Article
Mathematics
Carmina Fjellstrom, Kaj Nystrom, Matias Vestberg
Summary: This paper introduces a new class of strongly degenerate nonlinear parabolic partial differential equations by combining the classical PDE of Kolmogorov and the normalized p-Laplace operator. The solutions are characterized in terms of an asymptotic mean value property and the results are connected to the analysis of certain tug-of-war games with noise. The value functions for the introduced games approximate solutions to the stated PDE when the parameter controlling the size of the possible steps tends to zero. Existence and uniqueness of viscosity solutions to the Dirichlet problem are established.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2023)
Review
Biochemistry & Molecular Biology
Batsheva Rozman, Tal Fisher, Noam Stern-Ginossar
Summary: Viral reproduction relies on host ribosomes for viral protein synthesis. Viruses have evolved strategies to hijack the host translational machinery for viral protein production and to hinder cellular defenses. This article discusses the methods viruses use to exploit translation machinery, the counter-strategies employed by host cells, and the potential roles of mRNA modifications and ribosome quality control in translational regulation and innate immunity. The focus is on the knowledge gaps in these mechanisms, particularly in viruses with pandemic potential, using the context of the COVID-19 pandemic.
Article
Chemistry, Multidisciplinary
Zhuoyue Chen, Yunru Yu, Jiahui Guo, Lingyu Sun, Yuanjin Zhao
Summary: A novel heterogeneous structural color microfiber designed for dynamic cardiac mechanics sensing is presented in this study. The microfiber contains non-close-packed colloidal arrays for quantitative optical sensing and bioactive GelMA for cardiac culture. It transforms microcosmic cell-generated force into macroscopic optical signals and has the potential to be an ideal platform for biomedical fields.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Review
Biochemistry & Molecular Biology
Simon Snoeck, Natalia Guayazan-Palacios, Adam D. Steinbrenner
Summary: This review discusses the mechanisms by which plants perceive and respond to chewing and piercing-sucking herbivores. It examines the recognition of herbivore-associated molecular patterns (HAMPs) and effectors by plant immune systems, and emphasizes the importance of these initial molecular interactions in resistance. The review also explores the potential evolution of immune receptor functions and the integration of sensing functions in plant-herbivore interactions.
Editorial Material
Biochemistry & Molecular Biology
Filip Van Hauwermeiren, Mohamed Lamkanfi
Summary: A recent study has discovered that Mycobacterium tuberculosis can evade the immune system by modifying the plasma membrane phospholipid composition of infected macrophages, thus preventing the host's pyroptosis response and allowing for chronic infection.
Review
Immunology
Noemie Alphonse, Ruth E. Dickenson, Charlotte Odendall
Summary: Type I and III interferons play important roles not only in antiviral immunity, but also in restricting bacterial infection by inducing ISGs and affecting antimicrobial signaling pathways. They are attractive targets for bacterial pathogens as they regulate a diverse range of anti-bacterial host responses.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Michael D. Nodine
Summary: Parental contributions affect early embryogenesis by regulating maternal resources distribution to offspring. A new study in Arabidopsis thaliana shows that signaling components from maternal sporophytic tissues and paternal gametes converge in zygotes to promote elongation of the extraembryonic suspensor, supporting embryo development.
Article
Engineering, Civil
Lin Zhang, Tao Zhang, Huajiang Ouyang, Tianyun Li, Genghui Xu
Summary: This paper presents a new method for robust assignment of natural frequencies using the receptance method. The method addresses the deviation between achieved and target frequencies, caused by uncertainties in passive structural modifications. The proposed method integrates a deviation expression into the optimization calculation to acquire highly robust modification parameters, without requiring knowledge of the probabilistic distribution of uncertainties.
INTERNATIONAL JOURNAL OF STRUCTURAL STABILITY AND DYNAMICS
(2023)
Review
Cell Biology
Apala Pal, Sachin Kumar Tripathi, Priya Rani, Meghana Rastogi, Saumitra Das
Summary: Host factor p53 plays crucial roles in viral infection by maintaining genomic integrity, regulating cellular pathways, and contributing to immune responses. Viruses have evolved strategies to manipulate p53 function for their own benefit, either by attenuating or exploiting its activity. Understanding these mechanisms provides insight into the pathogenesis of positive-strand RNA viruses.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Editorial Material
Biochemistry & Molecular Biology
Clara Paola Igisch, Christine Miege, Yvon Jaillais
Summary: ROP GTPases regulate the complex morphogenesis of leaf pavement cells through the activation and inhibition of proteins.
Article
Nanoscience & Nanotechnology
Xin Fan, Lingshuang Rong, Lushi Kong, Yuxin Li, Junrong Huang, Yungang Cao, Wei-Hong Zhong
Summary: This study introduces a multifunctional air filter zNFs-Ag@PT composed of a substrate made from silver nanoparticles-paper towel microfibers and an upper layer formed from aligned corn zein nanofibers. By incorporating silver nanoparticles, the filter gains effective antimicrobial activity and improved filtration performance, enhancing overall filtration efficiency.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Physics, Multidisciplinary
Hongda Jiang, Shenshen Wang
Summary: The adaptive immune system improves its protection against future pathogens by constantly modifying its lymphocyte repertoire. Recent experiments have shown that B cells physically extract antigens using active forces, and this extraction level determines clonal fitness. These observations challenge the prevailing view that the equilibrium constant of receptor-antigen binding determines selective advantage. A theoretical framework was proposed to explore the impact of tug-of-war antigen extraction on the quality and diversity of an evolved B cell repertoire. The results suggest that active forces play a multifaceted role in immune adaptation, rationalizing key observations on repertoire dynamics.
Article
Geosciences, Multidisciplinary
A. D. Gronewold, H. X. Do, Y. Mei, C. A. Stow
Summary: The past decade was the wettest on record for much of central and eastern North America. Research shows that during this period, overlake precipitation on the Laurentian Great Lakes rose to extraordinary levels, while overlake evaporation diminished rapidly in 2014. In the era of climate change, it is important to pay attention to the impacts of competing hydrologic forces on large freshwater systems.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Article
Cell Biology
Brianna Dailey-Krempel, Andrew L. Martin, Ha-Neul Jo, Harald J. Junge, Zhe Chen
Summary: Dynamic and coordinated axonal responses are crucial for establishing neural connections, especially during commissural axon migration across the CNS midline. It is hypothesized that the switch in axonal responses from attraction to repulsion is mediated by the silencing of Netrin1/DCC attraction and activation of SLIT/ROBO1 repulsion. In vivo experiments using CRISPR-Cas9-engineered mouse models demonstrate that commissural axons maintain responsiveness to both Netrin and SLIT during midline crossing, with the possibility of quantitatively different levels. Full-length DCC, in collaboration with ROBO3, can antagonize ROBO1 repulsion in vivo, suggesting an integrated and balanced signaling mechanism for proper guidance decisions.
Review
Cell Biology
Hunter J. Hill, Kent G. Golic
Summary: This article reviews the studies on centromere strength over the past 70 years, with a special focus on the characterization of Drosophila melanogaster kinetochores, in order to determine if the current evidence supports the previous conclusions.
Correction
Biotechnology & Applied Microbiology
Michiko Nemoto, Sayako Iwaki, Hisao Moriya, Yuki Monden, Takashi Tamura, Kenji Inagaki, Shigeki Mayama, Kiori Obuse
MARINE BIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yuta Tsunematsu, Naoya Maeda, Michio Sato, Kodai Hara, Hiroshi Hashimoto, Kenji Watanabe, Christian Hertweck
Summary: Epidithiodiketopiperazines (ETPs) are a class of ecologically and medicinally important cyclodipeptides with a reactive transannular disulfide bridge. A novel oxidoreductase (AcIR) has been discovered to catalyze both carbon-sulfur bond migration and spiro-ring formation, with a pathway involving cryptic acetylation. The discovery highlights the specialized role of the thioredoxin oxidoreductase family enzyme in the ETP pathway and expands the chemical diversity of small molecules bearing an aberrant disulfide pharmacophore.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Zhuan Zhang, Yui Tamura, Mancheng Tang, Tianzhang Qiao, Michio Sato, Yoshihiro Otsu, Satoshi Sasamura, Masatoshi Taniguchi, Kenji Watanabe, Yi Tang
Summary: The study characterized the biosynthetic pathway of the immunosuppressant (-)-FR901483 (1) through heterologous expression and enzymatic assays, proposing a possible target of 1 based on the biosynthetic studies. The biosynthetic logic involves aza-spiro annulation of dityrosyl-piperazine to form a ketoaldehyde intermediate, followed by regioselective aldol condensation, stereoselective ketoreduction, and phosphorylation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Oncology
Motoki Iwasaki, Rieko Kanehara, Taiki Yamaji, Ryoko Katagiri, Michihiro Mutoh, Yuta Tsunematsu, Michio Sato, Kenji Watanabe, Koji Hosomi, Yasuo Kakugawa, Hiroaki Ikematsu, Kinichi Hotta, Jun Kunisawa, Keiji Wakabayashi, Takahisa Matsuda
Summary: This study investigated the association between the presence of polyketide synthase in Escherichia coli and the prevalence of colorectal neoplasia, finding no significant association overall. However, positive associations were suggested under certain intake levels of cereals or vegetables.
Article
Biochemistry & Molecular Biology
Shinya Matsuda, Yuta Tsunematsu, Takuma Matsushita, Yuji Ogata, Shihomi Hachiya, Shinji Kishimoto, Noriyuki Miyoshi, Kenji Watanabe
Summary: The study demonstrates that HeLa cells harboring fma-P450 can biosynthesize 5-hydroxyl-beta-trans-bergamoten and cytotoxic 5-epi-demethoxyfumagillol when supplemented with the nontoxic precursor beta-trans-bergamotene. While the production level was insufficient to effect cell death, it shows that programming human cells to autogenerate antibiotics by introducing a heterologous biosynthetic gene is feasible.
Article
Biochemistry & Molecular Biology
Daniel Evans-Yamamoto, Francois D. Rouleau, Piyush Nanda, Koji Makanae, Yin Liu, Philippe C. Despres, Hitoshi Matsuo, Motoaki Seki, Alexandre K. Dube, Diana Ascencio, Nozomu Yachie, Christian R. Landry
Summary: Barcode fusion genetics (BFG) utilizes deep sequencing to improve the throughput of protein-protein interaction (PPI) screening. This technology expands the scope of PPI research by leveraging clone collections from any species of interest and demonstrates high sensitivity and specificity for capturing known interactions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Satoshi Horiuchi, Shotaro Namba, Nozomu Saeki, Ayano Satoh, Hisao Moriya
Summary: Eukaryotic cells are composed of organelles, each containing proteins crucial for their function. In this study, novel mitochondrially localized proteins in yeast were identified using a fluorescent protein that is degraded in the cytoplasm. The findings revealed 35 uncharacterized proteins potentially localized to mitochondria, some of which are upregulated during mitochondrial development, suggesting their involvement in mitochondrial function.
Article
Chemistry, Multidisciplinary
Shinji Kishimoto, Yuya Matsubara, Kenji Watanabe
Summary: Ergopeptines are representative ergoline alkaloids with a tripeptide extension on the lysergic acid core. In this study, we characterized newly isolated ergopeptine-like compounds called lentopeptins from Aspergillus lentulus, which differ from traditional ergopeptines in structure and biosynthetic pathway. Targeted deletion of len cluster biosynthetic genes predicted from the genome sequence revealed the atypical biosynthetic pathway of lentopeptins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Genetics & Heredity
Shotaro Namba, Hisaaki Kato, Shuji Shigenobu, Takashi Makino, Hisao Moriya
Summary: The overexpression of EGFP, a harmless protein, causes cell elongation in yeast, and this phenomenon is associated with the content of cysteine. The abnormal cell morphology triggered by EGFP overexpression is observed in different types of yeast. The perturbation of the proteasome by the exposed cysteine of the overexpressed protein leads to cell elongation.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yuichiro Hirayama, Michio Sato, Kenji Watanabe
Summary: Recent studies have identified a gene cluster in Escherichia coli that produces a genotoxic secondary metabolite known as colibactin, which is suspected to be a risk factor for colorectal cancer. There is a need to develop simple detection methods for colibactin-producing strains and understand the mechanism of colibactin-induced oncogenesis to improve early screening and prevention of colorectal cancer. This review discusses recent efforts in identifying the structure of colibactin and developing detection methods using polymerase chain reaction and isothermal amplification techniques.
Article
Chemistry, Medicinal
Takuma Kobayashi, Shinji Kishimoto, Shogo Watanabe, Yasukiyo Yoshioka, Takeshi Toyoda, Kumiko Ogawa, Kenji Watanabe, Yukari Totsuka, Keiji Wakabayashi, Noriyuki Miyoshi
Summary: This study identifies the formation of several p-semidine-type dimers, including MMBD and MxMxBD, during the metabolic conversion of o-Tol and o-Ans. The dimers containing the o-Ans moiety showed faster dimerization rates but decreased levels with prolonged incubation. These findings suggest the potential significance of the homo-and hetero-dimers of monocyclic aromatic amines in bladder carcinogenesis and the combined exposure risk.
CHEMICAL RESEARCH IN TOXICOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Shinji Kishimoto, Ayumi Minami, Yoshimitsu Aoki, Yuya Matsubara, Shogo Watanabe, Kenji Watanabe
Summary: Pathogenic fungi of Aspergillus section Fumigati are capable of producing various secondary metabolites. This study reports the isolation of fumimycin and a new compound named lentofuranine from A. lentulus. These compounds were found to be assembled through a nonenzymatic condensation involving a polyketide intermediate from the terrein biosynthetic pathway and a highly reactive azlactone intermediate. The formation of an unusual carbon skeleton is attributed to the reactivity of azlactone.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Kanji Niwa, Masao Ohashi, Kaili Xie, Chen-Yu Chiang, Cooper S. Jamieson, Michio Sato, Kenji Watanabe, Fang Liu, K. N. Houk, Yi Tang
Summary: We have discovered biosynthetic pathways that can produce and transform conjugated octaenes and nonaenes into complex natural products. The biosynthesis of (-)-PF1018 involves an enzyme called PfB, which controls the regio-, stereo-, and periselectivity of multiple reactions starting from a conjugated octaene. By using PfB as a starting point, we found a homologous enzyme, BruB, that facilitates diene isomerization, tandem 8π-6π-electrocyclization, and a 1,2-divinylcyclobutane Cope rearrangement to generate a novel compound not previously found in nature.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Genetics & Heredity
Nozomu Saeki, Chie Yamamoto, Yuichi Eguchi, Takayuki Sekito, Shuji Shigenobu, Mami Yoshimura, Yoko Yashiroda, Charles Boone, Hisao Moriya
Summary: The study focused on how overexpression of genes can help organisms adapt to stress. A new method was developed to identify functionally adaptive genes when overexpressed in yeast under stress. The results showed that adaptive overexpression compensated for deficiencies and improved stress tolerance, such as calcium under salt stress. The study also investigated the influence of different genetic backgrounds on these genes, revealing variations among yeast strains. Additionally, calcium was found to play a role in adapting to salt stress by preventing mitochondrial outbursts. These findings highlight the importance of adaptive overexpression in maximizing stress adaptability within a specific environment and genetic context.
Article
Genetics & Heredity
Tao Zhou, Takayuki Ando, Akihiro Kudo, Michio Sato, Noriyuki Miyoshi, Michihiro Mutoh, Hideki Ishikawa, Keiji Wakabayashi, Kenji Watanabe
Summary: The study established an efficient screening system for identifying ClbP-specific inhibitors. Two different assays were used to screen a large number of compounds, resulting in the identification of one compound with moderate inhibitory activity against ClbP. This screening method is believed to be reliable and useful in developing potential prophylactic agents for colorectal cancer.
GENES AND ENVIRONMENT
(2023)
