Biology subjects

Kumagai, H.

Publications and source records attributed to Kumagai, H..

4 recordsLinked to original sources

bioRxiv2026

Evaluation of fluorescent proteins for compatibility with STED microscopy systems using two-color spectroscopies

Stimulated emission depletion (STED) microscopy is a super-resolution fluorescence imaging technique that achieves high spatial and temporal resolution by exploiting stimulated emission to induce fluorescence depletion (FD) and is expected to have substantial utility for imaging applications using fluorescent proteins. However, the compatibility of fluorescent proteins with STED microscopy systems has been understood primarily through empirical observations, and there is no established methodology for the rational selection of fluorescent proteins for STED microscopy. In this study, we systematically evaluated the compatibility of commonly used fluorescent proteins with STED microscopy systems by measuring FD properties using transient absorption spectroscopy and fluorescence dip spectroscopy, both of which are classified as two-color spectroscopy (TCS). Fluorescent proteins identified as compatible with the STED microscopy system based on the TCS measurements were employed for three-dimensional STED imaging of cellular samples expressing each protein. In all samples, three-dimensional spatial resolution was improved relative to confocal laser microscopy, with particularly marked improvements in z-axis resolution. These findings demonstrate that measurements of FD properties via TCS provide a robust approach for evaluating the compatibility of fluorescent proteins with the STED microscopy system and for selecting suitable fluorescent proteins for STED imaging.

biophysics↗

bioRxiv2026

Nuclear Mitochondrial Interaction Test Reveals Sex-Dependent Mitochondrial SNPs Interacting with Klotho Variants on Diabetes Risk

ContextThe environmental or other genetic factors might influence the effect of Klotho (KL) on glucose metabolism. ObjectiveWe investigated mitochondrial genetic variants that interact with KL single nucleotide polymorphisms (SNPs) to modulate diabetes risk. MethodsWe used the data from 7,047 non-Hispanic white participants of the Health and Retirement Study, a prospective observational study including adults aged 50 years and older from the United States. First, we performed single gene-wide association scans to identify KL SNPs associated with diabetes. Next, we performed a nuclear-by-mitochondrial interaction test (NuMIT) in which we use an identified KL SNP from the gene-wide scan to evaluate potential interactions with 85 mitochondrial SNPs in relation to diabetes. ResultsWe failed to identify a significant association between diabetes and the KL SNP in our single gene-wide association test. However, we identified a novel variant (KL rs9563121) which showed a trend of increasing klotho mRNA levels with each additional minor allele. A NuMIT analysis identified mitochondrial SNPs, which showed significant interactions with rs9563121 in relation to diabetes risk. MitoG15929A showed significant interactions with rs9563121 in both men and women. MitoG15929A diminished the potential beneficial effect of KL rs9563121 on diabetes risk in women. Among men with the MitoG15929A variant, KL rs9563121 was associated with higher prevalence of diabetes. ConclusionThe NuMIT approach revealed significant interactions between mitochondrial and nuclear DNA variants of KL. Furthermore, MitoG15929A may have a role in the interaction between diabetes and KL in a sex-dependent manner.

genetics↗

bioRxiv2023

Characteristics of the rumen virome in Japanese cattle

The rumen microbiome is a highly complex ecosystem that includes bacteria, archaea, protozoa, fungi, and viruses. Viruses have a high potential to modify the rumen digestion of feeds via infection and cell lysis of prokaryotes in the rumen; however, understanding of the rumen virome is substantially less advanced due to limitations of the reference genome database. In this study, we conducted metagenomic sequencing of virus-like particles (VLPs) in the rumens of 22 Japanese cattle to construct a reference viral genome catalog of the rumen and uncover the rumen virome characteristics. We succeeded in construction of 8 232 nonredundant viral genomes ([≥]5 kb length and [≥]50% completeness). Among them, putative hosts of 1 223 virus genomes were predicted, and 1 053 virus genomes were taxonomically classified, mainly Siphoviridae, Myoviridae, and Podoviridae. Additionally, 2 764 putative auxiliary metabolic genes (AMGs) were identified in the viral genomes. Importantly, 22 viral genomes associated with archaea in the rumen were identified. Some archaeal viruses have AMGs related to DNA synthesis, suggesting that archaeal viruses control archaeal populations in the rumen and affect methane production from the rumen. Furthermore, we revealed that most rumen viruses were highly rumen-and individual-specific and related to rumen-specific prokaryotes. Overall, the rumen viral catalog and findings of this study will help future analyses to uncover the roles of rumen viruses in feed digestion, productivity, and methane production.

microbiology↗

bioRxiv2019

A Pro-Diabetogenic mtDNA Polymorphism in the Mitochondrial-Derived Peptide, MOTS-c

Type 2 Diabetes (T2D) is an emerging public health problem in Asia. An Asian mitochondrial DNA variation m.1382A>C (rs111033358) leads to a K14Q amino acid replacement in MOTS-c, an insulin sensitizing mitochondrial-derived peptide. Meta-analysis of three cohorts (n=27,527, J-MICC, MEC, and TMM) showed that males but not females with the C-allele exhibit a higher prevalence of T2D. Furthermore, in J-MICC, only males with the C-allele in the lowest tertile of physical activity increased their prevalence of T2D, demonstrating a kinesio-genomic interaction. High-fat fed, male mice injected with MOTS-c showed reduced weight and improved glucose tolerance, but not K14Q-MOTS-c treated mice. Like the human data, female mice were unaffected. Mechanistically, K14Q-MOTS-c leads to diminished insulin-sensitization in vitro. Thus, the m.1382A>C polymorphism is associated with susceptibility to T2D in men, possibly interacting with exercise, and contributing to the risk of T2D in sedentary males by reducing the activity of MOTS-c.

genetics↗