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  1. Article ; Online: Chromatin dynamics and subnuclear gene positioning for transcriptional regulation.

    Sakamoto, Takuya / Matsunaga, Sachihiro

    Current opinion in plant biology

    2023  Volume 75, Page(s) 102431

    Abstract: Plants have been found to exhibit diverse characteristics and functions of chromatin organization, showing both similarities and differences to animals. It is becoming clear how chromatin organization is linked to transcriptional regulation in response ... ...

    Abstract Plants have been found to exhibit diverse characteristics and functions of chromatin organization, showing both similarities and differences to animals. It is becoming clear how chromatin organization is linked to transcriptional regulation in response to environmental stresses. Regulation of specific chromatin positions in the nuclear space is important for transcription, and the mechanisms that enable such chromatin dynamics are gradually being unveiled. Genes move between subdomains responsible for transcriptional activation or suppression in the subnuclear space in a gene repositioning cycle. We propose a model of localized chromatin interaction in nuclear subdomains, in which the dynamics of local chromatin interactions have a more important impact on the regulation of gene expression than large-scale chromatin organization. In this mini-review, we highlight recent findings on chromatin dynamics, particularly involving transcriptional regulation, and discuss future directions in the study of chromatin organization in plants.
    MeSH term(s) Animals ; Chromatin/genetics ; Gene Expression Regulation
    Chemical Substances Chromatin
    Language English
    Publishing date 2023-08-08
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1418472-2
    ISSN 1879-0356 ; 1369-5266
    ISSN (online) 1879-0356
    ISSN 1369-5266
    DOI 10.1016/j.pbi.2023.102431
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  2. Book ; Online: Stepped-frequency DORT Imaging with Singular Value Decomposition for a Single-antenna Ultrawideband Radar in Multi-path Environments

    Sakamoto, Takuya

    2021  

    Abstract: Ultrawideband radar is an attractive technology for a variety of applications including security systems. As such, it is essential to develop low-cost systems that produce clear target images. Electromagnetic inverse scattering with time-reversal imaging ...

    Abstract Ultrawideband radar is an attractive technology for a variety of applications including security systems. As such, it is essential to develop low-cost systems that produce clear target images. Electromagnetic inverse scattering with time-reversal imaging has been studied for a variety of applications. The time-reversal method, however, uses large-scale antenna arrays, making the system potentially more costly. In this study, we propose an ultrawideband radar imaging algorithm, namely the stepped-frequency DORT algorithm, that uses multi-path scattering for a single antenna. The proposed imaging method is an extension of the conventional DORT method, and uses a frequency-frequency matrix that is suitable for a system with a single antenna. The performance of the proposed method is verified through numerical simulations.

    Comment: 7 pages, 10 figures
    Keywords Electrical Engineering and Systems Science - Signal Processing
    Subject code 518
    Publishing date 2021-10-13
    Publishing country us
    Document type Book ; Online
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  3. Article ; Online: Chromatin dynamics and subnuclear gene positioning for transcriptional regulation

    Sakamoto, Takuya / Matsunaga, Sachihiro

    Current Opinion in Plant Biology. 2023 Oct., v. 75 p.102431-

    2023  

    Abstract: Plants have been found to exhibit diverse characteristics and functions of chromatin organization, showing both similarities and differences to animals. It is becoming clear how chromatin organization is linked to transcriptional regulation in response ... ...

    Abstract Plants have been found to exhibit diverse characteristics and functions of chromatin organization, showing both similarities and differences to animals. It is becoming clear how chromatin organization is linked to transcriptional regulation in response to environmental stresses. Regulation of specific chromatin positions in the nuclear space is important for transcription, and the mechanisms that enable such chromatin dynamics are gradually being unveiled. Genes move between subdomains responsible for transcriptional activation or suppression in the subnuclear space in a gene repositioning cycle. We propose a model of localized chromatin interaction in nuclear subdomains, in which the dynamics of local chromatin interactions have a more important impact on the regulation of gene expression than large-scale chromatin organization. In this mini-review, we highlight recent findings on chromatin dynamics, particularly involving transcriptional regulation, and discuss future directions in the study of chromatin organization in plants.
    Keywords chromatin ; genes ; models ; plant biology ; transcription (genetics) ; transcriptional activation ; Chromatin organization ; Centromeres ; Lamina ; Gene positioning ; Super-enhancer
    Language English
    Dates of publication 2023-10
    Publishing place Elsevier Ltd
    Document type Article ; Online
    ZDB-ID 1418472-2
    ISSN 1879-0356 ; 1369-5266
    ISSN (online) 1879-0356
    ISSN 1369-5266
    DOI 10.1016/j.pbi.2023.102431
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  4. Book ; Online: Signal Separation Using a Mathematical Model of Physiological Signals for the Measurement of Heart Pulse Wave Propagation With Array Radar

    Sakamoto, Takuya

    2020  

    Abstract: The arterial pulse wave, which propagates along the artery, is an important indicator of various cardiovascular diseases. By measuring the displacement at multiple parts of the human body, pulse wave velocity can be estimated from the pulse transit time. ...

    Abstract The arterial pulse wave, which propagates along the artery, is an important indicator of various cardiovascular diseases. By measuring the displacement at multiple parts of the human body, pulse wave velocity can be estimated from the pulse transit time. This paper proposes a technique for signal separation using an antenna array, so that pulse wave propagation can be measured in a non-contact manner. The body displacements due to the pulse wave at different body parts are highly correlated, and cannot be accurately separated using techniques that assume independent or uncorrelated signals. The proposed method formulates the signal separation as an optimization problem, based on a mathematical model of the arterial pulse wave. The objective function in the optimization comprises four terms that are derived based on a small-displacement approximation, unimodal impulse response approximation, and a causality condition. The optimization process was implemented using a genetic algorithm. The effectiveness of the proposed method is demonstrated through numerical simulations and experiments.

    Comment: This paper has been published in IEEE Access (Early Access), 12 pages, 17 figures
    Keywords Electrical Engineering and Systems Science - Signal Processing
    Subject code 530
    Publishing date 2020-08-20
    Publishing country us
    Document type Book ; Online
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  5. Book ; Online: Ultra-Wideband Radar and Wireless Human Sensing

    Sakamoto, Takuya

    2020  

    Abstract: This study presents the progress of our recent research regarding wireless measurements of the human body. First, we explain radar imaging algorithms for screening passengers at security checkpoints that can process data faster than existing algorithms ... ...

    Abstract This study presents the progress of our recent research regarding wireless measurements of the human body. First, we explain radar imaging algorithms for screening passengers at security checkpoints that can process data faster than existing algorithms to generate accurate and high-resolution images of human bodies. Second, we introduce signal processing techniques for accurately measuring radar micro-Doppler signals associated with human motions and activities. Finally, we present radar signal processing algorithms for measuring human respiration, heartbeat, and other types of motion. Such algorithms can be applied in various fields including healthcare, security, biometric identification, and man-machine interfaces. These fields have one thing in common: prior knowledge about the human shape, motion, and physiology are effectively exploited to improve performance by optimizing the radar systems and signal processing algorithms.

    Comment: 9 pages and 13 figures
    Keywords Electrical Engineering and Systems Science - Signal Processing
    Subject code 006
    Publishing date 2020-12-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Book ; Online: Personal Identification Using Ultrawideband Radar Measurement of Walking and Sitting Motions and a Convolutional Neural Network

    Sakamoto, Takuya

    2020  

    Abstract: This study proposes a personal identification technique that applies machine learning with a two-layered convolutional neural network to spectrogram images obtained from radar echoes of a target person in motion. The walking and sitting motions of six ... ...

    Abstract This study proposes a personal identification technique that applies machine learning with a two-layered convolutional neural network to spectrogram images obtained from radar echoes of a target person in motion. The walking and sitting motions of six participants were measured using an ultrawideband radar system. Time-frequency analysis was applied to the radar signal to generate spectrogram images containing the micro-Doppler components associated with limb movements. A convolutional neural network was trained using the spectrogram images with personal labels to achieve radar-based personal identification. The personal identification accuracies were evaluated experimentally to demonstrate the effectiveness of the proposed technique.

    Comment: 9 pages, 7 figures, and 3 tables
    Keywords Electrical Engineering and Systems Science - Signal Processing
    Publishing date 2020-08-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Novel whole-mount FISH analysis for intact root of Arabidopsis thaliana with spatial reference to 3D visualization.

    Kikuchi, Suzuka / Sakamoto, Takuya / Matsunaga, Sachihiro / Iwamoto, Akitoshi

    Journal of plant research

    2023  Volume 136, Issue 3, Page(s) 423–428

    Abstract: Whole-mount fluorescent in situ hybridization (WM-FISH) is an effective tool to observe chromosome behavior in tissues or organs. However, it is difficult to obtain a precise spatial profile of fluorescent signals in roots using conventional WM-FISH ... ...

    Abstract Whole-mount fluorescent in situ hybridization (WM-FISH) is an effective tool to observe chromosome behavior in tissues or organs. However, it is difficult to obtain a precise spatial profile of fluorescent signals in roots using conventional WM-FISH mainly because of the severe damage caused during the processing. To address this problem, we established a novel WM-FISH analysis for intact roots of Arabidopsis thaliana and successfully obtained a precise spatial profile of nuclear size and centromere signals. The two main improvements in the novel WM-FISH analysis are: (i) hybridization was performed directly on MAS-coated glass slides covered with silicon wells and (ii) conditions for enzyme treatment were optimized (37 °C, 45 s). After the WM-FISH using a centromere probe, we analyzed the results by 3D data processing to quantify the nuclear volume and number of centromere signals of the obtained cortical cell files and determined the position of each nucleus in intact roots. Then we plotted the nuclear volume and number of centromere signals versus distance from the quiescent center to evaluate the precise spatial profile of each parameter.
    MeSH term(s) Arabidopsis/genetics ; In Situ Hybridization, Fluorescence/methods ; Imaging, Three-Dimensional/methods ; Cell Nucleus/genetics
    Language English
    Publishing date 2023-01-31
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 2077362-6
    ISSN 1618-0860 ; 0918-9440
    ISSN (online) 1618-0860
    ISSN 0918-9440
    DOI 10.1007/s10265-023-01438-8
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  8. Article ; Online: Nuclear pore complex proteins are involved in centromere distribution.

    Ito, Nanami / Sakamoto, Takuya / Oko, Yuka / Sato, Hikaru / Hanamata, Shigeru / Sakamoto, Yuki / Matsunaga, Sachihiro

    iScience

    2024  Volume 27, Issue 2, Page(s) 108855

    Abstract: The subnuclear distribution of centromeres is cooperatively regulated by condensin II and the linker of nucleoskeleton and cytoskeleton (LINC) complex. However, other nuclear membrane structures and nuclear proteins are probably involved in centromere ... ...

    Abstract The subnuclear distribution of centromeres is cooperatively regulated by condensin II and the linker of nucleoskeleton and cytoskeleton (LINC) complex. However, other nuclear membrane structures and nuclear proteins are probably involved in centromere dynamics and distribution. Here, we focused on the nuclear pore complex (NPC), which is known to regulate gene expression, transcription memory, and chromatin structure in addition to transport between the cytoplasm and nucleoplasm. We report here that some nucleoporins (Nups), including Nup85, Nup133, CG1, Nup93b, and NUA, are involved in centromere scattering in
    Language English
    Publishing date 2024-01-11
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2024.108855
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  9. Article: Antecedents and Outcomes of Work Engagement among Psychiatric Nurses in Japan.

    Kato, Yuichi / Chiba, Rie / Shimazu, Akihito / Hayashi, Yuta / Sakamoto, Takuya

    Healthcare (Basel, Switzerland)

    2023  Volume 11, Issue 3

    Abstract: While previous studies have examined antecedents and outcomes of work engagement among general nurses, studies among psychiatric nurses remain limited. This study aimed to explore the antecedents (i.e., job crafting and nursing practice environment) and ... ...

    Abstract While previous studies have examined antecedents and outcomes of work engagement among general nurses, studies among psychiatric nurses remain limited. This study aimed to explore the antecedents (i.e., job crafting and nursing practice environment) and outcomes (i.e., strength-oriented care attitudes, mental health, and turnover intention) of work engagement among psychiatric nurses in Japan. This cross-sectional study included 309 nurses from three psychiatric hospitals in Japan (valid response rate: 60.4%). Data collection using the self-administered questionnaire took place from July to August 2021. We performed Structural Equation Modeling to examine the directional relationships among variables. Job crafting (β = 0.57,
    Language English
    Publishing date 2023-01-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2721009-1
    ISSN 2227-9032
    ISSN 2227-9032
    DOI 10.3390/healthcare11030295
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  10. Article ; Online: Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry.

    Berendzen, Kenneth W / Grefen, Christopher / Sakamoto, Takuya / Slane, Daniel

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2698, Page(s) 57–73

    Abstract: The past two decades in biomedical research have experienced an explosion of cell type-specific and single-cell studies, especially concerning the concomitant dissection of regulatory and transcriptional landscapes of those under investigation. ... ...

    Abstract The past two decades in biomedical research have experienced an explosion of cell type-specific and single-cell studies, especially concerning the concomitant dissection of regulatory and transcriptional landscapes of those under investigation. Additionally, leveraging next-generation sequencing (NGS) platforms efforts have been undertaken to evaluate the effects of chromatin accessibility, histone modifications, or even transcription factor binding sites. We have shown that Fluorescence-Activated Nuclear Sorting (FANS) is an effective means to characterize the transcriptomes of nuclei from different tissues. In light of our own technical and experimental developments, we extend this effort to combine FACS/FANS with Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) for profiling individual cell types according to their chromatin and transcriptional states.
    MeSH term(s) Chromatin/genetics ; Histone Code ; Flow Cytometry ; Protein Processing, Post-Translational ; Cell Nucleus
    Chemical Substances Chromatin
    Language English
    Publishing date 2023-09-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3354-0_5
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