Article
Biochemistry & Molecular Biology
Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas
Summary: The article introduces a major upgrade of the eggNOG-mapper tool, optimized for functional annotation of vast genomic and metagenomic datasets, including database updates, efficiency enhancements, and new features such as de novo gene prediction and fast protein domain discovery.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Editorial Material
Multidisciplinary Sciences
Anthony J. Hannan
Summary: The study found a link between tandem repeats in DNA and autism spectrum disorder, which could provide insights into other human disorders. Bioinformatic analysis was used to study tandem repeat mutations in autism.
Editorial Material
Multidisciplinary Sciences
Amber Dance
Summary: Methods that combine imaging with sequencing are revealing the organizational principles of the genome and its impact on cell fates.
Review
Microbiology
Kendra A. Turk-Kubo, Mary R. Gradoville, Shunyan Cheung, Francisco M. Cornejo-Castillo, Katie J. Harding, Michael Morando, Matthew Mills, Jonathan P. Zehr
Summary: This review paper provides a comprehensive understanding of the biology, ecology, and biogeography of marine non-cyanobacterial diazotrophs (NCDs) through the synthesis of multiple datasets. The authors discuss recent advances in studying the diversity, distribution, and ecophysiology of NCDs, as well as their significance to the nitrogen cycle in well-lit oxygenated euphotic waters.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Engineering, Electrical & Electronic
Jan Voges, Mikel Hernaez, Marco Mattavelli, Joern Ostermann
Summary: Advancements in high-throughput sequencing technologies have significantly reduced the cost of DNA sequencing, enabling the potential for personalized medicine. However, the associated costs of storing, transmitting, and processing large amounts of data remain a challenge. To address this issue, the MPEG-G standard has been developed, allowing for higher levels of compression and new functionalities.
PROCEEDINGS OF THE IEEE
(2021)
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Analysis of protein shapes reveals unexpected forms and connections.
Review
Biotechnology & Applied Microbiology
Alexander B. Alleman, John W. Peters
Summary: The availability of fixed nitrogen is a limiting factor in ecosystem productivity, but diazotrophs can convert atmospheric dinitrogen to ammonia to overcome this limitation. Diazotrophs are diverse bacteria and archaea that utilize various metabolisms to generate low potential reducing equivalents for the nitrogenase enzyme. Understanding the electron transport systems in diazotrophs is essential for future engineering strategies to enhance biological nitrogen fixation in agriculture.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Editorial Material
Multidisciplinary Sciences
Jeffrey A. Farrell
Summary: CellOracle, a computational tool, can predict the interaction of gene networks in programming cell identity during embryonic development. This tool will contribute to a better understanding of the regulation of development.
Article
Microbiology
Tatiana Dvorkina, Anton Bankevich, Alexei Sorokin, Fan Yang, Boahemaa Adu-Oppong, Ryan Williams, Keith Turner, Pavel A. Pevzner
Summary: The study introduces a gene prediction tool called ORFograph that can predict IPGs in assembly graphs and has discovered numerous novel IPGs from (meta)genomic datasets. Analysis of assembly graphs reveals potential candidate IPGs, including known genes hidden in assembly graphs and potential new IPGs. ORFograph is a fast tool that could potentially identify even more novel IPGs for phenotypic testing from (meta)genomic assembly graphs than traditional gene-finding methods.
Article
Soil Science
Khalil Kariman, Benjamin Moreira-Grez, Craig Scanlan, Saleh Rahimlou, Gustavo Boitt, Zed Rengel
Summary: This controlled-environment study found synergistic interactions between the arbuscular mycorrhizal fungus Austroboletus occidentalis and soil free-living diazotrophs. Inoculating these microorganisms significantly increased wheat plant growth and nutrient uptake, and altered the soil microbiome. Additionally, the FM fungus exhibited limited saprotrophic capacity similar to ectomycorrhizal fungi.
BIOLOGY AND FERTILITY OF SOILS
(2022)
Editorial Material
Multidisciplinary Sciences
Luke M. M. Evans, Pamela N. Romero N. Villela
Summary: An analysis of rare genetic variants shows their impact on human traits is mediated through similar biological pathways as common variants, enhancing our understanding of their influence on complex traits.
Editorial Material
Multidisciplinary Sciences
Roser Vento-Tormo, Roser Vilarrasa-Blasi
Summary: The HuBMAP consortium has created spatially resolved cell atlases for the human intestine, kidney, and placenta, providing unprecedented detail for analyzing tissue organization.
Review
Agronomy
Jagdish K. Ladha, Mark B. Peoples, Pallavolu M. Reddy, Jatish C. Biswas, Alan Bennett, Mangi L. Jat, Timothy J. Krupnik
Summary: This review examines the importance of biological nitrogen fixation in crop production and the contribution of nitrogen sources on a global scale. Strategies to enhance the efficiency of biological nitrogen fixation are discussed, along with the challenges and potential of introducing biological nitrogen fixation into conventional and alternative crop management systems.
FIELD CROPS RESEARCH
(2022)
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Microbial molecules from soil, seawater, and human bodies are among the least understood substances on Earth.
Article
Multidisciplinary Sciences
Xia Liu, Minghui Wang, Ao Li
Summary: This study introduces a novel deep-learning framework called PhosVarDeep for predicting phospho-variants, which significantly improves prediction performance through two identical subnetworks and a prediction module. The experimental results demonstrate the effectiveness of this method and its favorable comparison with existing conventional machine learning methods.
Article
Soil Science
Kazumori Mise, Runa Maruyama, Yuichi Miyabara, Takashi Kunito, Keishi Senoo, Shigeto Otsuka
APPLIED SOIL ECOLOGY
(2020)
Article
Ecology
Kazumori Mise, Yuki Koyama, Arisa Matsumoto, Kazuki Fujita, Takashi Kunito, Keishi Senoo, Shigeto Otsuka
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2020)
Article
Microbiology
Zhenxing Xu, Yoko Masuda, Chie Hayakawa, Natsumi Ushijima, Keisuke Kawano, Yutaka Shiratori, Keishi Senoo, Hideomi Itoh
Article
Multidisciplinary Sciences
Kazumori Mise, Wataru Iwasaki
Article
Microbiology
Hideomi Itoh, Zhenxing Xu, Yoko Masuda, Natsumi Ushijima, Chie Hayakawa, Yutaka Shiratori, Keishi Senoo
Summary: Three novel bacterial strains were isolated from soil in Japan, identified as new species in the genus Geomonas based on 16S rRNA gene sequences and genome-related analysis, named Geomonas silvestris sp. nov., Geomonas paludis sp. nov., and Geomonas limicola sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Zhengcheng Zhang, Zhenxing Xu, Yoko Masuda, Xueding Wang, Natsumi Ushijima, Yutaka Shiratori, Keishi Senoo, Hideomi Itoh
Summary: Bacteria in the family Geobacteraceae play important roles in anaerobic environments and global biogeochemical processes. Three newly isolated strains showed distinctive physiological and phylogenetic characteristics, leading to the proposal of a new genus and two independent species within the family.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yuya Sato, Seonghan Jang, Kazutaka Takeshita, Hideomi Itoh, Hideaki Koike, Kanako Tago, Masahito Hayatsu, Tomoyuki Hori, Yoshitomo Kikuchi
Summary: The study reveals a symbiotic bacteria that degrades insecticide into a non-insecticidal but bactericidal compound, offering a new strategy to address insecticide resistance.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Hideomi Itoh, Zhenxing Xu, Kazumori Mise, Yoko Masuda, Natsumi Ushijima, Chie Hayakawa, Yutaka Shiratori, Keishi Senoo
Summary: Three novel bacterial strains belonging to the Anaeromyxobacter genus were isolated from paddy soils in Japan. They displayed distinct genomic, physiological, and chemotaxonomic characteristics that distinguished them from other strains within the genus.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Ecology
Mar Benavides, Louis Conradt, Sophie Bonnet, Ilana Berman-Frank, Stephanie Barrillon, Anne Petrenko, Andrea Doglioli
Summary: The study reports a unique case of worker-dependent microbiota in the ant Diacamma cf. indicum from Japan. The dominant bacterium is found in the hindgut of workers but is scarce or absent in the reproductive castes, indicating a novel pattern of ant-associated bacterial symbiosis.
ISME COMMUNICATIONS
(2021)
Article
Biology
Kota Ishigami, Seonghan Jang, Hideomi Itoh, Yoshitomo Kikuchi
Summary: Recent studies have shown that gut microorganisms can mediate insect resistance by detoxifying plant toxins and man-made insecticides, such as Burkholderia mediating insecticide resistance in beetles. This symbiosis significantly increases the host's resistance to insecticides.
Article
Biotechnology & Applied Microbiology
Yu Maeda, Kazumori Mise, Wataru Iwasaki, Akira Watanabe, Susumu Asakawa, Rasit Asiloglu, Jun Murase
MICROBES AND ENVIRONMENTS
(2020)
Article
Microbiology
Kazumori Mise, Shigeto Otsuka
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)