-dependent germination assays. Consistent with these gene-expression patterns, the amount of bioactive GA was higher in the pil5 mutant and lower in the PIL5 overexpression line. Lastly, we showed that red and far-red light signals trigger PIL5 protein degradation through the 26S proteasome, thus releasing the inhibition of bioactive GA biosynthesis by PIL5. Taken together, our data indicate that phytochromes promote seed germination by degrading PIL5, which leads to increased GA biosynthesis and decreased GA degradation
タンパクシツフォールディングトミスフォールディングノホウカツテキリカイ
No full textMasahiro Noji, Masatomo So, Keiichi Yamaguchi, Hironobu Hojo, Maki Onda, Yoko Akazawa-Ogawa, Yoshihisa Hagihara, and Yuji Goto Biochemistry 2018 57 (37), 5415-5426Masahiro Noji, Kenji Sasahara, Keiichi Yamaguchi, Masatomo So, Kazumasa Sakurai, József Kardos, Hironobu Naiki, and Yuji Goto “Heating during agitation of β2-microglobulin reveals that supersaturation breakdown is required for amyloid fibril formation at neutral pH” Journal of Biological Chemistry (ASBMB Publications), 294 (43), 15826–15835, 2019This is the author’s version of a work that was accepted for publication in Communications Biology. The doctoral dissertation and the accepted paper are both based on the same data, but the style of the figures is different for each. Masahiro Noji, Tatsushi Samejima, Keiichi Yamaguchi, Masatomo So, Keisuke Yuzu, Eri Chatani, Yoko Akazawa-Ogawa, Yoshihisa Hagihara, Yasushi Kawata, Kensuke Ikenaka, Hideki Mochizuki, József Kardos, Daniel E. Otzen, Vittorio Bellotti, Johannes Buchner, and Yuji Goto “Breakdown of supersaturation barrier links protein folding to amyloid formation” Communications Biology (Springer Nature), 4, 120, 202
非流暢性要因としての同音誤字が文章理解に及ぼす効果
No full text文章中に含まれる一部の文字を薄い色で表示したり読みにくいフォントを使ったりすることによって，文章の内容記憶に良い影響を与える「非流暢性効果」の存在が多くの先行研究で示されている．しかしながら，従来の研究で取り扱われてきた非流暢性は，ほぼ全てが視覚的な困難に基づく非流暢性であり，それ以外の要因に基づく非流暢性の影響に関する研究は極めて少ない．本研究では，文章中に含まれる一部の文字の意味認知における非流暢性が与える影響について検証する．具体的には，正しい読みで読むことができるが誤った漢字である「同音誤字」を含めることが文章理解に与える影響について実験を行い調査した．その結果，同音誤字は文章の内容記憶にむしろ負の影響を与え，特に作業記憶容量が多い人にとってその影響が強いことが示された．Many previous studies have shown the existence of the “disfluency effect”, in which the use of a light color or a difficult-to-read font for some of the characters in a sentence has a positive effect on the memorization of the content of the sentence. However, almost all of the disfluency effects dealt with in previous studies were based on visual difficulties, and there have been very few studies on the effects of disfluency based on other factors. In this study, we examine the impact of difficulties in recognizing the meaning of certain characters in a sentence. Specifically, we conducted experiments to investigate the impact of including “homophonic Kanji errors” - A kanji that can be read with the correct pronunciation but is not correct in terms of meaning - on sentence comprehension. The results showed that homophonic Kanji errors had a negative impact on sentence comprehension, and that this impact was particularly strong for people with high working memory capacity
6.K_2ZnF_4中に孤立させたCu^<2+>イオンのEPR : 孤立Cu^<2+>のJahn-Teller効果(千葉大学大学院理学研究科物理学専攻,修士論文題目・アブストラクト(1988年度))
No full textこの論文は国立情報学研究所の電子図書館事業により電子化されました
SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5
No full textLight absorbed by seed phytochromes of Arabidopsis thaliana modulates abscisic acid (ABA) and gibberellic acid (GA) signaling pathways at least partly via PHYTOCHROME-INTERACTING FACTOR3-LIKE5 (PIL5), a phytochrome-interacting basic helix-loop-helix transcription factor. Here, we report a new mutant, somnus (som), that germinates in darkness, independently of various light regimens. SOM encodes a nucleus-localized CCCH-type zinc finger protein. The som mutant has lower levels of ABA and elevated levels of GA due to expressional changes in ABA and GA metabolic genes. Unlike PIL5, however, SOM does not regulate the expression of GA-INSENSITIVE and REPRESSOR OF GA1 (RGA/RGA1), two DELLA genes encoding GA negative signaling components. Our in vivo analysis shows that PIL5 activates the expression of SOM by binding directly to its promoter, suggesting that PIL5 regulates ABA and GA metabolic genes partly through SOM. In agreement with these results, we also observed that the reduced germination frequency of a PIL5 overexpression line is rescued by the som mutation and that this rescue is accompanied by expressional changes in ABA and GA metabolic genes. Taken together, our results indicate that SOM is a component in the phytochrome signal transduction pathway that regulates hormone metabolic genes downstream of PIL5 during seed germination
Flow-induced Alignment of Amyloid Protofilaments Revealed by Linear Dichroism
No full textThis research was originally published in the Journal of Biological Chemistry. Rumi Adachi, Kei-ichi Yamaguchi, Hisashi Yagi, Kazumasa Sakurai, Hironobu Naiki and Yuji Goto. Flow-induced Alignment of Amyloid Protofilaments Revealed by Linear Dichroism. J. Biol. Chem. 2007; 282, 8978-8983. © the American Society for Biochemistry and Molecular BiologyAmyloid fibrils underlying various serious amyloidoses including Alzheimer and prion diseases form characteristic deposits in which linear fibrils with an unbranched and rigid morphology associate laterally or radially, e.g. radial senile amyloid plaques of amyloid β. To clarify the formation of these high order amyloid deposits, studying the rheology is important. A 22-residue K3 peptide fragment of β2-microglobulin, a protein responsible for dialysis-related amyloidosis, forms long and homogeneous protofilament-like fibrils in 20% (v/v) 2,2,2-trifluoroethanol and 10 mm HCl (pH ∼2). Here, using circular dichroism and linear dichroism, we observed the flow-induced alignment of fibrils. Analysis of far- and near-UV linear dichroism spectra suggested that both the net π-π* transition moment of the backbone carbonyl group and Lb transition moment of the Tyr26 side chain are oriented in parallel to the fibril axis, revealing the structural details of amyloid protofilaments. Moreover, the intensities of flow-induced circular dichroism or linear dichroism signals depended critically on the length and type of fibrils, suggesting that they are useful for detecting and characterizing amyloid fibrils
Metal Ion-dependent Effects of Clioquinol on the Fibril Growth of an Amyloid β Peptide
No full textThis research was originally published in the Journal of Biological Chemistry. Bakthisaran Raman, Tadato Ban, Kei-ichi Yamaguchi, Miyo Sakai, Tomoji Kawai, Hironobu Naiki and Yuji Goto. Metal Ion-dependent Effects of Clioquinol on the Fibril Growth of an Amyloid β Peptide. J. Biol. Chem. 2005; 280, 16157-16162. © the American Society for Biochemistry and Molecular BiologyAlthough metal ions such as Cu2+, Zn2+, and Fe3+ are implicated to play a key role in Alzheimer disease, their role is rather complex, and comprehensive understanding is not yet obtained. We show that Cu2+ and Zn2+ but not Fe3+ renders the amyloid β peptide, Aβ1–40, nonfibrillogenic in nature. However, preformed fibrils of Aβ1–40 were stable when treated with these metal ions. Consequently, fibril growth of Aβ1–40 could be switched on/off by switching the molecule between its apo- and holo-forms. Clioquinol, a potential drug for Alzheimer disease, induced resumption of the Cu2+-suppressed but not the Zn2+-suppressed fibril growth of Aβ1–40. The observed synergistic effect of clioquinol and Zn2+ suggests that Zn2+-clioquinol complex effectively retards fibril growth. Thus, clioquinol has dual effects; although it disaggregates the metal ion-induced aggregates of Aβ1–40 through metal chelation, it further retards the fibril growth along with Zn2+. These results indicate the mechanism of metal ions in suppressing Aβ amyloid formation, as well as providing information toward the use of metal ion chelators, particularly clioquinol, as potential drugs for Alzheimer disease
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