Yield Spread: A Novel
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Back to tab navigation Download options Please wait Article type: Edge Article. DOI: Download Citation: Chem. A novel strategy for facile serum exosome isolation based on specific interactions between phospholipid bilayers and TiO 2 F. Gao, F. Jiao, C. Xia, Y. Zhao, W. Ying, Y. Xie, X. Guan, M. This process was repeated 20 times, one time for each gene in the training dataset. The false positive rate of the model was estimated based on the incorrectly classified genes. The ratio between the true and false positive rate was used to determine an optimal threshold score for a gene to be classified as B1BL.
To optimize the threshold score for the model when applied to metagenomic data, the cross-validation was additionally performed for gene fragments. The excluded B1 gene was randomly cut into 10, fragments, each nucleotides long, corresponding to the most common read length for Illumina sequence data, and then was analyzed by the model.
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The true positive rate was then calculated as the proportion of correctly classified fragments. The false positive rate was estimated by both 1 fragmented genes from the MBL superfamily as described above and 2 fragments randomly selected from bacterial genomes from NCBI RefSeq , from which every predicted MBL subclass B1 gene had been removed. Based on the results of the cross-validation, the score threshold for the full-length genes was set to All putative B1BL genes that were assembled from metagenomic data were subjected to an additional quality control. Contigs where the physical coverage was zero at any nucleotide position were excluded from the analysis.
Finally, the full-length genes were analyzed by the model again, and genes with a score of less than the threshold for full-length genes were discarded. To assess the functionality of the predicted novel genes, 21 of the candidate novel genes ORFs were synthesized at ThermoFisher Scientific, Germany, using the GeneArt gene synthesis service. The expression of the cloned gene was induced using anhydroteteracycline aTc.
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Phylogenetic analysis was performed to summarize the results and to visualize the evolutionary relationships between the predicted B1BL genes. Livermore DM. Has the era of untreatable infections arrived? J Antimicrob Chemother. Carbapenems: past, present, and future. Antimicrob Agents Chemother. Palzkill T. Metallo-beta-lactamase structure and function. Ann N Y Acad Sci. Bush K, Jacoby GA. Fast W, Sutton LD.
Metallo-beta-lactamase: inhibitors and reporter substrates. Biochim Biophys Acta. Standard numbering scheme for class B beta-lactamases. The rapid spread of carbapenem-resistant Enterobacteriaceae. Drug Resist Updat. Queenan AM, Bush K. Clin Microbiol Rev. The emerging NDM carbapenemases. Trends Microbiol. Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol.
The shared antibiotic resistome of soil bacteria and human pathogens. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Front Microbiol.
Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Sci Total Environ. The structure and diversity of human, animal and environmental resistomes. The scourge of antibiotic resistance: the important role of the environment.
Clin Infect Dis. A novel method to discover fluoroquinolone antibiotic resistance qnr genes in fragmented nucleotide sequences. BMC Genomics. Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets. Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil. ISME J. Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins. Appl Environ Microbiol. The soil microbiota harbors a diversity of carbapenem-hydrolyzing beta-lactamases of potential clinical relevance.
Diverse antibiotic resistance genes in dairy cow manure.
Development of a novel cultivation technique for uncultured soil bacteria
One origin for metallo-beta-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees. J Mol Evol. Nucleic Acids Res. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol.
Grynberg M, Godzik A. Trends Biochem Sci. Roy CR, Cherfils J. Structure and function of Fic proteins. TetX is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics. J Biol Chem. Tigecycline is modified by the flavin-dependent monooxygenase TetX. Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS One. Identification of a metagenomic gene cluster containing a new class A beta-lactamase and toxin-antitoxin systems.
Molecular characterization of the recently emerged poultry pathogen ornithobacterium rhinotracheale by multilocus sequence typing. Antibiotic resistance mechanisms of Myroides sp. J Zhejiang Univ Sci B. Systematic analysis of metallo-beta-lactamases using an automated database. Novel and diverse integron integrase genes and integron-like gene cassettes are prevalent in deep-sea hydrothermal vents. Environ Microbiol. Int J Burns Trauma.