Biology subjects

Tajima, A.

Publications and source records attributed to Tajima, A..

12 recordsLinked to original sources

bioRxiv2026

Click-Prep: An Interactive Data Preparation Tool for Click-qPCR

Click-qPCR is a browser-based application for relative qPCR analysis that requires a tidy-format CSV file containing four columns: sample, group, gene, and Cq. Preparing this input from qPCR instrument output typically requires manual reformatting and calculation of mean Cq values for technical replicates. To simplify this process, we developed Click-Prep (https://kubo-azu.shinyapps.io/Click-Prep/), an interactive web-based application designed specifically to create Click-qPCR input files. Click-Prep imports CSV, TXT, TSV, and XLS/XLSX files and supports skipping of instrument-generated metadata rows, interactive column mapping, and manual assignment of experimental groups. Users can review technical-replicate measurements, exclude selected rows according to predefined quality-control criteria, and calculate mean Cq values for each sample-group-target combination. Missing or nonnumeric Cq values are flagged for review and must be resolved before the mean is calculated. Click-Prep can also combine compatible formatted CSV files, such as datasets obtained from separate qPCR plates. The resulting dataset is exported as a standardized CSV file containing the four fields required by Click-qPCR. By integrating these operations into a guided browser-based workflow, Click-Prep enables users to prepare Click-qPCR input files rapidly and consistently without programming.

bioinformatics↗

bioRxiv2026

Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation

Social isolation (SI) during adolescence is associated with neurobiological alterations; however, its effect on the hippocampal epigenome and transcriptome remains unclear. We performed ATAC-seq and RNA-seq of hippocampal CA1 in an adolescent mouse SI model, with single-cell RNA-seq reference mapping and cell type deconvolution. ATAC-seq identified candidate SI-associated chromatin accessibility alterations, with nominal functional enrichment linking increased enhancer-associated regions to calcium transport and decreased promoter regions to synaptic organization. Motif analysis showed enrichment of the activator protein 1 (AP-1) motif among candidate regions with reduced accessibility. RNA-seq identified 106 differentially expressed genes (DEGs), including upregulated Fosl2 and Hdac9 and downregulated Fbxw7, with enrichment of myelination-related pathways. Although global concordance between chromatin accessibility and transcriptional changes was limited, integrated analysis showed directional concordance between expression and nearby candidate accessibility changes for a subset of DEGs. Cell type analyses suggested that SI-downregulated transcriptional signatures were linked to excitatory neurons, whereas SI-upregulated signatures were enriched in non-neuronal populations, particularly oligodendrocytes. Deconvolution suggested higher estimated oligodendrocyte representation and lower estimated excitatory neuron representation in isolated mice. These findings suggest that adolescent SI is associated with significant transcriptomic remodeling and candidate chromatin accessibility changes within hippocampal CA1, accompanied by distinct neuronal- and glial-associated transcriptional signatures.

neuroscience↗

bioRxiv2026

PANDA: Read-Level Phased Analysis of DNA Amplicons for Methylation Studies

Targeted bisulfite amplicon sequencing is widely used to examine methylation at defined genomic loci, but site-wise methylation estimates can obscure phased patterns among individual reads. We developed PANDA (Phased Analysis for DNA Amplicons), an open-source platform for read-level analysis of targeted bisulfite amplicons generated by Sanger sequencing or amplicon NGS, with graphical and command-line interfaces built on a shared computational core (https://github.com/kubo-azu/PANDA). PANDA integrates reference-coordinate methylation calling and visualization, motif-based haplotype filtering, coordinate linkage of unmerged paired reads, and group comparison. It also implements three complementary heterogeneity metrics: Amplicon PDR (proportion of discordant reads), Window Epipolymorphism, and Amplicon qFDRP (quantitative fraction of discordant read pairs). These metrics use retained read-count weighting and explicit eligibility criteria. Synthetic demonstration datasets illustrated global methylation estimation, sequence-defined haplotype selection, and CpG-level group comparison. The heterogeneity metrics illustrated different aspects of the predefined methylation states. Re-analysis of public chimpanzee and rhesus macaque placental datasets was consistent with the previously reported species-associated methylation contrast and demonstrated coordinate-linked analysis of unmerged paired reads without imputing the unsequenced interval. PANDA provides a reproducible framework for examining phased methylation patterns and within-sample heterogeneity alongside site-wise methylation estimates in amplicon sequencing.

bioinformatics↗

bioRxiv2026

Systems-level Investigation of the Anxiolytic Gut-Brain Interactions induced by Paraprobiotic Lactobacillus brevis SBC8803 in Zebrafish

Anxiety disorders are among the most prevalent mental health conditions worldwide, and interest in psychobiotics--live or inactivated microorganisms that beneficially modulate the microbiota-gut-brain axis--is increasing. Heat-killed Lactobacillus brevis SBC8803 enhances serotonin (5-hydroxytryptamine; 5-HT) signaling and ameliorates stress-related phenotypes in mammals, although the gut-brain pathways mediating these effects remain incompletely defined. Here, we investigated the anxiolytic effects and underlying molecular mechanisms of oral SBC8803 administration in adult zebrafish. Adult male AB-strain zebrafish were fed a diet containing heat-killed SBC8803 for 4 weeks, and anxiety-like behavior was evaluated using the novel tank test. SBC8803-treated fish exhibited a shorter latency to enter the upper half of the tank and more frequent transitions into the upper half, consistent with reduced anxiety-like behavior. To explore underlying mechanisms, we performed brain RNA sequencing and 16S rRNA gene sequencing of intestinal contents, followed by integrative multi-omics analyses. Brain transcriptomic profiling identified differentially expressed genes and enrichment of serotonin receptor, CREB, and oxytocin signaling pathways, suggesting enhanced monoaminergic and plasticity-related signaling. Microbiome functional prediction indicated SBC8803-associated shifts in lipid and vitamin metabolism, including pathways related to riboflavin (vitamin B2) and tryptophan. Gene set variation analysis combined with DIABLO-based data integration revealed coordinated changes between microbial metabolic and brain signaling pathways, consistent with a vitamin B-serotonin-anti-inflammatory axis linking gut metabolism to neural regulation. Furthermore, residual correlation analysis showed innate gut-brain coordination independent of SBC8803 effect, such as the coupling between brain arachidonic acid and gut histidine metabolism. These findings support the biological validity of SBC8803 administration-associated interactions observed in the multi-omics analyses. Collectively, these findings indicate that the paraprobiotic SBC8803 exerts anxiolytic-like effects in zebrafish and reshapes gut-brain network states at behavioral, microbial, and transcriptomic levels, providing a mechanistic framework for considering heat-killed SBC8803 as a candidate psychobiotic for anxiety-related conditions.

microbiology↗

bioRxiv2025

Click-qPCR: an ultra-simple tool for interactive qPCR data analysis

Real-time quantitative PCR (qPCR) is a pivotal technique for analyzing gene expression and DNA copy number variation. However, the limited availability of easy-to-use software tools remains a significant challenge for experimental biologists without programming expertise. To address this issue, we developed Click-qPCR, a user-friendly, web-based Shiny application that requires no local installation. Click-qPCR streamlines {Delta}Cq and {Delta}{Delta}Cq calculations using user-uploaded CSV data files. The application allows users to dynamically select genes and groups, and to perform Welchs t-tests for pairwise comparisons and one-way ANOVA with Dunnetts post-hoc test for multi-group comparisons. Results are immediately visualized as interactive bar plots (mean {+/-} SD with individual data points) and can be downloaded as publication-quality images, along with statistical summaries. Click-qPCR enables researchers to efficiently process, interpret, and visualize their qPCR data regardless of programming experience, thereby accelerating data processing and improving the accessibility of routine analysis. The Shiny application of Click-qPCR is freely available at https://kubo-azu.shinyapps.io/Click-qPCR/. The source code and user guide for Click-qPCR are openly available on GitHub at https://github.com/kubo-azu/Click-qPCR.

bioinformatics↗

bioRxiv2025

Housing environment bilaterally alters transcriptomic profile in the rat hippocampal CA1 region

Brain asymmetry is a fundamental feature of neural organization. However, the molecular basis of hippocampal lateralization in response to environmental stimuli remains poorly understood. Here, we examined the transcriptomic profiles of the left and right hippocampal CA1 regions in rats reared under isolated or enriched housing conditions to elucidate hemisphere-specific responses and shared molecular adaptations. RNA-sequencing analysis revealed lateralized differences in the number and identity of differentially expressed genes, accompanied by distinct biological themes, as indicated by overrepresentation and gene set enrichment analysis. The left CA1 region was prominently engaged in pathways related to synaptic organization and mitochondrial function, whereas the right CA1 region exhibited enrichment in transcriptional regulation and RNA metabolic processes. Despite these asymmetries, co-expression and protein-protein interaction network analyses revealed shared molecular architectures. Immediate early genes formed consistent central hubs across both hemispheres, and a common Mecp2-Grin2b-Cdkl5-Tet3 protein interaction cluster was identified as a potential integrative regulatory module. Additional enrichment analysis of differentially expressed genes shared between hemispheres further highlighted conserved responses, particularly in synaptic plasticity and cell-cell communication. Together, these findings demonstrate that the left and right CA1 regions employ distinct yet partially convergent transcriptional programs to adapt to environmental stimuli. This coordinated molecular asymmetry provides novel insights into hippocampal lateralization and its role in experience-dependent brain plasticity.

neuroscience↗

bioRxiv2022

An RFX transcription factor regulated ciliogenesis in the progenitors of choanoflagellates and animals

Little is known about the origins of the transcriptional modules that coordinate cell-type specific functions in animals. The controlled expression of one cellular feature - the cilium - was likely critical during early animal evolution. Two key transcription factors, RFX and FoxJ1, coordinate ciliogenesis in animals but are absent from the genomes of most other ciliated eukaryotes, raising the question of how the transcriptional regulation of ciliogenesis has evolved. To reconstruct the evolution of the RFX/FoxJ1 transcriptional module and its role in the regulation of ciliogenesis, we investigated RFX and FoxJ1 function in one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta. Targeted disruption of the S. rosetta RFX homolog cRFXa resulted in delayed cell proliferation and aberrant ciliogenesis, marked by the collapse and resorption of nascent cilia. Ciliogenesis genes and foxJ1 were significantly down-regulated in cRFXa mutants, consistent with a pre-animal ancestry for this transcriptional module. We also found that cRFXa protein preferentially binds to a sequence motif that is enriched in the promoters of S. rosetta ciliary genes and matches the sequence motif bound by animal RFX proteins. These findings suggest that RFX coordinated ciliogenesis before the divergence of animals and choanoflagellates, and that the deployment of this module may have provided a mechanism to differentiate ciliated and non-ciliated cell types in early animal evolution.

evolutionary biology↗

bioRxiv2021

Astroglial CD38 regulates social memory and synapse formation through SPARCL1 in the medial prefrontal cortex

Social behavior is essential for the health, survival and reproduction of animals, yet the role of astrocytes in social behavior is largely unknown. CD38 is critical for social behaviors by regulating oxytocin release from hypothalamic neurons. On the other hand, CD38 is most abundantly expressed in astrocytes especially in the postnatal cortex, and is important for astroglial development. Here, we demonstrate that astroglial CD38 plays a pivotal role in the social behavior. Selective deletion of CD38 in postnatal astrocytes, but not in adult astrocytes, specifically impaired social memory without any other behavioral abnormalities. Morphological analysis revealed reductions in spine numbers, mature spines and excitatory synapse numbers in the pyramidal neurons of the medial prefrontal cortex (mPFC) due to deletion of astroglial CD38 in the postnatal brain. Astrocyte-conditioned medium (ACM) of CD38 KO astrocytes reduced synaptogenesis of cortical neurons by reducing extracellular SPARCL1, a synaptogenic protein. Finally, the release of SPARCL1 from astrocytes is regulated by CD38/cADPR/calcium signaling. Our data indicate that astroglial CD38 developmentally regulates social memory and neural circuit formation in the developing brain by promoting synaptogenesis through SPARCL1.

neuroscience↗

bioRxiv2021

The ATF6β-calreticulin axis protects hippocampal neurons against endoplasmic reticulum stress and excitotoxicity

While ATF6 plays a central role in the endoplasmic reticulum (ER) stress response, the function of ATF6{beta} is largely unknown. Here, we demonstrate that ATF6{beta} is highly expressed in the hippocampus of the brain, and specifically regulates the expression of calreticulin, a molecular chaperone in the ER with a high Ca2+-binding capacity. Calreticulin expression was reduced to ~50% in the central nervous system of Atf6b-/- mice, and restored by ATF6{beta}. Analysis using cultured hippocampal neurons revealed that ATF6{beta} deficiency reduced Ca2+ stores in the ER and enhanced ER stress-induced death, which was rescued by ATF6{beta}, calreticulin, Ca2+-modulating reagents such as BAPTA-AM and 2-APB, and ER stress inhibitor salubrinal. In vivo, kainate-induced neuronal death was enhanced in hippocampi of Atf6b-/- and Calr+/- mice, and restored by 2-APB and salubrinal. These results suggest that the ATF6{beta}-calreticulin axis plays a critical role in the neuronal survival by improving Ca2+ homeostasis under ER stress.

cell biology↗

bioRxiv2019

Jomon genome sheds light on East Asian population history

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

genomics↗

bioRxiv2019

Exploring deep-time relationships between cultural and genetic evolution in Northeast Asia

Culture evolves in ways that are analogous to, but distinct from, genomes. Previous studies examined similarities between cultural variation and genetic variation (population history) at small scales within language families, but few studies empirically investigated such parallels across language families using diverse cultural data. We report an analysis comparing culture and genomes from in and around Northeast Asia spanning 11 language families. We extract and summarize the variation in language (grammar, phonology, lexicon), music (song structure, performance style), and genomes (genome-wide SNPs) and test for correlations. We find that grammatical structure correlates with population history. Recent contact and shared descent fail to explain the signal, suggesting relationships that arose before the formation of current families. Our results suggest that grammar might be a cultural indicator of population history, while also demonstrating differences among cultural and genetic relationships that highlight the complex nature of human history.

evolutionary biology↗

bioRxiv2018

A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes

To analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, ring finger protein 213, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome region with substantial length.

genomics↗