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Biology subjects

Ishihara, A.

Publications and source records attributed to Ishihara, A..

3 recordsLinked to original sources

Length estimation of fish detected as non-occluded using a smartphone application and deep learning techniques

Uncertainty in stock assessment can be reduced if accurate and precise length composition of catch is available. Length data are usually manually collected, although this method is costly and time-consuming. Recently, some studies have estimated fish species and length from images using deep learning by installing camera systems in fishing vessels or a fish auction center. Once the deep learning model is properly trained, it does not require expensive and time-consuming manual labor. However, several previous studies have focused on monitoring fishing practices using an electronic monitoring system (EMS); therefore, it is necessary to solve many challenges, such as counting the total number of fish in the catch. In this study, we proposed a new deep learning-based method to estimate fish length using images. Species identification was not performed by the model, and images were taken manually by the measurers; however, length composition was obtained only for non-occluded fish detected by the model. A smartphone application was developed to calculate scale information (cm/pixel) from a known size fish box in fish images, and the Mask R-CNN (Region-based convolutional neural networks) model was trained using 76,161 fish to predict non-occluded fish. Two experiments were conducted to confirm whether the proposed method resulted in errors in the length composition. First, we manually measured the total length (TL) for each of the five fish categories and estimated the TL using deep learning and calculated the bias. Second, multiple fish in a fish box were photographed simultaneously, and the difference between the mean TL estimated from the non-occluded fish and the true TL from all fish was calculated. The results indicated that the biases of all five species categories were within {+/-} 3%. Moreover, the difference was within {+/-} 1.5% regardless of the number of fish in the fish box. In the proposed method, deep learning was used not to replace the measurer but to increase their measurement efficiency. The proposed method is expected to increase opportunities for the application of deep learning-based fish length estimation in areas of research that are different from the scope of conventional EMS.

ecology↗

Exploring the Complexity of Protein-Level Dosage Compensation that Fine-Tunes Stoichiometry of Multiprotein Complexes

Proper control of gene expression levels upon various perturbations is a fundamental aspect of cellular robustness. Protein-level dosage compensation is one mechanism buffering perturbations to stoichiometry of multiprotein complexes through accelerated proteolysis of unassembled subunits. Although N-terminal acetylation- and ubiquitin-mediated proteasomal degradation by the Ac/N-end rule pathway enables selective compensation of excess subunits, it is unclear how dominant this pathway contributes to stoichiometry control. Here we report that dosage compensation depends only partially on the Ac/N-end rule pathway. Our analysis of genetic interactions between 18 subunits and 10 quality control factors in budding yeast demonstrated that multiple E3 ubiquitin ligases and N-acetyltransferases are involved in dosage compensation. We find that N-acetyltransferases-mediated compensation is not simply predictable from N-terminal sequence despite their sequence specificity for N-acetylation. We also find that the compensation of Pop3 and Bet4 is due in large part to a minor N-acetyltransferase NatD. Furthermore, canonical NatD substrates histone H2A/H4 were compensated even in its absence, suggesting N-acetylation-independent compensation. Our study reveals the complexity and robustness of the stoichiometry control system.

genetics↗

Laminin heparin-binding peptides promiscuously bind growth factors and enhance diabetic wound healing

Laminin, as a key component of the basement membrane extracellular matrix (ECM), regulates tissue morphogenesis. We show that multiple laminin isoforms promiscuously bind to growth factors (GFs) with high affinity, through their heparin binding domains (HBDs) located in the a chain LG domains. Interestingly, these domains also bind to syndecan cell-surface receptors, promoting attachment of fibroblasts and endothelial cells. We next explore application of these multifunctional laminin HBDs in skin healing in the type 2 diabetic mouse. We demonstrate that covalent incorporation of laminin HBDs into fibrin matrix enables the slow-release of GFs. Incorporation of the 33043-3067 laminin HBD significantly enhances in vivo wound-healing efficacy of vascular endothelial cell growth factor (VEGF)-A165 and platelet-derived growth factor (PDGF)-BB, under conditions where the GFs alone in fibrin are inefficacious. This laminin HBD peptide may be clinically useful by improving biomaterials as both GF reservoirs and cell scaffolds, leading to effective tissue regeneration.

bioengineering↗