Biology subjects

Kaneko, H.

Publications and source records attributed to Kaneko, H..

9 recordsLinked to original sources

bioRxiv2023

Wide scope analysis of bioactive lipids, including steroids, bile acids, and polyunsaturated fatty acid metabolites, in human plasma by LC/MS/MS

Quantitative information on blood metabolites has the potential to be utilized in medical strategies such as early disease detection and prevention. Monitoring of bioactive lipids, such as steroids, bile acids, and polyunsaturated fatty acid (PUFA) metabolites, could be a valuable indicator for health status. However, a method for simultaneous measurement of these bioactive lipids has not been reported at present. Here, we report a liquid chromatography tandem mass spectrometry (LC/MS/MS) method that can simultaneously measure more than 140 bioactive lipids, including steroids, bile acids, and PUFA metabolites, from human plasma, and a sample preparation method for these targets. Protein removal in methanol precipitation and purification operations of bioactive lipids by solid-phase extraction improved the recovery of targeted compounds in human plasma samples, demonstrating the importance of sample preparation methods in a wide range of bioactive lipid analyses. Using the developed method, we measured plasma from healthy human volunteers and confirmed the presence of bioactive lipid molecules associated with sex differences and circadian rhythms. The practical bioactive lipid analysis method developed is expected to be applied to health monitoring and disease biomarker discovery for precision medicine.

systems biology↗

bioRxiv2023

Genomic adaptation of giant viruses in polar oceans

Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptative strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and demonstrate that temperature drives dramatic changes in the virus-host network at the polar/nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is independent of the polar adaptation of their hosts.

microbiology↗

bioRxiv2022

Global observation of plankton communities from space

Satellite remote sensing from space is a powerful way to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here we present an approach to identify representative communities from a global plankton network that included both zooplankton and phytoplankton and using global satellite observations to predict their biogeography. Six representative plankton communities were identified from a global co-occurrence network inferred using a novel rDNA 18S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to train a model that predicted these representative communities from satellite data. The model showed an overall 67% accuracy in the prediction of the representative communities. The prediction based on 17 satellite-derived parameters showed better performance than based only on temperature and/or the concentration of chlorophyll a. The trained model allowed to predict the global spatiotemporal distribution of communities over 19-years. Our model exhibited strong seasonal changes in the community compositions in the subarctic-subtropical boundary regions, which were consistent with previous field observations. This network-oriented approach can easily be extended to more comprehensive models including prokaryotes as well as viruses.

ecology↗

bioRxiv2021

Stem cell therapy for skin regeneration using mesenchymal stem cells derived from the progeroid Werner syndrome-specific iPS cells

Adult progeria, Werner syndrome (WS), is an autosomal recessive disorder that develops accelerated aging-associated symptoms after puberty. Refractory skin ulcer of limbs, which is one of the symptoms specific to WS, is seriously painful and sometimes results in amputation. In recent years, cell therapy using mesenchymal stem cells (MSCs) has been attracting attention; however, the effect of WS-derived MSCs on skin ulcers is still unclear. In this study, we generated iPS cells from a patient with WS and a normal subject, differentiated them into MSCs (WS- and NM-iMSC, respectively), and performed cell therapy to a refractory skin ulcer mouse model. As a result, WS-iMSC recapitulated premature senescence phenotypes in vitro. Upon subcutaneous injection around the wounds of mice, WS-iMSC was significantly inferior in wound healing effect compared to NM-iMSC. Proteome and transcriptome analysis revealed altered expression of genes related to angiogenesis, inflammation, and proliferation in WS-iMSC with remarkable downregulation of VEGF, a potent angiogenic factor. In addition, simultaneous administration of recombinant human VEGF and WS-iMSC improved the wound healing effect in vivo. These results indicate that the expression of angiogenic factors is reduced in WS-iMSC, and its supplementation restores the wound healing ability. This finding may pave the way to develop the treatment of intractable skin ulcers of WS.

cell biology↗

bioRxiv2021

Locomotion induced by medial septal glutamatergic neurons is linked to intrinsically generated persistent firing

The medial septum and diagonal band of Broca (MSDB) serve as a central hub in an ascending brainstem pathway that conveys sensory and motor signals to the limbic system. However, the cellular and circuit mechanisms underlying these functions remain unclear. Here, we show that transient optogenetic activation of MSDB VGluT2 neurons initiates a structured arousal sequence - beginning with facial movements, followed by pupil dilation and locomotion. Neuropixels recordings reveal persistent MSDB neuronal activity that strongly correlates with arousal-related behaviors. We demonstrate that persistent firing (PF) is an intrinsic property of a subset of MSDB neurons, independent of ongoing synaptic input. PF neurons and putative GABAergic theta-bursting neurons predicted movement initiation, with population activity scaling with initiation magnitude, unlike other MSDB populations. These findings identify PF in the MSDB as a central neural mechanism that orchestrates the transition from preparatory movements to full behavioral engagement, bridging sensory input with locomotor arousal and supporting state transitions within the limbic system.

neuroscience↗

bioRxiv2021

Temporal enhancement of cross-adaptation between density and size perception based on the theory of magnitude

The estimation of spatial distances is one of the most important perceptual outputs of vision and can easily be deduced even with detached objects. However, how the visual system encodes distances between objects and object sizes is unclear. Hisakata, Nishida, and Johnston (2016) reported a new adaptation effect, in which the perceived distance between objects and the size of an object shrink after adaptation to a dense texture. They proposed that the internal representation of density plays a role in a spatial metric system that measures distance and size. According to the theory of magnitude (Walsh, 2003), the estimation of spatial extent (distance and size) shares common metrics with the estimation of temporal length and numerosity magnitudes and is processed at the same stage. Here, we show the existence of temporal enhancement in cross-adaptation between density and size perception. We used the staircase method to measure the temporal property. The test stimuli were two circles, and the adapting stimulus had a dotted texture. The adapting texture refreshed every 100 or 300 ms, or not at all (static), during the adaptation. The results showed that the aftereffects from a refreshing stimulus were larger than those under the static condition. On the other hand, density adaptation lacked such enhancement. This result indicates that repetitive presentation of an adapting texture enhanced the density-size cross-aftereffect. According to the theory of magnitude, a common mechanism encodes spatial and temporal magnitude estimation and the adaptation to temporal density explains this cross-adaptation enhancement.

neuroscience↗

bioRxiv2020

Quantitative assessment of NCLDV-host interactions predicted by co-occurrence analyses

Nucleocytoplasmic DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships four-fold compared with random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by twelve-fold. Finally, we inferred virophage - NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments. ImportanceNCLDVs can infect a wide range of eukaryotes although their life cycle is less dependent on hosts compared with other viruses. However, our understanding of NCLDV- host systems is highly limited because few of these viruses have been isolated so far. Co-occurrence information has been assumed to be useful to predict virus-host interactions. In this study, we quantitatively show the effectiveness of co-occurrence inference for NCLDV host prediction. We also improve the prediction performance with a phylogeny-guided method, which leads to a concise list of candidate host lineages for three NCLDV families. Our results underpin the usage of co-occurrence approach for metagenomic exploration of the ecology of this diverse group of viruses.

microbiology↗

bioRxiv2019

Viruses of the eukaryotic plankton are predicted to increase carbon export efficiency in the global sunlit ocean

The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earths carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral "shunt" and "shuttle"). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.

ecology↗

bioRxiv2018

Restoring memory by optogenetic synchronization of hippocampal oscillations in an Alzheimer’s disease mouse model

Disrupted neural oscillations are a feature of Alzheimers disease (AD). We observed reduced frequency of theta oscillations in the hippocampal local field potential (LFP) in a mouse model of beta-amyloidosis. By restoring the temporal organization of theta oscillations using LFP-guided closed-loop optogenetic stimulation of parvalbumin-positive interneurons, we could rescue memory deficits of APP/PS1 mice in the novel object recognition test.

neuroscience↗