Biology subjects

Kawakami, S.

Publications and source records attributed to Kawakami, S..

8 recordsLinked to original sources

bioRxiv2026

Long-read sequencing reveals transposable element-derived chimeric transcripts at zygotic genome activation in mammalian embryos

BackgroundTransposable elements (TEs) are mobile genomic sequences that constitute one-third to one-half of the mammalian genome. Recently, TEs have been recognized for their important roles as cis-regulatory elements. TEs are broadly activated during zygotic genome activation (ZGA) in mammalian embryos, where they function as alternative promoters of host genes and drive the transcription of chimeric transcripts. However, the construction of comprehensive chimeric transcript databases based on short-read sequencing remains limited due to the repetitive and abundant nature of TEs in the genome. Here, we used long-read RNA sequencing to construct a comprehensive dataset of chimeric transcripts expressed in ZGA mouse and bovine embryos. ResultsWe identified 11,996 and 4,755 chimeric transcripts variants derived from 2,695 and 1,200 host genes in mouse and bovine, respectively, exceeding the numbers reported in previous short-read-based studies. Among them, 114 orthologous pairs produced chimeric transcripts in both species. Gene Ontology analysis revealed significant enrichment of terms related to transcriptional regulation and protein modification in mouse, whereas no terms were significantly enriched in bovine. Assessment of the protein-coding potential of the TE-driven transcripts using predicted open reading frames (ORFs) revealed that the proportion of "Protein-coding" transcripts was lower, whereas that of "LncRNA" (long non-coding RNA) was higher compared with all transcripts in both species. Among the ORFs classified as "Protein-coding", comparison with canonical ORFs revealed a tendency for the N terminus to be truncated while the C terminus remained intact in both species. TE-derived promoters used in mouse were enriched for mouse-specific TEs, whereas those in bovine were enriched for older TEs conserved among eutherians. In addition, long-read sequencing detected a greater number and proportion of TEs used as promoters in mouse and bovine than short-read sequencing. Although motif analysis identified KLF5 and OTX2 binding sites upstream of TE-derived promoters in both species, the specific TEs containing these motifs differed between the two species. ConclusionsThis study presents the first long-read sequencing analysis of chimeric transcripts in mammalian embryos in two species. Our approach revealed the functional similarities of chimeric transcripts between species, as well as species-specific differences in their TE compositions.

developmental biology↗

bioRxiv2025

3D-printed microfluidic chip for modeling retinal organoid-endothelial co-culture

Pathological angiogenesis, such as that observed in wet age-related macular degeneration (AMD), is challenging to reproduce in vitro. While previous organ-on-chip approaches have incorporated retinal pigment epithelium (RPE) and endothelial barriers, models integrating human retinal organoids with vascular networks remain limited. Here, we report the development of a fully 3D-printed microfluidic device for co-culture of human induced pluripotent stem cell (hiPSC)-derived retinal organoids containing RPE regions with endothelial cells. The device, fabricated from flexible thermoplastic polyurethane (TPU) on a transparent polyvinyl chloride (PVC) substrate, enables direct organoid-endothelial interaction within a fibrin-Matrigel matrix without physical barriers. In this system, endothelial cells formed choroid-like networks that integrated with retinal organoids. Vascular network density and invasion into RPE regions were enhanced by VEGF stimulation, recapitulating features of wet AMD. Furthermore, fluorescent liposomes distributed along endothelial structures and accumulated at the organoid interface, supporting the application of this model for nanoparticle delivery studies. This 3D-printed retinal organoid-on-chip provides a simple, reproducible, and physiologically relevant platform that complements existing retinal models for investigating angiogenesis and evaluating therapeutic strategies.

bioengineering↗

bioRxiv2025

Single-cell-based evidence for GLS1 inhibitor as a bona fide senolytic agent in vivo

A plethora of senolytic compounds and technologies have been identified. However, the efficacy of these treatments in eliminating senescent cells and the suppression of chronic inflammation remains to be substantiated in vivo. Here, we employ single-cell RNA sequencing and find the selective elimination of highly inflammatory fibroblasts, endothelial cells in the lung, and proximal tubule cells in the kidney from the GLS1 inhibitor BPTES-treated aged mice. The eliminated fibroblasts share typical phenotypes with in vitro human senescent cells. These cells predominantly express Dpp4 (CD26) and Cadm3, showing activated IFN signaling and lysosomal membrane damage. Cells eliminated by BPTES in lungs exhibit transcriptomes similar to those eliminated in p16-DTR mice, where DTR expression is limited in p16-expressing cells. BPTES treatment results in the T cell population shift from cytotoxic to a protective state, suggesting the suppression of age-related chronic inflammation. CellChat analysis revealed that multiple cytokine signals are transmitted from inflammatory fibroblasts and proximal tubular cells to immune cells in lungs and kidneys. These results provide evidence that GLS1 inhibitor functions as a bona fide senolytic drug to eliminate inflammatory cells, including a subset of senescent cells, and suppresses age-related chronic inflammation.

cell biology↗

bioRxiv2024

In vitro activity of cefiderocol against carbapenemase-producing and meropenem-nonsusceptible gram-negative bacteria collected in the Japan Antimicrobial Resistant Bacterial Surveillance (JARBS-GNR)

The treatment options available for infections caused by multidrug-resistant gram-negative pathogens are often limited. Cefiderocol (CFDC) is a novel siderophore cephalosporin that exhibits activity against multidrug-resistant gram-negative pathogens. Several studies have reported the in vitro activity of CFDC using clinical isolates from Europe, the United States, and China. However, no large-scale studies on the in vitro activities of CFDC have been conducted using all isolates with available genomic backgrounds based on whole-genome sequencing (WGS). We evaluated the antimicrobial activities of CFDC, ceftolozane/tazobactam (CTLZ/TAZ), imipenem-relebactam (IPM/REL), and ceftazidime/avibactam (CAZ/AVI) against carbapenemase-producing Enterobacterales, carbapenemase-non-producing meropenem-nonsusceptible Enterobacterales, and carbapenemase-producing non-fermentative bacteria. We selected 603 isolates (528 Enterobacterales, 18 Pseudomonas aeruginosa, and 57 Acinetobacter spp.) from the recent surveillance of clinical isolates in Japan using WGS data. Among these, 97.7% (300/307 strains) of carbapenemase-producing Enterobacterales, 100% (18/18 strains) of carbapenemase-producing P. aeruginosa, and 91.2% (52/57 strains) of carbapenemase-producing Acinetobacter spp. were susceptible to CFDC, showing better antimicrobial activity than the other antimicrobial agents evaluated in this study. In addition, CFDC was highly effective against class A, B, and D {beta}-lactamase harboring isolates when compared to the other antimicrobial agents in this study. While {beta}-lactam antibiotics were essentially ineffective against CFDC-resistant Enterobacterales, minocycline was the most effective, and gentamicin and amikacin were also effective. This is the first large-scale study to systematically demonstrate the efficacy of CFDC using carbapenemase-producing strains with transparent genomic backgrounds.

microbiology↗

bioRxiv2024

A Cell Model for the Detection of a Planar Surface Using Motion Stereo in Area MST of the Visual Cortex

I propose a series of modeled cells for detecting three plane parameters (i.e. a time-to-contact to a plane, its orientation, and its shortest distance) with motion stereo. This series is composed of lateral geniculate nucleus cells, nondirectionally selective simple cells, directionally selective (DS) simple cells, DS complex cells, motion-detection cells, and planar-surface-detection cells. These cell types perform the time delay, Hough transform, spatio-temporal correlation, accumulation, inverse Hough transform, and a combinations of the cross-ratio and polar transforms (or a small-circle transform) to detect these plane parameters, respectively. Each connection of the neural network connecting this series of cell types is modeled mathematically one by one using these transforms. The selective responses of SDCs to planar parameters are consistent with those of physiological experiments.

neuroscience↗

bioRxiv2023

Nationwide genome surveillance of carbapenem-resistant Pseudomonas aeruginosa in Japan

Japan is a country with an approximate 10 % prevalence rate of carbapenem-resistant Pseudomonas aeruginosa (CRPA). Currently, a comprehensive overview of the genotype and phenotype patterns of CRPA in Japan is lacking. Herein, we conducted genome sequencing and quantitative antimicrobial susceptibility testing for 382 meropenem-resistant CRPA isolates that were collected from 78 hospitals across Japan from 2019 to 2020. CRPA exhibited susceptibility rates of 52.9%, 26.4%, and 88.0% against piperacillin-tazobactam, ciprofloxacin, and amikacin, respectively, whereas 27.7% of CRPA isolates were classified as difficult-to-treat resistance P. aeruginosa. Of the 148 sequence types detected, ST274 (9.7%) was predominant, followed by ST235 (7.6%). The proportion of urine isolates in ST235 was higher than that in other STs (P = 0.0056, chi-square test). Only 4.1% of CRPA isolates carried the carbapenemase genes: blaGES (2) and blaIMP (13). One ST235 isolate carried the novel blaIMP variant blaIMP-98 in the chromosome. Regarding chromosomal mutations, 87.1% of CRPA isolates possessed inactivating or other resistance mutations in oprD, and 28.8% showed mutations in the regulatory genes (mexR, nalC, and nalD) for the MexAB-OprM effux pump. Additionally, 4.7% of CRPA isolates carried a resistance mutation in the PBP3-encoding gene ftsI. The findings from this study and other surveillance studies collectively demonstrate that CRPA exhibits marked genetic diversity and that its multidrug resistance in Japan is less prevailed than in other regions. This study contributes a valuable dataset that addresses a gap in genotype/phenotype information regarding CRPA in the Asia-Pacific region, where the epidemiological background markedly differs between regions.

microbiology↗

bioRxiv2022

Mesophyll specific expression of a bacterial mercury transporter-based vacuolar sequestration machinery sufficiently enhances mercury tolerance of Arabidopsis.

We aimed to efficiently enhance plant Hg(II) tolerance by the transgenic approach utilizing a bacterial mercury transporter MerC, an Arabidopsis mesophyll specific promoter pRBCS1A, and a vacuolar membrane targeting syntaxin AtVAM3/SYP22. We generated two independent homozygous Arabidopsis pRBCS1A-TCV lines expressing mT-Sapphire-MerC-AtVAM3 under the control of pRBCS1A. Quantitative RT-PCR showed that the transgene was expressed specifically in shoots of pRBCS1A-TCV lines. Confocal analyses further demonstrated the leaf mesophyll specific expression of mT-Sapphire-MerC-AtVAM3. Confocal observation of the protoplast derived from the F1 plants of the pRBCS1A-TCV line and the tonoplast marker line p35S-GFP-{delta}TIP showed the tonoplast colocalization of mT-Sapphire-MerC-AtVAM3 and GFP-{delta}TIP. These results clearly demonstrated that mT-Sapphire-MerC-AtVAM3 expression in Arabidopsis is spatially regulated as designed at the transcript and the membrane trafficking levels. We then examined the Hg(II) tolerance of the pRBCS1A-TCV lines as well as the p35S-driven MerC-AtVAM3 expressing line p35S-CV under the various Hg(II) stress conditions. Short-term (12 d) Hg(II) treatment indicated the enhanced Hg(II) tolerance of both pRBCS1A-TCV and p35S-CV lines. The longer (3 weeks) Hg(II) treatment highlighted the better shoot growth of the transgenic plants compared to the wild-type Col-0 and the pRBCS1A-TCV lines were more tolerant to Hg(II) stress than the p35S-CV line. These results suggest that mesophyll-specific expression of MerC-AtVAM3 is sufficient or even better to enhance the Arabidopsis Hg(II) tolerance. The Hg accumulation in roots and shoots did not differ between the wild-type Col-0 and the MerC-AtVAM3 expressing plants, suggesting that the boosted Hg(II) tolerance of the transgenic lines would be attributed to vacuolar Hg-sequestration by the tonoplast-localized MerC. Further perspectives of the MerC-based plant engineering are also discussed.

plant biology↗

bioRxiv2020

Patterns of functional and structural brain information are preserved over generations

There is clear evidence of intergenerational transmission of life values, cognitive traits, psychiatric disorders, and even aspects of daily decision making. To investigate biological substrates of this phenomenon, brain has received increasing attention as a measurable biomarker and potential target for intervention. However, no previous study has quantitatively and comprehensively investigated the effects of intergenerational transmission on functional and structural brain networks from parents to their children. Here, by employing an unusually large cohort dataset, we show that patterns of functional and structural brain networks are preserved over a generation. We also demonstrate that several demographic and behavioural phenotypes have effects on brain similarity. Collectively, our results provide a comprehensive picture of neurobiological substrates of parent-child similarity, and demonstrate the usability of our dataset for investigating the neurobiological substrates of intergenerational transmission.

neuroscience↗