Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a

Background

On most common microarray platforms many genes are represented by multiple probes. Although this is quite common no one has systematically explored the concordance between probes mapped to the same gene.

Results

Here we present an analysis of all the cases of multiple probe sets measuring the same gene on the Affymetrix U133a GeneChip and found that although in the majority of cases both measurements tend to agree there are a significant number of cases in which the two measurements differ from each other. In these cases the measurements can not be simply averaged but rather should be handled individually.

Conclusion

Our analysis allows us to provide a comprehensive list of the correlation between all pairs of probe sets that are mapped to the same gene and thus allows microarray users to sort out the cases that deserve further analysis. Comparison between the set of highly correlated pairs and the set of pairs that tend to differ from each other reveals potential factors that may affect it.     

Basic structure of the oligosaccharide repeating-unit of the Shigella flexneri O-antigens.

The reaction of sodium D-glucuronate with a synthetic peptide, AcTyrLysGlyNH₂ acetate, under physiological conditions, gave as major product the sodium salt of AcTyr-N-(D-arabino-5-carboxy-2,3,4,5-tetrahydroxy-1-pentenyl)-N-(D-arabino- 5-carboxy-3,4,5-trihydroxy-2-oxopentylidene)LysGlyNH₂ (2). The structure was elucidated on the basis of p.m.r., ¹³C-n.m.r., i.r., and u.v. spectra, and pH titration. Compound 2 is the product of oxidation of the sodium salt of AcTyr-N,N-bis(D- arabino-5-carboxy-2,3,4,5-tetrahydroxy-1-pentenyl)LysGlyNH₂, the bis-enol form of the di-D-fructuronic acid peptide obtained through the Amadori rearrangement. A new type of condensation that gives a product having a conjugated enol-keto-immonium group might take place when D-glucuronic acid reacts with peptides or proteins containing a lysine residue.     

Structural and immunochemical studies of the lipopolysaccharide from a new provisional serotype of Shigella flexneri

The chemical structure of the O-antigen of a proposed new provisional serotype of Shigella flexneri has been determined. Methylation analysis, GLC-MS, 1H-NMR and 13C-NMR showed that the linear O-antigenic polysaccharide is the same as for all S. flexneri [Kenne, L., Lindberg, B., Petersson, K. & Romanowska, E. (1977) Carbohydr. Res. 56, 363-370]. A novel structural feature is that the disaccharide alpha-D-Glcp-(1----2)-alpha-D-Glcp is linked to O4 of the N-acetyl-glucosamine residue. (Formula: see text) Western blotting of the lipopolysaccharide with an E. coli R3 core-specific monoclonal antibody, suggested the presence of an E. coli R3 core.     

A case of shigellosis caused by Shigella dysenteriae type 1 and Shigella flexneri type 5B

Shigella dysenteriae type 1 and Shigella flexneri type 5b strains were isolated as causative agents of bacterial dysentery in a patient having visited South-East Asia. Both strains are a rare finding for Bulgaria. S. dysenteriae 1 strains have not been isolated since 1962, and there were only single isolates of S. flexneri 5b. The strains were of the same antibiotic resistance patterns. Conjugation experiments showed that resistance is determined by transferrable R-plasmids having identical characteristics. It is assumed that in the patient's gut transfer of an R-plasmid occurs from E. coli of the normal flora to the pathogenic shigellae.     

The immunochemistry of Shigella flexneri O-antigens. The biochemical basis of smooth to rough mutation

1. Smooth to rough mutation has the same biochemical basis in Shigella as in Salmonella. It is the result of enzyme defects blocking the incorporation of the O-specific side chains that characterize the smooth lipopolysaccharide with the consequent exposure of the underlying basal structures that determine `rough'-specificity. 2. The Shigella flexneri basal structure resembles its Salmonella analogue in that it has the same qualitative sugar composition, and enzyme defects in its biosynthetic pathway give rise to `rough'-lipopolysaccharides that are indistinguishable from those of Salmonella chemotypes Ra, Rb, Rc and Rd. However, the Salmonella and Shigella basal structures are not identical as judged by quantitative analysis and the absence of serological cross-reaction. 3. The Sh. flexneri basal structure side chain has been isolated and characterized as an α-N-acetylglucosaminyl-(1→4)-galactosyl-(1→3)-glucose sequence with α-glucosyl radicals substituted on the 3- and 4-positions of the galactose and glucose respectively. The different sugar types in this side chain are incorporated into the growing molecule in the same order as in Salmonella, which explains why the enzyme defects associated with smooth to rough mutation produce the same series of R-chemotypes from both genera. The terminal α-glucosyl and α-N-acetylglucosaminyl-(1→4)-galactosyl residues of the Sh. flexneri basal structure are sufficiently different from the terminal α-galactosyl and α-N-acetylglucosaminylglucosyl residues of the Salmonella analogue that they offer an explanation for the absence of serological cross-reaction between these two basal structures.     

福氏志贺氏2a及Y变种保护性抗原的研究

福氏志贺菌Y变种曾经作为一种痢疾疫苗的候选株,其特有的抗原结构在疫苗的有效性抗原研究中起主要作用。以Y变种毒株与无毒株、野生型F2a株与T32株及失去Ⅱ型抗原结构的T32-1株之间分别进行了各种毒力表型的检测、四种外膜侵袭蛋白表达、菌株的外膜蛋白提取物(OMPs)分析、质粒DNA图谱和小鼠主动免疫、被动保护试验的对比分析,了解其抗原特性。结果显示：细菌外膜蛋白抗原和具有完整型特异性抗原结构的福氏菌LPS在动物机体免疫中都发挥着重要的作用。这些抗原物质的共同存在似乎能达到更好的免疫效果。