Biology subjects

Shibata, T.

Publications and source records attributed to Shibata, T..

4 recordsLinked to original sources

bioRxiv2018

Monkey Features Location Identification Using Convolutional Neural Networks

Understanding animal behavior in its natural habitat is a challenging task. One of the primary step for analyzing animal behavior is feature detection. In this study, we propose the use of deep convolutional neural network (CNN) to locate monkey features from raw RGB images of monkey in its natural environment. We train the model to identify features such as the nose and shoulders of the monkey at about 0.01 model loss.

animal behavior and cognition↗

bioRxiv2018

Synthetic mammalian pattern formation driven by differential diffusivity of Nodal and Lefty

Pattern formation is fundamental for embryonic development. Although synthetic biologists have created several patterns, a synthetic mammalian reaction-diffusion pattern has yet to be realized. TGF-{beta} family proteins Nodal and Lefty have been proposed to meet the conditions for reaction-diffusion patterning: Nodal is a short-range activator that enhances the expression of Nodal and Lefty whereas Lefty acts as a long-range inhibitor against Nodal. However, the pattern forming possibility of the Nodal-Lefty signaling has never been directly tested, and the underlying mechanisms of differential diffusivity of Nodal and Lefty remain unclear. Here, through a combination of synthetic biology and theoretical modeling, we show that a reconstituted minimal network of the Nodal-Lefty signaling spontaneously gives rise to a pattern in mammalian cell culture. Surprisingly, extracellular Nodal was confined underneath the cells as small clusters, resulting in a narrow distribution range compared with Lefty. We further found that the finger 1 domain of the Nodal protein is responsible for its short-range distribution. By transplanting the finger 1 domain of Nodal into Lefty, we converted the originally long-range distribution of Lefty to a short-range one, successfully preventing the pattern formation. These results indicate that the differences in the localization and domain structures between Nodal and Lefty, combined with the activator-inhibitor topology, are sufficient for reaction-diffusion pattern formation in mammalian cells.

synthetic biology↗

bioRxiv2018

Three-dimensional cell geometry controls excitable membrane signaling in Dictyotelium cells

Phosphatidylinositol (3,4,5)-trisphosphate (PtdInsP3) is known to propagate as waves on the plasma membrane and is related to the membrane protrusive activities in Dictyostelium and mammalian cells. While there have been a few attempts to study the three-dimensional dynamics of these processes, most studies have focused on the dynamics extracted from single focal planes. However, the relation between the dynamics and three-dimensional cell shape remains elusive, due to the lack of signaling information about the unobserved part of the membrane. Here we show that PtdInsP3 wave dynamics are directly regulated by the three-dimensional geometry - size and shape - of the plasma membrane. By introducing an analysis method that extracts the three-dimensional spatiotemporal activities on the entire cell membrane, we show that PtdInsP3 waves self-regulate their dynamics within the confined membrane area. This leads to changes in speed, orientation and pattern evolution, following the underlying excitability of the signal transduction system. Our findings emphasize the role of the plasma membrane topology in reaction-diffusion driven biological systems and indicate its importance in other mammalian systems.

biophysics↗

bioRxiv2017

Genome-wide stability of the DNA replication program in single mammalian cells

Here, we report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.

genomics↗