Biology subjects

Taniguchi, Y.

Publications and source records attributed to Taniguchi, Y..

9 recordsLinked to original sources

bioRxiv2026

Natural variation in rice mitogen-activated protein kinase 4 contributes to increased photosynthetic rate under field conditions

Improving rice (Oryza sativa L.) yield requires a balanced enhancement of both sink size and source capacity. While many QTLs for sink size have been identified, only a few are known for source capacity, which is essential for achieving high yield. Here we identified qHP10 as a major QTL for increased photosynthetic rate by using chromosome segment substitution lines derived from a cross between the high-yielding indica cultivar Takanari and the average-yielding japonica cultivar Koshihikari. High-resolution mapping combined with CRISPR/Cas9-induced mutagenesis revealed that the causative gene underlying qHP10 is Mitogen-Activated Protein Kinase 4 (OsMPK4). A near-isogenic line carrying the OsMPK4Takanari allele (NIL-OsMPK4) had a 15-25% higher photosynthetic rate than Koshihikari. NIL-OsMPK4 also had higher stomatal conductance than Koshihikari but similar stomatal pore size and density, indicating that increased stomatal aperture increases photosynthetic rate. This enhancement is likely attributable to the down-regulation of OsMPK4 expression, which increases stomatal conductance and thus promotes CO2 uptake. Our findings demonstrate that OsMPK4 is a promising genetic target for increasing source capacity and, potentially, rice yield through molecular breeding. (175 words)

plant biology↗

bioRxiv2026

Comprehensive molecular profiling of single-cell proteome via gel electrophoresis and 3D single-molecule imaging

Recent advances in shotgun proteomics and immunoassays have yielded powerful single-cell proteomics technologies. However, current methods lack the sensitivity required to comprehensively quantify protein abundances in individual cells. Here, we present single-cell PAGE-PISA, an ultra-sensitive proteome profiling strategy that combines gel electrophoresis with 3D single-molecule fluorescence imaging. Our approach labels all proteins in single cells with fluorescent dyes, separates them by electrophoresis, and counts with single-molecule resolution. This technique quantified over 107 protein copies from a single mammalian cell with the sensitivity to detect low-abundance proteins down to 104 copies per species. Single-cell PAGE-PISA successfully classified cells into distinct cell types based on their proteomic profiles. Furthermore, our single-cell proteome data strongly correlated with predicted developmental states during cardiomyocyte differentiation, providing complementary information to single-cell transcriptome data. Together, single-cell PAGE-PISA enables highly sensitive and quantitative proteome profiling at the single-cell level, capturing subtle proteomic differences that distinguish diverse cellular states.

biophysics↗

bioRxiv2025

High-Coverage Jomon Genomes Provide Insights into Population Structure and Genetic Traits of Ancient Japanese Hunter-Gatherers

We analyzed eight high-coverage Jomon genomes spanning 9,000-2,800 years ago across the Japanese archipelago. Population genomic analyses revealed substantial genetic homogeneity across time and space reflecting post-glacial isolation, yet temporal stratification emerged: Initial Jomon (Iyai) individuals formed the earliest branch with weaker affinities to present-day Japanese. Using genomes from Todoroki and Chidorikubo sites, we estimated Jomon ancestry in mainland Japanese at [~]20%, substantially higher than previous estimates ([~]13%). Polygenic score analyses, based on the direct analysis of Jomon genomes, provided the genetic evidence for their phenotypic predispositions, including elevated BMI and metabolic trait scores, reduced immune-related scores, and larger cardiac dimensions, patterns consistent with hunter-gatherer adaptations. These ancestral genetic influences, including elevated risks for obesity and dyslipidemia, persist in present-day Japanese. Our findings demonstrate that Jomon populations maintained genetic continuity despite ecological diversity, while their greater-than-expected contribution to present-day Japanese reshapes population history models and reveals how ancient adaptations continue influencing contemporary disease susceptibility.

genomics↗

bioRxiv2024

PISA: versatile microscope for 3D single molecule light sheet imaging

Light sheet microscopy combines high sensitivity and imaging speeds with low photodamage, however a remaining hurdle to its widespread adoption is its requirement for special sample preparation. Our new microscope - planar illumination microscope for single molecule imaging for all purpose (PISA) - significantly relieves these restrictions to enable light sheet imaging of coverslip-mounted samples as commonly analyzed in biological microscopes. We show how this technology now permits high-throughput imaging using multi-well plates. Further, the ability of 3D single molecule imaging in microlitre or mm3 scale volumes over the coverslip improves the sensitivity of biochemical gel-based fluorometric assays to atto/zepto molar levels. PISA will facilitate widespread adoption of light sheet imaging for a variety of biological, biochemical and medical investigations.

biophysics↗

bioRxiv2024

Comparative transcriptome and variant analyses of the pancreatic islets of a rat model of obese type 2 diabetes identifies a frequently distributed nonsense mutation in the lipocalin 2 gene

We have recently established the Zucker fatty diabetes mellitus (ZFDM) rat as a novel model of obese type 2 diabetes (T2D), originating from the obese Zucker fatty (ZF) rat harboring a missense mutation in the leptin receptor gene. Pathogenesis of dysfunction of the pancreatic islets and genetic factors of T2D in ZFDM rats remain unknown. Here, we perform comparative transcriptome and variant analyses of the pancreatic islets between the two strains. Among differentially expressed genes irrespective of obesity and glucose intolerance states, we identify a nonsense mutation, c.409C>T (p.Gln137X), in the lipocalin 2 (Lcn2) gene which encodes a secreted protein called neutrophil gelatinase-associated lipocalin, a well-known biomarker for inflammation. Interestingly, we find that the Lcn2 mutation is distributed widely in rat species, such as commonly used DA and F344 strains. We examine the Lcn2 mutation as a strong candidate gene for T2D in ZFDM rats by using genome editing of ZFDM rats in which the nonsense mutation is replaced with a wild-type nucleotide. We find that the genome editing well works but also observe that there is no significant difference in the development of T2D between genome-edited and original ZFDM rats. Finally, we perform a genetic linkage analysis by using backcross progeny between ZF and ZFDM rats and confirm that the Lcn2 mutation exhibits no significant association with the onset of T2D. Our data indicate that several rat strains would serve as Lcn2 deficient models, contributing to elucidate pathophysiological roles of Lcn2 in a wide variety of phenotypes.

genetics↗

bioRxiv2024

High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasian

The migration of prehistoric humans led to intriguing interactions and changes in cultural and genetic heritage. In Eurasia, prehistoric migration and population replacement have affected present-day humans. The available high-quality genetic evidence for prehistoric migration in eastern Eurasia, particularly in the Far East, is still limited. We succeeded in obtaining low-contaminant, high-coverage genomes from middle-Yayoi (>46-fold coverage) and Initial Jomon (>67-fold coverage) individuals from mainland Japan. This study demonstrated that the Yayoi individual exhibited a genetic profile distinct from that of the indigenous Jomon population of the Japanese archipelago, suggesting that Yayoi ancestry was connected to the peopling of the Eurasian continent. Our high-coverage genome provides interesting insights into the evolution of copy number polymorphisms related to the dietary styles of ancient Japanese people. The copy number estimates of the amylase gene for the Yayoi individual were comparable to those of present-day East Asians who have diets high in starch. This suggests that the population in the middle Yayoi period may have already adapted to high-starch diets, which may have been related to paddy rice agriculture introduced from the continent. Furthermore, the individual from the initial Jomon period showed high amylase copy numbers comparable to those from modern East Eurasia, including modern Japanese. This suggests that some Jomon people may have consumed a high-starch diet then. The high-coverage whole-genome sequence also revealed differences in the demographic backgrounds of the two ancestral populations during the Yayoi and Jomon periods. Our results shed light on the prehistorical events and origins of related migrations from Eurasia at that time and their genetic background, cultural transformations, and links to modern Japanese people.

genomics↗

bioRxiv2023

Precise immunofluorescence canceling for highly multiplexed imaging capturing specific cell state

Cell states are regulated by the response of signaling pathways to receptor ligand-binding and inter-cellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we developed Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes.

cell biology↗

bioRxiv2019

PHi-C: deciphering Hi-C data into polymer dynamics

Computational modelling methods for Hi-C data have revealed averaged and static features of the 3D genome in cell nuclei. Here, we describe a 4D simulation method, PHi-C (Polymer dynamics deciphered from Hi-C data), that depicts dynamic 3D genome features through polymer modelling. This method allows for demonstrations of dynamic characteristics of genomic loci and chromosomes, as observed in live-cell imaging experiments, and provides physical insights into Hi-C data.

bioinformatics↗

bioRxiv2018

Broad applicability of a streamlined Ethyl Cinnamate-based clearing procedure

Turbidity and opaqueness are inherent properties of tissues which limit the capacity to acquire microscopic images through large tissues. Creating a uniform refractive index, known as tissue clearing, overcomes most of these issues. These methods have enabled researchers to image large and complex 3D structures with unprecedented depth and resolution. However, tissue clearing has been adopted to a limited extent due to a combination of cost, time, complexity of existing methods and potential negative impact on fluorescence signal. Here we describe 2Eci (2nd generation Ethyl cinnamate based clearing method) which can be used to clear a wide range of tissues, including cerebral organoids, Drosophila melanogaster, zebrafish, axolotl, and Xenopus laevis in as little as 1-5 days while preserving a broad range of fluorescence proteins including GFP, mCherry, Brainbow, and alexa-fluorophores. Ethyl cinnamate is non-toxic and can easily be used in multi-user microscope facilities. This method will open up clearing to a much broader group of researchers, due to its broad applicability, ease of use, and non-toxic nature of Ethyl cinnamate.\n\nSummary statementThe non-toxic, broadly applicable, and simplified protocol of 2Eci tissue clearing makes it possible for non-specialist labs to use clearing approaches on conventional inverted microscopes.

developmental biology↗