Biology subjects

Kawato, S.

Publications and source records attributed to Kawato, S..

5 recordsLinked to original sources

bioRxiv2026

gbdraw: a genome diagram generator for microbes and organelles

MotivationGenerating graphical diagrams of microbial and organellar genomes is a common and essential task in bioinformatics. Existing tools often present a trade-off; while powerful programming libraries that require coding skills, graphical applications require server processing or local installation with complex dependency. This highlights the need for a tool that offers both programmatic control for batch processing and graphical accessibility for ease of use. ResultsTo fill this gap, I developed gbdraw, a web application that generates circular and linear genome diagrams from self-contained GenBank or DDBJ files or combinations of GFF3 annotation and FASTA sequence files. Its core functions include visualizing annotated features, plotting GC content/skew tracks, and optionally generating pairwise sequence comparisons for comparative genomics. It is available as both a GUI web application and a command-line utility. Unlike existing web-based tools that require data upload to a remote server, gbdraw operates entirely within the users web browser. This serverless architecture ensures that sensitive sequence data never leaves the local machine, providing a secure environment for visualizing unpublished genomic data. Availability and Implementationgbdraw is implemented in Python 3 (version 3.10+) and is freely available under the MIT license. The web app is available at https://gbdraw.app/. Source code and documentation are available at https://github.com/satoshikawato/gbdraw. The local version can be installed from the Bioconda channel using a conda-compatible package manager.

bioinformatics↗

bioRxiv2025

Age-related decline of synaptic plasticity is regulated by neuro-androgen and neuro-estrogen in normal aging of hippocampus

We revealed a good relationship between age-dependent decrease in the hippocampal dendritic spine density and age-dependent decrease in hippocampal androgen and estrogen levels with normal aging of male rats. Approximately 25% decrease in the spine density was observed in hippocampal CA1 region by going from 3 month-old (3m; young adult) to 24 month-old (24m; aged). We found a significant age-induced decrease in hippocampal neuro-androgen levels by going from 3m to 24 m using mass-spectrometric analysis. The hippocampal levels of testosterone (T) and dihydrotestosterone (DHT) dramatically decreased from 17 nM T and 7 nM DHT at 3 m to 17/100 nM T and 7/15 nM DHT at 24 m. On the other hand, hippocampal estradiol (E2) was moderately decreased with aging, from 8 nM at 3 m to 2 nM at 24m. Comprehensive analysis of mRNAs of hippocampal steroidogenic enzymes and receptors showed an age-dependent decrease in their expression levels by approximately 50% (P450(17)), 25% (17-hydroxysteroid dehydrogenase) and 0% (5-reductase and P450arom). Androgen receptor AR was moderately decreased but estrogen receptor ER was not decreased with aging. The 25% decrease in the spine density with aging may be due to a balance between considerably decreased T and DHT levels (spine decrease factor) and remained moderately high E2 level (spine increase factor) in the 24m hippocampus. Aged hippocampus still has moderate capacity of sex-steroid synthesis and their functions. Interestingly, DHT-supplementation and T-supplementation recovered the spine density at 24m.

neuroscience↗

bioRxiv2025

Rethinking synthesis and function of neuro-estrogen and neuro-androgen in the hippocampus: some methodological problems and possible solutions

Local synthesis and action of neuro-estrogen and neuro-androgen (including neuro-estradiol (nE2) and neuro-testosterone (nT) have become recognized as key mechanisms in modulation of neural plasticity and cognitive performance, in addition to the contribution of circulating sex steroids. However, still several methodological problems are left to be solved in order to get an better understanding of functions of neural sex steroids in the brain. Here we describe and discuss important improvements in the methods for determination of accurate concentrations of nE2 and nT in rat hippocampus (Section 1), and in methods for analysis of the dendritic spine density in castrated male rat hippocampus (Section 2). The improvements are discussed in order to solve the following two problems. One problem is that the previously reported nE2 concentrations in the hippocampus were widely distributed between [~]3 pg/g tissue and [~]2 ng/g tissue (i.e., between [~]11 pM and [~]7 nM) (Section 1). The other problem is that the degree of decrease in hippocampal spine density by castration in male rat hippocamps was strongly dependent on surgical skills of operators (surgeons) (Section 2).

neuroscience↗

bioRxiv2024

Inhibition of PDE5 induces rapid non-genomic increase in hippocampal dendritic spines via specific kinases

Cyclic guanosine monophosphate (cGMP) is a typical neuromodulator that is used in neuronal synapses. Inhibitor of phosphodiesterase 5 (PDE5) could regulates signaling pathways by elevating cGMP levels. In the current study, we found that the treatments with tadalafil, a PDE5 inhibitor, for 2 h rapidly and non-genomically increased the total density of dendritic spines, using confocal imaging of Lucifer Yellow-injected hippocampal CA1 pyramidal neurons. Since inhibition of PDE5 elevates cGMP levels at synapses, we analyzed downstream nongenomic signaling. We analyzed the involvement of kinase signaling, because rapid postsynaptic modulation often involves kinase networks as observed from many investigations of synaptic functions. Upon co-treatments of PKG inhibitor (KT5823) with tadalafil, the spine increase was considerably blocked. In addition, co-treatments of GSK-3 inhibitor (I8) also blocked the spine increase induced by tadalafil. However, inhibitors of other representative synaptic kinases, including LIMK, Erk/MAPK, PKA, PKC and PI3K, did not suppress the tadalafil-induced spine increases. PDE5 inhibitors have attracted attention on their recovery effects from pathological damages, including memory improvement from cognitive impairment by Stroke, Amyloid beta accumulation and tau phosphorylation. The current finding of tadalafil function about rapid modulation of neural plasticity may add new elemental steps of anti-aging capacity against cognitive decline.

neuroscience↗

bioRxiv2023

Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans

Crustacean genomes harbor sequences originating from nimaviruses, a family of large double-stranded DNA viruses infecting crustaceans. In this study, we recovered metagenome-assembled genomes of 25 endogenous nimaviruses from crustacean genome data. Phylogenetic analysis revealed four major lineages within Nimaviridae, and for three of these lineages, we propose novel genera of endogenous nimaviruses: "Majanivirus" and "Pemonivirus" identified from penaeid shrimp genomes, and "Clopovirus" identified from terrestrial isopods. Majanivirus genomes contain multiple eukaryotic-like genes such as baculoviral inhibitor of apoptosis repeat-containing genes, innexins, and heat shock protein 70-like genes, some of which contain introns. An alignment of long reads revealed that that each endogenous nimavirus species specifically inserts into host microsatellites or within 28S rDNA. This insertion preference was associated with the type of virus-encoded DNA recombination enzymes, the integrases. Majaniviruses, pemoniviruses, some whispoviruses, and possibly clopoviruses specifically insert into the arthropod telomere repeat motif (TAACC/GGTTA)n and all possessed a specific tyrosine recombinase family. Pasiphaea japonica whipovirus and Portunus trituberculatus whispovirus, the closest relatives of white spot syndrome virus, integrate into the host 28S rDNA and are equipped with members of another family of tyrosine recombinases that are distantly related to telomere-specific tyrosine recombinases. Endogenous nimavirus genomes identified from sesarmid crabs, which lack tyrosine recombinases and are flanked by a 46-bp inverted terminal repeat, integrate into (AT/TA)n microsatellites through the acquisition of a Ginger2-like cut- and-paste DDE transposase. These results suggest that endogenous nimaviruses are giant transposable elements that occupy different sequence niches through the acquisition of different integrase families. ImportanceCrustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.

microbiology↗