Biology subjects

Takeuchi, M.

Publications and source records attributed to Takeuchi, M..

14 recordsLinked to original sources

bioRxiv2026

Multi-Omics Mapping of Human Kidney Reveals Complement-Mediated Cellular Dynamics During Progression of Focal Segmental Glomerulosclerosis

Focal segmental glomerulosclerosis (FSGS) is a major cause of glucocorticoid-resistant nephrosis, yet its pathogenesis remains unclear. To define the molecular and cellular landscape of FSGS, we employed multi-omics approaches on independent human kidney biopsy cohorts. Proteomics revealed enhanced immune and complement activation. Spatial transcriptomics using a target gene panel constructed from the proteomics highlighted alternative pathway activation driven by complement factor D as a prominent feature. Complement activation emerged in glomeruli alongside altered signaling in podocytes and parietal epithelial cells (PECs): Podocytes displayed reduced PECAM1 and elevated macrophage migration inhibitory factor (MIF) signaling, and PECs display complement and collagen signaling as early events, and progressively acquired cellular activation, prompting glomerular fibrosis. These pathogenic signals propagated into adjacent interstitial regions, paralleling immune cell infiltration and fibrosis. These results uncover dynamics of dysregulated intercellular interactions originated from podocyte and PECs underlying the pathogenesis of FSGS, which provides insights into potential stage-specific interventions.

systems biology↗

bioRxiv2026

Sodium ion-assisted structural lipidomics for sphingolipid profiling

Sphingolipids are diverse lipids with sphingobases and N-acyl fatty acids as the hydrophobic moieties. While the importance of the in-depth elucidation of hydrophobic structures is widely recognized in lipid biology, mass spectrometry-based annotation of ceramides in the commonly used protonated form is often hindered by in-source dehydration during electrospray ionization in the heated state and variable water losses in the product ion spectrum. In this study, we investigated the sodium ion form and its product ions in ceramides with the use of electron-activated dissociation tandem mass spectrometry (EAD MS/MS) in addition to collision-induced dissociation to facilitate indepth structural elucidation. While dehydrated ions from the protonated form were frequently observed, the sodium adduct ions remained stable because of their higher activation energy compared with the protonated form, which was validated using quantum chemical calculations. Using the three adduct forms under optimized conditions increased confidence in annotating the ceramide peaks through retention-time matching. Furthermore, EAD MS/MS of the sodium adduct ions facilitated the positional determination of double bonds and hydroxyl groups in the ceramide hydrophobic moiety. Our approach is showcased by the annotation of phytoceramides with N-acyl 2- and 3-hydroxyl groups in mouse feces and ceramides with N-acyl n-6 very long-chain polyunsaturated 2-hydroxy fatty acids in mouse testis.

bioengineering↗

bioRxiv2025

Differential quantitative requirements for pre-mRNA splicing-regulated shelterin protein levels in distinct telomere functions

Telomeres perform multiple functions to maintain genome stability, including telomere length regulation, chromosome end protection, and meiotic chromosome dynamics. These functions are governed by shelterin, a telomere-binding protein complex. Here, we show that efficient pre-mRNA splicing of the Schizosaccharomyces pombe shelterin components Rap1 and Poz1 ensures sufficient protein levels, which are critical for telomere maintenance. Our analyses revealed that Tls1 and Cay1 act at distinct steps in splicing, specifically affecting rap1 and poz1 transcripts: Tls1 strongly interacts with Brr2 (a splicing factor), whereas Cay1 preferentially associates with introns. Accordingly, deletion of tls1 and cay1 synergistically impaired splicing of rap1 and poz1 transcripts and reduced their protein levels, leading to abnormal telomere elongation. Removal of introns from the rap1 and poz1 genes restored normal protein levels and telomere length, confirming that defective splicing underlies these defects. Analyses of the phenotypes of single and double tls1{Delta} and cay1{Delta} mutants revealed that different telomere functions vary in their dependence on Rap1 levels: telomere length regulation and, to a lesser extent, meiosis require higher protein abundance, whereas chromosome end protection can be sustained with minimal amounts. These findings reveal a hierarchical requirement for Rap1 across telomere functions and establish a framework for understanding how splicing-dependent regulation of shelterin components coordinates multiple aspects of telomere biology.

molecular biology↗

bioRxiv2025

Retrospective metabolomics via dual-dimensional deconvolution using ZT Scan DIA 2.0

We present a scanning data-independent acquisition (DIA) strategy, ZT Scan DIA, combined with dual-dimensional tandem mass spectrometry spectral filtering and deconvolution along both the quadrupole and retention time axes to reconstruct compound-specific MS2 spectra from complex mixtures. This approach is particularly effective for hydrophilic metabolomics data, where spectral similarity-based annotation is widely used, increasing annotation rates by 119-193% compared with conventional data-dependent acquisition (DDA) and window-based DIA methods. In lipidomics, deconvolution improved annotation precision by removing contaminant product ions and enabled separate quantification of co-eluting isomers using MS2 chromatograms, although common diagnostic ions could also be erroneously removed. Nevertheless, optimization of analysis parameters minimized this negative effect. Furthermore, we developed a practical data processing pipeline in which raw ZT Scan DIA-MS2 chromatograms are directly used for isomer separation and MS2-based quantification, covering 1,393 and 3,020 molecules for human plasma and mouse liver tissues, respectively. All data processing steps, including direct import of vendor raw data, are supported in MS-DIAL.

bioengineering↗

bioRxiv2024

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn- and double-bond positions of eye-specific phosphatidylcholine molecules containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology.

bioinformatics↗

bioRxiv2023

A procedure for solid phase extractions using metal oxide coated silica column in lipidomics

Lipid enrichment is indispensable for enhancing the coverage of targeted molecules in mass spectrometry (MS)-based lipidomics studies. In this study, we developed a simple stepwise fractionation method using a titanium- and zirconium-dioxide-coated solid-phase extraction (SPE) silica column that separates neutral lipids, phospholipids, and other lipids, including fatty acids (FAs) and glycolipids. Chloroform was used to dissolve the lipids, and neutral lipids, including steryl esters and di- and triacylglycerols, were collected in the loading fraction. Second, methanol with formic acid (99:1, v/v) was used to retrieve FAs, ceramides, and glycolipids, including glycosylated ceramides and glycosylated diacylglycerols, by competing for affinity with the Lewis acid sites on the metal oxide surface. Finally, phospholipids strongly retained via chemoaffinity interactions were eluted using a solution containing 5% ammonia and high water content (45:50 v/v, 2-propanol:water), which canceled the electrostatic and chelating interactions with the SPE column. High average reproducibility of <10% and coverage of [~]100% compared to those of the non-SPE samples were demonstrated by untargeted lipidomics of human plasma and mouse brain, testis, and feces. The advantage of our procedure was showcased by characterizing minor lipid subclasses, including dihexosylceramides containing very long-chain polyunsaturated FA in the testis, mono- and digalactosyl monoacylglycerols in feces, and acetylated and glycolylated derivatives of gangliosides in the brain that were not detected using conventional solvent extraction methods. Likewise, the value of our method in biology is maximized during glycolipidome profiling in the absence of neutral lipids and phospholipids that cover more than 80% of the chromatographic peaks. Table of Contents artwork O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/562428v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@170b451org.highwire.dtl.DTLVardef@4e4d3forg.highwire.dtl.DTLVardef@b1a1d4org.highwire.dtl.DTLVardef@1f77b31_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Functional opsin patterning for Drosophila color vision is established through signaling pathways in adjacent object-detection neurons

Vision is mainly based on two different tasks, object detection and color discrimination through activities of photoreceptor (PR) cells. Drosophila compound eye consists of [~]800 ommatidia. Every ommatidium contains eight PR cells; six outer cells (R1-R6) and two inner cells (R7 and R8) by which object detection and color vision are achieved, respectively. Expression of opsin genes in R7 and R8 is highly coordinated through the instructive signal from R7 to R8, and two major ommatidial subtypes are distributed stochastically; pale type expresses Rh3/Rh5, while yellow type expresses Rh4/Rh6 in R7/R8. The homeodomain protein Defective proventriculus (Dve) is expressed in yellow-type R7 and in six outer PRs, and it is involved in Rh3 repression to specify the yellow-type R7. dve mutant eyes exhibited atypical coupling, Rh3/Rh6 and Rh4/Rh5, indicating that the Dve activity is required for proper opsin coupling. Surprisingly, Dve activity in R1 is required for instructive signal, whereas those in R6 and R7 block the signal. Our results indicate that functional coupling of two different neurons is established through signaling pathways from adjacent neurons that are functionally different. Summary StatementDve activity is required for proper opsin coupling of two neurons that is established through signaling pathways from adjacent neurons that are functionally different.

developmental biology↗

bioRxiv2023

Multicellular dynamics on 3D scaffolds: Stress concentration is a key to controlling complex microtissue morphology on engineered surfaces

Tissue engineers have utilized a variety of three-dimensional (3D) scaffolds for controlling multicellular dynamics and the resulting tissue microstructures. In particular, cutting-edge microfabrication technologies, such as 3D bioprinting, provide increasingly complex structures. However, unpredictable microtissue detachment from scaffolds, which ruins desired tissue structures, is becoming an evident problem. To overcome this issue, we elucidated the mechanism underlying collective cellular detachment by combining a new computational simulation method with quantitative tissue-culture experiments. We first quantified the stochastic processes of cellular detachment shown by vascular smooth muscle cells on model curved scaffolds and found that microtissue morphologies vary drastically depending on cell contractility, substrate curvature, and cell-substrate adhesion strength. To explore this mechanism, we developed a new particle-based model that explicitly describes stochastic processes of multicellular dynamics, such as adhesion, rupture, and large deformation of microtissues on structured surfaces. Computational simulations using the developed model successfully reproduced characteristic detachment processes observed in experiments. Crucially, simulations revealed that cellular contractility-induced stress is locally concentrated at the cell-substrate interface, subsequently inducing a catastrophic process of collective cellular detachment, which can be suppressed by modulating cell contractility, substrate curvature, and cell-substrate adhesion. These results show that the developed computational method is useful for predicting engineered tissue dynamics as a platform for prediction-guided scaffold design.

biophysics↗

bioRxiv2022

Characterisation of an Escherichia coli line that completely lacks ribonucleotide reduction yields insights into the evolution of obligate intracellularity.

All life requires ribonucleotide reduction for de novo synthesis of deoxyribonucleotides. A handful of obligate intracellular species are known to lack ribonucleotide reduction and are instead dependent on their host for deoxyribonucleotide synthesis. As ribonucleotide reduction has on occasion been lost in obligate intracellular parasites and endosymbionts, we reasoned that it should in principle be possible to knock this process out entirely under conditions where deoxyribonucleotides are present in the growth media. We report here the creation of a strain of E. coli where all three ribonucleotide reductase operons have been fully deleted. Our strain is able to grow in the presence of deoxyribonucleosides and shows slowed but substantial growth. Under limiting deoxyribonucleoside levels, we observe a distinctive filamentous cell morphology, where cells grow but do not appear to divide regularly. Finally, we examined whether our lines are able to adapt to limited supplies of deoxyribonucleosides, as might occur in the evolutionary switch from de novo synthesis to dependence on host production during the evolution of parasitism or endosymbiosis. Over the course of an evolution experiment, we observe a 25-fold reduction in the minimum concentration of exogenous deoxyribonucleosides necessary for growth. Genome analysis of replicate lines reveals that several lines carry mutations in deoB and cdd. deoB codes for phosphopentomutase, a key part of the deoxyriboaldolase pathway, which has been hypothesised as an alternative to ribonucleotide reduction for deoxyribonucleotide synthesis. Rather than synthesis via this pathway complementing the loss of ribonucleotide reduction, our experiments reveal that mutations appear that reduce or eliminate the capacity for this pathway to catabolise deoxyribonucleotides, thus preventing their loss via central metabolism. Mutational inactivation of both deoB and cdd is also observed in a number of obligate intracellular bacteria that have lost ribonucleotide reduction. We conclude that our experiments recapitulate key evolutionary steps in the adaptation to intracellular life without ribonucleotide reduction.

microbiology↗

bioRxiv2022

The Intestinal Microbiome, Dietary Habits, and Physical and Psychological Resilience in Postpartum Women

The population of postpartum women suffering from mental illness is increasing steadily, particularly under conditions of the COVID-19 pandemic. Identifying factors that contribute to resilience in postpartum women is urgently needed to decrease risks of poor physical and psychological functioning. Studies have linked variations in the intestinal microbiota to depression in clinical samples, but the impacts in postpartum women in a Japanese population are unknown. We conducted two studies to examine the links between intestinal microbiota, physical condition, and psychological state in nonclinical, postpartum Japanese women. Our results show that decreasing Lachnospira and alpha diversity of microbiome is related to high mental health risk (i.e., parenting stress and/or depression). Psychological resilience and physical conditions were associated with relative abundances of genera Blautia, Clostridium, Eggerthella. This study contributes to further understanding of the gut-brain axis mechanisms and supports proposals for interventions to enhance resilience in postpartum women.

microbiology↗

bioRxiv2021

Synergy of turbulence and fishing reduce aquatic biomass

A universal scaling relationship exists between organism abundance and body size1,2. Within ocean habitats this relationship deviates from that generally observed in terrestrial systems2-4, where marine macro-fauna display steeper size-abundance scaling than expected. This is indicative of a fundamental shift in food-web organization, yet a conclusive mechanism for this pattern has remained elusive. We demonstrate that while fishing has partially contributed to the reduced abundance of larger organisms, a larger effect comes from ocean turbulence: the energetic cost of movement within a turbulent environment induces additional biomass losses among the nekton. These results identify turbulence as a novel mechanism governing the marine size-abundance distribution, highlighting the complex interplay of biophysical forces that must be considered alongside anthropogenic impacts in processes governing marine ecosystems.

ecology↗

bioRxiv2020

Lipopolysaccharide stimulation of RAW264.7 cells is a model for identifying novel clients of Hsc70

Heat shock cognate protein 71 kDa (Hsc70, Hspa8, Hspa10, Hsp73) is a member of the heat shock protein 70 kDa family of molecular chaperones. These chaperones function to aid the correct folding of client proteins using an ATP-dependent mechanism. Though Hsc70 is accepted to be a constitutively expressed protein, it has a well-documented function in modulating the induction of the pro-inflammatory cytokine TNF by the LPS/TLR4 pathway. In this work we attempt to identify protein clients of Hsc70 to gain insight into those which may be responsible for this regulatory effect. RAW264.7 cells were cultured in the absence or presence of 1 g/mL LPS for 0 to 24 hours. Herein we describe of a large number of newly-categorized Hsc70 clients using immunoprecipitation and nanoLC-MS/MS and we validate several novel Hsc70/client interactions using co-immunoprecipitation. After performing immunoprecipitation using a commercially available antibody, eluted fractions were proteolytically digested either immediately after immunoprecipitation or after separation by SDS-PAGE and sequence analyzed using nanoLC-MS/MS with a Q-Exactive Plus triple-quadrupole/orbitrap mass spectrometer. Using these methods, 292 total unique protein hits were identified with high confidence; 34 of which were only detected in LPS-treated cells.

biochemistry↗

bioRxiv2020

Clinical factors affecting evoked magnetic fields in patients with Parkinson's disease

Studies on evoked responses in Parkinsons disease (PD) may be useful for elucidating the etiology and quantitative evaluation of PD. However, in previous studies, the association between evoked responses and detailed motor symptoms or cognitive functions has not been clear. This study investigated the characteristics of the visual (VEF), auditory (AEF), and somatosensory (SEF) evoked magnetic fields in patients with Parkinsons disease (PD), and the correlations between evoked fields and the patients clinical characteristics, motor symptoms, and cognitive functions. Twenty patients with PD and 10 healthy controls (HCs) were recruited as participants. We recorded VEF, AEF, and SEF, collected clinical characteristics, performed physical examinations, and administered 10 cognitive tests. We investigated differences in the latencies of the evoked fields between patients with PD and HCs. We also evaluated the correlation of the latencies with motor symptoms and cognitive functioning. There were significant differences between the two groups in 6 of the cognitive tests, all of which suggested mild cognitive impairment in patients with PD. The latencies of the VEF N75m, P100m, N145m, AEF P50m, P100m, and SEF P60m components were greater in the patients with PD than in the HCs. The latencies mainly correlated with medication and motor symptoms, less so with cognitive tests, with some elements of the correlations remaining significant after Bonferroni correction. In conclusion, the latencies of the VEF, AEF, and SEF were greater in PD patients than in HCs and were mainly correlated with medication and motor symptoms rather than cognitive functioning. Findings from this study suggest that evoked fields may reflect basal ganglia functioning and are candidates for assessing motor symptoms or the therapeutic effects of medication in patients with PD.

neuroscience↗

bioRxiv2019

Subcellular localization of glypican-5 associates with dynamic cell motility and cell communication of the human mesenchymal stem cell line U3DT

Glypican-5 (GPC5) is a heparan sulfate proteoglycan (HSPG) localized to the plasma membrane. We previously reported that in the human mesenchymal stem cell line UE6E7T3, GPC5 is overexpressed in association with transformation and promotes cell proliferation by acting as a co-receptor for Sonic hedgehog signaling. In this study, we found using an immunofluorescence microscopy that in transformed cells (U3DT), GPC5 localized not only at primary cilia on the cell surface, but also at the leading edge of migrating cells, at the intercellular bridge and blebs during cytokinesis, and in extracellular vesicles. In each subcellular region, GPC5 colocalized with the small GTPase Rab11. These observations suggest that the colocalization of GPC5 with Rab11 is crucial for its function, and that its activity in each subcellular compartment promotes proliferation of U3DT cells. Our findings indicate that GPC5 plays active and essential roles in regulation of U3DT cell proliferation, and provides several insights into the functions of GPC5 that could be elucidated by future studies.

cell biology↗