Details of a Researcher - Tomita, Masaru

Papers - Tomita, Masaru

Division display 41 - 60 of about 520 ／ All the affair displays >>

Relationship between standard uptake values of positron emission tomography/computed tomography and salivary metabolites in oral cancer: A pilot study

Ishikawa S., Hiraka T., Kirii K., Sugimoto M., Shimamoto H., Sugano A., Kitabatake K., Toyoguchi Y., Kanoto M., Nemoto K., Soga T., Tomita M., Iino M.

Journal of Clinical Medicine (Journal of Clinical Medicine) 9 ( 12 ) 1 - 8 2020.12

ISSN 2077-0383

18F-fluorodeoxyglucose (18F-FDG) positron emission tomography (PET)/computed tomography (CT) is usually used for staging or evaluation of treatment response rather than for cancer screening. However,18F-FDG PET/CT has also been used in Japan for cancer screening in people with no cancer symptoms, and accumulating evidence supports this application of18F-FDG PET/CT. Previously, we have observed a correlation between the saliva and tumor metabolomic profiles in patients with oral cancer. Hence, if salivary metabolites demonstrate a significant correlation with PET parameters such as the maximum standardized uptake value (SUVmax), they may have the potential to be used as a screening tool before PET/CT to identify patients with high SUVmax. Hence, in this study, we aimed to explore the relationship between salivary metabolites and SUVmax of18F-FDG PET/CT using previously collected data.18F-FDG PET/CT was performed for staging 26 patients with oral cancer. The collected data were integrated and analyzed along with quantified salivary hydrophilic metabolites obtained from the same patients with oral cancer and controls (n = 44). In total, 11 metabolites showed significant correlations with SUVmax in the delayed phases. A multiple logistic regression model of the two metabolites showed the ability to discriminate between patients with oral cancer and controls, with an area under the receiver operating characteristic curve of 0.738 (p = 0.001). This study uniquely confirmed a relationship between salivary metabolites and SUVmax of PET/CT in patients with oral cancer; salivary metabolites were significantly correlated with SUVmax. These salivary metabolites can be used as a screening tool before PET/CT to identify patients with high SUVmax, i.e., to detect the presence of oral cancer.

Access to Document (DOI)

Comprehensive dipeptide analysis revealed cancer-specific profile in the liver of patients with hepatocellular carcinoma and hepatitis

Ozawa H., Hirayama A., Shoji F., Maruyama M., Suzuki K., Yamanaka-Okumura H., Tatano H., Morine Y., Soga T., Shimada M., Tomita M.

Metabolites (Metabolites) 10 ( 11 ) 1 - 11 2020.11

ISSN 2218-1989

As the physical properties and functionality of dipeptides differ from those of amino acids, they have attracted attention in metabolomics; however, their functions in vivo have not been clarified in detail. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, and its major cause is chronic hepatitis. This study was conducted to explore tumor-specific dipeptide characteristics by performing comprehensive dipeptide analysis in the tumor and surrounding nontumor tissue of patients with HCC. Dipeptides were analyzed by liquid chromatography tandem mass spectrometry and capillary electrophoresis tandem mass spectrometry. Principal component analysis using 236 detected dipeptides showed differences in the dipeptide profiles between nontumor and tumor tissues; however, no clear difference was observed in etiological comparison. In addition, the N-and C-terminal amino acid compositions of the detected dipeptides significantly differed, suggesting the substrate specificity of enzyme proteins, such as peptidase. Furthermore, hepatitis-derived HCC may show a characteristic dipeptide profile even before tumor formation. These results provide insight into HCC pathogenesis and may help identify novel biomarkers for diagnosis.

Access to Document (DOI)

Effects of feed crops and boiling on chicken egg yolk and white determined by a metabolome analysis

Ogura T., Wakayama M., Ashino Y., Kadowaki R., Sato M., Soga T., Tomita M.

Food Chemistry (Food Chemistry) 327 127077 2020.10

ISSN 03088146

Compositional analyses of eggs have primarily focused on nutritional components, including large molecules, such as proteins. However, few reports have investigated the effects of heating and hen feed crops on taste components, such as free amino acids and sugars. Herein, water-soluble metabolites in raw and boiled eggs produced from chickens raised with corn- or rice-fed were analyzed. Each egg was separated into yolk and white, and freeze-dried samples were analyzed by CE-MS and LC-MS. Abundant metabolites included amino acids in yolks and sugars in whites. Compared to corn-fed, rice-fed resulted in three times higher betaine and uridine monophosphate concentrations in yolks and whites, respectively. Boiled whites contained more than four times higher concentrations of amino acids and fructose than raw whites. Metabolites in yolks exhibited minimal changes after boiling. Our findings support the use of water-soluble metabolomics to evaluate the effects of heating and feed crops on taste components.

Access to Document (DOI)

Conjunctival injection reduction in patients with atopic keratoconjunctivitis due to synergic effect of bovine enteric-coated lactoferrin in 0.1% tacrolimus ophthalmic suspension

Fujishima H., Okada N., Matsumoto K., Shimizu E., Fukuda S., Tomita M.

Journal of Clinical Medicine (Journal of Clinical Medicine) 9 ( 10 ) 1 - 9 2020.10

ISSN 2077-0383

Lactoferrin (LF), a multifunctional glycoprotein found in mammalian milk, is reported to have immunoregulatory effects. The present study aimed to evaluate whether enteric-coated LF (eLF) could improve symptoms in patients with atopic keratoconjunctivitis (AKC). This randomized double-blind placebo-controlled single-center trial comprised Japanese patients (n = 20; aged 22–60 years) with AKC. Patients treated with 0.1% tacrolimus ophthalmic suspension (TALYMUS®) were administered eLF (400 mg/d of bovine LF) or placebo tablets for 12 weeks. Conjunctival injection was examined, papillae formation in the palpebral conjunctiva was evaluated, and corneal fluorescein score, itchy sensation in end-point itching scale, and serum allergic parameters were assessed. Conjunctival injection was significantly reduced in the LF group than in the placebo group (p = 0.0017, Mann–Whitney U-test). Papillae formation in the palpebral conjunctiva showed a statistical decrease in the LF group than in the placebo group (p = 0.010, unpaired T-test). LF combined with TALYMUS® could be a promising treatment strategy to mitigate AKC.

Access to Document (DOI)

Pre-treatment with D942, a furancarboxylic acid derivative, increases desiccation tolerance in an anhydrobiotic tardigrade Hypsibius exemplaris

Kondo K., Mori M., Tomita M., Arakawa K.

FEBS Open Bio (FEBS Open Bio) 10 ( 9 ) 1774 - 1781 2020.09

The tardigrade Hypsibius exemplaris can undergo anhydrobiosis. Several chemicals that inhibit successful anhydrobiosis in H. exemplaris have been identified, and these chemicals inhibit the activity of signaling molecules. In the present study, we investigated whether upregulation of the activity of these signaling molecules could improve desiccation tolerance of H. exemplaris. Pre-treatment with an indirect activator of AMP-activated protein kinase [AMPK; which directly inhibits mammalian NAD(P)H dehydrogenase [quinone] 1 [NQO1] of mitochondrial complex I (D942)] significantly improved desiccation tolerance of H. exemplaris, whereas a direct activator of AMPK did not. To elucidate the underlying molecular mechanisms, we examined the proteome of tardigrades treated with D942. Two proteins, putative glutathione S-transferase and pirin-like protein, were upregulated by treatment. Both of these proteins are known to be associated with the response to oxidative stress. One of the downregulated proteins was serine/threonine-proteinphosphatase 2A (PP2A) 65-kDa regulatory subunit A alpha isoform, and it is interesting to note that PP2A activity was previously suggested to be required for successful anhydrobiosis in H. exemplaris. Taken together, our results suggest that D942 treatment may partially induce responses common to those of desiccation stress. The identification of a chemical that improves desiccation tolerance of H. exemplaris may facilitate further investigation into desiccation tolerance mechanisms.

Access to Document (DOI)

Comprehensive Dipeptide Profiling and Quantitation by Capillary Electrophoresis and Liquid Chromatography Coupled with Tandem Mass Spectrometry

Ozawa H., Hirayama A., Ishikawa T., Kudo R., Maruyama M., Shoji F., Doke T., Ishimoto T., Maruyama S., Soga T., Tomita M.

Analytical Chemistry (Analytical Chemistry) 92 ( 14 ) 9799 - 9806 2020.07

ISSN 00032700

Dipeptides have attracted much attention as post-amino acids with physical properties and functions different from those of amino acids. However, a given dipeptide cannot be distinguished by mass spectrometry from its structural isomer with an opposite amino acid binding order unless these isomers are separated before introduction, which complicates the comprehensive analysis of dipeptides. Herein, a novel analytical platform for dipeptide analysis by capillary electrophoresis tandem mass spectrometry and liquid chromatography tandem mass spectrometry is developed. This method is used to quantitate 335 dipeptides and achieves excellent separation of structural isomers with opposite binding orders, high correlation coefficients, and low instrumental detection limits (0.088-83.1 nM). Moreover, acceptable recoveries (70-135%) are observed for most tested dipeptides in chicken liver samples spiked both before and after preparation. The developed method is also applied to the quantitation of dipeptides in the livers of mice fed different diets to detect 236 dipeptides, and the shift from a normal diet to a high-fat diet is shown to increase/decrease (p < 0.05, fold-change < 0.5) the contents of 0/29 dipeptides, respectively. The developed method is expected to facilitate the search for new dipeptide applications such as novel functional components of foods and biomarkers of diseases.

Access to Document (DOI)

Base editors for simultaneous introduction of C-to-T and A-to-G mutations

Sakata R.C., Ishiguro S., Mori H., Tanaka M., Tatsuno K., Ueda H., Yamamoto S., Seki M., Masuyama N., Nishida K., Nishimasu H., Arakawa K., Kondo A., Nureki O., Tomita M., Aburatani H., Yachie N.

Nature Biotechnology (Nature Biotechnology) 38 ( 7 ) 865 - 869 2020.07

ISSN 10870156

Access to Document (DOI)

Draft Genome Sequence of Geobacter sp. Strain SVR, Isolated from Antimony Mine Soil

Warashina T., Harada M., Nakajima N., Yamamura S., Tomita M., Suzuki H., Amachi S.

Microbiology Resource Announcements (Microbiology Resource Announcements) 9 ( 26 ) 2020.06

Access to Document (DOI)

The use of a double coaxial electrospray ionization sprayer improves the peak resolutions of anionic metabolites in capillary ion chromatography-mass spectrometry

Hirayama A., Tabata S., Kudo R., Hasebe M., Suzuki K., Tomita M., Soga T.

Journal of Chromatography A (Journal of Chromatography A) 1619 460914 2020.05

ISSN 00219673

Recently, ion chromatography coupled with mass spectrometry has been used for the determination of anionic metabolites. However, connection with a mass spectrometer in this method is not straightforward because backpressure produced by the addition of a make-up solution often affects the peak resolutions of the target metabolites. To overcome this problem, we developed a capillary ion chromatography-mass spectrometry method utilizing a double coaxial electrospray ionization sprayer. This method was not affected by backpressure and the number of theoretical plates was about three times that of a conventional sprayer. Under optimized conditions, 44 anionic metabolites, including organic acids, sugar phosphates, nucleotides, and cofactors, were successfully separated and selectively detected with a Q Exactive mass spectrometer. The calibration curves of the tested metabolites showed excellent linearity within the range of 1–100,000 nmol/L and the correlation coefficient was greater than 0.991. The detection limits for these metabolites were between 1 and 500 nmol/L (0.4 and 200 fmol). The developed method was applied to the quantitation of anionic metabolites in cultured cancer cell samples with tumor necrosis factor (TNF)-α stimulation. This allowed for the successful determination of 105 metabolites. The levels of tricarboxylic acid cycle intermediates changed significantly after TNF-α stimulation. These results demonstrate that the developed method is a promising new tool for comprehensive analysis of anionic metabolites.

Access to Document (DOI)

Effect of blanching on the concentration of metabolites in two parts of Undaria pinnatifida, Wakame (leaf) and Mekabu (sporophyll)

Hamid S.S., Wakayama M., Ashino Y., Kadowaki R., Soga T., Tomita M.

Algal Research 47 2020.05

ISSN 22119264

Undaria pinnatifida is a seaweed native to Japan, where it is cultivated and sold commercially as food. Fresh seaweed commonly blanches before consumption. However, the effects of blanching on metabolites present in different parts of U. pinnatifida, namely, Wakame (leaf) and Mekabu (sporophyll), are not well understood. Here, we investigated changes in metabolites in these two seaweed parts after blanching for different periods. The samples were freeze-dried and extracted using methanol-water, and metabolite concentration was quantitated using liquid chromatography mass spectrometry and capillary electrophoresis mass spectrometry. The concentration of most metabolites was the highest in raw samples, decreasing drastically within 20 s of blanching in Wakame and decreasing gradually in Mekabu. In contrast, the concentration of some fatty acids, such as octanoate, increased in both parts. During blanching, seaweed color changed from brown to green, and blanching did not significantly affect amino acid or the sugar composition. Finally, a relationship was found between metabolite and blanching-related characteristics, such as color and drying percentage.

Access to Document (DOI)

Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress

Murai J., Zhang H., Pongor L., Tang S.W., Jo U., Moribe F., Ma Y., Tomita M., Pommier Y.

Cell Reports (Cell Reports) 30 ( 12 ) 4137 - 4151.e6 2020.03

Access to Document (DOI)

Sensory properties and metabolomic profiles of dry-cured ham during the ripening process

Sugimoto M., Sugawara T., Obiya S., Enomoto A., Kaneko M., Ota S., Soga T., Tomita M.

Food Research International (Food Research International) 129 108850 2020.03

ISSN 09639969

Dry-cured ham with a long ripening period is a valuable product worldwide. Ripening time is a key determinant of the endogenous metabolites that characterize the flavor and taste of ham products. While various studies have analyzed the relationship between ripening duration and sensory characteristics, no studies have evaluated ham products produced in Japan. Here, we conducted time-course metabolomic profiling, taste sensor-based analyses, and sensory evaluations by non-trained consumers during ripening. Capillary electrophoresis-mass spectrometry was used to quantify non-volatile metabolites, such as amino acids, organic acids, and nucleotides. In an analysis of eight time-points during 680 days of ripening, the highest score for the after-taste of umami was observed on day 540, despite subtle changes in the scores for other properties. The concentrations of aspartic acid and glutamic acid relative to those of total amino acids were the highest at this point. This approach can contribute to the understanding of the relationship between the metabolite profile and ripening duration.

Access to Document (DOI)

Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics

Masuda T., Sugiyama N., Tomita M., Ohtsuki S., Ishihama Y.

Journal of Proteome Research (Journal of Proteome Research) 19 ( 1 ) 75 - 84 2020.01

ISSN 15353893

We found that nuclear envelopes stabilize against surfactants in the presence of ethylene glycol (EG). We, therefore, developed a novel subcellular fractionation approach for proteomics using RIPA buffer containing EG and phase transfer surfactants. This method involves separating the cells into the cytoplasm, organelles, and nucleus, including intermediate filaments without ultracentrifugation. These fractions are directly applicable to sample preparation for shotgun proteomics as they have no mass spectrometry (MS)-incompatible chemicals, whereas those separated by traditional fractionation protocols require desalting. This protocol is successfully applied to subcellular fractionation with only 3.5 × 10 cells. Here, it was combined with phosphoproteomics and proteomics to identify phosphorylation sites regulating protein subcellular localization. In total, 59 phosphorylation sites on 42 phosphopeptides and 32 proteins showing different enrichment patterns between phosphoproteomics and the corresponding proteomics were identified, which are potential candidate sites to regulate the protein subcellular localization, including serine 706 on CD44 and serine 22 on lamin A/C. 5

Access to Document (DOI)

Stable mutants of restriction-deficient/modification-proficient Bacillus subtilis 168: Hub strains for giant DNA engineering

Itaya M., Sato M., Watanabe S., Yoshikawa H., Tomita M., Sato R.

Journal of Biochemistry (Journal of Biochemistry) 25 ( 1 ) 231 - 236 2020.01

ISSN 0021924X

Bacillus subtilis 168 has been explored as a platform for the synthesis and transmission of large DNA. Two inherent DNA incorporation systems, natural transformation and pLS20-based conjugation transfer, enable rapid handling of target DNA. Both systems are affected by the Bsu restriction-modification system that recognizes and cleaves unmethylated XhoI sites, limiting the choice of target DNA. We constructed B. subtilis 168 with stable mutation for restriction-deficient and modification-proficient (r m ). It was demonstrated that the r m strains can incorporate and transfer synthesized DNA with multiple XhoI sites. These should be of value as hub strains to integrate and disseminate giant DNA between B. subtilis 168 derivatives. - + - +

Access to Document (DOI)

Does the Gut Microbiota Modulate Host Physiology through Polymicrobial Biofilms?

Yang J, Yang Y, Ishii M, Nagata M, Aw W, Obana N, Tomita M, Nomura N, Fukuda S.

Microbes Environ 2020

Access to Document (DOI)

Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals

Tsukimi T, Watabe T, Tanaka K, Sato MP, Suzuki H, Tomita M, Fukuda S.

J Genomics 8 37 - 42 2020

ISSN 1839-9940

Access to Document (DOI)

Comparison of the transcriptomes of two tardigrades with different hatching coordination

Yoshida Y., Sugiura K., Tomita M., Matsumoto M., Arakawa K.

BMC Developmental Biology (BMC Developmental Biology) 19 ( 1 ) 24 2019.12

Background: Tardigrades are microscopic organisms, famous for their tolerance against extreme environments. The establishment of rearing systems of multiple species has allowed for comparison of tardigrade physiology, in particular in embryogenesis. Interestingly, in-lab cultures of limnic species showed smaller variation in hatching timing than terrestrial species, suggesting a hatching regulation mechanism acquired by adaptation to their habitat. Results: To this end, we screened for coordinated gene expression during the development of two species of tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, and observed induction of the arthropod molting pathway. Exposure of ecdysteroids and juvenile hormone analog affected egg hatching but not embryonic development in only the limnic H. exemplaris. Conclusion: These observations suggest a hatching regulation mechanism by the molting pathway in H. exemplaris.

Access to Document (DOI)

Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue

Kono N., Nakamura H., Ohtoshi R., Moran D., Shinohara A., Yoshida Y., Fujiwara M., Mori M., Tomita M., Arakawa K.

Scientific Reports (Scientific Reports) 9 ( 1 ) 8380 2019.12

© 2019, The Author(s). Members of the family Araneidae are common orb-weaving spiders, and they produce several types of silks throughout their behaviors and lives, from reproduction to foraging. Egg sac, prey capture thread, or dragline silk possesses characteristic mechanical properties, and its variability makes it a highly attractive material for ecological, evolutional, and industrial fields. However, the complete set of constituents of silks produced by a single species is still unclear, and novel spidroin genes as well as other proteins are still being found. Here, we present the first genome in genus Araneus together with the full set of spidroin genes with unamplified long reads and confirmed with transcriptome of the silk glands and proteome analysis of the dragline silk. The catalogue includes the first full length sequence of a paralog of major ampullate spidroin MaSp3, and several spider silk-constituting elements designated SpiCE. Family-wide phylogenomic analysis of Araneidae suggests the relatively recent acquisition of these genes, and multiple-omics analyses demonstrate that these proteins are critical components in the abdominal spidroin gland and dragline silk, contributing to the outstanding mechanical properties of silk in this group of species.

Access to Document (DOI)

AMPK activity is required for the induction of anhydrobiosis in a tardigrade Hypsibius exemplaris, and its potential up-regulator is PP2A

Kondo K., Mori M., Tomita M., Arakawa K.

Genes to Cells (Genes to Cells) 24 ( 12 ) 768 - 780 2019.12

ISSN 13569597

The anhydrobiotic tardigrade, Hypsibius exemplaris, was previously considered to require de novo gene expression and protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A) activity for successful anhydrobiosis. These indicate that H. exemplaris has signal transduction systems responding to desiccation stress, with the involvement of phosphorylation events. To this end, we carried out time-series phosphoproteomics of H. exemplaris exposed to mild desiccation stress and detected 48 phosphoproteins with significant differential regulations. Among them, immediate and successive reduction of phosphorylation levels of AMP-activated protein kinase (AMPK) was observed. The subsequent chemical genetic approach showed that AMPK was activated during the preconditioning stage for anhydrobiosis, and inhibition of its activity impaired successful anhydrobiosis. As PP2A is known to dephosphorylate AMPK in other organisms, we suggested that decreased phosphorylation levels of AMPK upon mild desiccation stress were caused by dephosphorylation by PP2A. Accordingly, phosphoproteomics of animals pre-treated with the PP1/PP2A inhibitor cantharidic acid (CA) lacked the decrease in phosphorylation levels of AMPK. These observations suggest that AMPK activity is required for successful anhydrobiosis in H. exemplaris, and its phosphorylation state is possibly regulated by PP2A.

Access to Document (DOI)

The bagworm genome reveals a unique fibroin gene that provides high tensile strength

Kono N., Nakamura H., Ohtoshi R., Tomita M., Numata K., Arakawa K.

Communications Biology (Communications Biology) 2 ( 1 ) 148 2019.12

Arthropod silk is known as a versatile tool, and its variability makes it an attractive biomaterial. Eumeta variegata is a bagworm moth (Lepidoptera, Psychidae) that uses silk throughout all life stages. Notably, the bagworm-specific uses of silk include larval development in a bag coated with silk and plant materials and the use of silk attachments to hang pupae. An understanding at the molecular level of bagworm silk, which enables such unique purposes, is an opportunity to expand the possibilities for artificial biomaterial design. However, very little is known about the bagworm fibroin gene and the mechanical properties of bagworm silk. Here, we report the bagworm genome, including a silk fibroin gene. The genome is approximately 700 Mbp in size, and the newly found fibroin gene has a unique repetitive motif. Furthermore, a mechanical property test demonstrates a phylogenetic relationship between the unique motif and tensile strength of bagworm silk.

Access to Document (DOI)

　 Previous page - Next page 　