|Koji Noshita||Last modified date：2021.06.12|
Assistant Professor / Department of Biology / Faculty of Sciences
|Koji Noshita||Last modified date：2021.06.12|
|1.||Shiryu Kirie, Hideo Iwasaki, Koji Noshita, Hiroyoshi Iwata, A theoretical morphological model for quantitative description of the three-dimensional floral morphology in water lily (Nymphaea), PLOS ONE, 10.1371/journal.pone.0239781, 15, 10, e0239781-e0239781, 2020.10.|
|2.||Guo, W., Fukano, Y., Noshita, K., Ninomiya, S. , Field‐based individual plant phenotyping of herbaceous species by unmanned aerial vehicle, Ecology and Evolution, 10.1002/ece3.6861, 10, 12318-12326, 2020.10.|
|3.||Lisa Sakamoto, Hiromi Kajiya-Kanegae, Koji Noshita, Hideki Takanashi, Masaaki Kobayashi, Toru Kudo, Kentaro Yano, Tsuyoshi Tokunaga, Nobuhiro Tsutsumi, Hiroyoshi Iwata, Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology, PloS one, 10.1371/journal.pone.0224695, 14, 11, 2019.11, Seed shape is an important agronomic trait with continuous variation among genotypes. Therefore, the quantitative evaluation of this variation is highly important. Among geometric morphometrics methods, elliptic Fourier analysis and semi-landmark analysis are often used for the quantification of biological shape variations. Elliptic Fourier analysis is an approximation method to treat contours as a waveform. Semi-landmark analysis is a method of superimposed points in which the differences of multiple contour positions are minimized. However, no detailed comparison of these methods has been undertaken. Moreover, these shape descriptors vary when the scale and direction of the contour and the starting point of the contour trace change. Thus, these methods should be compared with respect to the standardization of the scale and direction of the contour and the starting point of the contour trace. In the present study, we evaluated seed shape variations in a sorghum (Sorghum bicolor Moench) germplasm collection to analyze the association between shape variations and genome-wide single-nucleotide polymorphisms by genomic prediction (GP) and genome-wide association studies (GWAS). In our analysis, we used all possible combinations of three shape description methods and eight standardization procedures for the scale and direction of the contour as well as the starting point of the contour trace; these combinations were compared in terms of GP accuracy and the GWAS results. We compared the shape description methods (elliptic Fourier descriptors and the coordinates of superposed pseudo-landmark points) and found that principal component analysis of their quantitative descriptors yielded similar results. Different scaling and direction standardization procedures caused differences in the principal component scores, average shape, and the results of GP and GWAS..|
|4.||Mitsuo Uchida, Koji Noshita, Hiroshi Koyama, Application of deep learning for the occupational health of VDT workers, Sangyo eiseigaku zasshi = Journal of occupational health, 10.1539/sangyoeisei.2018-040-C, 61, 6, 256-260, 2019.11.|
|5.||Daniel Reynolds, Frederic Baret, Claude Welcker, Aaron Bostrom, Joshua Ball, Francesco Cellini, Argelia Lorence, Aakash Chawade, Mehdi Khafif, Koji Noshita, Mark Mueller-Linow, Ji Zhou, François Tardieu, What is cost-efficient phenotyping? Optimizing costs for different scenarios, Plant Science, 10.1016/j.plantsci.2018.06.015, 282, 14-22, 2019.05, Progress in remote sensing and robotic technologies decreases the hardware costs of phenotyping. Here, we first review cost-effective imaging devices and environmental sensors, and present a trade-off between investment and manpower costs. We then discuss the structure of costs in various real-world scenarios. Hand-held low-cost sensors are suitable for quick and infrequent plant diagnostic measurements. In experiments for genetic or agronomic analyses, (i) major costs arise from plant handling and manpower; (ii) the total costs per plant/microplot are similar in robotized platform or field experiments with drones, hand-held or robotized ground vehicles; (iii) the cost of vehicles carrying sensors represents only 5–26% of the total costs. These conclusions depend on the context, in particular for labor cost, the quantitative demand of phenotyping and the number of days available for phenotypic measurements due to climatic constraints. Data analysis represents 10–20% of total cost if pipelines have already been developed. A trade-off exists between the initial high cost of pipeline development and labor cost of manual operations. Overall, depending on the context and objsectives, “cost-effective” phenotyping may involve either low investment (“affordable phenotyping”), or initial high investments in sensors, vehicles and pipelines that result in higher quality and lower operational costs..|
|6.||Yuya Fukano, Wei Guo, Koji Noshita, Shoko Hashida, Shotaka Kamikawa, Genotype-aggregated planting improves yield in Jerusalem artichoke (Helianthus tuberosus) due to self/non-self-discrimination, Evolutionary Applications, 10.1111/eva.12735, 12, 3, 508-518, 2019.03, Accumulating evidence indicates that plants are capable of self/non-self and kin/stranger discrimination. Plants increase biomass of and resource allocation to roots when they encounter roots of conspecific non-self-neighbors, but not when they encounter self roots. Root proliferation usually occurs at the expense of reproductive investment. Therefore, if clonal crops are capable of self/non-self-discrimination, spatially aggregated planting with seedlings of the same genotype may decrease root proliferation and produce a higher yield than planting without considering seedling genotype. To test this idea, we grew Helianthus tuberosus (Jerusalem artichoke) in pot and field conditions and examined self/non-self-discrimination and the effectiveness of genotype-aggregated planting. Plants grown in self pairs allocated less to root biomass than plants grown in non-self pairs in both pot and field conditions; in field conditions, the self pairs produced 40% more tubers by weight than the non-self pairs. When six sprouts from seed tuber of two different genotypes were grown together, with the two genotypes planted aggregately (AGG) or alternately (ALT), plants in the AGG group produced 14% more tubers than plants in the ALT group. These results suggest that spatial aggregation of genotypes increases tuber production in H. tuberosus. Because we found no evidence for trade-offs between root biomass and tuber production, suppression of root proliferation may not be the only mechanism behind the benefits of genotype aggregation. By applying the concept of self/non-self-discrimination, farmers can increase crop production without additional external inputs or expansion of agricultural land use..|
|7.||Mitsuo Uchida, Koji Noshita, Yasuhiro Tsutsui, Hiroshi Koyama, Application of a deep learning for occupational health and safety recognition
a pilot study in a logistics industry, Sangyo eiseigaku zasshi = Journal of occupational health, 10.1539/sangyoeisei.2018-022-C, 60, 6, 191-195, 2018.12.
|8.||Yue Mu, Yuichiro Fujii, Daisuke Takata, Bangyou Zheng, Koji Noshita, Kiyoshi Honda, Seishi Ninomiya, Wei Guo, Characterization of peach tree crown by using high-resolution images from an unmanned aerial vehicle, Horticulture Research, 10.1038/s41438-018-0097-z, 5, 1, 2018.12, In orchards, measuring crown characteristics is essential for monitoring the dynamics of tree growth and optimizing farm management. However, it lacks a rapid and reliable method of extracting the features of trees with an irregular crown shape such as trained peach trees. Here, we propose an efficient method of segmenting the individual trees and measuring the crown width and crown projection area (CPA) of peach trees with time-series information, based on gathered images. The images of peach trees were collected by unmanned aerial vehicles in an orchard in Okayama, Japan, and then the digital surface model was generated by using a Structure from Motion (SfM) and Multi-View Stereo (MVS) based software. After individual trees were identified through the use of an adaptive threshold and marker-controlled watershed segmentation in the digital surface model, the crown widths and CPA were calculated, and the accuracy was evaluated against manual delineation and field measurement, respectively. Taking manual delineation of 12 trees as reference, the root-mean-square errors of the proposed method were 0.08 m (R
= 0.99) and 0.15 m (R
= 0.93) for the two orthogonal crown widths, and 3.87 m
for CPA (R
= 0.89), while those taking field measurement of 44 trees as reference were 0.47 m (R
= 0.91), 0.51 m (R
= 0.74), and 4.96 m
= 0.88). The change of growth rate of CPA showed that the peach trees grew faster from May to July than from July to September, with a wide variation in relative growth rates among trees. Not only can this method save labour by replacing field measurement, but also it can allow farmers to monitor the growth of orchard trees dynamically..
|9.||Keisuke Shimizu, Katsunori Kimoto, Koji Noshita, Masahide Wakita, Tetsuichi Fujiki, Takenori Sasaki, Phylogeography of the pelagic snail Limacina helicina (Gastropoda
Thecosomata) in the subarctic western North Pacific, Journal of Molluscan Studies, 10.1093/mollus/eyx040, 84, 1, 30-37, 2018.02, The genetic diversity of one of the most abundant species in the Arctic and subarctic oceans, the pelagic snail Limacina helicina, has not yet been characterized in the north Pacific. This species has different â €? forma' (L. helicina forma helicina, acuta, pacifica and ochotensis), but whether or not the morphological differences between these forma are caused by phenotypic plasticity or genetic differentiation remains unclear. Here, we analysed partial nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I gene in L. helicina from the subarctic western North Pacific Ocean (SWNP; L. helicina f. acuta) and compared them with those from Svalbard (L. helicina f. helicina) and other localities (Beaufort Sea, eastern Pacific, northern Sea of Japan and western Atlantic). The results show clear genetic differentiation between populations in the SWNP and Svalbard (? ▪ CT = 0.59282, P < 0.001). These genetic differences are consistent with the previous description of the two forma L. h. f. acuta (SWNP) and L. h. f. helicina (Svalbard) based on shell morphology..
|10.||Wei Guo, Bangyou Zheng, Andries B. Potgieter, Julien Diot, Kakeru Watanabe, Koji Noshita, David R. Jordan, Xuemin Wang, James Watson, Seishi Ninomiya, Scott C. Chapman, Aerial imagery analysis – Quantifying appearance and number of sorghum heads for applications in breeding and agronomy, Frontiers in Plant Science, 10.3389/fpls.2018.01544, 871, 2018.01, Sorghum (Sorghum bicolor L. Moench) is a C4 tropical grass that plays an essential role in providing nutrition to humans and livestock, particularly in marginal rainfall environments. The timing of head development and the number of heads per unit area are key adaptation traits to consider in agronomy and breeding but are time consuming and labor intensive to measure. We propose a two-step machine-based image processing method to detect and count the number of heads from high-resolution images captured by unmanned aerial vehicles (UAVs) in a breeding trial. To demonstrate the performance of the proposed method, 52 images were manually labeled; the precision and recall of head detection were 0.87 and 0.98, respectively, and the coefficient of determination (R
) between the manual and new methods of counting was 0.84. To verify the utility of the method in breeding programs, a geolocation-based plot segmentation method was applied to pre-processed ortho-mosaic images to extract >1000 plots from original RGB images. Forty of these plots were randomly selected and labeled manually; the precision and recall of detection were 0.82 and 0.98, respectively, and the coefficient of determination between manual and algorithm counting was 0.56, with the major source of error being related to the morphology of plants resulting in heads being displayed both within and outside the plot in which the plants were sown, i.e., being allocated to a neighboring plot. Finally, the potential applications in yield estimation from UAV-based imagery from agronomy experiments and scouting of production fields are also discussed..
|11.||Katsuhito Fujiu, Munehiko Shibata, Yukiteru Nakayama, Fusa Ogata, Sahohime Matsumoto, Koji Noshita, Shingo Iwami, Susumu Nakae, Issei Komuro, Ryozo Nagai, Ichiro Manabe, A heart-brain-kidney network controls adaptation to cardiac stress through tissue macrophage activation, Nature medicine, 10.1038/nm.4326, 23, 5, 611-622, 2017.05, Heart failure is a complex clinical syndrome characterized by insufficient cardiac function. In addition to abnormalities intrinsic to the heart, dysfunction of other organs and dysregulation of systemic factors greatly affect the development and consequences of heart failure. Here we show that the heart and kidneys function cooperatively in generating an adaptive response to cardiac pressure overload. In mice subjected to pressure overload in the heart, sympathetic nerve activation led to activation of renal collecting-duct (CD) epithelial cells. Cell-cell interactions among activated CD cells, tissue macrophages and endothelial cells within the kidney led to secretion of the cytokine CSF2, which in turn stimulated cardiac-resident Ly6C lo macrophages, which are essential for the myocardial adaptive response to pressure overload. The renal response to cardiac pressure overload was disrupted by renal sympathetic denervation, adrenergic β2-receptor blockade or CD-cell-specific deficiency of the transcription factor KLF5. Moreover, we identified amphiregulin as an essential cardioprotective mediator produced by cardiac Ly6C lo macrophages. Our results demonstrate a dynamic interplay between the heart, brain and kidneys that is necessary for adaptation to cardiac stress, and they highlight the homeostatic functions of tissue macrophages and the sympathetic nervous system..|
|12.||Koji Noshita, Keisuke Shimizu, Takenori Sasaki, Geometric analysis and estimation of the growth rate gradient on gastropod shells, Journal of Theoretical Biology, 10.1016/j.jtbi.2015.10.011, 389, 11-19, 2016.01, The morphology of gastropod shells provides a record of the growth rate at the aperture of the shell, and molecular biological studies have shown that the growth rate gradient along the aperture of a gastropod shell can be closely related to gene expression at the aperture. Here, we develop a novel method for deriving microscopic growth rates from the macroscopic shapes of gastropod shells. The growth vector map of a shell provides information on the growth rate gradient as a vector field along the aperture, over the growth history. However, it is difficult to estimate the growth vector map directly from the macroscopic shape of a specimen, because the degree of freedom of the growth vector map is very high. In order to overcome this difficulty, we develop a method of estimating the growth vector map based on a growing tube model, where the latter includes fewer parameters to be estimated. In addition, we calculate an aperture map specifying the magnitude of the growth vector at each location, which can be compared with the expression levels of several genes or proteins that are important in morphogenesis. Finally, we show a concrete example of how macroscopic shell shapes evolve in a morphospace when microscopic growth rate gradient changes..|
|13.||Koji Noshita, Quantification and geometric analysis of coiling patterns in gastropod shells based on 3D and 2D image data, Journal of Theoretical Biology, 10.1016/j.jtbi.2014.08.010, 363, 93-104, 2014.12, The morphology of gastropod shells has been a focus of analyses in ecology and evolution. It has recently emerged as an important issue in developmental biology, thanks to recent advancements in molecular biological techniques. The growing tube model is a theoretical morphological model for describing various coiling patterns of molluscan shells, and it is a useful theoretical tool to relate local tissue growth with global shell morphology. However, the growing tube model has rarely been adopted in empirical research owing to the difficulty in estimating the parameters of the model from morphological data. In this article, I solve this problem by developing methods of parameter estimation when (1) 3D Computed Tomography (CT) data are available and (2) only 2D image data (such as photographs) are available. When 3D CT data are available, the parameters can be estimated by fitting an analytical solution of the growing tube model to the data. When only 2D image data are available, we first fit Raup's model to the 2D image data and then convert the parameters of Raup's model to those of the growing tube model. To illustrate the use of these methods, I apply them to data generated by a computer simulation of the model. Both methods work well, except when shells grow without coiling. I also demonstrate the effectiveness of the methods by applying the model to actual 3D CT data and 2D image data of land snails. I conclude that the method proposed in this article can reconstruct the coiling pattern from observed data..|
|14.||Koji Noshita, Takahiro Asami, Takao Ubukata, Functional constraints on coiling geometry and aperture inclination in gastropods, Paleobiology, 10.1666/10060.1, 38, 2, 322-334, 2012.03, We studied the morphological diversity of gastropod shell forms from the viewpoint of theoretical morphology, emphasizing the relationships of shell form to postural stability and the available space for soft body, which we assessed in terms of the moment of force and soft-tissue ratio calculations, respectively. The results of computer simulations suggest a functional trade-off between postural stability and available space for soft body: a compact shell possessing a low spire and small umbilicus exhibits high postural stability, whereas a less overlapped shell form with a high spire and large umbilicus makes available space for soft body. A functional morphospace analysis using theoretical models reveals that outward and downward inclination of the aperture moderates the functional trade-off between these parameter values and permits compatibility between stable posture and efficient shell construction. The hypothetical optimum that realizes this compatibility is consistent with the observed range of forms estimated from 359 extant gastropod species. The biometric results also suggest that land snails are more highly constrained than marine species in achieving a balance between postural stability and available space for soft body..|
|15.||Koji Noshita, Spiral Shell Form
A computer software package for theoretical morphological analysis of spiral shell form, Geoscience Reports of the Shizuoka University, 37, 57-73, 2010.07, The Spiral Shell Form was developed as an original computer software package designed for theoretical morphological analysis of gastropod shell forms using the Raup's model. It is composed of the following three programs. Spiral Shell Measure is a software for capturing coordinate data of the points of interest on computer image files of a specimen. Raup's Parameter Calculator is a Mathematica program for calculation of Raup's parameters from coordinate data that were collected using the Spiral Shell Measure. Spiral Shell Properties is a Mathematica program for computing physical properties of a theoretical model such as shell volume, area of the aperture, center of gravity, soft-body ratio and length of trajectory of centroid of aperture..