Results 51 to 60 of about 138,246 (299)

metagenome-atlas/atlas: Use parquet and pyfastx to handle large gene catalogs

, 2022
What's Changed Make atlas handle large gene catalogs using parquet and pyfastx (Fix #515) parquet files can be opened in python with import pandas as pd coverage = pd.read_parquet("working_dir/Genecatalog/counts/median_coverage.parquet") coverage ...
Silas Kieser, Richard Allen White III, Joe Brown, Vladimir Mikryukov, Roshni Biswas, Yan Hui, Jackson M. Tsuji, Christopher Bottoms, Cedric Midoux, Jie Zhu, Sean M. Colby, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +15 more
core   +1 more source

Reconstructing enzyme evolution by protein engineering

FEBS Letters, EarlyView.
Natural enzyme evolution can be retraced by protein engineering methods such as directed evolution, rational design, and ancestral sequence reconstruction. These approaches reveal how enzymes emerged from ligand‐binding scaffolds, developed varying substrate preferences, formed oligomeric complexes, adapted to environmental changes, and evolved novel ...
Lukas Drexler, Markus R. Busch, Reinhard Sterner   +2 more
wiley   +1 more source

Noncanonical Peloruside A Biosynthesis by an Uncultivated Verrucomicrobiota Symbiont

Angewandte Chemie, EarlyView.
Noncanonical biochemistry of the peloruside PKS characterized in this work, comprising double bond generation by a noncanonical tridomain (blue), acetyl‐CoA recycling (orange), and proofreading systems (purple and yellow). The Z‐double bond is installed by TEB1 through O‐acetylation and acetate elimination. The acyl ligase PelB (AL, orange) selectively
Amy E. Fraley, Michael Rust, Moritz Wagner, Ida R. Hipfinger, Paul J. N. Böhm, Cora L. Dieterich, Christopher M. Field, Michael J. Page, Jeremy G. Owen, Robert A. Keyzers, Shinichi Sunagawa, Jörn Piel   +11 more
wiley   +2 more sources

Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours

Nature Communications
Urinary tract infections (UTIs) affect 405 million people worldwide. Current diagnostics rely on cultures, which can take 2 to 4 days. This study evaluates eleven culture-independent methods for sample preparation from 78 complicated UTI patients ...
Anurag Basavaraj Bellankimath, Sverre Branders, Isabell Kegel, Jawad Ali, Fatemeh Asadi, Truls E. Bjerklund Johansen, Can Imirzalioglu, Torsten Hain, Florian Wagenlehner, Rafi Ahmad   +9 more
doaj   +1 more source

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms [PDF]

, 2013
Eikmeyer FG, Rademacher A, Hanreich A, et al. Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms.
Sebastian Jaenicke, Eikmeyer, Felix Gregor ; https://orcid.org/, Zakrzewski, Martha, Schlüter, Andreas, Jaenicke, Sebastian, Antje Rademacher, Maus, Irena, Eikmeyer, Felix G., Alfred Pühler, Hennig, Magdalena, Klocke, Michael, Wibberg, Daniel, Michael Klocke, Andreas Schlüter, Schlüter, Andreas ; https://orcid.org/, Rademacher, Antje, Angelika Hanreich, Martha Zakrzewski, Daniel Wibberg, Magdalena Hennig, Pühler, Alfred, Pühler, Alfred ; https://orcid.org/, Felix G Eikmeyer, Hanreich, Angelika, Irena Maus   +24 more
core   +1 more source

Polyphenol‐Inspired Materials for Agricultural Applications

Advanced Materials, EarlyView.
This review outlines the use of polyphenol‐inspired materials for sustainable agriculture, highlighting their molecular design, interfacial assembly, structure–property relationships, and prospects toward precision agriculture, climate resilience, ecosystem protection, and circular bioeconomy strategies.
Haofu Liu, Omid Mazaheri, Zhixing Lin, Tianzheng Wang, Jingqu Chen, Yuang Gu, Xia Liang, Deli Chen, Frank Caruso   +8 more
wiley   +1 more source

metagenome-atlas/atlas: Allow parameters in init qc

, 2020
ATLAS - Three commands to start analysing your metagenome ...
Silas Kieser, Jackson M. Tsuji, Richard Allen White III, Christopher Bottoms, Joe Brown, Sean M. Colby, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +10 more
core   +1 more source

A Comprehensive Microbial Gene Catalog of the Human Airway Microbiome Across Anatomical Sites and Geographic Regions

Advanced Science, EarlyView.
An integrated Human Airway Microbiome Gene Catalog (iHAMGC) is constructed from 12,273 metagenomic airway samples, providing a high‐resolution reference of respiratory microbial genes. The catalog enables systematic exploration of taxonomic and functional variation across airway niches and geographic regions, revealing site‐specific and region ...
Qing Zhang, Dashu Li, Bo Liu, Yue Zhang, Min Li, Ruochun Guo, Yawen Ni, Shibin Chen, Biao Ni, Lijie Qiu, Guorui Xing, He Dong, Qiulong Yan, Shenghui Li, Xiaohui Zou, Bin Cao   +15 more
wiley   +1 more source

Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC‑9

, 2020
At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms.
Jayda E. Meisel (1583992), Larry Mullins, Paul B. Hatzinger, Katarzyna H. Kucharzyk, Craig M. Bartling, Simon Vainberg (2288551), Steven A. Higgins (8610837), Steven A. Higgins, Simon Vainberg, Robert W. Murdoch (5943200), Jayda E. Meisel, Katarzyna H. Kucharzyk (8610831), Paul B. Hatzinger (1741243), Frank E. Löffler (1598887), Robert W. Murdoch, Frank E. Löffler, Fadime Kara-Murdoch (8610834), Fadime Kara-Murdoch, Larry Mullins (8610840), Craig M. Bartling (2350426)   +19 more
core   +2 more sources

Revolutionising Agricultural Sustainability: New ‘Furrow Tillage’ can Mitigate Short‐Term Soil‐to‐Atmosphere CO2 Flux and Promote Soil‐Plant‐Microbe Health

Advanced Science, EarlyView.
Furrow tillage resolves the conventional‐vs.‐no‐tillage trade‐off by simultaneously cutting CO2 efflux to 2.0–3.0 g C m−2 d−1 and unlocking high nutrient availability for the rice rhizosphere. This scalable agronomic solution strengthens soil health, enhances plant physiology, reshapes microbial metabolism, and shifts paddy systems toward a net ...
Arnab Majumdar, Munish Kumar Upadhyay, Argha Ghosh, Rakesh Biswas, Ioly Kotta Loizou, Martin Buck, Mark Tibbett, Biswajit Giri, Debojyoti Moulick, Manoj Kumar Jaiswal, Tarit Roychowdhury   +10 more
wiley   +1 more source