Biology subjects

Hatakeyama, M.

Publications and source records attributed to Hatakeyama, M..

9 recordsLinked to original sources

bioRxiv2026

A vagal sensory pathway for satiety suppression by intestinal fructose

Mammals primarily use glucose as an energy source, but they can also utilize other isocaloric monosaccharides, such as galactose and fructose. Since the gustatory system cannot distinguish between different sugars in ingested foods, it remains unclear whether and how mammals control the intake of different monosaccharides. Here we perform in vivo calcium imaging of the nodose ganglion in mice and find that intestinal glucose and fructose activate distinct populations of vagal sensory neurons. While glucose suppresses food intake in fed mice, fructose does not, resulting in increased calorie intake. However, after vagotomy, both glucose and fructose suppressed food intake, suggesting that vagal circuits activated by fructose facilitate feeding. This specialized vagal sensory pathway for fructose may partly explain the excess calorie intake induced by a fructose-rich diet.

neuroscience↗

bioRxiv2026

A chorionic gonadotropin assay enables non-invasive detection of ovulation and early pregnancy in a New World primate model

Early detection of ovulation and pregnancy in the common marmoset is crucial for reproductive studies, yet hCG kits lack cross-reactivity with marmoset CG, and current methods remain labor-intensive. Here, we developed monoclonal antibodies against marmoset CG and CG{beta}, and established a non-invasive immunochromatographic CG assay. By eliminating invasive blood sampling, this assay supports 3Rs principles and enables practical endocrine monitoring. The assay detected urinary CG surges preceding ovulation, enabling efficient embryo recovery through artificial insemination (75%). Early pregnancy was detected at approximately 17 days post-ovulation. In addition, pregnancy detection in squirrel monkeys suggests conservation of CG features among certain New World primates. Overall, this simple, non-invasive assay provides a practical tool for marmoset research and establishes a foundation for future conservation-oriented reproductive monitoring following appropriate species-specific validation.

physiology↗

bioRxiv2025

A super-enhancer actuated by heterodimerization of a specific YAP1 isoform, YAP1-2α, with TAZ endows cancer stemness and drug resistance

The pro-oncogenic transcriptional coactivator YAP1 comprises multiple splice isoforms, including YAP1-2, which retains an intact leucine zipper by skipping exon 6. Here, we show that YAP1-2 has a markedly greater capacity to form nuclear condensates via liquid-liquid phase separation (LLPS) than other YAP1 isoforms. Mechanistically, the YAP1-2/TEAD complex interacts with the TAZ/TEAD complex through the leucine zippers on YAP1 -2 and TAZ, forming a tetrameric complex that is further assembled multivalently by BRD4 to induce LLPS. The resulting YAP1-2 /TAZ/TEAD/BRD4 complexes activate TEAD-associated super-enhancers and strongly stimulate pro-oncogenic gene expression. Cancer cells with elevated YAP1-2 display enhanced malignant traits, including sphere formation, invasion, and chemoresistance. In high-grade serous ovarian cancers (HGSOCs), higher YAP1-2 mRNA levels are associated with nuclear YAP1 biomolecular condensates and more advanced clinical stages. Our study shows that YAP1-2 drives cancer cell aggressiveness, identifying the LLPS-induced YAP1-2/TAZ/TEAD super-enhancers as a promising target for the treatment of refractory cancers.

cancer biology↗

bioRxiv2024

Comprehensive expression data for two honey bee species, Apis mellifera and Apis cerana japonica

Comprehensive expression datasets were constructed for Apis mellifera and Apis cerana japonica. Post-oviposition day 6 to day 58 samples of A. mellifera workers (larva to adult); day 9, 10, 12, and 13 samples of A. mellifera queen (larva to pupa); and day 9 to day 18 samples of A. cerana japonica workers (larva to adult) were prepared, and RNA-Seq data were obtained. For A. cerana japonica, reference transcript sequence data, predicted amino acid sequence data, and functional annotation data were generated based on the genome sequence and RNA-Seq data. Using the transcript sequence and RNA-Seq data, comprehensive expression data for all transcripts of A. mellifera and A. cerana japonica were prepared. Hierarchical clustering analyses and the used sample preparation method ensured that both sets of expression data were reliable for use as comprehensive reference expression datasets. Therefore, these data are applicable for honey bee research or for comparative or evolutionary studies on insect species or social insect species at the genetic and molecular levels.

genetics↗

bioRxiv2022

PlantServation: time-series phenotyping using machine learning revealed seasonal pigment fluctuation in diploid and polyploid Arabidopsis

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers, but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software to analyze field images, where the plant shape, color, and background vary over months. We estimated the anthocyanin contents of small individuals of four Arabidopsis species using color information and verified the results experimentally. We obtained >4 million plant images over three field seasons to study anthocyanin fluctuations. We found significant effects of past radiation, coldness, and precipitation on the anthocyanin content in the field. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation pipeline facilitates the study of plant responses to complex environments termed "in natura."

plant biology↗

bioRxiv2019

Highly efficient direct conversion of human monocytes into neuronal cells using a small molecule combination

Previous studies reported that human fibroblasts and astrocytes were successfully converted into neuronal cells by small molecules without introducing ectopic transgenes. Induced neuronal cells--reprogrammed directly from dermal fibroblasts or brain astrocytes--were obtained from some donors; however, the clinical applications of this approach would be limited because it requires an invasive biopsy to harvest enough cells for derivation. Here, we report that adult human peripheral blood monocytes may be directly converted into neuron-like cells using only a combination of small molecules without transgene integration. This method enables neuronal cell generation from TUJ1-positive cells after 3 days of induction (at over 80% conversion efficacy). These cells presented neuronal morphologies and markers, suggesting that terminally differentiated human cells may be efficiently transdifferentiated into a distantly related lineage. Overall, our study provides a strategy to develop neuronal cells directly from human adult peripheral blood monocytes using a generate transgene-free, chemical-only approach.

cell biology↗

bioRxiv2019

Fine-scale ecological and transcriptomic data reveal niche differentiation of an allopolyploid from diploid parents in Cardamine

Polyploidization, or whole genome duplication, is one of the major mechanisms of plant speciation. Allopolyploids (species that harbor polyploid genomes originating from hybridization of different diploid species) have been hypothesized to occupy a niche with intermediate, broader, or fluctuating environmental conditions compared with parental diploids. It remains unclear whether empirical data support this hypothesis and whether specialization of expression patterns of the homeologs (paralogous gene copies resulting from allopolyploidization) relates to habitat environments. Here, we studied the ecology and transcriptomics of a wild allopolyploid Cardamine flexuosa and its diploid parents C. hirsuta and C. amara at a fine geographical scale in their native area in Switzerland. We found that the diploid parents favored opposite extremes in terms of soil moisture, soil carbon-to-nitrogen ratios, and light availability. The habitat of the allopolyploid C. flexuosa was broader compared with those of its parental species and overlapped with those of the parents, but not at its extremes. In C. flexuosa, the genes related to water availability were overrepresented among those at both the expression level and the expression ratio of homeolog pairs, which varied among habitat environments. These findings provide empirical evidence for niche differentiation between an allopolyploid and its diploid parents at a fine scale, where both ecological and transcriptomic data indicated water availability to be the key environmental factor for niche differentiation.Significance statement Polyploidization, or whole genome duplication, is common in plants and may contribute to their ecological diversification. However, little is known about the niche differentiation of wild allopolyploids relative to their diploid parents and the gene expression patterns that may underlie such ecological divergence. We detected niche differentiation between the allopolyploid Cardamine flexuosa and its diploid parents C. amara and C. hirsuta along water availability gradient at a fine scale. The ecological differentiation was mirrored by the dynamic control of water availability-related gene expression patterns according to habitat environments. Thus, both ecological and transcriptomic data revealed niche differentiation between an allopolyploid species and its diploid parents.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2018

Homeolog expression quantification methods for allopolyploids

Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi, and plants, and is especially common in crop plants. There is increasing interest in the study of allopolyploids due to advances in polyploid genome assembly, however the high level of sequence similarity in duplicated gene copies (homeologs) pose many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (> 10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (< 1% using EAGLE-RC, < 2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method. In general, disagreement in low expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision.

bioinformatics↗

bioRxiv2018

The Genomic Basis of Arthropod Diversity

BackgroundArthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.\n\nResultsUsing 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality and chemoperception.\n\nConclusionsThese analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

genomics↗