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Article ; Online: Selective Genome Packaging Mechanisms of Influenza A Viruses.

Noda, Takeshi

Cold Spring Harbor perspectives in medicine

2021 Volume 11, Issue 7

Abstract: The genome of influenza A virus (IAV) comprises eight segmented, single-stranded, negative-sense RNAs. The genome packaging mechanism of IAV was a long-standing enigma, but it is now widely accepted that IAV packages one copy of each of the eight viral ... ...

Abstract	The genome of influenza A virus (IAV) comprises eight segmented, single-stranded, negative-sense RNAs. The genome packaging mechanism of IAV was a long-standing enigma, but it is now widely accepted that IAV packages one copy of each of the eight viral RNA (vRNA) segments in a selective manner. Accumulating evidence over the last decade suggests that the eight unique vRNAs are selected via intersegment interactions mediated by their segment-specific genome packaging signals; however, the characteristics of these RNA-based interactions largely remain unknown. This review summarizes our current knowledge of IAV selective genome packaging and the possible mechanisms underlying the selection of the eight unique vRNAs.
MeSH term(s)	Genome, Viral ; Influenza A virus/genetics ; RNA, Viral/genetics ; Virus Assembly
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	2157-1422
ISSN (online)	2157-1422
DOI	10.1101/cshperspect.a038497
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Foreword- A Decade of Cross-Boundary Cooperation: UICC-ARO and the University of Tokyo.

Noda, Tetsuo

Japanese journal of clinical oncology

2021 Volume 51, Issue 12 Suppl 2, Page(s) i1

MeSH term(s)	Humans ; International Cooperation ; Neoplasms ; Tokyo
Language	English
Publishing date	2021-05-18
Publishing country	England
Document type	Journal Article
ZDB-ID	190978-2
ISSN	1465-3621 ; 0368-2811
ISSN (online)	1465-3621
ISSN	0368-2811
DOI	10.1093/jjco/hyab016
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Zs.A 1298: Show issues

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Article ; Online: Stochastic resonance in sparse neuronal network: functional role of ongoing activity to detect weak sensory input in awake auditory cortex of rat.

Noda, Takahiro / Takahashi, Hirokazu

Cerebral cortex (New York, N.Y. : 1991)

2023 Volume 34, Issue 1

Abstract: The awake cortex is characterized by a higher level of ongoing spontaneous activity, but it has a better detectability of weak sensory inputs than the anesthetized cortex. However, the computational mechanism underlying this paradoxical nature of awake ... ...

Abstract	The awake cortex is characterized by a higher level of ongoing spontaneous activity, but it has a better detectability of weak sensory inputs than the anesthetized cortex. However, the computational mechanism underlying this paradoxical nature of awake neuronal activity remains to be elucidated. Here, we propose a hypothetical stochastic resonance, which improves the signal-to-noise ratio (SNR) of weak sensory inputs through nonlinear relations between ongoing spontaneous activities and sensory-evoked activities. Prestimulus and tone-evoked activities were investigated via in vivo extracellular recording with a dense microelectrode array covering the entire auditory cortex in rats in both awake and anesthetized states. We found that tone-evoked activities increased supralinearly with the prestimulus activity level in the awake state and that the SNR of weak stimulus representation was optimized at an intermediate level of prestimulus ongoing activity. Furthermore, the temporally intermittent firing pattern, but not the trial-by-trial reliability or the fluctuation of local field potential, was identified as a relevant factor for SNR improvement. Since ongoing activity differs among neurons, hypothetical stochastic resonance or "sparse network stochastic resonance" might offer beneficial SNR improvement at the single-neuron level, which is compatible with the sparse representation in the sensory cortex.
MeSH term(s)	Rats ; Animals ; Auditory Cortex/physiology ; Wakefulness/physiology ; Reproducibility of Results ; Neurons/physiology ; Vibration
Language	English
Publishing date	2023-11-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1077450-6
ISSN	1460-2199 ; 1047-3211
ISSN (online)	1460-2199
ISSN	1047-3211
DOI	10.1093/cercor/bhad428
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Article ; Online: Filovirus helical nucleocapsid structures.

Hu, Shangfan / Noda, Takeshi

Microscopy (Oxford, England)

2022 Volume 72, Issue 3, Page(s) 178–190

Abstract: Filoviruses are filamentous enveloped viruses belonging to the family Filoviridae, in the order Mononegavirales. Some filovirus members, such as Ebola virus and Marburg virus, cause severe hemorrhagic fever in humans and non-human primates. The filovirus ...

Abstract	Filoviruses are filamentous enveloped viruses belonging to the family Filoviridae, in the order Mononegavirales. Some filovirus members, such as Ebola virus and Marburg virus, cause severe hemorrhagic fever in humans and non-human primates. The filovirus ribonucleoprotein complex, called the nucleocapsid, forms a double-layered helical structure in which a non-segmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (NP), viral protein 35 (VP35), VP24, VP30 and RNA-dependent RNA polymerase (L). The inner layer consists of the helical NP-RNA complex, acting as a scaffold for the binding of VP35 and VP24 that constitute the outer layer. Recent structural studies using cryo-electron microscopy have advanced our understanding of the molecular mechanism of filovirus nucleocapsid formation. Here, we review the key characteristics of the Ebola virus and Marburg virus nucleocapsid structures, highlighting the similarities and differences between the two viruses. In particular, we focus on the structure of the helical NP-RNA complex, the RNA binding mechanism and the NP-NP interactions in the helix. The structural analyses reveal a possible mechanism of nucleocapsid assembly and provide potential targets for the anti-filovirus drug design.
MeSH term(s)	Animals ; Cryoelectron Microscopy ; Nucleocapsid/chemistry ; Nucleocapsid/metabolism ; Ebolavirus/chemistry ; Ebolavirus/metabolism ; Marburgvirus/chemistry ; Marburgvirus/metabolism ; Viral Proteins/analysis ; Viral Proteins/chemistry ; Viral Proteins/metabolism ; RNA/analysis ; RNA/metabolism
Chemical Substances	Viral Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2022-10-14
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	2707496-1
ISSN	2050-5701 ; 2050-5698
ISSN (online)	2050-5701
ISSN	2050-5698
DOI	10.1093/jmicro/dfac049
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Article ; Online: Unsaturated polyurethanes degradable by conjugate substitution reactions with amines and carboxylate anions.

Noda, Takumi / Tanaka, Anri / Akae, Yosuke / Kohsaka, Yasuhiro

RSC advances

2023 Volume 13, Issue 29, Page(s) 20336–20341

Abstract: Main-chain scission of polymers induces a significant decrease in molecular weight and accompanying changes in physical properties and is important for applications in materials engineering, such as in photoresists and adhesive dismantling. In this study, ...

Abstract	Main-chain scission of polymers induces a significant decrease in molecular weight and accompanying changes in physical properties and is important for applications in materials engineering, such as in photoresists and adhesive dismantling. In this study, we focused on methacrylates substituted with carbamate groups at the allylic positions for the purpose of developing a mechanism that efficiently cleaves the main chain in response to chemical stimuli. Dimethacrylates substituted with hydroxy groups at the allylic positions were synthesized by the Morita-Baylis-Hillman reaction of diacrylates and aldehydes. The polyaddition with diisocyanates afforded a series of poly(conjugated ester-urethane)s. These polymers underwent a conjugate substitution reaction with diethylamine or acetate anion at 25 °C, resulting in main-chain scission accompanied by decarboxylation. A side reaction by the re-attack of the liberated amine end to the methacrylate skeleton proceeded, whereas it was suppressed for the polymers with an allylic substitute of the phenyl group. Therefore, the methacrylate skeleton substituted with phenyl and carbamate groups at the allylic position is an excellent decomposition point that induces selective and quantitative main-chain scission with weak nucleophiles, such as carboxylate anions.
Language	English
Publishing date	2023-07-07
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d3ra03461e
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Article ; Online: Regulation of Autophagy through TORC1 and mTORC1.

Noda, Takeshi

Biomolecules

2017 Volume 7, Issue 3

Abstract: Autophagy is an intracellular protein-degradation process that is conserved across eukaryotes including yeast and humans. Under nutrient starvation conditions, intracellular proteins are transported to lysosomes and vacuoles via membranous structures ... ...

Abstract	Autophagy is an intracellular protein-degradation process that is conserved across eukaryotes including yeast and humans. Under nutrient starvation conditions, intracellular proteins are transported to lysosomes and vacuoles via membranous structures known as autophagosomes, and are degraded. The various steps of autophagy are regulated by the target of rapamycin complex 1 (TORC1/mTORC1). In this review, a history of this regulation and recent advances in such regulation both in yeast and mammals will be discussed. Recently, the mechanism of autophagy initiation in yeast has been deduced. The autophagy-related gene 13 (Atg13) and the unc-51 like autophagy activating kinase 1 (Ulk1) are the most crucial substrates of TORC1 in autophagy, and by its dephosphorylation, autophagosome formation is initiated. Phosphorylation/dephosphorylation of Atg13 is regulated spatially inside the cell. Another TORC1-dependent regulation lies in the expression of autophagy genes and vacuolar/lysosomal hydrolases. Several transcriptional and post-transcriptional regulations are controlled by TORC1, which affects autophagy activity in yeast and mammals.
MeSH term(s)	Animals ; Autophagy ; Autophagy-Related Protein-1 Homolog/metabolism ; Autophagy-Related Proteins/metabolism ; Gene Expression Regulation ; Humans ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Phosphorylation ; Protein Transport
Chemical Substances	Autophagy-Related Proteins ; Autophagy-Related Protein-1 Homolog (EC 2.7.11.1) ; Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1)
Language	English
Publishing date	2017-07-07
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom7030052
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Article ; Online: Interactive effects of two rodent species on the seed dispersal of Japanese walnut.

Okawa, Ryunosuke / Saitoh, Takashi / Noda, Takashi

Scientific reports

2023 Volume 13, Issue 1, Page(s) 18098

Abstract: The effects of seed dispersers on plant fitness (seed dispersal effectiveness, SDE) have been evaluated based on the number (quantity) and recruitment probability (quality) of dispersed seeds. Although seeds of most zoochorous species are dispersed by ... ...

Abstract	The effects of seed dispersers on plant fitness (seed dispersal effectiveness, SDE) have been evaluated based on the number (quantity) and recruitment probability (quality) of dispersed seeds. Although seeds of most zoochorous species are dispersed by two or more animal species, which may interact with each other, SDE has often been studied assuming a one-plant and one-animal species system. We compared the SDE of Japanese walnut (Juglans ailanthifolia) between squirrel-only and squirrel-mouse sites in natural forests of Hokkaido, Japan, and found that the SDE from the red squirrel (Sciurus vulgaris), considered a primary seed disperser, was altered by an alternative seed disperser species, the Japanese wood mouse (Apodemus speciosus). Seed removal rates at the squirrel-mouse site were significantly higher than those at the squirrel-only site, and both dispersed seeds and seedlings were less aggregated, with a strongly repulsive relationship with adult conspecific trees at the squirrel-mouse site. Seedlings established themselves at a location with fewer medium-sized trees (< 10 cm DBH) at the squirrel-mouse site. These results suggest that the interactive effect of the rodent species affects the SDE of Japanese walnut.
MeSH term(s)	Animals ; Mice ; Feeding Behavior ; Juglans ; Sciuridae ; Seed Dispersal ; Seedlings ; Seeds ; Japan ; Behavior, Animal
Language	English
Publishing date	2023-10-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-44513-9
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Article: Molecular characterization of Satsuma mandarin (

Hasan, Nazmul / Tokuhara, Naoki / Noda, Takayuki / Kotoda, Nobuhiro

Plant biotechnology (Tokyo, Japan)

2023 Volume 40, Issue 1, Page(s) 51–62

Abstract: Shortening the juvenility is a burning issue in breeding fruit trees such as Satsuma mandarin ( ...

Abstract	Shortening the juvenility is a burning issue in breeding fruit trees such as Satsuma mandarin (
Language	English
Publishing date	2023-12-27
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2210142-1
ISSN	1347-6114 ; 1342-4580
ISSN (online)	1347-6114
ISSN	1342-4580
DOI	10.5511/plantbiotechnology.23.0122a
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Article: Tartary Buckwheat Bran: A Review of Its Chemical Composition, Processing Methods and Food Uses.

Noda, Takahiro / Ishiguro, Koji / Suzuki, Tatsuro / Morishita, Toshikazu

Plants (Basel, Switzerland)

2023 Volume 12, Issue 10

Abstract: Tartary buckwheat ( ...

Abstract	Tartary buckwheat (
Language	English
Publishing date	2023-05-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants12101965
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Article ; Online: Research note changes in the number of outpatient visits in Japan during the COVID-19 pandemic.

Machida, Munehito / Nishioka, Yuichi / Noda, Tatsuya / Imamura, Tomoaki

BMC research notes

2023 Volume 16, Issue 1, Page(s) 70

Abstract: Objective: This study aimed to determine the change in the number of outpatient visits in Japan since the beginning of the COVID-19 pandemic, using data on the outpatient claims submitted by medical institutions to insurers in 2019 and 2020, from the ... ...

Abstract	Objective: This study aimed to determine the change in the number of outpatient visits in Japan since the beginning of the COVID-19 pandemic, using data on the outpatient claims submitted by medical institutions to insurers in 2019 and 2020, from the National Database of Health Insurance Claims and Specific Health Check-ups. We calculated the total number of outpatient visits, and number of visits for individual diseases according to the International Classification of Diseases-10 codes on the claim form. Results: The number of outpatient visits per million people decreased by 9.98% in 2020 compared to 2019. Of the diseases included in the analysis, 71 showed a decrease in the number of visits by ≥ 1%. There were significant decreases in the number of visits related to infectious diseases (influenza, acute bronchitis, and acute laryngitis, etc.), and chronic diseases (hemorrhoids, cystic kidney disease, dyspepsia, and chronic sinusitis, etc.). The observed decreased rate of outpatient visit might have been due to, a decrease in the incidence of disease, a decreased frequency of visit by patients with the disease, or both. Our analysis method using actual health insurance claim data can be applied worldwide, where researchers have access to national information on health insurance claims.
MeSH term(s)	Humans ; Outpatients ; Japan/epidemiology ; Pandemics ; COVID-19/epidemiology ; Insurance, Health ; Chronic Disease
Language	English
Publishing date	2023-05-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2413336-X
ISSN	1756-0500 ; 1756-0500
ISSN (online)	1756-0500
ISSN	1756-0500
DOI	10.1186/s13104-023-06336-9
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