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Structural and Genetic Characterization of the Shigella boydii Type 13 O Antigen. Lu Feng, 2004.Shigella is an important human pathogen . It is generally agreed that Shigella and Escherichia coli constitute a single species; the only exception is Shigella boydii type 13, which is more distantly related to E . coli and other Shigella forms and seems to represent another species . This gives S . boydii type 13 an important status in evolution . O antigen is the polysaccharide part of the lipopolysaccharide in the outer membrane of gram-negative bacteria and plays an important role in pathogenicity . The chemical structure and genetic organization of the S . boydii type 13 O antigen were investigated . The O polysaccharide was found to be acid labile owing to the presence of a glycosyl phosphate linkage in the main chain . The structure of the linear pentasaccharide phosphate repeating unit (O unit) was established by nuclear magnetic resonance spectroscopy, including two-dimensional COSY, TOCSY, ROESY, and H-detected 1H,13C and 1H,31P HMQC experiments, along with chemical methods . The O antigen gene cluster of S . boydii type 13 was located and sequenced . Genes for synthesis of UDP-2-acetamido-2,6-dideoxy-L-glucose and genes that encode putative sugar transferases, O unit flippase, and O antigen polymerase were identified . Seven genes were found to be specific to S . boydii type 13 . The S . boydii type 13 O antigen gene cluster has higher levels of sequence similarity with Vibrio cholerae gene clusters and may be evolutionarily related to these gene clusters .
 -Galactosylceramide and Novel Synthetic Glycolipids Directly Induce the Innate Host Defense Pathway and Have Direct Activity against Hepatitis B and C Viruses.Anand S. Mehta, 2004. -Galactosylceramide is a glycolipid derived from marine sponges that is currently in human clinical trials as an anticancer agent . It has also been shown to be effective in reducing the amount of hepatitis B virus (HBV) DNA detected in mice that produce HBV constitutively from a transgene . It was assumed that all of the antiviral and antitumor activities associated with
-galactosylceramide were mediated through the activation of NK T cells . However, we report here an additional unpredicted activity of
-galactosylceramide as a direct antiviral agent and inducer of the innate host defense pathway . To exploit this activity, we have developed a new class of smaller, orally available glycolipids that also induce the innate host defense pathway and have direct activity against HBV and hepatitis C virus .
Detection of Molecular Diversity in Bacillus atrophaeus by Amplified Fragment Length Polymorphism Analysis. S. A. Burke, 2004.Phenotypically, Bacillus atrophaeus is indistinguishable from the type strain of Bacillus subtilis except by virtue of pigment production on certain media . Several pigmented variants of B . subtilis have been reclassified as B . atrophaeus, but several remain ambiguous in regard to their taxonomic placement . In this study, we examined strains within the American Type Culture Collection originally deposited as Bacillus globigii, B . subtilis var . niger, or Bacillus niger using 16S rRNA gene sequencing and amplified fragment length polymorphism (AFLP) analysis to determine the level of molecular diversity among these strains and their relationship with closely related taxa . The 16S rRNA gene sequences revealed little variation with one base substitution between the B . atrophaeus type strain ATCC 49337 and the other pigmented bacilli . AFLP analysis produced high-quality DNA fingerprints with sufficient polymorphism to reveal strain-level variation . Cluster analysis of Dice similarity coefficients revealed that three strains, ATCC 31028, ATCC 49760, and ATCC 49822, are much more closely related to B . atrophaeus than to B . subtilis and should be reclassified as B . atrophaeus . A very closely related cluster of B . atrophaeus strains was also observed; this cluster was genetically distinct from the type strain . The level of variation between the two groups was approximately the same as the level of variation observed between members of the two B . subtilis subspecies, subtilis and spizizenii . It is proposed that the cluster of strains typified by ATCC 9372 be designated a new subspecies, B . atrophaeus subsp . globigii . Increasing the Carbon Flux toward Synthesis of Short-Chain-Length—Medium-Chain-Length Polyhydroxyalkanoate in the Peroxisome of Saccharomyces cerevisiae through Modification of the ß-Oxidation Cycle. Valeria Cora de Oliveira, 2004. The DsbA Signal Sequence Directs Efficient, Cotranslational Export of Passenger Proteins to the Escherichia coli Periplasm via the Signal Recognition Particle Pathway. Clark F. Schierle, 2003.The Escherichia coli cytoplasmic protein thioredoxin 1 can be efficiently exported to the periplasmic space by the signal sequence of the DsbA protein (DsbAss) but not by the signal sequence of alkaline phosphatase (PhoA) or maltose binding protein (MBP) . Using mutations of the signal recognition particle (SRP) pathway, we found that DsbAss directs thioredoxin 1 to the SRP export pathway . When DsbAss is fused to MBP, MBP also is directed to the SRP pathway . We show directly that the DsbAss-promoted export of MBP is largely cotranslational, in contrast to the mode of MBP export when the native signal sequence is utilized . However, both the export of thioredoxin 1 by DsbAss and the export of DsbA itself are quite sensitive to even the slight inhibition of SecA . These results suggest that SecA may be essential for both the slow posttranslational pathway and the SRP-dependent cotranslational pathway . Finally, probably because of its rapid folding in the cytoplasm, thioredoxin provides, along with gene fusion approaches, a sensitive assay system for signal sequences that utilize the SRP pathway .
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