Biolog Phenotype MicroArray
     Serious Technology for Serious Microbiology December 2015
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Mobile Genetic Elements Studied with Phenotype MicroArrays

Phenotype MicroArray
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Horizontal genomics or study of the mobilome focuses on plasmids, bacteriophages, transposons, genomic islands, and genome plasticity. Phenotype MicroArrays have been used in the comparison of these different genomic states revealing phenotypes including metabolic substrate utilization, relative antibiotic sensitivity, and relative sensitivity to environmental stressors. In this issue, we present five papers from the scientific literature on this topic:
 
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  A Novel Family of Integrases Associated with Prophages and Genomic Islands Integrated Within the tRNA-Dihydrouridine Synthase A (dusA) Gene
A novel tyrosine recombinase was discovered embedded in the gene that encodes tRNA-dihydrouridine synthase A in over 200 bacteria. Using Phenotype MicroArrays, no phenotypic differences were found between a genomic island deletion strain and the wild type strain. The genomic islands were found to be highly diverse while the integrase was a common feature.
 
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  Modulation of primary cell function of host Pseudomonas bacteria by the conjugative plasmid pCAR1
A new fluorescence-based thermal shift assay for detection of ligand binding was used in conjunction with Biolog's PM3 plate, which contains diverse nitrogen substrates, to create ligand binding profiles for several chemoreceptor ligand binding domains. P. syringae homologs of previously characterized P. aeruginosa chemoreceptors were studied. Results show distinct ligand binding profiles and a critical amino acid residue in one homolog that determines specificity.
 
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  Genomic comparison on Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, prophage heterogeneity, including shiga toxin encoding phage stx2
Lei and Bochner developed a new assay for toxin quantification. They combined the new assay with Phenotype MicroArrays as a source of diverse culture conditions. After testing 768 conditions, they identified metabolic substrates that either induce or repress toxin production. They propose that this new functional cytotoxin quantification method be applied to toxigenic microorganisms.
 
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  Cryptic prophages help bacteria cope with adverse environments
Donald Gardiner's group used Phenotype MicroArrays and a GFP reporter gene to identify inducers of tricothecene biosynthesis. The TRI5-GFP reporter (05T0017) was grown in Phenotype MicroArrays and read for fluorescence and turbidity. PM Substrates inducing the reporter gene suggest involvment of the arginine-polyamine biosynthetic pathway in plants.
 
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  Phenotypic diversity of Escherichia coli O157:H7 strains associated with the plasmid O157
Donald Gardiner's group used Phenotype MicroArrays and a GFP reporter gene to identify inducers of tricothecene biosynthesis. The TRI5-GFP reporter (05T0017) was grown in Phenotype MicroArrays and read for fluorescence and turbidity. PM Substrates inducing the reporter gene suggest involvment of the arginine-polyamine biosynthetic pathway in plants.
 
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Phenotype MicroArray Technology
Biolog's Phentoype MicroArray technology enables researchers to evaluate nearly 2000 phenotypes of a microbial cell in a single experiment. This integrated system of cellular assays, instrumentation and bioinformatics software provides cellular knowledge that complements molecular information, helping you interpret and find the relevant aspects in massive amounts of gene expression or proteomics data. Through comprehensive and precise quantitation of phenotypes, researchers are able to obtain an unbiased perspective of the effect on cells of genetic differences, environmental change, exposure to chemicals or drugs, and more.
 
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