Article
Multidisciplinary Sciences
Rosa Maria Chura-Chambi, Alvaro Rossan De Brandao Prieto-da-Silva, Matheus Martins Di Lela, Joao Ezequiel Oliveira, Patricia Estima Antonia Abreu, Luciana Regina Meireles, Heitor Franco de Andrade Junior, Ligia Morganti
Summary: In this study, a method for the expression and refolding of SARS-CoV-2 N protein was introduced, which ensured high yield and purity while avoiding non-specific binding with antibodies from patients previously infected with other coronaviruses. The refolding process was simple and fast, and could be used to effectively distinguish between sera with SARS-CoV-2 antibodies and those without.
Article
Environmental Sciences
Hirokuni Miyamoto, Nobuhiro Kawachi, Atsushi Kurotani, Shigeharu Moriya, Wataru Suda, Kenta Suzuki, Makiko Matsuura, Naoko Tsuji, Teruno Nakaguma, Chitose Ishii, Arisa Tsuboi, Chie Shindo, Tamotsu Kato, Motoaki Udagawa, Takashi Satoh, Satoshi Wada, Hiroshi Masuya, Hisashi Miyamoto, Hiroshi Ohno, Jun Kikuchi
Summary: Coastal aquaculture significantly impacts the distribution of seagrass and seaweed. A study found an exceptional area near the onshore aquaculture facility where seagrass thrives. The sediment in this area is suitable for seagrass growth and harbors beneficial bacterial populations. These findings have important implications for the conservation of coastal ecosystems and blue carbon.
ENVIRONMENTAL RESEARCH
(2023)
Article
Computer Science, Interdisciplinary Applications
He Liu, Chuanjun Dai, Hengguo Yu, Qing Guo, Jianbing Li, Aimin Hao, Jun Kikuchi, Min Zhao
Summary: This paper presents an analytical and numerical investigation of a stochastic non-autonomous phytoplankton-zooplankton system with toxin-producing phytoplankton (TPP) and impulsive perturbations. The study examines the impact of white noise, impulsive perturbations, and TPP on the system dynamics. Mathematical derivations are used to analyze threshold conditions for the existence of global positive solution, population extinction, and persistence in the mean. The results demonstrate the effects of white noise, impulsive control parameter, and toxin liberation rate on population extinction and persistence in the mean. The findings contribute to a better understanding of the dynamics of aquatic ecosystems in fluctuating environments.
MATHEMATICS AND COMPUTERS IN SIMULATION
(2023)
Article
Biochemistry & Molecular Biology
Hirokuni Miyamoto, Jun Kikuchi
Summary: The natural world is undergoing constant changes, with planetary boundaries warning about biodiversity and the cycles of carbon, nitrogen, and phosphorus. Furthermore, social issues like global warming and food shortages are spreading across different fields. These seemingly unrelated problems are closely interconnected, but a comprehensive understanding is still a work in progress. However, advancements in analytical technologies, such as next-generation sequencers (NGS) and mass spectrometry, have made it possible to obtain various forms of molecular information. Additionally, the development of environmental analytical instruments and measurement facilities have increased the availability of data for different environmental factors. Computational science plays a vital role in integrating and understanding these disparate data sets through techniques like machine learning and statistical causal inference.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Analytical
Tharatorn Rungreungthanapol, Chishu Homma, Ken-ichi Akagi, Masayoshi Tanaka, Jun Kikuchi, Hideyuki Tomizawa, Yoshiaki Sugizaki, Atsunobu Isobayashi, Yuhei Hayamizu, Mina Okochi
Summary: Researchers designed an olfactory receptor mimetic peptide-modified graphene field-effect transistor (gFET) to address the low specificity challenge of graphene-based sensors for volatile organic compound (VOC) sensing. Peptides mimicking a fruit fly olfactory receptor were designed using a high-throughput analysis method and successfully achieved sensitive and selective detection of limonene. The peptide probe was bifunctionalized and facilitated facile sensor functionalization. This study demonstrates the advancement of a precise VOC detection system using a target-specific peptide selection and functionalization strategy for gFET sensors.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Shunji Yamada, Yuuri Tsuboi, Daiki Yokoyama, Jun Kikuchi
Summary: As the focus on global environmental sustainability grows, the development of ecofriendly materials, including addressing the issue of marine plastics, is flourishing. The vast parameter space of materials poses a challenge for efficient search. Time-domain nuclear magnetic resonance offers a way to gather information about material properties through complex T2 relaxation curves. In this research, we used a pulse sequence to assess water affinity in polymers and evaluated their relaxation properties using various techniques. By separating the relaxation curves and utilizing polymer properties, we developed a method to optimize polymer composition for desired water affinity and rigidity.
JOURNAL OF MAGNETIC RESONANCE
(2023)
Article
Multidisciplinary Sciences
Shunnosuke Okada, Yudai Inabu, Hirokuni Miyamoto, Kenta Suzuki, Tamotsu Kato, Atsushi Kurotani, Yutaka Taguchi, Ryoichi Fujino, Yuji Shiotsuka, Tetsuji Etoh, Naoko Tsuji, Makiko Matsuura, Arisa Tsuboi, Akira Saito, Hiroshi Masuya, Jun Kikuchi, Yuya Nagasawa, Aya Hirose, Tomohito Hayashi, Hiroshi Ohno, Hideyuki Takahashi
Summary: Reducing antibiotic usage among livestock animals to prevent antimicrobial resistance has become an urgent issue worldwide. This study evaluated the effects of administering chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentrations of calves. The results showed that CTC administration had an impact on the correlation between fecal organic acids and bacterial genera, and also affected the populations of various types of fecal bacteria.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Hideaki Shima, Kenji Sakata, Jun Kikuchi
Summary: Aquaculture is being acknowledged as a solution to the global food problem. This study focuses on the impact of fish and their environment on the stability and quality of fish meat. Nuclear magnetic resonance is used to non-destructively acquire metabolite information, while machine learning and artificial neural network analysis provide comprehensive analysis. It was found that the antioxidant anserine is reduced in fish muscles at low water temperature, affecting other metabolites. The relationship between water temperature and fish intestinal microbiota was also established.
APPLIED SCIENCES-BASEL
(2023)
Article
Environmental Sciences
Daiki Yokoyama, Jun Kikuchi
Summary: In this study, the assembly processes of particle-associated and free-living surface water microbiomes in an urban river in Japan were analyzed. The variation in microbiomes was successfully explained by environmental factors, such as organic matter, nitrogen metabolism, and salinity. The study also revealed the dominance of stochastic processes over deterministic processes in community assembly, and the potential enhanced contribution of heterogeneous selection to community assembly in areas with salinity gradient.
ENVIRONMENTAL RESEARCH
(2023)
Article
Environmental Sciences
Hiroshi Kudo, Ning Han, Daiki Yokoyama, Tomoko Matsumoto, Mei-Fang Chien, Jun Kikuchi, Chihiro Inoue
Summary: Phytoextraction is a cost-effective and eco-friendly method for removing pollutants from contaminated soil. Bayesian network analysis revealed that the microbial strain Pseudomonas sp. m307 and MND1 order microbes positively contribute to arsenic accumulation in P. vittata.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Ecology
Hirokuni Miyamoto, Katsumi Shigeta, Wataru Suda, Yasunori Ichihashi, Naoto Nihei, Makiko Matsuura, Arisa Tsuboi, Naoki Tominaga, Masahiko Aono, Muneo Sato, Shunya Taguchi, Teruno Nakaguma, Naoko Tsuji, Chitose Ishii, Teruo Matsushita, Chie Shindo, Toshiaki Ito, Tamotsu Kato, Atsushi Kurotani, Hideaki Shima, Shigeharu Moriya, Satoshi Wada, Sankichi Horiuchi, Takashi Satoh, Kenichi Mori, Takumi Nishiuchi, Hisashi Miyamoto, Hiroaki Kodama, Masahira Hattori, Hiroshi Ohno, Jun Kikuchi, Masami Yokota Hirai
Summary: The study investigated the effects of compost on the growth and quality of carrots and the soil bacterial composition. The results showed that exposure to compost significantly improved carrot productivity, antioxidant activity, color, and taste. It also altered the soil bacterial composition and influenced the levels of characteristic metabolites. Structural equation modeling revealed the optimal linkages between amino acids, antioxidant activity, flavonoids and/or carotenoids in plants, and the involvement of Paenibacillus genus and nitrogen compounds in the soil during exposure to compost. These findings suggest the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by compost.
ISME COMMUNICATIONS
(2023)
Article
Ecology
Daiki Yokoyama, Ayari Takamura, Yuuri Tsuboi, Jun Kikuchi
Summary: In this study, the authors compared the microbiomes and degradation processes of different biodegradable polymers using prompt evaluation systems. They found differences in the microbial community compositions among the polymer materials, with the largest differences observed in one particular polymer material, PHBH. Time-series sampling showed several stages of microbial succession during polymer degradation. Metagenome prediction revealed functional changes, including the adhesion of free-swimming microbes onto the polymer and the formation of a biofilm by certain microbes.
ISME COMMUNICATIONS
(2023)
Correction
Plant Sciences
Ryosuke Mega, Fumitaka Abe, June-Sik Kim, Yuuri Tsuboi, Keisuke Tanaka, Hisato Kobayashi, Yoichi Sakata, Kousuke Hanada, Hisashi Tsujimoto, Jun Kikuchi, Sean R. Cutler, Masanori Okamoto
Review
Toxicology
Gandhi Radis-Baptista
Summary: Fragrance compounds, whether synthetic or natural, are used in personal care and household products to mask unpleasant odors and enhance olfactory perception. However, these compounds can negatively impact human health, causing skin, respiratory, and systemic reactions.
JOURNAL OF XENOBIOTICS
(2023)
Article
Biology
Ana Paula dos Santos, Roberta Carolina Rangel de Oliveira, Bianca Oliveira Louchard, Antonia Flavia Justino Uchoa, Nagila Maria Pontes Silva Ricardo, Luzia Kalyne Almeida Moreira Leal, Gandhi Radis-Baptista, Tamara Goncalves de Araujo
Summary: This article reports the preparation and optimized formulation of Ctn[15-34] anti-infective peptide using poly(lactic acid-co-glycolic acid) (PLGA) nanoparticles. The prepared nanoparticles showed smaller particle size, better stability, and higher zeta potential values. The loaded nanoparticles demonstrated sustained release and enhanced antifungal activity compared to the free peptide.
BRAZILIAN ARCHIVES OF BIOLOGY AND TECHNOLOGY
(2023)