Article
Agricultural Engineering
Victor Pozzobon, Na Cui, Alissa Moreaud, Emilie Michiels, Wendie Levasseur
Summary: The addition of nitrite triggered growth rate inhibition in Chlorella vulgaris, while there was no impact on the pigment contents. Nitrate uptake rate increased with nitrate content, but nitrite uptake remained constant.
BIORESOURCE TECHNOLOGY
(2021)
Article
Chemistry, Physical
Li Cai, Jinrui Guo, Ting Liu, Jing Tian, Zhaoli Wang, Yong Liu, Mohamed S. Hamdy, Xuping Sun
Summary: In this study, a novel Cu@Fe-Cu-CuFe2O4-x photocatalyst was prepared and used to selectively reduce NO3- to N-2 with a two-step reduction process. The first step achieved 91.0% NO3- reduction to NO2- and N-2, while the second step further enhanced the selectivity of NO2- reduction to N2 through the introduction of H2C2O4 and H2O2. The overall process achieved high NO3- removal efficiency and N-2 selectivity.
Article
Multidisciplinary Sciences
Chongzhao You, Yumu Zhang, Youwei Xu, Peiyu Xu, Zhen Li, Huadong Li, Sijie Huang, Zecai Chen, Jingru Li, Eric Xu, Yi Jiang
Summary: Motilin is an endogenous peptide hormone that is mainly expressed in the human gastrointestinal tract. It activates the motilin receptor (MTLR), a type of G protein-coupled receptor (GPCR), and promotes GI motility. This study presents the structures of MTLR bound to motilin and erythromycin, revealing the recognition mechanism of these ligands. The findings provide insights into the physiological regulation of MTLR and offer guidance for drug design targeting MTLR for the treatment of GI motility disorders.
Article
Medicine, Legal
Francesco Taus, Nicola Pigaiani, Federica Bortolotti, Guido Mazzoleni, Michele Brevi, Franco Tagliaro, Rossella Gottardo
Summary: The study describes the optimization and validation of an analytical method for the determination of nitrite and nitrate in biological fluids using capillary ion analysis (CIA) with UV detection. The method was successfully applied to two authentic cases of death by nitrite intake, where high concentrations of nitrate were found in cadaveric blood samples. Nitrite was detected in trace amounts due to its instability in cadaveric blood. This new method offers a more sensitive and precise diagnostic tool for forensic cases compared to traditional methemoglobin analysis.
FORENSIC SCIENCE INTERNATIONAL
(2021)
Article
Agriculture, Multidisciplinary
Shuanghong Zhang, Ziyi Wu, Jian Wang, Sicong Zhang, Shuna Zhao, He Li, Jinli Zhao
Summary: This study investigated bacterial community successions during sugar production processes and their correlation with nitrate/nitrite content. Results revealed dominant genera in the samples and significant changes in bacterial communities, as well as communities capable of nitrate and nitrite metabolism. Furthermore, experiments showed a decline in nitrate levels, indicating the contribution of bacterial communities to nitrate and nitrite transformation.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2022)
Article
Polymer Science
Thakshila Nadeeshani Dharmapriya, Hsin-Yin Shih, Po-Jung Huang
Summary: This study aimed to develop facile, reusable hydrogel-based anion exchange resins for the adsorption of nitrate and nitrite in water. The results demonstrated that the developed adsorbents exhibited high adsorption capacities and cycling capabilities, making them potential alternatives to carbon-based sorbents.
Article
Medicine, General & Internal
Jeffry Florian, Murali K. Matta, Ryan DePalma, Victoria Gershuny, Vikram Patel, Cheng-Hui Hsiao, Robbert Zusterzeel, Rodney Rouse, Kristin Prentice, Colleen Gosa Nalepinski, Insook Kim, Sojeong Yi, Liang Zhao, Miyoung Yoon, Susan Selaya, David Keire, Joyce Korvick, David G. Strauss
Summary: This study involving 18 healthy participants found that oral ranitidine did not significantly increase urinary excretion of NDMA compared to placebo under different dietary conditions.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2021)
Article
Chemistry, Applied
Marisa B. Navas, Hernan P. Bideberrripe, Carmen I. Cabello, Delia Gazzoli, Monica L. Casella, Maria A. Jaworski
Summary: In this study, PdCu-based catalysts supported on CeO2 and 10% ZrO2 were prepared and investigated for the elimination of NO3-, NO2- and BrO3-. The results showed that PdCu/10ZrCe catalyst exhibited the highest efficiency in removing oxyanions, especially NO3-.
Article
Chemistry, Physical
Jeonghoon Lim, Yu Chen, David A. Cullen, Seung Woo Lee, Thomas P. Senftle, Marta C. Hatzell
Summary: By controlling the copper surface coverage, palladium nanocubes as electrocatalysts can effectively reduce nitrate (NO3-) and increase the selectivity for the reduction of nitrite (NO2-) to N2 or NH4+. Partial copper-coated Pd nanocubes can reduce 95% of NO3- and have 89% selectivity for NO2- reduction over 20 cycles (80 h). Complete copper-covered Pd nanocubes can reduce about 99% of NO3- and selectively reduce NO2- to NH4+ with a 70% selectivity over 20 cycles (80 h).
Article
Microbiology
Clara Duffner, Anja Wunderlich, Michael Schloter, Stefanie Schulz, Florian Einsiedl
Summary: Bioremediation of polluted groundwater, especially nitrate contaminated groundwater, is a challenging task due to high nitrate concentrations exceeding drinking water limits. Stimulating autotrophic denitrifiers with hydrogen injection may be a promising remediation strategy, but challenges like cost and potential accumulation of cytotoxic intermediates and greenhouse gases need to be addressed.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Engineering, Environmental
Lai Yip Khen, Safia Syazana Mohtar, Farhana Aziz, Wan Norharyati Wan Salleh, Norhaniza Yusof, Juhana Jaafar, Ahmad Fauzi Ismail
Summary: In this study, visible-light active perovskite photocatalysts (LFO) were successfully synthesized in composites with floating photocatalysts (EP and MEP) for ammonia degradation. The LFO/MEP composite showed the best performance, with an optimal degradation efficiency of 45.7%. The reusable and environmentally friendly photocatalyst demonstrated high stability and low by-product production, making it an effective method for removing ammonia from water.
JOURNAL OF WATER PROCESS ENGINEERING
(2021)
Article
Agriculture, Multidisciplinary
Zebron Nchimunya Tembo, Seker Fatma Aygun
Summary: Teas and traditional herbs are commonly used for health purposes, but they may contain carcinogenic contaminants. This study developed a quick method using capillary electrophoresis for simultaneous determination of nitrate, nitrite, and bromate ions in selected plants and tea samples. Optimal conditions were determined, and the method was found to be quick and efficient with detection achievable within 6 minutes.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Article
Agricultural Engineering
Lei He, Xuejie He, Xing Fan, Shuohui Shi, Tao Yang, Hongyuan Li, Jian Zhou
Summary: This study found that the use of S. oneidensis MR-1 in combination with denitrifying microbial community can significantly enhance the bio-denitrification process through interspecies electron transfer (IET). The nitrogen removal rate was increased by 74.74% and the accumulation of nitrite was greatly reduced. The results also indicated that mediated interspecies electron transfer (MIET) played a role in enhancing denitrification, as observed when S. oneidensis MR-1 was separated by a dialysis bag.
BIORESOURCE TECHNOLOGY
(2023)
Article
Environmental Sciences
Weilai Wang, Kaixuan Wang, Lei Xu, Yang Li, Junfeng Niu
Summary: Raney nickel coupled with nascent hydrogen (Nas-H-2) can efficiently catalyze the reduction of nitrate and nitrite (NOX-). The micro/nano-sized Nas-H-2 bubbles with fine dispersion of hydrogen molecules exhibit increased reactivity, and the alkaline environment positively maintains the activity of R-Ni. By introducing fine hydrogen resources, an efficient catalytic hydrogenation technique without noble metals can be developed.
Article
Computer Science, Artificial Intelligence
Chen Zhang, Yiming Fan, Yu Xie, Bin Yu, Chunyi Li, Ke Pan
Summary: The proposed Dynamic Network Embedding via Structural Attention (DNESA) method integrates attention mechanism into network embedding, focusing on task-related parts of the given graph while avoiding noisy parts, capturing the evolving characteristic of dynamic networks. Empirical experiments demonstrate the efficiency of DNESA, outperforming state-of-the-art network embedding methods in applications like link prediction and node classification.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Fei Jin, Minxuan Sun, Takashi Fujii, Yurika Yamada, Jin Wang, Andres D. Maturana, Miki Wada, Shichen Su, Jinbiao Ma, Hironori Takeda, Tsukasa Kusakizako, Atsuhiro Tomita, Yoshiko Nakada-Nakura, Kehong Liu, Tomoko Uemura, Yayoi Nomura, Norimichi Nomura, Koichi Ito, Osamu Nureki, Keiichi Namba, So Iwata, Ye Yu, Motoyuki Hattori
Summary: Our study revealed the transmembrane structure of MgtE in the absence of Mg2+ ions through cryo-electron microscopy, showing the Mg2+-dependent pore opening mechanism and the kink motions of TM2 and TM5 helices at glycine residues crucial for channel activity. This provides structure-based mechanistic insights into the channel gating of MgtE.
Article
Biology
Kazumasa Oda, Takashi Nomura, Takanori Nakane, Keitaro Yamashita, Keiichi Inoue, Shota Ito, Johannes Vierock, Kunio Hirata, Andres D. Maturana, Kota Katayama, Tatsuya Ikuta, Itsuki Ishigami, Tamaki Izume, Rie Umeda, Ryuun Eguma, Satomi Oishi, Go Kasuya, Takafumi Kato, Tsukasa Kusakizako, Wataru Shihoya, Hiroto Shimada, Tomoyuki Takatsuji, Mizuki Takemoto, Reiya Taniguchi, Atsuhiro Tomita, Ryoki Nakamura, Masahiro Fukuda, Hirotake Miyauchi, Yongchan Lee, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Michihiro Sugahara, Tetsunari Kimura, Tatsuro Shimamura, Takaaki Fujiwara, Yasuaki Yamanaka, Shigeki Owada, Yasumasa Joti, Kensuke Tono, Ryuichiro Ishitani, Shigehiko Hayashi, Hideki Kandori, Peter Hegemann, So Iwata, Minoru Kubo, Tomohiro Nishizawa, Osamu Nureki
Summary: Channelrhodopsins (ChRs) are microbial light-gated ion channels used in optogenetics for controlling neural activity with light. Time-resolved crystallographic analyses revealed conformational changes in ChR following photoactivation, suggesting early changes in the pore-forming helices trigger the opening of the ion conducting pore.
Article
Biochemistry & Molecular Biology
Koichiro E. Kishi, Yoon Seok Kim, Masahiro Fukuda, Masatoshi Inoue, Tsukasa Kusakizako, Peter Y. Wang, Charu Ramakrishnan, Eamon F. X. Byrne, Elina Thadhani, Joseph M. Paggi, Toshiki E. Matsui, Keitaro Yamashita, Takashi Nagata, Masae Konno, Sean Quirin, Maisie Lo, Tyler Benster, Tomoko Uemura, Kehong Liu, Mikihiro Shibata, Norimichi Nomura, So Iwata, Osamu Nureki, Ron O. Dror, Keiichi Inoue, Karl Deisseroth, Hideaki E. Kato
Summary: ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, has opened new possibilities in optogenetics with its unique properties. The cryo-EM structure of ChRmine, revealed at 2.0A resolution, uncovers architectural features distinct from other channelrhodopsins and lays the foundation for the creation of new channelrhodopsins for various biological applications.
Article
Multidisciplinary Sciences
Rieko Suenaga, Mizuki Takemoto, Asuka Inoue, Ryuichiro Ishitani, Osamu Nureki
Summary: The crystal structure of LPA(6) revealed a lateral gap structure that allows the lipophilic ligand to directly enter the binding pocket through the membrane. The flexibility of the gap structure on the membrane enables the lateral entrance of the ligand, facilitating the transition state of the ligand binding process.
Article
Multidisciplinary Sciences
Naotaka Tsutsumi, Shoji Maeda, Qianhui Qu, Martin Vogele, Kevin M. Jude, Carl-Mikael Suomivuori, Ouliana Panova, Deepa Waghray, Hideaki E. Kato, Andrew Velasco, Ron O. Dror, Georgios Skiniotis, Brian K. Kobilka, K. Christopher Garcia
Summary: This study reports the cryo-electron microscopy structures of HCMV-encoded GPCRs US28 and US27 forming nonproductive and productive complexes with host G proteins, providing new insights into their functional mechanisms in viral pathogenesis.
Article
Multidisciplinary Sciences
So Takamoto, Chikashi Shinagawa, Daisuke Motoki, Kosuke Nakago, Wenwen Li, Iori Kurata, Taku Watanabe, Yoshihiro Yayama, Hiroki Iriguchi, Yusuke Asano, Tasuku Onodera, Takafumi Ishii, Takao Kudo, Hideki Ono, Ryohto Sawada, Ryuichiro Ishitani, Marc Ong, Taiki Yamaguchi, Toshiki Kataoka, Akihide Hayashi, Nontawat Charoenphakdee, Takeshi Ibuka
Summary: Researchers have developed a neural network potential that can handle any combination of 45 elements, showcasing its applicability in multiple domains. This technology provides a highly useful tool for material discovery.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
Ryuichiro Ishitani, Toshiki Kataoka, Kentaro Rikimaru
Summary: The automatic design of molecules with specific chemical and biochemical properties is crucial in material informatics and computational drug discovery. This study introduces a novel representation of molecules, called Reversible Junction Tree (RJT), which can be converted back to the original molecule without external information. By utilizing deep reinforcement learning, the molecular design and optimization problem is formulated as a tree-structure construction, enabling efficient optimization in simple benchmark tasks. The applicability of the method is further demonstrated in multiobjective optimization and fine-tuning of reinforcement learning models in drug discovery.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Kazuhiro Kobayashi, Kouki Kawakami, Tsukasa Kusakizako, Hirotake Miyauchi, Atsuhiro Tomita, Kan Kobayashi, Wataru Shihoya, Keitaro Yamashita, Tomohiro Nishizawa, Hideaki E. Kato, Asuka Inoue, Osamu Nureki
Summary: This study reports the cryoelectron microscopic structures of the human PTH1R-Gs complex in the presence of endogenous parathyroid hormone and PTH-related peptide, revealing distinct ligand-receptor interactions and signaling durations induced by these two ligands.
Article
Biochemistry & Molecular Biology
Miki Wada, Koichi Ito
Summary: Heterologous expression of human ABCE1 in S. cerevisiae cannot replace the function of Rli1, but shows low but significant growth at high temperature. This may be attributed to heterologous co-functionality of ABCE1 with S. cerevisiae factor(s) and functional upregulation of human ABCE1 at its functional temperature.
Article
Multidisciplinary Sciences
Haon Futamata, Masahiro Fukuda, Rie Umeda, Keitaro Yamashita, Atsuhiro Tomita, Satoe Takahashi, Takafumi Shikakura, Shigehiko Hayashi, Tsukasa Kusakizako, Tomohiro Nishizawa, Kazuaki Homma, Osamu Nureki
Summary: Outer hair cell electromotility, driven by prestin, is essential for mammalian cochlear amplification. In this study, the cryo-EM structures of thermostabilized prestin in the presence of different anions are reported, providing insights into the mechanisms of mammalian cochlear amplification.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Koichiro E. Kishi, Hideaki E. Kato
Summary: Channelrhodopsins are microbial rhodopsins that function as light-gated ion channels to control specific cells' membrane potential in a light-dependent manner. Optogenetics, the technology utilizing this, has revolutionized neuroscience, and various channelrhodopsin variants have been discovered or engineered for expanding its applications. Pump-like channelrhodopsins (PLCRs), a recent subfamily with high sequence similarity to ion-pumping rhodopsins, have gained attention for their unique properties such as high light sensitivity and ion selectivity. This review summarizes the current understanding of PLCRs' structure-function relationships and discusses the challenges and opportunities of channelrhodopsin research.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Miki Wada, Koichi Ito
Summary: The CGA codon is inefficiently decoded in Saccharomyces cerevisiae by wobble pairing with Arg-tRNA(ICG). The tRNA(Arg)(ICG) is edited post-transcriptionally from tRNA(Arg)(ACG) by the Tad2/Tad3 complex. Ribosome stalling caused by consecutive CGA codons leads to a reduction in protein product. Increasing the supply of tRNA(Arg)(ACG) genes that produce decoding Arg-tRNA(ICG) can enhance the product level, indicating that the reduction in product is mainly due to inefficient decoding and deficiency in tRNA supply. The ratio of mature tRNA(Arg)(ICG) to precursor tRNA(Arg)(ACG) is less than 30% and is responsive to the expression level of Tad2/Tad3.
Article
Biochemistry & Molecular Biology
Hiroshi Otsuka, Kei Endo, Miki Wada, Koichi Ito
Summary: Translation elongation is hindered by obstacles like rare codons or RNA structures, causing ribosomal stalling. Ribosome rescue pathways resolve persistent stalling states. The study identified the critical regions in ribosomal proteins S20 and Asc1 required for ribosome rescue, and revealed their interaction with the E3 ubiquitin ligase Hel2 and their crucial role at the collided ribosome interface.
