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Wayne M Barnes

Publications and source records attributed to Wayne M Barnes.

5 recordsLinked to original sources
PubMed2004

The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition.

ETT2 is a second cryptic type III secretion system in Escherichia coli which was first discovered through the analysis of genome sequences of enterohemorrhagic E. coli O157:H7. Comparative analyses of Escherichia and Shigella genome sequences revealed that the ETT2 gene cluster is larger than was previously thought, encompassing homologues of genes from the Spi-1, Spi-2, and Spi-3 Salmonella pathogenicity islands. ETT2-associated genes, including regulators and chaperones, were found at the same chromosomal location in the majority of genome-sequenced strains, including the laboratory strain K-12. Using a PCR-based approach, we constructed a complete tiling path through the ETT2 gene cluster for 79 strains, including the well-characterized E. coli reference collection supplemented with additional pathotypes. The ETT2 gene cluster was found to be present in whole or in part in the majority of E. coli strains, whether pathogenic or commensal, with patterns of distribution and deletion mirroring the known phylogenetic structure of the species. In almost all strains, including enterohemorrhagic E. coli O157:H7, ETT2 has been subjected to varying degrees of mutational attrition that render it unable to encode a functioning secretion system. A second type III secretion system-associated locus that likely encodes the ETT2 translocation apparatus was found in some E. coli strains. Intact versions of both ETT2-related clusters are apparently present in enteroaggregative E. coli strain O42.

Escherichia coli↗
PubMed2003

Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR.

Although the thermophilic bacterium Thermus aquaticus grows optimally at 70 degrees C and cannot grow at moderate temperatures, its DNA polymerase I has significant activity at 20-37 degrees C. This activity is a bane to some PCRs, since it catalyzes non-specific priming. We report mutations of Klentaq (an N-terminal deletion variant) DNA polymerase that have markedly reduced activity at 37 degrees C yet retain apparently normal activity at 68 degrees C and resistance at 95 degrees C. The first four of these mutations are clustered on the outside surface of the enzyme, nowhere near the active site, but at the hinge point of a domain that has been proposed to move at each cycle of nucleotide incorporation. We show that the novel cold-sensitive mutants can provide a hot start for PCR and exhibit slightly improved fidelity.

Binding Sites↗
PubMed2002

Magnesium precipitate hot start method for PCR.

For the amplification of HIV-1 gag gene, and other challenging targets, a simple new hot start PCR protocol is presented which consists simply and entirely of the buffer system. This novel buffer composition and reaction assembly protocol for PCR includes magnesium and phosphate combined at high concentration in addition to standard buffer reagents. The resulting magnesium-containing precipitate provides a hot start for PCR, since the magnesium in the precipitate is unavailable to DNA polymerase until thermal cycling. No extra manipulations at the thermal cycler or changes to standard thermal cycling profiles are necessary. Upon normal cycling, the magnesium becomes fully available within the first 3 cycles. The method effectively prevents premature primer extension by several DNA polymerases or mixtures of DNA polymerases tested, including Klentaql, KlentaqLA, Pfu, and full-length wild-type DNA polymerase. Once the precipitate is formed, the hot start buffer is stable and functional for at least a week at -20 degrees, 4 degrees , or 25 degrees. We demonstrate that the method is as effective as a manual hot start (addition of magnesium at or above primers'annealing temperatures) for several target gene amplifications which require a hot start.

Animals↗