SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena

Tohsato, Yukako; Ho, Kenneth H. L.; Kyoda, Koji; Onami, Shuichi

doi:10.1093/bioinformatics/btw417

Cited by 45 publications

(31 citation statements)

References 43 publications

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“…7 and 8). The datasets generated during the current studies are available in the System Science of Biological Dynamics (SSBD) database 60 . Source data are provided with this paper.…”

Section: Data Availabilitymentioning

confidence: 99%

Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells

et al. 2020

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The periodic cartilage and smooth muscle structures in mammalian trachea are derived from tracheal mesoderm, and tracheal malformations result in serious respiratory defects in neonates. Here we show that canonical Wnt signaling in mesoderm is critical to confer trachea mesenchymal identity in human and mouse. At the initiation of tracheal development, endoderm begins to express Nkx2.1, and then mesoderm expresses the Tbx4 gene. Loss of βcatenin in fetal mouse mesoderm causes loss of Tbx4 + tracheal mesoderm and tracheal cartilage agenesis. The mesenchymal Tbx4 expression relies on endodermal Wnt activation and Wnt ligand secretion but is independent of known Nkx2.1-mediated respiratory development, suggesting that bidirectional Wnt signaling between endoderm and mesoderm promotes trachea development. Activating Wnt, Bmp signaling in mouse embryonic stem cell (ESC)-derived lateral plate mesoderm (LPM) generates tracheal mesoderm containing chondrocytes and smooth muscle cells. For human ESC-derived LPM, SHH activation is required along with WNT to generate proper tracheal mesoderm. Together, these findings may contribute to developing applications for human tracheal tissue repair.

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“…7 and 8). The datasets generated during the current studies are available in the System Science of Biological Dynamics (SSBD) database 60 . Source data are provided with this paper.…”

Section: Data Availabilitymentioning

confidence: 99%

Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells

et al. 2020

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“…The C. elegans swimming activity time series and movie data reported in this paper have been deposited in Systems Science of Biological Dynamics (SSBD) database 1 , http://ssbd.qbic.riken.jp/set/20190401/…”

Section: Data Depositionmentioning

confidence: 99%

C. elegansepisodic swimming is driven by multifractal kinetics

Ikeda

Jurica

Kimurâ

et al. 2020

Preprint

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Fractal scaling is a common property of temporal change in various modes of animal behavior. The molecular mechanisms of fractal scaling in animal behaviors remain largely unexplored. The nematode C. elegans alternates between swimming and resting states in a liquid solution. Here, we report that C. elegans episodic swimming is characterized by scale-free kinetics with long-range temporal correlation and local temporal clusterization, which is characterized as multifractal kinetics. Residence times in actively-moving and inactive states were distributed in a power law-based scale-free manner. Multifractal analysis showed that temporal correlation and temporal clusterization were distinct between the actively-moving state and the inactive state. These results indicate that C. elegans episodic swimming is driven by transition between two behavioral states, in which each of two transition kinetics follows distinct multifractal kinetics. We found that a conserved behavioral modulator, cyclic GMP dependent kinase (PKG) may regulate the multifractal kinetics underlying an animal behavior. Our combinatorial analysis approach involving molecular genetics and kinetics provides a platform for the molecular dissection of the fractal nature of physiological and behavioral phenomena.

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“…The oocyte images will be available at the Systems Science of Biological Dynamics database (SSBD) [40]…”

Section: Additional Filesmentioning

confidence: 99%

Statistical image processing quantifies the changes in cytoplasmic texture associated with aging inCaenorhabditis elegansoocytes

Imakubo

Takayama

Okada

et al. 2020

Preprint

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BackgroundOocyte quality decreases with aging, thereby increasing errors in fertilization, chromosome segregation, and embryonic cleavage. Oocyte appearance also changes with aging, suggesting a functional relationship between oocyte quality and appearance. However, no methods are available to objectively quantify age-associated changes in oocyte appearance.ResultsWe show that statistical image processing of Nomarski differential interference contrast microscopy images can be used to quantify age-associated changes in Caenorhabditis elegans oocyte appearance. Max-min Value (mean difference between the maximum and minimum intensities within each moving window) quantitatively characterized the difference in oocyte cytoplasmic texture between 1- and 3-day-old adults (Day 1 and Day 3 oocytes, respectively). With an appropriate parameter set, the gray level co-occurrence matrix (GLCM)-based texture feature Correlation (COR) more sensitively characterized this difference than the Max-min Value. Manipulating the smoothness of and/or adding irregular structures to the cytoplasmic texture of Day 1 oocyte images reproduced the difference in Max-min Value but not in COR between Day 1 and Day 3 oocytes. Increasing the size of granules in synthetic images recapitulated the age-associated changes in COR. Manual measurements validated that the cytoplasmic granules in oocytes become larger with aging.ConclusionsThe Max-min Value and COR objectively quantify age-related changes in C. elegans oocyte in Nomarski DIC microscopy images. Our methods provide new opportunities for understanding the mechanism underlying oocyte aging.

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SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena

Cited by 45 publications

References 43 publications

Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells

Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells

C. elegansepisodic swimming is driven by multifractal kinetics

Statistical image processing quantifies the changes in cytoplasmic texture associated with aging inCaenorhabditis elegansoocytes

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