Biology subjects

Ishikawa, A.

Publications and source records attributed to Ishikawa, A..

6 recordsLinked to original sources

bioRxiv2025

Operant House: A Versatile Open-Source Platform for Automated Operant Conditioning Testing of Mice in Home Cages

Operant conditioning is a valuable method for studying cognitive functions, yet its adoption is limited by low throughput, labor intensity, and high costs. Here, we developed "Operant House," a low-cost, programmable device featuring a touchscreen, retractable levers, and a water reward port, designed for flexible, automated operant conditioning tasks. To validate its utility, we implemented two protocols to assess working memory in mice: a delayed non-match-to-position test and a two-choice spatial discrimination test. Using these protocols, we examined a mouse model of Alzheimers disease carrying familial Alzheimers disease-associated amyloid precursor protein mutations. Results revealed significant working memory deficits as early as 5 months of age. These findings highlight the Operant House as a cost-effective, high-throughput platform for evaluating higher cognitive functions in mice, offering an accessible tool for investigating models of neurological and neuropsychiatric disorders.

neuroscience↗

bioRxiv2024

Discovering cancer stem-like cells using Spatial transcriptomic analysis: Nuclear factor I X as a novel therapeutic target for gastric cancer

BackgroundGastric cancer (GC) is characterized by significant intratumoral heterogeneity and stem cells presenting as promising therapeutic targets. Despite advancements in spatial transcriptome analysis, unexplored targets for addressing cancer stemness remain unknown. This study aims to identify Nuclear Factor IX (NFIX) as a critical regulator of cancer stemness in GC and evaluate its clinicopathological significance and function. MethodsSpatial transcriptome analysis was conducted on GC. NFIX expressions correlation with clinicopathological factors and prognosis was assessed through immunostaining in 127 GC cases. Functional analyses in cancer cell lines validated these findings. ResultsSpatial transcriptome analysis stratified GC tissues based on genetic profiles, pinpointing CSC-like cells and further refined the classification to identify and highlight the NFIXs significance, validated by Monocle 3 and CytoTRACE analyses. Knockdown experiments in cancer cell lines demonstrated the involvement of NFIX in cancer cell proliferation and kinase activity. ConclusionsThis study underscores spatial transcriptome analysiss role in refining GC tissue classification and identifying therapeutic targets, highlighting NFIX as pivotal. NFIX expression correlates with poor prognosis and drives GC progression, suggesting its potential as a novel therapeutic target for personalized GC therapies.

pathology↗

bioRxiv2020

Tracking tau fibrillogenesis and consequent primary phagocytosis of neurons mediated by microglia in a living tauopathy model

Fibrillary tau pathologies have been implicated in Alzheimers and allied neurodegenerative diseases, while mechanisms by which neurons bearing tau tangles die remain enigmatic. To address this issue, we pursued tau and related key pathologies macroscopically by PET and MRI and microscopically by intravital two-photon laser optics. Time-course macroscopic assays of tau transgenic mice demonstrated intimate associations of tau deposition and increase of an inflammatory microglial marker, translocator protein (TSPO), with regional brain atrophy. Longitudinal microscopy of these mice revealed a rapid turnover of tau lesions resulting from continuous generation of new tau aggregates followed by loss of neurons and their fibrillar contents. This technology also allowed the capturing of the disappearance of tangle-bearing neurons several days after being engulfed by activated microglia. Notably, a therapeutic TSPO ligand profoundly suppressed the mobility and phagocytotic activity of microglia and improved neuronal survival in this model, supporting the involvement of primary phagocytosis of viable neurons by microglia in tau-primed neuronal death. Finally, partial depletion of microglia revealed roles of immune factors, MFG-E8 and C1q, as eat-me signals for an immediate attraction of phagocytic microglia towards the elimination of tangle-loaded neurons.

neuroscience↗

bioRxiv2020

Chromosome-level genome construction of a Japanese stickleback species using ultra-dense linkage analysis using single-cell sequencing of sperms

The presence of high quality genomes at the chromosome level is very useful in the search for the causal genes of mutants and in genetic breeding. The advent of next-generation sequencers has made it easier to decode genomes, but it is still difficult to construct the genomes of higher organisms. In order to construct the genome of a higher organism, the genome sequence of the organism is extended to the length of the chromosome by linkage analysis after assembly and scaffolding. However, in the past linkage analysis, it was difficult to make a high-density linkage map, and it was not possible to analyze organisms without an established breeding system. As an innovative alternative to conventional linkage analysis, we devised a method for genotyping sperm using 10x single-cell genome (CNV) sequencing libraries to generate a linkage map without interbreeding individuals. The genome was constructed using sperm from Gasterosteus nipponicus, and single-cell genotyping yielded 1,864,430 very dense hetero-SNPs. The average coverage per sperm cell is 0.13x. The number of sperm used is 1,738, which is an order of magnitude higher than the number of sperm used for conventional linkage analysis. We have improved the linkage analysis tool SELDLA (Scaffold Extender with Low Depth Linkage Analysis) so that we can analyze the data in accordance with the characteristics of single-cell genotyping data. Finally, we were able to determine the location and orientation on the chromosome for 85.6% of the contigs in the 456 Mbase genome of Gasterosteus nipponicus sequenced in nanopores. A total of 95.6% of the contigs in which a cross-reaction was detected within the contigs.

genomics↗

bioRxiv2020

bak1-5 mutation uncouples tryptophan-dependent and independent postinvasive immune pathways triggered in Arabidopsis by multiple fungal pathogens

Robust nonhost resistance of Arabidopsis thaliana against the nonadapted hemibiotrophic fungus Colletotrichum tropicale requires PEN2-dependent preinvasive and CYP71A12/CYP71A13-dependent postinvasive resistance, which both rely on tryptophan (Trp) metabolism. Here we report that CYP71A12 and CYP71A13 are critical for Arabidopsis postinvasive resistance toward both the necrotrophic Alternaria brassicicola and the adapted hemibiotrophic C. higginsianum fungi. Metabolite analyses suggest that the production of indole-3-carboxylic acid derivatives (ICAs) and camalexin is induced upon pathogen invasion, while phenotypic comparison of cyp79B2 cyp79B3 and pen2 cyp71A12 cyp71A13 plants indicates that the contribution of ICAs to postinvasive resistance is dose-dependent. We also found that the disruption of intact pattern recognition receptor complex caused by bak1-5 mutation significantly reduced postinvasive resistance against C. tropicale and A. brassicicola, indicating that pattern recognition commonly contributes to this second defense-layer against pathogens with distinct infection strategies. However, the bak1-5 mutation had no detectable effects on Trp-metabolite accumulation triggered by pathogen invasion. Together with this, further comparative gene expression analyses suggested that pathogen invasion in Arabidopsis activates (i) bak1-5 insensitive Trp-metabolism that leads to antimicrobial secondary metabolites, and (ii) a bak1-5 sensitive immune pathway that activates the expression of antimicrobial proteins.

plant biology↗

bioRxiv2019

White matter abnormalities across different epilepsy syndromes in adults: an ENIGMA Epilepsy study

The epilepsies are commonly accompanied by widespread abnormalities in cerebral white matter. ENIGMA-Epilepsy is a large quantitative brain imaging consortium, aggregating data to investigate patterns of neuroimaging abnormalities in common epilepsy syndromes, including temporal lobe epilepsy, extratemporal epilepsy, and genetic generalized epilepsy. Our goal was to rank the most robust white matter microstructural differences across and within syndromes in a multicentre sample of adult epilepsy patients. Diffusion-weighted MRI data were analyzed from 1,069 non-epileptic controls and 1,249 patients: temporal lobe epilepsy with hippocampal sclerosis (N=599), temporal lobe epilepsy with normal MRI (N=275), genetic generalized epilepsy (N=182) and nonlesional extratemporal epilepsy (N=193). A harmonized protocol using tract-based spatial statistics was used to derive skeletonized maps of fractional anisotropy and mean diffusivity for each participant, and fiber tracts were segmented using a diffusion MRI atlas. Data were harmonized to correct for scanner-specific variations in diffusion measures using a batch-effect correction tool (ComBat). Analyses of covariance, adjusting for age and sex, examined differences between each epilepsy syndrome and controls for each white matter tract (Bonferroni corrected at p<0.001). Across "all epilepsies" lower fractional anisotropy was observed in most fiber tracts with small to medium effect sizes, especially in the corpus callosum, cingulum and external capsule. Less robust effects were seen with mean diffusivity. Syndrome-specific fractional anisotropy and mean diffusivity differences were most pronounced in patients with hippocampal sclerosis in the ipsilateral parahippocampal cingulum and external capsule, with smaller effects across most other tracts. Those with temporal lobe epilepsy and normal MRI showed a similar pattern of greater ipsilateral than contralateral abnormalities, but less marked than those in patients with hippocampal sclerosis. Patients with generalized and extratemporal epilepsies had pronounced differences in fractional anisotropy in the corpus callosum, corona radiata and external capsule, and in mean diffusivity of the anterior corona radiata. Earlier age of seizure onset and longer disease duration were associated with a greater extent of microstructural abnormalities in patients with hippocampal sclerosis. We demonstrate microstructural abnormalities across major association, commissural, and projection fibers in a large multicentre study of epilepsy. Overall, epilepsy patients showed white matter abnormalities in the corpus callosum, cingulum and external capsule, with differing severity across epilepsy syndromes. These data further define the spectrum of white matter abnormalities in common epilepsy syndromes, yielding new insights into pathological substrates that may be used to guide future therapeutic and genetic studies.

neuroscience↗