Biology subjects

Fukuda, H.

Publications and source records attributed to Fukuda, H..

12 recordsLinked to original sources

bioRxiv2026

Pyramiding panicle-level heat avoidance and grain-level heat tolerance improves rice grain appearance under high-temperature grain filling

High temperature during grain filling increases rice grain chalkiness and deteriorates grain appearance under climate warming. Although several loci that reduce chalkiness have been identified, breeding strategies that integrate grain level heat tolerance with panicle level heat avoidance remain limited. Here we characterized SL2033, a chromosome segment substitution line carrying a long IR64 derived segment on chromosome 10, and evaluated the combination of the chromosome 10 segment with Appearance quality of brown rice 1 (Apq1), a quantitative trait locus associated with reduced heat induced chalkiness that acts at the grain level. Compared with its recurrent parent Koshihikari, SL2033 had longer flag leaves, altered vertical plant architecture, and lower panicle temperature. Total starch and protein contents were comparable between the two genotypes, whereas RNAseq analysis of the developing endosperm identified specific differences in heat, stress, and cell wall related transcripts. In a two year field trial, a pyramided line combining the SL2033 derived segment with Apq1 had the highest proportion of perfect grains and lowest frequencies of multiple chalky kernel types during the year with hotter grain filling conditions, with no detectable yield penalty. The pyramided line combined longer flag leaves, as in SL2033, with shorter panicle exsertion, as in an Apq1 near isogenic line, and had the lowest panicle temperature among the tested genotypes. Time series unmanned aerial vehicle imaging also detected genotype dependent differences in plant height during early grain filling, supporting distinct temporal patterns of plant development among the lines. These findings demonstrate that pyramiding genetic loci that confer panicle level and grain level heat tolerance is a promising strategy for improving rice grain appearance under high temperature field conditions, which are becoming increasingly prevalent.

plant biology↗

bioRxiv2026

Rice Cultivars Carrying the Semi Dwarfing Allele Enables High Yield without Lodging under Hairy Vetch based Green Manure

Green manure is a promising strategy for reducing dependence on chemical fertilizers in crop production. However, vigorous growth due to green manure often leads to high yield accompanied by lodging in rice, hindering its practical use in rice cultivation. Here, we show that rice cultivars carrying a semi-dwarfing sd1/ga20ox2 allele achieve high grain yield without lodging under hairy vetch-based green manure conditions. The leading Japanese cultivar Koshihikari exhibited enhanced vegetative growth, increased panicle number, and consequently higher grain yield and quality under green manure conditions in 2023 and 2024 compared with chemical fertilizer management, although this was accompanied by increased culm length and widespread lodging. Among the four GA20-oxidase genes, green manure significantly upregulated Sd1/GA20ox2 mRNA levels. A temperate japonica cultivar, Nijinokirameki, and an indica cultivar, Hokuriku-193, carrying a non-functional sd1/ga20ox2 allele exhibited no lodging under hairy vetch-based green manure management while achieving improved yield performance. Notably, yields obtained under our hairy vetch-based cultivation system were comparable to or exceeded a recently reported high-yield benchmark observed for Hokuriku-193 under chemical fertilizer management in the same region of Japan. These findings suggest that cultivars harboring non-functional sd1/ga20ox2 alleles enable the practical implementation of annual hairy-vetch-rice rotation for sustainable rice production.

plant biology↗

bioRxiv2025

Dissecting Agronomically Favorable Genotypes in Temperate Japonica Rice via Haplotype Analysis of a Japan-MAGIC Population

O_LICrop breeding assembles genomic variants into cultivars via crossing and selection. Phenotypic selection has improved yield and lodging tolerance but has limited genetic insights. We show how specific genomic variants and their combinations underpin advances in modern rice breeding in Japan. C_LIO_LIThrough genome-wide association study using a multi-parent advanced-generation intercross population derived from four temperate japonica cultivars, we identified 11 quantitative trait loci (QTLs) for key agronomic traits, including days to heading, shoot biomass, panicle length, and culm length under field conditions. GA20ox1, GA20ox2, and Hd1 were among the QTLs, and their natural variants were well conserved in temperate japonica cultivars bred in Japan, underscoring distinct selection pressures at these loci. C_LIO_LIBy integrating genotype data with 5-year yield-performance-evaluation trials of elite cultivars, we found that cultivars carrying multiple-copy GA20ox1 and functional Hd1, together with non-functional ga20ox2, tended to have shorter culms and higher grain yield than cultivars with multiple-copy GA20ox1, functional Hd1, and GA20ox2. This yield advantage was consistent across latitudes in Japan. C_LIO_LIThese results reveal favorable genotype combinations underlying modern japonica improvement and provide a genomic framework for breeding semi-dwarf, high-yielding cultivars adapted to temperate rice-growing regions in Asia. C_LI

genomics↗

bioRxiv2025

Rad18 suppresses the late step of human immunodeficiency virus type 1 replication

The Rad18 DNA repair protein plays a central role in the response to DNA damage and has been suggested to bind to the human immunodeficiency virus type 1 (HIV-1) integrase (IN) and restrict the early steps of HIV-1 infection. However, the inhibitory mechanism of Rad18 is not fully understood. Here, we describe a series of experiments that indicate that Rad18 can suppress the late step of HIV-1 replication by inhibiting selective viral post-transcription and the production of infectious HIV-1 virions. Notably, Rad18 interacted with HIV-1 IN, Tat, and Vif proteins and hijacked them in the nucleoli. Therefore, Rad18 seems to suppress multiple steps of HIV-1 infection, including viral post-transcription, production, and infectivity. ImportanceRad18, which contributes to damage bypass and DNA post-replication repair, is known to bind to HIV-1 IN and suppress HIV-1 infection. In this study, we found for the first time that Rad18 suppresses the late stages of HIV-1 infection. In addition to IN, we identified Tat and Vif as Rad18-interacting proteins. Rad18 may suppress multiple steps of the HIV-1 life cycle, including the early steps of HIV-1 infection, reverse transcription and integration, and the late steps of HIV-1 infection, viral post- transcription, viral production, and viral infectivity. These findings highlight the protective role of DNA repair proteins against retroviral infection and L1 retrotransposition as guardians of the human genome.

microbiology↗

bioRxiv2025

Metabolic reprogramming of protists within the microbiome of sinking particles

Protists play a crucial role in the biological carbon pump, yet their metabolic activity and function in sinking particles, which drive the aggregation and degradation of organic carbon, remains poorly characterized. Here, we examined transcriptional dynamics of protists in sinking and suspended particles collected by marine snow catcher in the Oyashio region to explore active lineages and their function during the sinking export. We found taxon-specific metabolic variations, with suspended particles showing up-regulated transcripts from diatoms, haptophytes, and chlorophytes, while sinking particles exhibited those from diatoms, ciliates, and dinoflagellates. Our data further revealed niche-dependent cellular metabolic reprogramming. The small diatoms Minidiscus variabilis and Thalassiosira oceanica upregulated more genes in suspended particles, while the chain-forming Thalassiosira rotula overexpressed more genes in sinking particles. The activity of both phototrophic and heterotrophic protists in sinking particles suggests the export of fresh organic carbon, with heterotrophic protists driving its degradation. Notably, the dinoflagellates Karlodinium veneficum and Karenia brevis exhibited significantly upregulated genes related to feeding and carbon metabolism in sinking particles. Additionally, the activity of RNA viruses was positively correlated with carbon flux. Overall, our study highlights the critical role of large-celled diatoms, heterotrophic dinoflagellate, ciliates and RNA viruses in organic carbon aggregation and degradation.

microbiology↗

bioRxiv2023

Probe capture enrichment sequencing of amoA genes discloses diverse ammonia-oxidizing archaeal and bacterial populations

The ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution, and activity of ammonia-oxidizing archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of amoA is a widely used method; however, it produces inaccurate results owing to the lack of a universal primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low concentration of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realizable sequencing depth. In this study, we developed a method for amoA enrichment sequencing using a hybridization capture technique. Using metagenomic mock community samples, our approach effectively enriched amoA genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or amoA gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 {+/-} 27.2%) than for non-capture samples (0.05 {+/-} 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.

microbiology↗

bioRxiv2021

VISUAL network analysis reveals the role of BEH3 as a stabilizer in the secondary vascular development in Arabidopsis

During secondary growth in plants, vascular stem cells located in the cambium continuously undergo self-renewal and differentiation throughout the lifetime. Recent cell-sorting technique enables to uncover transcriptional regulatory framework for cambial cells. However, the mechanisms underlying the robust control of vascular stem cells have not been understood yet. By coexpression network analysis using multiple transcriptome datasets of an ectopic vascular cell transdifferentiation system using Arabidopsis cotyledons, VISUAL, we newly identified a cambium-specific gene module from an alternative approach. The cambium gene list included a transcription factor BES1/BZR1 homolog 3 (BEH3), whose homolog BES1 is known to control vascular stem cell maintenance negatively. Interestingly, the vascular size of the beh3 mutants showed a large variation, implying the role of BEH3 as a stabilizer. BEH3 almost lost the transcriptional repressor activity and functioned antagonistically with other BES/BZR members via competitive binding to the same motif BRRE. Indeed, mathematical modeling suggests that the competitive relationship among BES/BZRs leads to the robust regulation of vascular stem cells.

developmental biology↗

bioRxiv2020

Phylogeography of Ryukyu insular cicadas: Extensive vicariance by island isolation vs accidental dispersal by super typhoon

Cicadas tend to be affected by vicariance reflecting poor mobility of nymphs underground and weak flying ability of adults. However, modern collection records of invasive cicada, combined with records of typhoon tracks, and newly obtained phylogeographic data suggest long distance, relatively instantaneous, dispersal of some vicariantly speciated cicadas. We address the importance of this typhoon dispersal mechanism applied to representative species of east Asian endemic cicadas of Cryptotympana, Mogannia, Euterpnosia and Meimuna. We combine BEAST-dated phylogenic and haplotype network analyses, modern collection data of non-native cicadas available in reports of the Japanese insect associations, modern typhoon records by Japan Meteorological Agency, and our own Quaternary geological constriction data. In conclusion, although Ryukyu endemic cicadas were vicariantly speciated, endemic cicadas on some islands were accidentally dispersed long distances to another island by typhoons, particularly those associated with super typhoons generated since 1.55 Ma.

evolutionary biology↗

bioRxiv2020

Synthesis and preclinical evaluation of MTP38 as a novel PET ligand for phophodiesterase 7 in the brain

PurposePhosphodiesterase (PDE) 7 is a potential therapeutic target for neurological and inflammatory diseases, although in-vivo visualization of PDE7 has not been successful. In this study, we aimed to develop [11C]MTP38 as a novel positron emission tomography (PET) ligand for PDE7. Methods[11C]MTP38 was radiosynthesized by 11C-cyanation of a bromo precursor with [11C]HCN. PET scans of rat and rhesus monkey brains and in-vitro autoradiography of brain sections derived from these species were conducted with [11C]MTP38. In monkeys, dynamic PET data were analyzed with an arterial input function to calculate the total distribution volume (VT). The non-displaceable binding potential (BPND) in the striatum was also determined by a reference tissue model with cerebellar reference. Finally, striatal occupancy of PDE7 by an inhibitor was calculated in monkeys according to changes in BPND. Results[11C]MTP38 was synthesized with radiochemical purity [≥] 99.4% and molar activity of 38.6 {+/-} 12.6 GBq/mol. Autoradiography revealed high radioactivity in the striatum and its reduction by non-radiolabeled ligands, in contrast with unaltered autoradiographic signals in other regions. In-vivo PET after radioligand injection to rats and monkeys demonstrated that radioactivity was rapidly distributed to the brain and intensely accumulated in the striatum relative to the cerebellum. Correspondingly, estimated VT values in the monkey striatum and cerebellum were 3.59 and 2.69 mL/cm3, respectively. The cerebellar VT value was unchanged by pretreatment with unlabeled MTP38. Striatal BPND was reduced in a dose-dependent manner after pretreatment with MTP-X, a PDE7 inhibitor. Relationships between PDE7 occupancy by MTP-X and plasma MTP-X concentration could be described by Hills sigmoidal function. ConclusionWe have provided the first successful preclinical demonstration of in-vivo PDE7 imaging with a specific PET radioligand. [11C]MTP38 is a feasible radioligand for evaluating PDE7 in the brain and is currently being applied to a first-in-human PET study.

neuroscience↗

bioRxiv2020

GSK3 activity is a cell fate switch that balances the ratio of vascular cell type

The phloem transports photosynthetic assimilates and signalling molecules. It mainly consists of sieve elements (SEs), which act as "highways" for transport, and companion cells (CCs), which serve as "gates" to load/unload cargos. Though SEs and CCs function together, it remains unknown what determines the ratio of SE/CC in the phloem. In this study, we develop a novel culture system for CC differentiation named VISUAL-CC, which reconstitutes the SE-CC complex formation. Comparative expression analysis in VISUAL-CC reveals that SE and CC differentiation tends to show negative correlation, while total phloem differentiation is unchanged. This varying SE/CC ratio is largely dependent on GSK3 kinase activity. Indeed, gsk3 hextuple mutants possess much more SEs and less CCs in planta. Conversely, gsk3 gain-of-function mutants induced by phloem-specific promoter partially increased the CC ratio. Taken together, GSK3 activity appears to function as a cell fate switch in the phloem, thereby balancing the SE/CC ratio.

plant biology↗

bioRxiv2019

Origination of the circadian clock system in stem cells regulates cell differentiation in Arabidopsis thaliana.

The circadian clock regulates various physiological responses. To achieve this, both animals and plants have distinct circadian clocks in each tissue that are optimized for that tissues respective functions. However, if and how the tissue-specific circadian clocks are involved in specification of cell types remains unclear. Here, by implementing a single-cell transcriptome with a new analytics pipeline, we have reconstructed an actual time-series of the cell differentiation process at single-cell resolution, and discovered that the Arabidopsis circadian clock is involved in the process of cell differentiation through transcription factor BRI1-EMS SUPPRESSOR 1 (BES1) signaling. In this pathway, direct repression of LATE ELONGATED HYPOCOTYL (LHY) expression by BES1 triggers reconstruction of the circadian clock in stem cells. The reconstructed circadian clock regulates cell differentiation through fine-tuning of key factors for epigenetic modification, cell-fate determination, and the cell cycle. Thus, the establishment of circadian systems precedes cell differentiation and specifies cell types.

plant biology↗

bioRxiv2018

Deep Neural Network for Protein Contact Prediction by Weighting Sequences in a Multiple Sequence Alignment

Protein contact prediction is a crucially important step for protein structure prediction. To predict a contact, approaches of two types are used: evolutionary coupling analysis (ECA) and supervised learning. ECA uses a large multiple sequence alignment (MSA) of homologue sequences and extract correlation information between residues. Supervised learning uses ECA analysis results as input features and can produce higher accuracy. As described herein, we present a new approach to contact prediction which can both extract correlation information and predict contacts in a supervised manner directly from MSA using a deep neural network (DNN). Using DNN, we can obtain higher accuracy than with earlier ECA methods. Simultaneously, we can weight each sequence in MSA to eliminate noise sequences automatically in a supervised way. It is expected that the combination of our method and other meta-learning methods can provide much higher accuracy of contact prediction.

bioinformatics↗