Results 71 to 80 of about 772,345 (307)

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

Genome Biology, 2021
We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have ...
Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal   +10 more
doaj   +1 more source

Dynamics of Bacteriophage Genome Ejection In Vitro and In Vivo

, 2010
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form helix, leading
Molineux, Ian J., Panja, Debabrata
core   +1 more source

Environmental shaping of codon usage and functional adaptation across microbial communities. [PDF]

, 2013
Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the ...
Achtman, Altschul, Arumugam, Boto, Botzman, Bruggemann, Burke, Caro-Quintero, Chen, Diene, Donner, Foerstner, Forsberg, Gill, Hershberg, Horvath, Hunyadkurti, Huson, Ikemura, István Nagy, Jensen, Johnson, Kanaya, Kanehisa, Karlin, Keeling, Keller, Kristian Vlahoviček, Kuo, Larimer, Malmstrom, Martin, Maša Roller, McDaniel, McDowell, Mira, Myers, Oda, Plotkin, R Development Core Team, Retchless, Rocha, Sharp, Sharp, Sowell, Staley, Supek, Supek, Tatusov, Tettelin, Tina Perica, Tringe, Tuller, Tuller, Tuller, Turnbaugh, Tyson, Vedran Lucić, Venter, Verberkmoes, Vieira-Silva, Whitman, Willenbrock, Wilmes   +63 more
core   +1 more source

Novel Bacterial Diversity and Fragmented eDNA Identified in Hyperbiofilm-Forming Pseudomonas aeruginosa Rugose Small Colony Variant [PDF]

, 2020
Pseudomonas aeruginosa biofilms represent a major threat to health care. Rugose small colony variants (RSCV) of P. aeruginosa, isolated from chronic infections, display hyperbiofilm phenotype.
Deng, Binbin, Ghatak, Piya Das, Ghatak, Subhadip, Khanna, Savita, Mathew-Steiner, Shomita S., McComb, David W., Roy, Sashwati, Sarkar, Subendu, Sen, Chandan K., Singh, Kanhaiya, Wozniak, Daniel J.   +10 more
core   +1 more source

Screening and epitope characterization of Nidogen‐2‐specific nanobodies

FEBS Open Bio, EarlyView.
Camel immunization and phage display were employed to generate high‐affinity VHH nanobodies against Nidogen‐2. After library construction, biopanning, ELISA screening, sequencing, and recombinant expression, selected nanobodies were purified and characterized, leading to the preliminary exploration of a nanobody‐based sandwich ELISA for specific ...
Jianchuan Wen, Qianqian Cui, Zhongyun Lan, Yingjun Wang, Shuaiying Zhao, Wenxuan Feng, Yunfeng Liu, Qiting Huang, Dongna Zhang, Jianfeng Xu   +9 more
wiley   +1 more source

Genetic Diversity and Spatial Segregation of Francisella tularensis Subspecies holarctica in Germany

Frontiers in Cellular and Infection Microbiology, 2019
Francisella tularensis is an intracellular pleomorphic bacterium and the causative agent of tularemia, a zoonotic disease with a wide host range. Among the F. tularensis subspecies, especially F. tularensis subsp.
Sandra Appelt, Kristin Köppen, Aleksandar Radonić, Oliver Drechsel, Daniela Jacob, Roland Grunow, Klaus Heuner   +6 more
doaj   +1 more source

Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage. [PDF]

, 2013
Sequence type (ST) 59 is an epidemic lineage of community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) isolates. Taiwanese CA-MRSA isolates belong to ST59 and can be grouped into 2 distinct clones, a virulent Taiwan clone and a ...
A Bera, A Holmes, AE Fossum, AM Milstone, B Loffler, BA Diep, BE Gonzalez, BE Gonzalez, C Goerke, C Weidenmaier, Chih-Jung Chen, CJ Chen, CJ Chen, CJ Chen, CJ Chen, CJC de Haas, Clemens Unger, CP Montgomery, dS Aires, FC Tenover, FJ Chen, Friedrich Götz, GM Pupo, GW Coombs, J Bubeck Wardenburg, J Bubeck Wardenburg, J Kaneko, JM Voyich, Jodi A. Lindsay, K Georgiades, KB Kiser, LY Hsu, M Labandeira-Rey, M Otto, MR Mulvey, MZ David, N Zetola, Paul J. Planet, PE Fournier, PL Ho, R Wang, S Herbert, SHM Rooijakkers, SL Kaplan, T Jin, T Jin, V Merhej, WJ Wannet, WJB van Wamel, Wolfgang Hoffmann, Y Gillet, YC Huang, YC Huang, YC Huang, YC Huang, Yhu-Chering Huang   +55 more
core   +3 more sources

Genomic Arrangement of Regulons in Bacterial Genomes

PLoS ONE, 2012
Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome.
Han Zhang, Yanbin Yin, Victor Olman, Ying Xu   +3 more
openaire   +4 more sources

Evolutionarily divergent DUF4465 domains have a common vitamin B12‐binding function

FEBS Open Bio, EarlyView.
We show that DUF4465 family proteins, widespread across bacteria from gut microbiomes, hydrothermal vents, and soil, share a common vitamin B12‐binding function. These augmented β‐jellyroll proteins bind vitamin B12 via extended loops. Our findings establish sequence‐diverse DUF4465 proteins as a widespread class of B12‐binding proteins, highlighting ...
Charlea Clarke, Michal Banasik, Rokas Juodeikis, Martin J. Warren, Richard W. Pickersgill   +4 more
wiley   +1 more source

Efficient dual-negative selection for bacterial genome editing

BMC Microbiology, 2020
Background Gene editing is key for elucidating gene function. Traditional methods, such as consecutive single-crossovers, have been widely used to modify bacterial genomes.
Francesca Romana Cianfanelli, Olivier Cunrath, Dirk Bumann   +2 more
doaj   +1 more source