Genome rearrangements induce biofilm formation in Escherichia coli C - an old model organism with a new application in biofilm research.

Background: Escherichia coli C forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E.

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps.

We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with or without creating or destroying restriction sites. We show that OMSV has high sensitivity and specificity, with clear performance gains over the latest method.

High-throughput single-molecule telomere characterization.

We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7-bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG)n tract length at the end of each large telomere-terminal DNA segment.

CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis.

We have developed a new, sequence-specific DNA labeling strategy that will dramatically improve DNA mapping in complex and structurally variant genomic regions, as well as facilitate high-throughput automated whole-genome mapping. The method uses the Cas9 D10A protein, which contains a nuclease disabling mutation in one of the two nuclease domains of Cas9, to create a guide RNA-directed DNA nick in the context of an in vitro-assembled CRISPR-CAS9-DNA complex. Fluorescent nucleotides are then incorporated adjacent to the nicking site with a DNA polymerase to label the guide RNA-determined target sequences.

Shifting from marine reserves to maritime zoning for conservation of Pacific bigeye tuna (Thunnus obesus).

Over 50% of the total bigeye tuna (BET) landed in the Western Central Pacific Ocean is caught incidentally in the purse seine fishery and sold for canning at prices less than US$2/kg. The remainder is landed in longline fisheries directed at BET and sold as fresh or frozen tuna at prices greater than US$10/kg. The combined fishing mortality by all gears will soon reduce the BET biomass in the Pacific Ocean to less than that capable of producing maximum sustainable yield.

Multiple factors insulate Msh2-Msh6 mismatch repair activity from defects in Msh2 domain I.

DNA mismatch repair (MMR) is a highly conserved mutation avoidance mechanism that corrects DNA polymerase misincorporation errors. In initial steps in MMR, Msh2-Msh6 binds mispairs and small insertion/deletion loops, and Msh2-Msh3 binds larger insertion/deletion loops. The msh2Δ1 mutation, which deletes the conserved DNA-binding domain I of Msh2, does not dramatically affect Msh2-Msh6-dependent repair.

"Wurster-type" ureas as redox-active receptors for anions.

Four redox-active receptors, 1-4, based on the incorporation of p-phenylenediamine(s) within a urea framework, were synthesized, and the affinities of two for a series of anions were quantified through UV-vis and NMR spectroscopic studies. The structure of 1 was confirmed by X-ray crystallography. For the oxoanions studied, complex stabilities approached 10(6) M(-1) in acetonitrile and decreased with the decreasing basicity of the anion (CH(3)COO(-) > C(6)H(5)COO(-) > H(2)PO(4)(-) > NO(2)(-) > NO(3)(-)).

The incidence and aetiology of epistaxis in infants: a population-based study.

Objective: To estimate the incidence and describe the aetiology of epistaxis in infants.

Design: Population-based study including a retrospective hospital admission database analysis and a postal questionnaire to clinicians.

Setting: Wales, United Kingdom.

C-reactive protein genotypes and haplotypes, polymorphisms in NSAID-metabolizing enzymes, and risk of colorectal polyps.

Introduction: C-reactive protein (CRP) is a nonspecific marker of inflammation linked to cardiovascular disease and possibly colon cancer. Polymorphisms in CRP have been associated with differential CRP concentrations among healthy adults, with some evidence for functional effects on CRP expression.

Methods: A linkage disequilibrium-based tag single nucleotide polymorphism (SNP)-selection algorithm identified six tagSNPs for Europeans (-821A>G, -390C>T/A, 90A>T, 838G>C, 2043G>A, and 4363C>A), defining six haplotypes with more than 1% frequency.

Wurster's crowns: a comparative study of ortho- and para-phenylenediamine-containing macrocyclic receptors.

Two series of isomeric, redox-responsive azacrown ethers based on ortho- and para-phenylenediamine (Wurster's crowns) have been synthesized and their properties explored through 13C NMR spectroscopy, electrospray ionization mass spectrometry, cyclic voltammetry, and X-ray crystallography. These crowns display strong affinity for alkali metal cations while maintaining comparable selectivity profiles to the parent crown ethers from which they are derived. Like Wurster's reagent (N,N,N',N'-tetramethyl-p-phenylenediamine or para-TMPD), the para-Wurster's crowns undergo two reversible one-electron oxidations.

Diagnosing abuse: a systematic review of torn frenum and other intra-oral injuries.

Introduction: A torn labial frenum is widely regarded as pathognomonic of abuse.

Methods: We systematically reviewed the evidence for this, and to define other intra-oral injuries found in physical abuse. Nine studies documented abusive torn labial frena in 27 children and 24 [corrected] were fatally abused: 22 were less than 5 years old.

Polymorphisms predicted to alter function in prostaglandin E2 synthase and prostaglandin E2 receptors.

Background And Objective: Prostaglandin synthesis is the primary target of aspirin and other nonsteroidal antiinflammatory drugs, and thus is a pathway of major interest to pharmacology, pharmacogenetics, and epidemiology. Several lines of evidence implicate prostaglandin E2 in carcinogenesis; this study aimed to identify genetic variants in genes related to prostaglandin E2 synthesis and signaling.

Methods: We resequenced the coding regions of human prostaglandin E2 synthase (PGES), and prostaglandin E2 receptors EP1, EP2, and EP4 in 48 African-Americans and 47 Caucasians.

Genetic variability in prostaglandin synthesis, fish intake and risk of colorectal polyps.

Dietary polyunsaturated fatty acids (PUFAs) can be converted to prostaglandins and leukotrienes. Metabolism of omega-6 (n-6) PUFAs results in the production of pro-inflammatory mediators whereas downstream products of omega-3 (n-3) PUFAs have lower inflammatory activity. Elevated n-3 PUFA intake from dietary fish may be associated with lower risk of colorectal neoplasia among those with genetic variants resulting in higher levels of pro-inflammatory mediators.

Biomass, size, and trophic status of top predators in the Pacific Ocean.

Fisheries have removed at least 50 million tons of tuna and other top-level predators from the Pacific Ocean pelagic ecosystem since 1950, leading to concerns about a catastrophic reduction in population biomass and the collapse of oceanic food chains. We analyzed all available data from Pacific tuna fisheries for 1950-2004 to provide comprehensive estimates of fishery impacts on population biomass and size structure. Current biomass ranges among species from 36 to 91% of the biomass predicted in the absence of fishing, a level consistent with or higher than standard fisheries management targets.

Which radiological investigations should be performed to identify fractures in suspected child abuse?

Aims: To determine which radiological investigations should be performed and which children should be investigated.

Materials And Methods: An all language literature search of original articles; from 1950-October 2005. Two reviewers independently reviewed each article.

Electron transfer vs coordination chemistry: isomer-specific binding of HgII by an ortho-Wurster's thiacrown ether.

Isomeric p- and o-phenylenediamine-containing macrocyclic hosts (Wurster's thiacrown ethers L1 and L2, respectively) were prepared and studied as Hg(II) ionophores. The distinct electrochemical properties of the two hosts allowed for the formation of a coordination compound with the ortho-Wurster's thiacrown ether but not the para isomer. In the latter case, the Hg(II) ion served as an oxidant in an electron-transfer reaction with the host.