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Nitrite-producing oral microbiome in adults and children

Yuria Sato-Suzuki, Jumpei Washio, Dimas Prasetianto Wicaksono, Takuichi Sato, Satoshi Fukumoto, Nobuhiro Takahashi
2020 Scientific Reports  
Recently, it was suggested that the nitrite (NO2−) produced from NO3− by oral bacteria might contribute to oral and general health. Therefore, we aimed to clarify the detailed information about the bacterial NO2-production in the oral biofilm. Dental plaque and tongue-coating samples were collected, then the NO2-producing activity was measured. Furthermore, the composition of the NO2−-producing bacterial population were identified using the Griess reagent-containing agar overlay method and
more » ... ular biological method. NO2−-producing activity per mg wet weight varied among individuals but was higher in dental plaque. Additionally, anaerobic bacteria exhibited higher numbers of NO2−-producing bacteria, except in the adults' dental plaque. The proportion of NO2−-producing bacteria also varied among individuals, but a positive correlation was found between NO2−-producing activity and the number of NO2−-producing bacteria, especially in dental plaque. Overall, the major NO2−-producing bacteria were identified as Actinomyces, Schaalia, Veillonella and Neisseria. Furthermore, Rothia was specifically detected in the tongue coatings of children. These results suggest that dental plaque has higher NO2−-producing activity and that this activity depends not on the presence of specific bacteria or the bacterial compositions, but on the number of NO2−-producing bacteria, although interindividual differences were detected.
doi:10.1038/s41598-020-73479-1 pmid:33024169 fatcat:rzjxdbxrsrgx3bjxfm7m3yebrm

Approximated logarithmic maps on Riemannian manifolds and their applications

Jumpei Goto, Hiroyuki Sato
2021 JSIAM Letters  
Recently, optimization problems on Riemannian manifolds involving geodesic distances have been attracting considerable research interest. To compute geodesic distances and their Riemannian gradients, we can use logarithmic maps. However, the computational cost of logarithmic maps on Riemannian manifolds is generally higher than that on the Euclidean space. To overcome this computational issue, we propose approximated logarithmic maps. We prove that the definition is closely related to the
more » ... e retractions. Numerical experiments for computing the Riemannian center of mass show that the proposed approximation significantly reduces the computational time while maintaining appropriate precision if the data diameter is sufficiently small.
doi:10.14495/jsiaml.13.17 fatcat:3eclyvb5cbbk5kbzthxhk3e7sq

Characterization of radioresistant epithelial stem cell heterogeneity in the damaged mouse intestine

Taku Sato, Miwako Sase, Shun Ishikawa, Mihoko Kajita, Jumpei Asano, Toshiro Sato, Yoshiyuki Mori, Toshiaki Ohteki
2020 Scientific Reports  
The small intestine has a robust regenerative capacity, and various cell types serve as "cells-of-origin" in the epithelial regeneration process after injury. However, how much each population contributes to regeneration remains unclear. Using lineage tracing, we found that Lgr5-expressing cell derivatives contained radioresistant intestinal stem cells (ISCs) crucial for epithelial regeneration in the damaged intestine after irradiation. Single-cell qRT-PCR analysis showed that surviving
more » ... pressing cell derivatives in the damaged intestine are remarkably heterogeneous, and that the expression levels of a YAP-target gene Sca1 were inversely correlated with their "stemness", suggesting that the YAP/Wnt signal balance in surviving crypt epithelial cells determines the cellular contribution to epithelial regeneration. Single-cell RNA sequencing of Sca1-Lgr5-derivatives revealed that expression of a tetraspanin family member CD81 correlated well with the expression of ISC- and proliferation-related genes. Consistent with these findings, organoid-forming ability was confined to the CD81hiSca1- fraction within the damaged crypt epithelial cells. Characterization of radioresistant epithelial stem cell heterogeneity in the damaged intestine may contribute to therapeutic strategies for gastrointestinal diseases.
doi:10.1038/s41598-020-64987-1 pmid:32444673 fatcat:mat7gawqnfhbfbmy3a2zwk6cfi

漢藥の原植物について
On the Chinese medical Plants

Jumpei SATO
1954 Acta Phytotaxonomica et Geobotanica  
漢 藥 の 原 植 物 に つ い て 佐 藤 潤 卆 Ju皿 pei SATo : On the Chinese Medical Plants 私 1 食 昨 年 10月 14目 中 國 引 揚 第 七 次 船 高 砂 丸 で 31 年 振 りで 砠 國 日 本 の 人 と な つ た も の で あ る 。  ... 
doi:10.18942/bunruichiri.kj00001077691 fatcat:5pb7ekm6j5h7noyiumr5njgslu

Amorphous 2D materials containing a conjugated-polymer network

Shoichiro Yano, Kosuke Sato, Jumpei Suzuki, Hiroaki Imai, Yuya Oaki
2019 Communications Chemistry  
Two-dimensional materials, such as layered compounds and nanosheets, have attracted interest for their characteristic structures and properties. If layered materials containing functional organic molecules are synthesized, designed nanosheets can be obtained by exfoliation. Here we show the design and synthesis of an amorphous organic layered material containing a conjugated-polymer network, its exfoliation into nanosheets, and their applications. Copolymerization of benzoquinone and pyrrole
more » ... erates random stacks of the conjugated polymer layers through successive C-C bond formation and pericyclic reaction under mild conditions at 60°C. The amorphous organic layered materials are efficiently exfoliated into nanosheets in 44.6% after 1 h. The nanosheets are used as a metal-free electrocatalyst for hydrogen evolution reaction with the overpotential 0.28 V (vs. RHE). The present approach may be applied to the design of functional nanosheets with graphenelike structures under mild conditions. :,; Prior to the LSV measurement, the BQ-Py polymer was reduced to recovery of the conjugation by chronoamperometry at -0.30 V vs. RHE for 5 h. The stability of the BQ-Py nanosheet for HER was studied using the sample after cyclic voltammetry in the range from 0 to -0.3 V vs. RHE for 500 times at the scan rate 100 mV s −1 . COMMUNICATIONS CHEMISTRY | https://doi.
doi:10.1038/s42004-019-0201-9 fatcat:qib7n2r56nh4xdoffmdj7254ku

Rapid evolution of antiviral APOBEC3 genes driven by the conflicts with ancient retroviruses [article]

Jumpei Ito, Robert J Gifford, Kei Sato
2019 bioRxiv   pre-print
The evolution of antiviral genes has been fundamentally shaped by antagonistic interactions with ancestral viruses. The AID/APOBEC family genes (AID and APOBEC1-4) encode cellular cytosine deaminases that target nucleic acids and catalyze C-to-U mutations. In the case of retroviral replication, APOBEC3 proteins induce C-to-U mutations in minus-stranded viral DNA, which results in G-to-A mutations in the viral genome. Previous studies have indicated that the expansion and rapid evolution of
more » ... lian APOBEC3 genes has been driven by an arms race with retroviral parasites, but this has not been thoroughly investigated. Endogenous retroviruses (ERVs) are retrotransposons originated from ancient retroviral infections. These sequences sometimes bear the hallmarks of APOBEC3-mediated mutations, and therefore serve as a record of the ancient conflict between retroviruses and APOBEC3 genes. Here we systematically investigated the sequences of ERVs and APOBEC3 genes in mammals to reconstruct details of the evolutionary conflict between them. We identified 1,420 AID/APOBEC family genes in a comprehensive screen of mammalian genome. Of the AID/APOBEC family genes, APOBEC3 genes have been selectively amplified in mammalian genomes and disclose evidence of strong positive selection - whereas the catalytic domain was highly conserved across species, the structure loop 7, which recognizes viral DNA/RNA substrates, was shown to be evolving under strong positive selection. Although APOBEC3 genes have been amplified by tandem gene duplication in most mammalian lineages, the retrotransposition-mediated gene amplification was found in several mammals including New World monkeys and prosimian primates. Comparative analysis revealed that G-to-A mutations are accumulated in ERVs, and that the G-to-A mutation signatures on ERVs is concordant with the target preferences of APOBEC3 proteins. Importantly, the number of APOBEC3 genes was significantly correlated with the frequency of G-to-A mutations in ERVs, suggesting that the amplification of APOBEC3 genes led to stronger attacks on ERVs and/or their ancestral retroviruses by APOBEC3 proteins. Furthermore, the numbers of APOBEC3 genes and ERVs in mammalian genomes were positively correlated, and in primates, the timings of APOBEC3 gene amplification was concordant with that of ERV invasions. Our findings suggest that conflict with ancient retroviruses was a major selective pressure driving the rapid evolution of APOBEC3 genes in mammals.
doi:10.1101/707190 fatcat:n2zpmm4davgz5dfdrv54n3abfm

The Anfu Parliament's 1919 fiscal budget
民国八(1919)年度予算案の編成と安福国会

Jumpei SATO
2018 Shakai keizai shigaku  
doi:10.20624/sehs.83.4_525 fatcat:taza6hfvinh37mn7dlurft4duq

A tissue level atlas of the healthy human virome

Ryuichi Kumata, Jumpei Ito, Kenta Takahashi, Tadaki Suzuki, Kei Sato
2020 BMC Biology  
Human-resident microbes can influence both health and disease. Investigating the microbiome using next-generation sequencing technology has revealed examples of mutualism and conflict between microbes and humans. Comparing to bacteria, the viral component of the microbiome (i.e., the "virome") is understudied. Somatic tissues of healthy individuals are usually inaccessible for the virome sampling; therefore, there is limited understanding of the presence and distribution of viruses in tissues
more » ... healthy individuals and how virus infection associates with human gene expression and perturbs immunological homeostasis. To characterize the human virome in a tissue-specific manner, here we performed meta-transcriptomic analysis using the RNA-sequencing dataset from the Genotype-Tissue Expression (GTEx) Project. We analyzed the 8991 RNA-sequencing data obtained from 51 somatic tissues from 547 individuals and successfully detected 39 viral species in at least one tissue. We then investigated associations between virus infection and human gene expression and human disease onset. We detected some expected relationships; for instance, hepatitis C virus infection in the liver was strongly associated with interferon-stimulated gene upregulation and pathological findings of chronic hepatitis. The presence of herpes simplex virus type 1 in one subject's brain strongly associated with immune gene expression. While torque teno virus was detected in a broad range of human tissues, it was not associated with interferon responses. Being notable in light of its association with lymphoproliferative disorders, Epstein-Barr virus infection in the spleen and blood was associated with an increase in plasma cells in healthy subjects. Human herpesvirus 7 was often detected in the stomach; intriguingly, it associated with the proportion of human leukocytes in the stomach as well as digestive gene expression. Moreover, virus infections in the local tissues associated with systemic immune responses in circulating blood. To our knowledge, this study is the first comprehensive investigation of the human virome in a variety of tissues in healthy individuals through meta-transcriptomic analysis. Further investigation of the associations described here, and application of this analytical pipeline to additional datasets, will be useful to reveal the impact of viral infections on human health.
doi:10.1186/s12915-020-00785-5 pmid:32493363 fatcat:wgxvsz3ngbdalhqzoyumozf2rm

漢蘂の原植物について3
On the Chinese medical Plants III

Jumpei SATO
1955 Acta Phytotaxonomica et Geobotanica  
漢 藥 の 原 植 物 に つ い て 3 Jumpei SATo : On the chinese medical Plants 3 8 獨 角 蓮 1950 年 頃 か そ れ ぽ よ く わ か ら な い が 或 時 私 の 學 校 (中 國 醫 科 大 學 藥 學 院 ) の 助 理 院 長 胡 振 鏃 氏 が 獨 角 蓮 と 穩 す る サ ト イ モ に 類 似 し た 地 下 莖 の  ... 
doi:10.18942/bunruichiri.kj00001077713 fatcat:kl7k7ijb3bdlzdfi66vj5ddkza

The Battle between Retroviruses and APOBEC3 Genes: Its Past and Present

Keiya Uriu, Yusuke Kosugi, Jumpei Ito, Kei Sato
2021 Viruses  
However, Ito, Gifford, and Sato [62] and Yang et al.  ...  However, Ito, Gifford, and Sato [62] and Yang et al.  ... 
doi:10.3390/v13010124 pmid:33477360 fatcat:awx4ikeqbnfb7gol4gqndk5qxm

Vital signs monitoring during injectable and inhalant anesthesia in mice

Atsushi TSUKAMOTO, Kazuya SERIZAWA, Reiichiro SATO, Jumpei YAMAZAKI, Tomo INOMATA
2015 Experimental animals  
Selecting the appropriate anesthetic protocol for the individual animal is an essential part of laboratory animal experimentation. The present study compared the characteristics of four anesthetic protocols in mice, focusing on the vital signs. Thirty-two male ddY mice were divided into four groups and administered anesthesia as follows: pentobarbital sodium monoanaesthesia; ketamine and xylazine combined (K/X); medetomidine, midazolam, and butorphanol combined (M/M/B); and isoflurane. In each
more » ... roup, rectal temperature, heart rate, respiratory rate, and O 2 saturation (SPO 2 ) were measured, and the changes over time and instability in these signs were compared. The anesthetic depth was also evaluated in each mouse, and the percentage of mice achieving surgical anesthesia was calculated. K/X anesthesia caused remarkable bradycardia, while the respiratory rate and SPO 2 were higher than with the others, suggesting a relatively strong cardiac influence and less respiratory depression. The M/M/B group showed a relatively lower heart rate and SPO 2 , but these abnormalities were rapidly reversed by atipamezole administration. The pentobarbital group showed a lower SPO 2 , and 62.5% of mice did not reach a surgical anesthetic depth. The isoflurane group showed a marked decrease in respiratory rate compared with the injectable anesthetic groups. However, it had the most stable SPO 2 among the groups, suggesting a higher tidal volume. The isoflurane group also showed the highest heart rate during anesthesia. In conclusion, the present study showed the cardiorespiratory characteristics of various anesthetic protocols, providing basic information for selecting an appropriate anesthetic for individual animals during experimentation.
doi:10.1538/expanim.14-0050 pmid:25312399 pmcid:PMC4329516 fatcat:5znxmnc7nzeafhuftb7dyuvx3u

Supplementary Information from Biochemical analysis of nucleosome targeting by Tn5 transposase

Shoko Sato, Yasuhiro Arimura, Tomoya Kujirai, Akihito Harada, Kazumitsu Maehara, Jumpei Nogami, Yasuyuki Ohkawa, Hitoshi Kurumizaka
2019 Figshare  
Tn5 transposase is a bacterial enzyme that integrates a DNA fragment into genomic DNA, and is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes. However, in chromatin, the DNA targeting by Tn5 transposase has remained unclear. In the present study, we reconstituted well-positioned 601 dinucleosomes, in which two nucleosomes are connected with a linker DNA, and studied the DNA integration sites in the dinucleosomes by Tn5 transposase in vitro. We found that Tn5
more » ... nsposase preferentially targets near the entry–exit DNA regions within the nucleosome. Tn5 transposase minimally cleaved the dinucleosome without a linker DNA, indicating that the linker DNA between two nucleosomes is important for the Tn5 transposase activity. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry–exit sites of the nucleosome. Intriguingly, this Tn5-targeting characteristic is conserved in a dinucleosome substrate with a different DNA sequence from the 601 sequence. Therefore, the Tn5-targeting preference in the nucleosomal templates reported here provides important information for the interpretation of Tn5 transposase-based genomics methods, such as ATAC-seq.
doi:10.6084/m9.figshare.9462290 fatcat:fo3im74qinajhgky6qb6452pue

Biochemical analysis of nucleosome targeting by Tn5 transposase

Shoko Sato, Yasuhiro Arimura, Tomoya Kujirai, Akihito Harada, Kazumitsu Maehara, Jumpei Nogami, Yasuyuki Ohkawa, Hitoshi Kurumizaka
2019 Open Biology  
Tn5 transposase is a bacterial enzyme that integrates a DNA fragment into genomic DNA, and is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes. However, in chromatin, the DNA targeting by Tn5 transposase has remained unclear. In the present study, we reconstituted well-positioned 601 dinucleosomes, in which two nucleosomes are connected with a linker DNA, and studied the DNA integration sites in the dinucleosomes by Tn5 transposase in vitro. We found that Tn5
more » ... nsposase preferentially targets near the entry-exit DNA regions within the nucleosome. Tn5 transposase minimally cleaved the dinucleosome without a linker DNA, indicating that the linker DNA between two nucleosomes is important for the Tn5 transposase activity. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry-exit sites of the nucleosome. Intriguingly, this Tn5-targeting characteristic is conserved in a dinucleosome substrate with a different DNA sequence from the 601 sequence. Therefore, the Tn5-targeting preference in the nucleosomal templates reported here provides important information for the interpretation of Tn5 transposase-based genomics methods, such as ATAC-seq.
doi:10.1098/rsob.190116 pmid:31409230 pmcid:PMC6731594 fatcat:xetifey3vbcxvfvut3xbc6kl44

Studies on the Detoxicating Hormone of the Liver (Yakriton)

Akira Sato, Michishiro Yamagishi, Jumpei Abe
1936 Tohoku journal of experimental medicine  
Sato. Tob oku J. Exp.  ...  Sato, a boy of 9 years and 2 months, admitted to the Hospital on the 8th day of the disease under the diagnosis scarlatina. When and how yakriton was used in each case.  ... 
doi:10.1620/tjem.28.156 fatcat:lnagn25y7bekrnhfjbfekkr5dy

Supplementary Information from Biochemical analysis of nucleosome targeting by Tn5 transposase

Shoko Sato, Yasuhiro Arimura, Tomoya Kujirai, Akihito Harada, Kazumitsu Maehara, Jumpei Nogami, Yasuyuki Ohkawa, Hitoshi Kurumizaka
2019 Figshare  
Tn5 transposase is a bacterial enzyme that integrates a DNA fragment into genomic DNA, and is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes. However, in chromatin, the DNA targeting by Tn5 transposase has remained unclear. In the present study, we reconstituted well-positioned 601 dinucleosomes, in which two nucleosomes are connected with a linker DNA, and studied the DNA integration sites in the dinucleosomes by Tn5 transposase in vitro. We found that Tn5
more » ... nsposase preferentially targets near the entry–exit DNA regions within the nucleosome. Tn5 transposase minimally cleaved the dinucleosome without a linker DNA, indicating that the linker DNA between two nucleosomes is important for the Tn5 transposase activity. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry–exit sites of the nucleosome. Intriguingly, this Tn5-targeting characteristic is conserved in a dinucleosome substrate with a different DNA sequence from the 601 sequence. Therefore, the Tn5-targeting preference in the nucleosomal templates reported here provides important information for the interpretation of Tn5 transposase-based genomics methods, such as ATAC-seq.
doi:10.6084/m9.figshare.9120032.v1 fatcat:a7fdrb5wt5d4to7upon737oyja
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