Publications by authors named "Takashi Akagi"

64 Publications

Editorial: Dioecy in Fruit Crops: The Gender Rise and Decline and Its Agronomic Impact.

Front Plant Sci 2021 15;12:719588. Epub 2021 Jul 15.

Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2021.719588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8320697PMC
July 2021

Increase in the intensity of an optical signal with fluorescein during proton and carbon-ion irradiation.

J Appl Clin Med Phys 2021 Jul 14;22(7):188-197. Epub 2021 Jun 14.

Hyogo Ion Beam Medical Center, Tatsuno, Japan.

Purpose: Although the imaging of luminescence emitted in water during irradiation of protons and carbon ions is a useful method for range and dose estimations, the intensity of the images is relatively low due to the low photon production of the luminescence phenomenon. Therefore, a relatively long time is required for the imaging. Since a fluorescent dye, fluorescein, may increase the intensity of the optical signal, we measured the luminescence images of water with different concentrations of fluorescein during irradiation of protons and carbon ions and compared the results with those by measurements with water.

Methods: A cooled charge-coupled device (CCD) camera was used for imaging a water phantom with different concentrations of fluorescein from 0.0063 to 0.025 mg/cm , in addition to a water phantom without fluorescein during irradiation of 150-MeV protons and 241.5-MeV/n carbon ions.

Results: For both protons and carbon ions, the intensity of the luminescence images increased as the concentration of fluorescein increased. With a fluorescein concentration of 0.025 mg/cm , the intensities increased to more than 10 times those of water for both protons and carbon ions. Although the shape of the depth profiles of luminescence images of water with fluorescein appeared similar to that of water for protons, those for carbon ions were different from those of water due to the increase in the Cherenkov light component at shallow depths by the decrease in the angular dependencies of the Cherenkov light.

Conclusion: We confirmed the increase in intensity of the luminescence of water by adding fluorescein for particle ions. With a small amount of Cherenkov light contamination in the images, such as protons, the relative distributions of the luminescence images with fluorescein were similar to that of water and will be used for range or dose determination in a short time.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/acm2.13309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292686PMC
July 2021

Possibility evaluation of the optical imaging of proton mini-beams.

Phys Med Biol 2021 06 7;66(12). Epub 2021 Jun 7.

Hyogo Ion Beam Medical Center, Japan.

Proton therapy using mini-beams is a promising method to reduce radiation damage to normal tissue. However, distribution measurements of mini-beams are difficult due to their small structures. Since optical imaging is a possible method to measure high-resolution two-dimensional dose distribution, we conducted optical imaging of an acrylic block during the irradiation of mini-beams of protons. Mini-beams were made from a proton pencil beam irradiated to 1 mm slits made of tungsten plate. During irradiation of the mini-beams to the acrylic block, we measured the luminescence of the acrylic block using a charge-coupled device camera. With the measurements, we could obtain slit beam images that have slit shapes in the shallow area while they were uniform in their Bragg peaks, which was similar to the case of simulated optical images by Monte Carlo simulations. We confirmed that high-resolution optical imaging of mini-beams is possible and provides a promising method for efficient quality assessment of mini-beams as well as research on mini-beam therapy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/ac02d7DOI Listing
June 2021

Shy Girl, a kiwifruit suppressor of feminization, restricts gynoecium development via regulation of cytokinin metabolism and signalling.

New Phytol 2021 05 28;230(4):1461-1475. Epub 2021 Feb 28.

The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.

Kiwifruit (Actinidia chinensis) is a dioecious, long-living woody perennial vine. Reduced generation time and induction of hermaphroditism can accelerate crop improvement and facilitate alternative farming for better food security in the face of climate change. Previous studies identified that CENTRORADIALIS genes CEN and CEN4 act to repress flowering, whilst the male-specific Shy Girl (SyGl) gene with homology to type-C cytokinin response regulators could repress gynoecium development in model plants. Here we use CRISPR/Cas9 to mutagenize CEN, CEN4 and SyGl in the male kiwifruit A. chinensis 'Bruce'. Biallelic mutations of CEN and CEN4 generated rapid-flowering male plants, and simultaneous targeting of CEN4 and SyGl gave rise to rapid-flowering hermaphrodites with restored gynoecial function and viable pollen, providing functional evidence for the role of SyGl in suppression of feminization. Analysis of ovary tissues identified genes that contribute to carpel development and revealed that SyGl affected both cytokinin profiles and the expression of genes involved in cytokinin metabolism and signalling. The plant lines generated by CEN4/SyGl knockout could self-pollinate and produce fast-flowering offspring. These results establish that SyGI acts as the suppressor of feminization in kiwifruit and demonstrate the potential for accelerated breeding in an outcrossing horticultural woody perennial.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.17234DOI Listing
May 2021

Measurements of temporal response of luminescence of water at lower energy than Cerenkov-light threshold during carbon-ion irradiation.

Biomed Phys Eng Express 2020 05 6;6(4):045002. Epub 2020 May 6.

Department of Radiological Sciences, Nagoya University Graduate School of Medicine, Japan.

Although the luminescence of water at lower energy than the Cerenkov-light threshold during carbon-ion irradiation was found and imaging was possible, the temporal response has not been measured, and so the difference from Cerenkov-light remains unclear. To clarify this point, we measured the temporal response of the luminescence of water at lower energy than the Cerenkov-light threshold and compared it with that of Cerenkov-light. We used silicon photomultiplier (Si-PM) modules to measure the temporal response at the Bragg peak area of a water phantom during irradiation of the carbon ion where the Cerenkov-light was not included. We also measured the temporal response at the shallow depth of the water phantom where the Cerenkov-light was included. In both areas, we measured the temporal waveforms of the light produced by the irradiation of the carbon ions in which the ripples of spills were clearly observed. We found no difference in the waveforms between the Bragg peak and the shallow depths of water. Our results do not contradict the hypothesis that the luminescence of water and Cerenkov-light are produced by the same mechanism.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/2057-1976/ab8b7eDOI Listing
May 2020

Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon.

Front Plant Sci 2020 22;11:567249. Epub 2020 Dec 22.

Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.

Sex expression in plants is often flexible and contributes to the maintenance of genetic diversity within a species. In diploid persimmons (the genus ), the sexuality is controlled by the Y chromosome-encoded small-RNA gene, , and its autosomal counterpart, . Hexaploid Oriental persimmon () evolved more flexible sex expression, where genetically male individuals carrying can produce both male and female flowers (monoecy). This is due to (semi-)inactivation of by the -SINE retrotransposon insertion on the promoter region and the resultant DNA methylations. Instead, flower sex determination in Oriental persimmon is also dependent on DNA methylation states of . Here, we focused on a cultivar, Kumemaru, which shows stable male flower production. Our results demonstrated that cv. Kumemaru carries with -SINE, which was highly methylated as well as in other monoecious cultivars; nevertheless, gene could have a basal expression level. Transcriptomic analysis between cv. Kumemaru and 14 cultivars that predominantly produce female flowers showed differentially expressed genes (DEGs) specific to cv. Kumemaru, which is mainly involved in stress responses. Co-expression gene networks focusing on the DEGs also suggested the involvement of stress signals, mainly via gibberellin (GA), salicylic acid (SA), and especially jasmonic acid (JA) signal pathways. We also identified potential regulators of this co-expression module, represented by the TCP4 transcription factor. Furthermore, we attempted to identify cv. Kumemaru-specific transcript polymorphisms potentially contributing to derepressed expression by cataloging subsequences (k-mers) in the transcriptomic reads from cv. Kumemaru and the other 14 female cultivars. Overall, although the direct genetic factor to activate remains to be solved, our results implied the involvement of stress signals in the release of silenced and the resultant continuous male production.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2020.567249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783364PMC
December 2020

Imaging of polarized components of Cerenkov light and luminescence of water during carbon-ion irradiation.

Med Phys 2021 Jan 4;48(1):427-433. Epub 2020 Dec 4.

Department of Integrated Health Science, Nagoya University Graduate School of Medicine, Nagoya, Japan.

Purpose: The luminescence image of water during the irradiation of carbon ions showed higher intensity at shallow depths than dose distribution due to the contamination of Cerenkov light from secondary electrons. Since Cerenkov light is coherent and polarized for the light produced during the irradiation of carbon ions to water, the reduction of Cerenkov light may be possible with a polarizer. In addition, there is no information on the polarization of the luminescence of water. To clarify these points, we measured the optical images of water during the irradiation of carbon ions with a polarizer by changing the directions of the transmission axis.

Methods: Imaging was conducted using a cooled charge-coupled device (CCD) camera during the irradiation of 241.5 MeV/n energy carbon ions to a water phantom with a polarizer in front of the lens by changing the transmission axis parallel and perpendicular to the carbon-ion beam.

Results: With the polarizer parallel to the carbon-ion beam, the intensity at the shallow depth was ~26% higher than that measured with the polarizer perpendicular to the beam. We found no significant intensity difference between these two images at deeper depths where the Cerenkov light was not included. The difference image of the parallel and perpendicular directions showed almost the same image as the simulated Cerenkov light distribution. Using the measured difference image, correction of the Cerenkov component was possible from the measured luminescence image of water during the irradiation of carbon ions.

Conclusion: We could measure the difference of the Cerenkov light component by changing the transmission axis of the polarizer. Also we clarified that there was no difference in the luminescence of water by changing the transmission axis of the polarizer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mp.14600DOI Listing
January 2021

Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume).

Plant J 2020 12 8;104(6):1551-1567. Epub 2020 Nov 8.

Graduate School of Agricultural Science, Kobe University, Nada-ku, Rokkodai 1-1, Kobe, 657-8501, Japan.

Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.15020DOI Listing
December 2020

Explainable Deep Learning Reproduces a 'Professional Eye' on the Diagnosis of Internal Disorders in Persimmon Fruit.

Plant Cell Physiol 2020 Dec;61(11):1967-1973

Field Science Education and Research Center, Kyoto University, Kyoto, 606-8502 Japan.

Recent rapid progress in deep neural network techniques has allowed recognition and classification of various objects, often exceeding the performance of the human eye. In plant biology and crop sciences, some deep neural network frameworks have been applied mainly for effective and rapid phenotyping. In this study, beyond simple optimizations of phenotyping, we propose an application of deep neural networks to make an image-based internal disorder diagnosis that is hard even for experts, and to visualize the reasons behind each diagnosis to provide biological interpretations. Here, we exemplified classification of calyx-end cracking in persimmon fruit by using five convolutional neural network models with various layer structures and examined potential analytical options involved in the diagnostic qualities. With 3,173 visible RGB images from the fruit apex side, the neural networks successfully made the binary classification of each degree of disorder, with up to 90% accuracy. Furthermore, feature visualizations, such as Grad-CAM and LRP, visualize the regions of the image that contribute to the diagnosis. They suggest that specific patterns of color unevenness, such as in the fruit peripheral area, can be indexes of calyx-end cracking. These results not only provided novel insights into indexes of fruit internal disorders but also proposed the potential applicability of deep neural networks in plant biology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pcaa111DOI Listing
December 2020

Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon.

DNA Res 2020 Jun;27(3)

Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.

Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/dnares/dsaa012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7406971PMC
June 2020

New algorithm using L1 regularization for measuring electron energy spectra.

Rev Sci Instrum 2020 Jul;91(7):075116

Kyushu University IGSES, Kasuga, Fukuoka 816-8580, Japan.

Retrieving the spectrum of physical radiation from experimental measurements typically involves using a mathematical algorithm to deconvolve the instrument response function from the measured signal. However, in the field of signal processing known as "Source Separation" (SS), which refers to the process of computationally retrieving the separate source components that generate an overlapping signal on the detector, the deconvolution process can become an ill-posed problem and crosstalk complicates the separation of the individual sources. To overcome this problem, we have designed a magnetic spectrometer for inline electron energy spectrum diagnosis and developed an analysis algorithm using techniques applicable to the problem of SS. An unknown polychromatic electron spectrum is calculated by sparse coding using a Gaussian basis function and an L1 regularization algorithm with a sparsity constraint. This technique is verified by using a specially designed magnetic field electron spectrometer. We use Monte Carlo simulations of the detector response to Maxwellian input energy distributions with electron temperatures of 5.0 MeV, 10.0 MeV, and 15.0 MeV to show that the calculated sparse spectrum can reproduce the input spectrum with an optimum energy bin width automatically selected by the L1 regularization. The spectra are reproduced with a high accuracy of less than 4.0% error, without an initial value. The technique is then applied to experimental measurements of intense laser accelerated electron beams from solid targets. Our analysis concept of spectral retrieval and automatic optimization of energy bin width by sparse coding could form the basis of a novel diagnostic method for spectroscopy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1063/1.5144897DOI Listing
July 2020

Antagonistic regulation of the gibberellic acid response during stem growth in rice.

Nature 2020 08 15;584(7819):109-114. Epub 2020 Jul 15.

Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.

The size of plants is largely determined by growth of the stem. Stem elongation is stimulated by gibberellic acid. Here we show that internode stem elongation in rice is regulated antagonistically by an 'accelerator' and a 'decelerator' in concert with gibberellic acid. Expression of a gene we name ACCELERATOR OF INTERNODE ELONGATION 1 (ACE1), which encodes a protein of unknown function, confers cells of the intercalary meristematic region with the competence for cell division, leading to internode elongation in the presence of gibberellic acid. By contrast, upregulation of DECELERATOR OF INTERNODE ELONGATION 1 (DEC1), which encodes a zinc-finger transcription factor, suppresses internode elongation, whereas downregulation of DEC1 allows internode elongation. We also show that the mechanism of internode elongation that is mediated by ACE1 and DEC1 is conserved in the Gramineae family. Furthermore, an analysis of genetic diversity suggests that mutations in ACE1 and DEC1 have historically contributed to the selection of shorter plants in domesticated populations of rice to increase their resistance to lodging, and of taller plants in wild species of rice for adaptation to growth in deep water. Our identification of these antagonistic regulatory factors enhances our understanding of the gibberellic acid response as an additional mechanism that regulates internode elongation and environmental fitness, beyond biosynthesis and gibberellic acid signal transduction.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-020-2501-8DOI Listing
August 2020

Prediction of dose distribution from luminescence image of water using a deep convolutional neural network for particle therapy.

Med Phys 2020 Sep 28;47(9):3882-3891. Epub 2020 Jul 28.

Hyogo Ion Beam Medical Center, Tatsuno, Japan.

Purpose: We recently obtained nearly the same depth profiles of luminescence images of water as dose for protons by subtracting the Cerenkov light component emitted by secondary electrons of prompt gamma photons. However, estimating the distribution of Cerenkov light with this correction method is time-consuming, depending on the irradiated energy of protons by Monte Carlo simulation. Therefore, we proposed a method of estimating dose distributions from the measured luminescence images of water using a deep convolutional neural network (DCNN).

Methods: In this study, we adopted the U-Net architectures as the DCNN. To prepare a large amount of image data for DCNN training, we calculated the training data pairs of two-dimensional (2D) dose distributions and luminescence images of water by Monte Carlo simulation for protons and carbon ions. After training the U-Net model for protons or carbon ions using these dose distributions and luminescence images calculated by Monte Carlo simulation, we predicted the dose distributions from the calculated and measured luminescence images of water using the trained U-Net model.

Results: All of the U-Net model's predicted images were in good agreement with the MC-calculated dose distributions and showed lower values of the root mean square percentage error (RSMPE) and higher values in the structural similarity index (SSIM) in comparison with these values for calculated or measured luminescence images.

Conclusion: We confirmed that the DCNN effectively predicts dose distributions in water from the measured as well as calculated luminescence images of water for particle therapy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mp.14372DOI Listing
September 2020

Estimation and correction of Cerenkov-light on luminescence image of water for carbon-ion therapy dosimetry.

Phys Med 2020 Jun 25;74:118-124. Epub 2020 May 25.

Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, Japan. Electronic address:

Purpose: The luminescence images of water during the irradiation of carbon-ions provide useful information such as the ranges and the widths of carbon-ion beams. However, measured luminescence images show higher intensities in shallow depths and wider lateral profiles than those of the dose distributions. These differences prevent the luminescence imaging of water from being applied to a quality assurance for carbon-ion therapy. We assumed that the differences were due to the contaminations of Cerenkov-light from the secondary electrons of carbon-ions as well as the prompt gamma photons in the measured image. In this study, we applied a correction method to a luminescence image of water during the irradiation of carbon-ion beams.

Methods: We estimated the distribution of the Cerenkov-light in water during the irradiation of carbon-ions by Monte Carlo simulation and subtracted the simulated Cerenkov-light from the depth and lateral profiles of the measured luminescence image for 241.5 MeV/u-carbon-ions.

Results: With these corrections, we successfully obtained depth and lateral profiles whose distributions are almost identical to the dose distributions of carbon-ions. The high intensities in the shallow depth areas decreased and the Bragg peak intensity increased. The beam widths of the measured images approached those of the ionization chamber.

Conclusions: These results indicate that the luminescence imaging of water with our proposed correction has potential to be used for dose distribution measurements for carbon-ion therapy dosimetry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejmp.2020.05.012DOI Listing
June 2020

Low temperature modulates natural peel degreening in lemon fruit independently of endogenous ethylene.

J Exp Bot 2020 08;71(16):4778-4796

Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.

Peel degreening is an important aspect of fruit ripening in many citrus fruit, and previous studies have shown that it can be advanced by ethylene treatment or by low-temperature storage. However, the important regulators and pathways involved in natural peel degreening remain largely unknown. To determine how natural peel degreening is regulated in lemon fruit (Citrus limon), we studied transcriptome and physiochemical changes in the flavedo in response to ethylene treatment and low temperatures. Treatment with ethylene induced rapid peel degreening, which was strongly inhibited by the ethylene antagonist, 1-methylcyclopropene (1-MCP). Compared with 25 ºC, moderately low storage temperatures of 5-20 °C also triggered peel degreening. Surprisingly, repeated 1-MCP treatments failed to inhibit the peel degreening induced by low temperature. Transcriptome analysis revealed that low temperature and ethylene independently regulated genes associated with chlorophyll degradation, carotenoid metabolism, photosystem proteins, phytohormone biosynthesis and signalling, and transcription factors. Peel degreening of fruit on trees occurred in association with drops in ambient temperature, and it coincided with the differential expression of low temperature-regulated genes. In contrast, genes that were uniquely regulated by ethylene showed no significant expression changes during on-tree peel degreening. Based on these findings, we hypothesize that low temperature plays a prominent role in regulating natural peel degreening independently of ethylene in citrus fruit.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jxb/eraa206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410192PMC
August 2020

Dose image prediction for range and width verifications from carbon ion-induced secondary electron bremsstrahlung x-rays using deep learning workflow.

Med Phys 2020 Aug 25;47(8):3520-3532. Epub 2020 May 25.

Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan.

Purpose: Imaging of the secondary electron bremsstrahlung (SEB) x rays emitted during particle-ion irradiation is a promising method for beam range estimation. However, the SEB x-ray images are not directly correlated to the dose images. In addition, limited spatial resolution of the x-ray camera and low-count situation may impede correctly estimating the beam range and width in SEB x-ray images. To overcome these limitations of the SEB x-ray images measured by the x-ray camera, a deep learning (DL) approach was proposed in this work to predict the dose images for estimating the range and width of the carbon ion beam on the measured SEB x-ray images.

Methods: To prepare enough data for the DL training efficiently, 10,000 simulated SEB x-ray and dose image pairs were generated by our in-house developed model function for different carbon ion beam energies and doses. The proposed DL neural network consists of two U-nets for SEB x ray to dose image conversion and super resolution. After the network being trained with these simulated x-ray and dose image pairs, the dose images were predicted from simulated and measured SEB x-ray testing images for performance evaluation.

Results: For the 500 simulated testing images, the average mean squared error (MSE) was 2.5 × 10 and average structural similarity index (SSIM) was 0.997 while the error of both beam range and width was within 1 mm FWHM. For the three measured SEB x-ray images, the MSE was no worse than 5.5 × 10 and SSIM was no worse than 0.980 while the error of the beam range and width was 2 mm and 5 mm FWHM, respectively.

Conclusions: We have demonstrated the advantages of predicting dose images from not only simulated data but also measured data using our deep learning approach.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/mp.14205DOI Listing
August 2020

Sensitivity improvement of YAP(Ce) cameras for imaging of secondary electron bremsstrahlung x-rays emitted during carbon-ion irradiation: problem and solution.

Phys Med Biol 2020 05 27;65(10):105008. Epub 2020 May 27.

Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya 461-8673, Japan.

Low-energy x-ray imaging of secondary electron bremsstrahlung x-rays emitted during carbon-ion irradiation is a promising method for range estimation and could be used for imaging with almost clinical dose levels of carbon ion. However, the number of counts in images with clinical dose levels is relatively small, making it difficult to obtain precise range estimations. Since improving the sensitivity of the x-ray camera may solve this issue, we developed two new types of x-ray cameras. One uses a 1 mm thick, 40 mm × 40 mm cerium-doped yttrium aluminum perovskite (YA1O: YAP(Ce)) scintillator plate combined with a 2 inch square flat panel photomultiplier tube (FP-PMT) contained in a 2 cm thick tungsten shield with a pinhole collimator positioned 50 mm from the scintillator; the other uses a 0.5 mm thick, 20 mm × 20 mm YAP(Ce) scintillator plate combined with a 1 inch square position sensitive photomultiplier tube (PSPMT) contained in the same tungsten shield with a pinhole collimator, but with the scintillator positioned closer (30 mm) to the pinhole collimator to obtain a similar field of view. For both cameras, we used a wider angle (∼55°) pinhole collimator to measure the phantom closer to improve sensitivity. Although the 40 mm × 40 mm YAP(Ce) camera had high system spatial resolution, the background count fractions were high and produced a high count area at the center of the images due to the pulse pileup of the signals. With the 20 mm × 20 mm YAP(Ce) camera, we obtained x-ray images with low background counts without a high count area at the image center. By smoothing the measured images, we were able to estimate the ranges even for clinical dose levels. We therefore confirmed that one of our newly developed YAP(Ce) cameras had high sensitivity and is promising for the imaging of secondary electron bremsstrahlung x-rays during irradiation of carbon ions in clinical conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/ab7a6eDOI Listing
May 2020

The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants.

PLoS Genet 2020 02 18;16(2):e1008566. Epub 2020 Feb 18.

Genome Center and Department of Plant Biology, University of California Davis, Davis, California, United States of America.

Most angiosperms bear hermaphroditic flowers, but a few species have evolved outcrossing strategies, such as dioecy, the presence of separate male and female individuals. We previously investigated the mechanisms underlying dioecy in diploid persimmon (D. lotus) and found that male flowers are specified by repression of the autosomal gene MeGI by its paralog, the Y-encoded pseudo-gene OGI. This mechanism is thought to be lineage-specific, but its evolutionary path remains unknown. Here, we developed a full draft of the diploid persimmon genome (D. lotus), which revealed a lineage-specific whole-genome duplication event and provided information on the architecture of the Y chromosome. We also identified three paralogs, MeGI, OGI and newly identified Sister of MeGI (SiMeGI). Evolutionary analysis suggested that MeGI underwent adaptive evolution after the whole-genome duplication event. Transformation of tobacco plants with MeGI and SiMeGI revealed that MeGI specifically acquired a new function as a repressor of male organ development, while SiMeGI presumably maintained the original function. Later, a segmental duplication event spawned MeGI's regulator OGI on the Y-chromosome, completing the path leading to dioecy, and probably initiating the formation of the Y-chromosome. These findings exemplify how duplication events can provide flexible genetic material available to help respond to varying environments and provide interesting parallels for our understanding of the mechanisms underlying the transition into dieocy in plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1008566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048303PMC
February 2020

Epigenetic Flexibility Underlies Somaclonal Sex Conversions in Hexaploid Persimmon.

Plant Cell Physiol 2020 Feb;61(2):393-402

Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan.

Epigenetic regulation adds a flexible layer to genetic variations, potentially enabling long-term, but reversible, changes to a trait, while maintaining genetic information. In the hexaploid Oriental persimmon (Diospyros kaki), genetically monoecious cultivars bearing male flowers require the Y-encoded small RNA (smRNA) gene, OGI. This gene represses the expression of its autosomal counterpart gene, MeGI, as part of the canonical male production system. However, a D. kaki cultivar, Saijo, which lacks the OGI gene and originally bears only female flowers, occasionally produces somaclonal mutant male and revertant female (RF) branches. In this study, we investigated the mechanisms underlying these somaclonal sex conversions in persimmon. Specifically, we aimed to unravel how a genetically female tree without the OGI gene can produce male flowers and RF flowers. Applying multi-omics approaches, we revealed that this noncanonical male production system is basically consistent with the canonical system, in which the accumulation of smRNA targeting MeGI and the considerable DNA methylation of MeGI are involved. The epigenetic status of MeGI on CGN and CHG was synchronized to the genome-wide methylation patterns, both in transition to and from the male production system. These results suggest that the somaclonal sex conversions in persimmon are driven by the genome-wide epigenetic regulatory activities. Moreover, flexibility in the epigenetic layers of long-lived plant species (e.g. trees) is important for overcoming genetic robustness.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pcz207DOI Listing
February 2020

Pleiotropic effects of sex-determining genes in the evolution of dioecy in two plant species.

Proc Biol Sci 2019 10 16;286(1913):20191805. Epub 2019 Oct 16.

Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.

One reason for studying sex chromosomes of flowering plants is that they have often evolved separate sexes recently, and the genomes of dioecious species may not yet have evolved adaptations to their changes from the ancestral state. An unstudied question concerns the relative importance of such adaptation, versus the effects of the mutations that led to separate sexes in the first place. Theoretical models for such an evolutionary change make the prediction that the mutations that created males must have sexually antagonistic effects, not only abolishing female functions, but also increasing male functions relative to the ancestral functional hermaphrodites. It is important to test this critical assumption. Moreover, the involvement of sexual antagonism also implies that plant sex-determining genes may directly cause some of the sexual dimorphisms observed in dioecious plants. Sex-determining genes are starting to be uncovered in plants, including species in the genera and (families Ebenaceae and Actinidiaceae, respectively). Here, we describe transgenic experiments in which the effects of the very different male-determining genes of these two dioecious species were studied in a non-dioecious plant, . The results indeed support the critical assumption outlined above.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1098/rspb.2019.1805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6834047PMC
October 2019

Two Y-chromosome-encoded genes determine sex in kiwifruit.

Nat Plants 2019 08 5;5(8):801-809. Epub 2019 Aug 5.

Graduate School of Agriculture, Kyoto University, Kyoto, Japan.

Dioecy, the presence of male and female individuals, has evolved independently in multiple flowering plant lineages. Although theoretical models for the evolution of dioecy, such as the 'two-mutations' model, are well established, little is known about the specific genes determining sex and their evolutionary history. Kiwifruit, a major tree crop consumed worldwide, is a dioecious species. In kiwifruit we previously identified a Y-encoded sex-determinant candidate gene acting as the suppressor of feminization (SuF), named Shy Girl (SyGI). Here, we identify a second Y-encoded sex-determinant that we named Friendly Boy (FrBy), which exhibits strong expression in tapetal cells. Gene-editing and complementation analyses in Arabidopsis thaliana and Nicotiana tabacum indicated that FrBy acts for the maintenance of male (M) functions, independently of SyGI, and that these functions are conserved across angiosperm species. We further characterized the genomic architecture of the small (<1 megabase pairs (Mb)) male-specific region of the Y chromosome (MSY), which harbours only two genes expressed extensively in developing gynoecia and androecia, respectively: SyGI and FrBy. Re-sequencing of the genome of a natural hermaphrodite kiwifruit revealed that this individual is genetically male but carries deletion(s) of parts of the Y chromosome, including SyGI. Additionally, expression of FrBy in female kiwifruit resulted in hermaphrodite plants. These results clearly indicate that Y-encoded SyGI and FrBy act independently as the SuF and M factors in kiwifruit, respectively, and provide insight into not only the evolutionary path leading to a two-factor sex-determination system, but also a new breeding approach for dioecious species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-019-0489-6DOI Listing
August 2019

Evolution of Lineage-Specific Gene Networks Underlying the Considerable Fruit Shape Diversity in Persimmon.

Plant Cell Physiol 2019 Nov;60(11):2464-2477

Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.

The shapes of plant organs reflect the evolution of each lineage and have been diversified according to lineage-specific adaptations to environment. Research on the molecular pathways responsible for organ shapes has traditionally been focused mainly on leaves or flowers. Thus, little is known about the pathways controlling fruit shapes, despite their diversity in some plant species. In this study, we analyzed oriental persimmon (Diospyros kaki), which exhibits considerable diversity in fruit shapes among cultivars, to elucidate the underlying molecular mechanism using transcriptomic data and quantitative evaluation. First, to filter the candidate genes associated with persimmon fruit shapes, the whole gene expression patterns obtained using mRNA-Seq analysis from 100 individuals, including a segregated population and various cultivars, were assessed to detect correlations with principal component scores for fruit shapes characterized with elliptic Fourier descriptors. Next, a gene co-expression network analysis with weighted gene co-expression network analysis (WGCNA) package revealed that class 1 KNOX family genes and SEEDSTICK function as integrators along with some phytohormone-related genes, to regulate the fruit shape diversity. On the other hand, the OVATE family genes also contribute to fruit shape diversity, of which pathway would be potentially shared with other plant species. Evolutionary aspects suggest that acquisition of a high lineage-specific and variable expression of class 1 KNOX gene, knotted-like homeobox of Arabidopsis thaliana 1 (KNAT1), in young fruit is important for establishing the persimmon-specific mechanism that determines fruit shape diversity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pcz139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839372PMC
November 2019

Detection of a novel locus involved in non-seed-shattering behaviour of Japonica rice cultivar, Oryzasativa 'Nipponbare'.

Theor Appl Genet 2019 Sep 20;132(9):2615-2623. Epub 2019 Jun 20.

Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.

Key Message: A novel locus, qCSS3, involved in the non-seed-shattering behaviour of Japonica rice cultivar, 'Nipponbare', was detected by QTL-seq analysis using the segregating population with the fixed known seed-shattering loci. Asian cultivated rice, Oryzasativa, was domesticated from its wild ancestor, O.rufipogon. Loss of seed shattering is one of the most recognisable traits selected during rice domestication. Three quantitative trait loci (QTLs), qSH1, qSH3, and sh4, were previously reported to be involved in the loss of seed shattering of Japonica cultivated rice, O.sativa 'Nipponbare'. However, the introgression line (IL) carrying 'Nipponbare' alleles at these three loci in the genetic background of wild rice, O.rufipogon W630, showed a lower value for detaching a grain from the pedicel than 'Nipponbare'. Here, we investigated abscission layer formation in the IL and found a partially formed abscission layer in the central region between the epidermis and vascular bundles. Based on QTL-seq analysis using the F population obtained from a cross between 'Nipponbare' and the IL, we detected two novel loci qCSS3 and qCSS9 (QTL for the Control of Seed Shattering in rice on chromosomes 3 and 9), which were found to be involved in the difference in seed-shattering degree between 'Nipponbare' and W630. Then, we further focused on qCSS3 in order to understand its potential role on the loss of seed shattering. The candidate region of qCSS3 was found to be located within a 526-kb region using substitution mapping analysis. Interestingly, the qCSS3 candidate region partially overlaps the selective sweep detected for Japonica but not for Indica rice cultivars, suggesting that this region harbours the mutation at a novel seed-shattering locus specifically selected for non-seed-shattering behaviour in Japonica cultivars.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-019-03376-3DOI Listing
September 2019

Imaging of fragment particles in water by nuclear spallation during carbon-ion irradiation.

Phys Med Biol 2019 07 2;64(13):13NT01. Epub 2019 Jul 2.

Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan. Department of Medical Technology, Nagoya University Hospital, Nagoya, Japan.

Recently we found that the luminescence imaging of water during carbon-ion irradiation was possible using a cooled charge-coupled device (CCD) camera and the method could be used for range estimation of the beam. In the luminescence image, we found luminescence from the fragment particles produced by the nuclear spallation reaction of carbon ions. The luminescence may be used for the estimation of the distribution of the fragment particles by the nuclear spallation. For this purpose, we irradiated carbon ions of 241.5 MeV u to a water phantom and measured the luminescence image of water using a CCD camera. Then, we carefully observed the luminescence distribution after the Bragg peak to find the luminescence from the nuclear spallation reaction. In the luminescence image, we could clearly observe the luminescence from the fragment particles produced by the nuclear spallation reaction during irradiation of carbon ions. The beam widths of the luminescence image of the nuclear spallation were compared with those measured by the ionization chamber. The relative difference of the beam width at FWHM between luminescence image and ionization chamber was 23%. With these results, we conclude that the luminescence image of water during carbon-ion irradiation has a potential to be a new and efficient method for the width estimation of the fragment particles by the nuclear spallation reaction.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/ab2920DOI Listing
July 2019

Development of a YAP(Ce) camera for the imaging of secondary electron bremsstrahlung x-ray emitted during carbon-ion irradiation toward the use of clinical conditions.

Phys Med Biol 2019 07 5;64(13):135019. Epub 2019 Jul 5.

Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya, 461-8673, Japan. These two authors equally contributed to this paper. Author to whom any correspondence should be addressed.

Low-energy x-ray imaging of the secondary electron bremsstrahlung (SEB) x-ray emitted during carbon-ion irradiation is a promising method for range estimation. However, it remains unclear whether the method can be used for imaging with the clinical dose levels of carbon-ion and whether the bremsstrahlung x-ray can be detected from the deeper part of the body. To clarify these points, we developed a new high resolution low-energy x-ray camera and conducted imaging of the SEB x-ray during the irradiation of carbon-ions of different energies and intensities. Imaging was also tried with an x-ray camera using a human-head-sized, 17 cm diameter cylindrical phantom. To develop a high resolution imaging detector for a low-energy x-ray, we used a 20  ×  20  ×  0.5 mm thick cerium-doped yttrium aluminum perovskite, YA1O (YAP(Ce)) scintillator plate, which was optically coupled to a 25 mm square high quantum efficiency (HQE) type position sensitive photomultiplier tube (PSPMT). The imaging detector was encased in a 2 cm thick tungsten container and a pinhole collimator was attached to its camera head. After evaluating the camera's performance, SEB x-ray imaging was tried during irradiation of the carbon-ion and compared the results with a Monte Carlo simulation. We imaged the beam tracks by the SEB x-ray in real-time during irradiation of the carbon-ion and imaging and range estimation were possible even with near clinical dose level of 7.5  ×  10 particles of carbon-ion. Clear images of a SEB x-ray were also obtained for a 17 cm diameter cylindrical phantom. The measured images were good agreement with the Monte Carlo simulation. We confirmed that our developed YAP(Ce) camera is promising for imaging SEB x-rays during irradiation of carbon-ions even near clinical conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/ab2072DOI Listing
July 2019

Gene networks orchestrated by MeGI: a single-factor mechanism underlying sex determination in persimmon.

Plant J 2019 04 14;98(1):97-111. Epub 2019 Feb 14.

Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.

Separating male and female sex organs is one of the main strategies used to maintain genetic diversity within a species. However, the genetic determinants and their regulatory mechanisms have been identified in only a few species. In dioecious persimmons, the homeodomain transcription factor, MeGI, which is the target of a Y chromosome-encoded small-RNA, OGI, can determine floral sexuality. The basic features of this system are conserved in the monoecious hexaploid Oriental persimmon, in which an additional epigenetic regulation of MeGI determines floral sexuality. The downstream regulatory pathways of MeGI remain uncharacterized. In this study, we examined transcriptomic data for male and female flowers from monoecious persimmon cultivars to unveil the gene networks orchestrated by MeGI. A network visualization and cistrome assessment suggested that class-1 KNOTTED-like homeobox (KNOX)/ovate family protein (OFP)/growth regulating factors (GRFs) and short vegetative phase (SVP) genes mediate the differences in gynoecium and androecium development between male and female flowers, respectively. The expression of these genes is directly controlled by MeGI. The gene networks also suggested that some cytokinin, auxin, and gibberellin signaling genes function cooperatively in the KNOX/OFP/GRF pathway during gynoecium differentiation. Meanwhile, SVP may repress PI expression in developing androecia. Overall, our results suggest that MeGI evolved the ability to promote gynoecium development and suppress androecium development by regulating KNOX/OFP/GRF and SVP expression levels, respectively. These insights may help to clarify the molecular mechanism underlying the production of unisexual flowers, while also elucidating the physiological background enabling a single-factor system to establish dioecy in plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.14202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850717PMC
April 2019

Treatment outcomes of proton or carbon ion therapy for skull base chordoma: a retrospective study.

Radiat Oncol 2018 Nov 26;13(1):232. Epub 2018 Nov 26.

Department of Radiology, Hyogo Ion Beam Medical Center, Tatsuno, Hyogo, Japan.

Background: The usefulness of particle therapy for skull base chordoma has not been established. The aim of this retrospective study was to analyse the treatment outcomes of proton therapy (PT) and carbon ion therapy (CIT) in patients with skull base chordoma at a single institution.

Methods: All patients who underwent PT or CIT with curative intent between 2003 and 2014 at Hyogo Ion Beam Medical Center were included in this study. Twenty-four patients were enrolled. Eleven (46%) received PT and 13 (54%) received CIT. Overall survival (OS), progression-free survival (PFS) and local control (LC) were calculated using the Kaplan-Meier method. Late toxicities were evaluated according to the Common Terminology Criteria for Adverse Events version 4.0.

Results: The median follow-up was 71.5 months (range, 14-175 months). The five-year LC, PFS and OS rates were 85, 81, and 86%, respectively. The LC (P = 0.048), PFS (P = 0.028) and OS (P = 0.012) were significantly improved in patients who had undergone surgery before particle therapy. No significant differences were observed in the LC rate and the incidence of grade 2 or higher late toxicities between patients who received PT and CIT.

Conclusions: Both PT and CIT appear to be effective and safe treatments and show potential to become the standard treatments for skull base chordoma. To increase the local control, surgery before particle therapy is preferable.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13014-018-1173-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260885PMC
November 2018

Evolution and diversification of the plant gibberellin receptor GID1.

Proc Natl Acad Sci U S A 2018 08 1;115(33):E7844-E7853. Epub 2018 Aug 1.

Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Aichi, Japan;

The plant gibberellin (GA) receptor GID1 shows sequence similarity to carboxylesterase (CXE). Here, we report the molecular evolution of GID1 from establishment to functionally diverse forms in eudicots. By introducing 18 mutagenized rice GID1s into a rice null mutant, we identified the amino acids crucial for GID1 activity in planta. We focused on two amino acids facing the C2/C3 positions of -gibberellane, not shared by lycophytes and euphyllophytes, and found that adjustment of these residues resulted in increased GID1 affinity toward GA, new acceptance of GA and GA carrying C13-OH as bioactive ligands, and elimination of inactive GAs. These residues rendered the GA perception system more sophisticated. We conducted phylogenetic analysis of 169 GID1s from 66 plant species and found that, unlike other taxa, nearly all eudicots contain two types of GID1, named A- and B-type. Certain B-type GID1s showed a unique evolutionary characteristic of significantly higher nonsynonymous-to-synonymous divergence in the region determining GA affinity. Furthermore, these B-type GID1s were preferentially expressed in the roots of , soybean, and lettuce and might be involved in root elongation without shoot elongation for adaptive growth under low-temperature stress. Based on these observations, we discuss the establishment and adaption of GID1s during plant evolution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1806040115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099883PMC
August 2018

Addition of luminescence process in Monte Carlo simulation to precisely estimate the light emitted from water during proton and carbon-ion irradiation.

Phys Med Biol 2018 06 20;63(12):125019. Epub 2018 Jun 20.

Department of Radiological Sciences, Nagoya University Graduate School of Medicine, Nagoya-shi, Aichi, Japan. These two authors contributed equally to this paper.

Although luminescence of water lower in energy than the Cerenkov-light threshold during proton and carbon-ion irradiation has been found, the phenomenon has not yet been implemented for Monte Carlo simulations. The results provided by the simulations lead to misunderstandings of the physical phenomenon in optical imaging of water during proton and carbon-ion irradiation. To solve the problems, as well as to clarify the light production of the luminescence of water, we modified a Monte Carlo simulation code to include the light production from the luminescence of water and compared them with the experimental results of luminescence imaging of water. We used GEANT4 for the simulation of emitted light from water during proton and carbon-ion irradiation. We used the light production from the luminescence of water using the scintillation process in GEANT4 while those of Cerenkov light from the secondary electrons and prompt gamma photons in water were also included in the simulation. The modified simulation results showed similar depth profiles to those of the measured data for both proton and carbon-ion. When the light production of 0.1 photons/MeV was used for the luminescence of water in the simulation, the simulated depth profiles showed the best match to those of the measured results for both the proton and carbon-ion compared with those used for smaller and larger numbers of photons/MeV. We could successively obtain the simulated depth profiles that were basically the same as the experimental data by using GEANT4 when we assumed the light production by the luminescence of water. Our results confirmed that the inclusion of the luminescence of water in Monte Carlo simulation is indispensable to calculate the precise light distribution in water during irradiation of proton and carbon-ion.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1361-6560/aac74bDOI Listing
June 2018
-->