Applied Biosystems

About: Applied Biosystems is a based out in . It is known for research contribution in the topics: Mass spectrometry & Nucleic acid. The organization has 1521 authors who have published 1579 publications receiving 285423 citations.

Selection of minimum subsets of single nucleotide polymorphisms to capture haplotype block diversity.

Abstract: We present a simple numerical algorithm to select the minimal subset of SNPs required to capture the diversity of haplotype blocks or other genetic loci. This algorithm can be used to quickly select the minimum SNP subset with no loss of haplotype information. In addition, the method can be used in a more aggressive mode to further reduce the original SNP set, with minimal loss of information. We demonstrate the algorithm performance with data from over 11,000 SNPs with average spacing of 6 to 11 Kb, across all the genes of chromosomes 6, 21, and 22, genotyped on DNA samples of 45 unrelated African-Americans and 45 Caucasians from the Coriell Human Diversity Collection. With no loss of information, we reduced the number of SNPs required to capture the haplotype block diversity by 25% for the African-American and 36% for the Caucasian populations. With a maximum loss of 10% of haplotype distribution information, the SNP reduction was 38% and 49% respectively for the two populations. All computations were performed in less than 1 minute for the entire dataset used.

A Second Outer-Core Region in Klebsiella pneumoniae Lipopolysaccharide

Abstract: Up to now only one major type of core oligosaccharide has been found in the lipopolysaccharide of all Klebsiella pneumoniae strains analyzed. Applying a different screening approach, we identified a novel Klebsiella pneumoniae core (type 2). Both Klebsiella core types share the same inner core and the outer-core-proximal disaccharide, GlcN-(1,4)-GalA, but they differ in the GlcN substituents. In core type 2, the GlcpN residue is substituted at the O-4 position by the disaccharide β-Glcp(1-6)-α-Glcp(1, while in core type 1 the GlcpN residue is substituted at the O-6 position by either the disaccharide α-Hep(1-4)-α-Kdo(2 or a Kdo residue (Kdo is 3-deoxy-d-manno-octulosonic acid). This difference correlates with the presence of a three-gene region in the corresponding core biosynthetic clusters. Engineering of both core types by interchanging this specific region allowed studying the effect on virulence. The replacement of Klebsiella core type 1 in a highly type 2 virulent strain (52145) induces lower virulence than core type 2 in a murine infection model.