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Article ; Online: The CGA codon decoding through tRNA

Wada, Miki / Ito, Koichi

2023 Volume 290, Issue 13, Page(s) 3480–3489

Abstract: The CGA codon is a rare codon in Saccharomyces cerevisiae and is known to be inefficiently decoded by wobble pairing with Arg-tRNA(ICG). The ... ...

Abstract	The CGA codon is a rare codon in Saccharomyces cerevisiae and is known to be inefficiently decoded by wobble pairing with Arg-tRNA(ICG). The tRNA
MeSH term(s)	Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; RNA, Transfer, Arg/genetics ; RNA, Transfer, Arg/metabolism ; Codon/genetics ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Anticodon/genetics ; Anticodon/metabolism
Chemical Substances	RNA, Transfer, Arg ; Codon ; RNA, Transfer (9014-25-9) ; Anticodon
Language	English
Publishing date	2023-03-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16760
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Article ; Online: The CGA codon decoding through tRNAArg(ICG) supply governed by Tad2/Tad3 in Saccharomyces cerevisiae

Wada, Miki / Ito, Koichi

The FEBS Journal. 2023 July, v. 290, no. 13 p.3480-3489

2023

Abstract: The CGA codon is a rare codon in Saccharomyces cerevisiae and is known to be inefficiently decoded by wobble pairing with Arg‐tRNA(ICG). The tRNAᴬʳᵍ(ICG) is post‐transcriptionally edited from tRNAᴬʳᵍ(ACG) by the anticodon first adenosine deamination ... ...

Abstract	The CGA codon is a rare codon in Saccharomyces cerevisiae and is known to be inefficiently decoded by wobble pairing with Arg‐tRNA(ICG). The tRNAᴬʳᵍ(ICG) is post‐transcriptionally edited from tRNAᴬʳᵍ(ACG) by the anticodon first adenosine deamination enzyme Tad2/Tad3 complex. Experimental consecutive CGA codons cause ribosome stalling to result in the reduction of the encoding protein product. In this study, the additional supply of tRNAᴬʳᵍ(ACG) genes that produce decoding Arg‐tRNA(ICG) promoted the product level from the CGA12‐luc reporter, revealing that the product reduction is essentially due to inefficient decoding and deficiency in the tRNA supply. The mature tRNAᴬʳᵍ(ICG) and the precursor tRNAᴬʳᵍ(ACG) ratios examined for cellular tRNA fraction revealed that the tRNAᴬʳᵍ(ICG) ratio is maintained at less than 30% and is responsive to the Tad2/Tad3 expression level.
Keywords	Saccharomyces cerevisiae ; adenosine ; codons ; deamination ; enzymes ; ribosomes
Language	English
Dates of publication	2023-07
Size	p. 3480-3489.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16760
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Neural Radiance Field-Inspired Depth Map Refinement for Accurate Multi-View Stereo.

Ito, Shintaro / Miura, Kanta / Ito, Koichi / Aoki, Takafumi

Journal of imaging

2024 Volume 10, Issue 3

Abstract: In this paper, we propose a method to refine the depth maps obtained by Multi-View Stereo (MVS) through iterative optimization of the Neural Radiance Field (NeRF). MVS accurately estimates the depths on object surfaces, and NeRF accurately estimates the ... ...

Abstract	In this paper, we propose a method to refine the depth maps obtained by Multi-View Stereo (MVS) through iterative optimization of the Neural Radiance Field (NeRF). MVS accurately estimates the depths on object surfaces, and NeRF accurately estimates the depths at object boundaries. The key ideas of the proposed method are to combine MVS and NeRF to utilize the advantages of both in depth map estimation and to use NeRF for depth map refinement. We also introduce a Huber loss into the NeRF optimization to improve the accuracy of the depth map refinement, where the Huber loss reduces the estimation error in the radiance fields by placing constraints on errors larger than a threshold. Through a set of experiments using the Redwood-3dscan dataset and the DTU dataset, which are public datasets consisting of multi-view images, we demonstrate the effectiveness of the proposed method compared to conventional methods: COLMAP, NeRF, and DS-NeRF.
Language	English
Publishing date	2024-03-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2824270-1
ISSN	2313-433X ; 2313-433X
ISSN (online)	2313-433X
ISSN	2313-433X
DOI	10.3390/jimaging10030068
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Article ; Online: Human ABCE1 exhibits temperature-dependent heterologous co-functionality in S. cerevisiae.

Wada, Miki / Ito, Koichi

FEBS open bio

2022 Volume 12, Issue 10, Page(s) 1782–1787

Abstract: ABCE1 protein (Rli1 in Saccharomyces cerevisiae) is a unique ribosome recycling factor that is composed of an N-terminal FeS cluster domain and two ATPase domains. Here, we report that heterologous expression of human ABCE1 in S. cerevisiae is unable to ... ...

Abstract	ABCE1 protein (Rli1 in Saccharomyces cerevisiae) is a unique ribosome recycling factor that is composed of an N-terminal FeS cluster domain and two ATPase domains. Here, we report that heterologous expression of human ABCE1 in S. cerevisiae is unable to complement conditional knockout of ABCE1 (Rli1), at a typical experimental temperature of 30 °C. However, low but significant growth was observed at high temperature, 37 °C. Considering the close interaction of ABCE1 with translation factors and ribosomal components, the observed temperature-dependent complementation may be attributed to heterologous co-functionality of ABCE1 with S. cerevisiae factor(s), and might reflect functional upregulation of human ABCE1 at its functional temperature.
MeSH term(s)	ATP-Binding Cassette Transporters/metabolism ; Adenosine Triphosphatases/metabolism ; Humans ; Ribosomes/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Temperature
Chemical Substances	ABCE1 protein, human ; ATP-Binding Cassette Transporters ; Adenosine Triphosphatases (EC 3.6.1.-)
Language	English
Publishing date	2022-07-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2651702-4
ISSN	2211-5463 ; 2211-5463
ISSN (online)	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13463
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Article ; Online: Human movement avoidance decisions during Coronavirus disease 2019 in Japan.

Omori, Ryosuke / Ito, Koichi / Kanemitsu, Shunsuke / Kimura, Ryusuke / Iwasa, Yoh

Journal of theoretical biology

2024 Volume 585, Page(s) 111795

Abstract: Understanding host behavioral change in response to epidemics is important to forecast the disease dynamics. To predict the behavioral change relevant to the epidemic situation (e.g., the number of reported cases), we need to know the epidemic situation ... ...

Abstract	Understanding host behavioral change in response to epidemics is important to forecast the disease dynamics. To predict the behavioral change relevant to the epidemic situation (e.g., the number of reported cases), we need to know the epidemic situation at the moment of decision, which is difficult to identify from the records of actually performed human mobility. In this study, the largest travel accommodation reservation data covering half of the existed accommodations in Japan was analyzed to observe decision-making timings and how it responded to the changing epidemic situation during Japan's Coronavirus Disease 2019 until February 2023. To this end, we measured mobility avoidance index proposed in Ito et al., 2022 to indicate people's decision of mobility avoidance and quantified it using the time-series of the accommodation booking/cancellation data. We observed matches of the peak dates of the mobility avoidance and the number of reported cases, and mobility avoidance changed proportional to the logarithmic number of reported cases. We also found that the slope of mobility avoidance against the change of the logarithmic number of reported cases were similar among the epidemic waves, while the intercept of that was much reduced as the first epidemic wave passed by. People measure the intensity of epidemic by logarithm of the number of reported cases. The sensitivity of their response is established during the first wave and the people's response became weakened after the first experience, as if the number of reported cases were multiplied by a constant small factor.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; Japan/epidemiology ; Epidemics ; Forecasting
Language	English
Publishing date	2024-03-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2972-5
ISSN	1095-8541 ; 0022-5193
ISSN (online)	1095-8541
ISSN	0022-5193
DOI	10.1016/j.jtbi.2024.111795
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Article ; Online: Systematic genetic identification of functional domains on collided di‐ribosomes responsible for rescue pathways upon translation arrest in Saccharomyces cerevisiae

Ōtsuka, Hiroshi / Endo, Kei / Wada, Miki / Ito, Koichi

The FEBS Journal. 2023 Aug., v. 290, no. 15 p.3748-3763

2023

Abstract: Translation elongation becomes arrested when various obstacles arise, such as a series of inefficient rare codons or stable RNA secondary structures, thus causing ribosomal stalling along the mRNA. Certain wasteful and persistent stalling states are ... ...

Abstract	Translation elongation becomes arrested when various obstacles arise, such as a series of inefficient rare codons or stable RNA secondary structures, thus causing ribosomal stalling along the mRNA. Certain wasteful and persistent stalling states are resolved by ribosome rescue pathways. For instance, collisions between stalled and subsequent ribosomes are thought to induce ubiquitination of ribosomal S20 protein by the E3 ubiquitin ligase Hel2, which triggers subsequent rescue reactions. Although structural studies have revealed specific contact sites between collided ribosomes, the ribosomal regions crucial for the rescue reaction remain uncharacterized. In this study, we performed a systematic genetic analysis to identify the molecular regions required for ribosome rescue in Saccharomyces cerevisiae. A series of dominant negative mutations capable of abolishing the rescue reaction were isolated in ribosomal proteins S20 and Asc1. Moreover, mutations in both proteins clustered on the surface of ribosomes between the collided ribosome interfaces, aligned in such a way that they seemingly faced each other. Further analysis via the application of the split‐TRP1 protein assay revealed that the mutation of either protein distinctively affected the functional interaction between Hel2 and Asc1, suggesting the development of differential functionality at the interface between collided ribosomes. Our results provide novel and complementary insights into the detailed molecular mechanisms of ribosomal rescue pathways.
Keywords	RNA ; Saccharomyces cerevisiae ; codons ; genetic analysis ; genetic testing ; mutation ; ribosomes ; ubiquitin-protein ligase ; ubiquitination
Language	English
Dates of publication	2023-08
Size	p. 3748-3763.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16781
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Article ; Online: Pose Estimation of Ultrasound Probe Using CNN and RNN with Image Reconstruction Loss.

Miura, Kanta / Ito, Koichi / Aoki, Takafumi / Ohmiya, Jun

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

2023 Volume 2023, Page(s) 1–4

Abstract: It is necessary to estimate the pose of the probe with high accuracy to reconstruct 3D ultrasound (US) images only from US image sequences scanned by a 1D-array probe. We propose the probe pose estimation method using Convolutional Neural Network (CNN) ... ...

Abstract	It is necessary to estimate the pose of the probe with high accuracy to reconstruct 3D ultrasound (US) images only from US image sequences scanned by a 1D-array probe. We propose the probe pose estimation method using Convolutional Neural Network (CNN) with training by image reconstruction loss. To calculate the image reconstruction loss, we use the image reconstruction network which consists of an encoder that extracts features from the two US images and a decoder that reconstructs the intermediate US image between the two images. CNN is trained to minimize the image reconstruction loss between the ground-truth image and the reconstructed image. Through experiments, we demonstrate that the proposed method exhibits efficient performance compared with the conventional methods.
MeSH term(s)	Image Processing, Computer-Assisted/methods ; Neural Networks, Computer ; Imaging, Three-Dimensional ; Ultrasonography
Language	English
Publishing date	2023-12-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2694-0604
ISSN (online)	2694-0604
DOI	10.1109/EMBC40787.2023.10340326
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Article: Competition model explains trends of long-term fertilization in plant communities.

Yamauchi, Atsushi / Ito, Koichi / Shibasaki, Shota

Ecology and evolution

2023 Volume 13, Issue 2, Page(s) e9832

Abstract: Over 40 years ago, Kempton ( ...

Abstract	Over 40 years ago, Kempton (
Language	English
Publishing date	2023-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.9832
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Article ; Online: Systematic genetic identification of functional domains on collided di-ribosomes responsible for rescue pathways upon translation arrest in Saccharomyces cerevisiae.

Otsuka, Hiroshi / Endo, Kei / Wada, Miki / Ito, Koichi

The FEBS journal

2023 Volume 290, Issue 15, Page(s) 3748–3763

Abstract	Translation elongation becomes arrested when various obstacles arise, such as a series of inefficient rare codons or stable RNA secondary structures, thus causing ribosomal stalling along the mRNA. Certain wasteful and persistent stalling states are resolved by ribosome rescue pathways. For instance, collisions between stalled and subsequent ribosomes are thought to induce ubiquitination of ribosomal S20 protein by the E3 ubiquitin ligase Hel2, which triggers subsequent rescue reactions. Although structural studies have revealed specific contact sites between collided ribosomes, the ribosomal regions crucial for the rescue reaction remain uncharacterized. In this study, we performed a systematic genetic analysis to identify the molecular regions required for ribosome rescue in Saccharomyces cerevisiae. A series of dominant negative mutations capable of abolishing the rescue reaction were isolated in ribosomal proteins S20 and Asc1. Moreover, mutations in both proteins clustered on the surface of ribosomes between the collided ribosome interfaces, aligned in such a way that they seemingly faced each other. Further analysis via the application of the split-TRP1 protein assay revealed that the mutation of either protein distinctively affected the functional interaction between Hel2 and Asc1, suggesting the development of differential functionality at the interface between collided ribosomes. Our results provide novel and complementary insights into the detailed molecular mechanisms of ribosomal rescue pathways.
MeSH term(s)	Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism ; Protein Biosynthesis ; Ubiquitination ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins ; Hel2 protein, S cerevisiae (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2023-03-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16781
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Article ; Online: Continuous irregular dynamics with multiple neutral trajectories permit species coexistence in competitive communities.

Yamauchi, Atsushi / Ito, Koichi / Shibasaki, Shota / Namba, Toshiyuki

Theoretical population biology

2023 Volume 149, Page(s) 39–47

Abstract: The colonization model formulates competition among propagules for habitable sites to colonize, which serves as a mechanism enabling coexistence of multiple species. This model traditionally assumes that encounters between propagules and sites occur as ... ...

Abstract	The colonization model formulates competition among propagules for habitable sites to colonize, which serves as a mechanism enabling coexistence of multiple species. This model traditionally assumes that encounters between propagules and sites occur as mass action events, under which species distribution can eventually reach an equilibrium state with multiple species in a constant environment. To investigate the effects of encounter mode on species diversity, we analyzed community dynamics in the colonization model by varying encounter processes. The analysis indicated that equilibrium is approximately neutrally-stable under perfect ratio-dependent encounter, resulting in temporally continuous variation of species' frequencies with irregular trajectories even under a constant environment. Although the trajectories significantly depend on initial conditions, they are considered to be "strange nonchaotic attractors" (SNAs) rather than chaos from the asymptotic growth rates of displacement. In addition, trajectories with different initial conditions remain different through time, indicating that the system involves an infinite number of SNAs. This analysis presents a novel mechanism for transient dynamics under competition.
MeSH term(s)	Models, Biological ; Ecosystem
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3948-2
ISSN	1096-0325 ; 0040-5809
ISSN (online)	1096-0325
ISSN	0040-5809
DOI	10.1016/j.tpb.2022.12.003
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