Search

Your search keyword '"Nomura, Nobuhiko"' showing total 680 results
Start Over Author "Nomura, Nobuhiko"
680 results on '"Nomura, Nobuhiko"'

2. Atrimonas thermophila gen. nov., sp. nov., a novel anaerobic thermophilic bacterium of the phylum Atribacterota isolated from deep subsurface gas field and proposal of Atrimonadaceae fam. nov. within the class Atribacteria in the phylum Atribacterota

Author

Kawamoto, Hiroki, Watanabe, Miho, Mochimaru, Hanako, Nakahara, Nozomi, Meng, Xiang-Ying, Sakamoto, Sachiko, Morinaga, Kana, Katayama, Taiki, Yoshioka, Hideyoshi, Nomura, Nobuhiko, and Tamaki, Hideyuki

Published
2024
Full Text
View/download PDF

3. Ratio of Electron Donor to Acceptor Influences Metabolic Specialization and Denitrification Dynamics in Pseudomonas aeruginosa in a Mixed Carbon Medium

Author

Zhang, Irene H, Mullen, Susan, Ciccarese, Davide, Dumit, Diana, Martocello, Donald E, Toyofuku, Masanori, Nomura, Nobuhiko, Smriga, Steven, and Babbin, Andrew R

Subjects
Pseudomonas aeruginosa, denitrification, rate-yield tradeoff, specialization, nitrite, Environmental Science and Management, Soil Sciences, Microbiology
Abstract

Denitrifying microbes sequentially reduce nitrate (NO3 -) to nitrite (NO2 -), NO, N2O, and N2 through enzymes encoded by nar, nir, nor, and nos. Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NOx -) utilization. Both exist within natural environments, but we lack an understanding of selective pressures driving the evolution toward each lifestyle. Here we investigate differences in growth rate, growth yield, denitrification dynamics, and the extent of intermediate metabolite accumulation under varying nutrient conditions between the model complete denitrifier Pseudomonas aeruginosa and a community of engineered specialists with deletions in the denitrification genes nar or nir. Our results in a mixed carbon medium indicate a growth rate vs. yield tradeoff between complete and partial denitrifiers, which varies with total nutrient availability and ratios of organic carbon to NOx -. We found that the cultures of both complete and partial denitrifiers accumulated nitrite and that the metabolic lifestyle coupled with nutrient conditions are responsible for the extent of nitrite accumulation.

Published
2021

17. Denitrification in low oxic environments increases the accumulation of nitrogen oxide intermediates and modulates the evolutionary potential of microbial populations.

Author

Takahashi, Kohei, Oshiki, Mamoru, Ruan, Chujin, Morinaga, Kana, Toyofuku, Masanori, Nomura, Nobuhiko, and Johnson, David R.

Subjects
DENITRIFICATION, NITROGEN oxides, ELECTROPHILES, NITRIC oxide, NATURAL selection, GENETIC variation, ANOXIC zones
Abstract

Denitrification in oxic environments occurs when a microorganism uses nitrogen oxides as terminal electron acceptors even though oxygen is available. While this phenomenon is well‐established, its consequences on ecological and evolutionary processes remain poorly understood. We hypothesize here that denitrification in oxic environments can modify the accumulation profiles of nitrogen oxide intermediates with cascading effects on the evolutionary potentials of denitrifying microorganisms. To test this, we performed laboratory experiments with Paracoccus denitrificans and complemented them with individual‐based computational modelling. We found that denitrification in low oxic environments significantly increases the accumulation of nitrite and nitric oxide. We further found that the increased accumulation of these intermediates has a negative effect on growth at low pH. Finally, we found that the increased negative effect at low pH increases the number of individuals that contribute to surface‐associated growth. This increases the amount of genetic diversity that is preserved from the initial population, thus increasing the number of genetic targets for natural selection to act upon and resulting in higher evolutionary potentials. Together, our data highlight that denitrification in low oxic environments can affect the ecological processes and evolutionary potentials of denitrifying microorganisms by modifying the accumulation of nitrogen oxide intermediates. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

28. Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR

Author

Obana, Nozomu, primary, Takada, Hiraku, additional, Crowe-McAuliffe, Caillan, additional, Iwamoto, Mizuki, additional, Egorov, Artyom A, additional, Wu, Kelvin J Y, additional, Chiba, Shinobu, additional, Murina, Victoriia, additional, Paternoga, Helge, additional, Tresco, Ben I C, additional, Nomura, Nobuhiko, additional, Myers, Andrew G, additional, Atkinson, Gemma C, additional, Wilson, Daniel N, additional, and Hauryliuk, Vasili, additional

Published
2023
Full Text
View/download PDF

29. Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR

Author

Obana, Nozomu, Takada, Hiraku, Crowe-Mcauliffe, Caillan, Iwamoto, Mizuki, Egorov, Artyom A, Wu, Kelvin J. Y, Chiba, Shinobu, Murina, Victoriia, Paternoga, Helge, Tresco, Ben I. C, Nomura, Nobuhiko, Myers, Andrew G, Atkinson, Gemma C, Wilson, Daniel N, Hauryliuk, Vasili, Obana, Nozomu, Takada, Hiraku, Crowe-Mcauliffe, Caillan, Iwamoto, Mizuki, Egorov, Artyom A, Wu, Kelvin J. Y, Chiba, Shinobu, Murina, Victoriia, Paternoga, Helge, Tresco, Ben I. C, Nomura, Nobuhiko, Myers, Andrew G, Atkinson, Gemma C, Wilson, Daniel N, and Hauryliuk, Vasili

Abstract

Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 from Streptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacterium Neobacillus vireti) and Clostridia (CplR from Clostridium perfringens, Clostridium sporogenes and Clostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. Finally, assisted by uORF4u, our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge.

Published
2023
Full Text
View/download PDF

36. Porous Pellicle Formation of a Filamentous Bacterium, Leptothrix

Author

Kunoh, Tatsuki, primary, Yamamoto, Tatsuya, additional, Prasad, Manoj, additional, Ono, Erika, additional, Li, Xiaojie, additional, Sugimoto, Shinya, additional, Iida, Eiji, additional, Obana, Nozomu, additional, Takeda, Minoru, additional, Nomura, Nobuhiko, additional, and Utada, Andrew S., additional

Published
2022
Full Text
View/download PDF

37. Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR

Author

Obana, Nozomu, primary, Takada, Hiraku, additional, Crowe-McAuliffe, Caillan, additional, Iwamoto, Mizuki, additional, Egorov, Artyom A., additional, Wu, Kelvin J.Y., additional, Murina, Victoriia, additional, Paternoga, Helge, additional, Tresco, Ben I.C., additional, Nomura, Nobuhiko, additional, Myers, Andrew G., additional, Atkinson, Gemma C., additional, Wilson, Daniel N., additional, and Hauryliuk, Vasili, additional

Published
2022
Full Text
View/download PDF

39. Treatment of DNA and Virus with Volcanic Water

Author

Komaba, Kyoka, TOYOFUKU, Masanori, NOMURA, Nobuhiko, and GOTO, Hiromasa

Abstract

FUTURUM as an open access journal has been launched by University of Tsukuba Library Research & Development Office Project 2016-2017 (Goto Project).

Published
2022

45. Membrane Vesicles Derived From Clostridium botulinum and Related Clostridial Species Induce Innate Immune Responses via MyD88/TRIF Signaling in vitro

Author

Kobayashi, Nobuhide, primary, Abe, Kimihiro, additional, Akagi, Sachiyo, additional, Kitamura, Mayu, additional, Shiraishi, Yoshitake, additional, Yamaguchi, Aki, additional, Yutani, Masahiro, additional, Amatsu, Sho, additional, Matsumura, Takuhiro, additional, Nomura, Nobuhiko, additional, Ozaki, Noriyuki, additional, Obana, Nozomu, additional, and Fujinaga, Yukako, additional

Published
2022
Full Text
View/download PDF

46. Bacterial Interactions

Author

Toyofuku, Masanori, primary, Tashiro, Yosuke, additional, Inaba, Tomohiro, additional, and Nomura, Nobuhiko, additional

Published
2016
Full Text
View/download PDF

47. Synergy between Sophorolipid Biosurfactant and SDS Increases the Efficiency of P. aeruginosa Biofilm Disruption

Author

TOYOFUKU, Masanori, NOMURA, Nobuhiko, UTADA, Andrew Shinichi, Nguyen, Bac V. G., and Nagakubo, Toshiki

Abstract

Biofilms are communities of bacteria encased in self-secreted extracellular polymeric substances (EPS) that adhere stubbornly to submerged surfaces. Once established, these communities can cause serious chronic illnesses in medical settings, while they can promote corrosion and biofouling in industrial settings. Due to the difficulty of their removal, strongly oxidizing chemicals and detergents can be used to degrade and remove biofilms by killing the cells and degrading the matrix; however, the choice of compounds is limited in delicate environments due to the potential damage they may cause. In the case of detergents, most are synthesized from nonrenewable petrochemicals that have a degree of aquatic toxicity. There is a growing need to identify and characterize alternatives to synthetic surfactants. Biosurfactants, which are surfactants produced by microorganisms, are a promising alternative since they can be synthesized from renewable resources, have low environmental toxicity, and have been shown to have higher degrees of specificity in the mechanism of action. Sophorolipids are a class of glycolipid surfactants produced by yeast that have demonstrated great promise due to large yields from renewable feedstocks and for antimicrobial properties; however, the effect of the application of sophorolipids to Gram-negative bacterial biofilms has not been well studied. We investigate the antibiofilm properties of sophorolipids by demonstrating its ability to cause the catastrophic disruption of Pseudomonas aeruginosa PAO1 biofilms in microfluidic channels. We show that while sophorolipids inflict little damage to the bacteria, they weaken the EPS biofilm matrix, leading to surface-detachment and breakup of the biofilm. Furthermore, we find that sophorolipids act cooperatively with the widely used surfactant, sodium dodecyl sulfate. When combined, concentrations ∼100-fold lower than the minimum effective concentration, when used independently, recover potency. Biosurfactants are typically expensive to produce, thus our work demonstrates a means to improve efficacy while simultaneously reducing both cost and the amount of environmentally harmful substances used.

Published
2020

Catalog

Books, media, physical & digital resources
See catalog results