Uropathogenic E. coli induces DNA damage in the bladder

Urinary tract infections (UTIs) are among the most common outpatient infections, with a lifetime incidence of around 60% in women. We analysed urine samples from 223 patients with community-acquired UTIs and report the presence of the cleavage product released during the synthesis of colibactin, a bacterial genotoxin, in 55 of the samples examined. Uropathogenic Escherichia coli strains isolated from these patients, as well as the archetypal E. coli strain UTI89, were found to produce colibactin. In a murine model of UTI, the machinery producing colibactin was expressed during the early hours of the infection, when intracellular bacterial communities form. We observed extensive DNA damage both in umbrella and bladder progenitor cells. To the best of our knowledge this is the first report of colibactin production in UTIs in humans and its genotoxicity in bladder cells.     

Cardboard nesting cavities may promote the development of Osmia cornuta and reduce infestation of kleptoparasitic mites

Mason bees (Osmia spp.) are receiving increasing attention as they are very effective pollinators of multiple crops. However, different bee-associated kleptoparasites are known which can be detrimental to the development of the bees’ offspring. To date, clear evidence-based guidelines to control these kleptoparasites are lacking for growers. This study investigates whether different types of artificial nesting materials—cardboard tubes and wooden grooved boards—influence the development of the European orchard bee (Osmia cornuta) as well as the infestation rate of kleptoparasitic mites in the bees’ nest. This preliminary study provides insight that cardboard tubes reduce the infestation rate of mites by 81.8% and as such promote successful development of the European orchard bee by 15.5%. Using cardboard tubes over wooden grooved boards should be advised to growers as an effective management strategy to avoid infestation of kleptoparasitic mites and to enhance successful bee development.     

Dr. Jekyll and Mr. Hyde: A short history of anthrax

The anthrax letters crisis, following the discovery of a major bacterial warfare program in the USSR and the realization that Irak had been on the verge of using anthrax as a weapon during the first Gulf war, had the consequence of putting anthrax back on the agenda of scientists. Fortunately, although it was mostly unknown by the public before these events, it was far from unknown by microbiologists. Already mentioned in the bible as a disease of herbivores, it remained a major cause of death for animals all over the planet until the end of the 19th century, with occasional, sometimes extensive, contamination of human beings. The aetiological agent, Bacillus anthracis, was identified by French and German scientists in the 1860s and 1870s. This was the first time that a disease could be attributed to a specific microorganism. The discovery by Koch that this bacterium formed spores greatly contributed to the understanding of the disease epidemiology. Studies on the pathophysiology of anthrax led to the identification of two major virulence factors, the capsule, protecting the bacilli against phagocytosis, and a tripartite toxin. The latter consists of two toxins with a common component (protecting antigen, PA) that allows the binding to and penetration into cells of two enzymes, the oedema factor EF, a calmodulin dependent adenylate cyclase, and the lethal factor LF, a specific zinc metalloprotease. The primary targets of these toxins would seem to be cells of innate immunity that would otherwise impair multiplication of the bacilli. If detected early enough, B. anthracis infections can be stopped by using antibiotics such as ciprofloxacin. Infection of animals can be prevented by the administration of vaccines, the first of which was developed by Pasteur after an historical testing at Pouilly-le-Fort which marked the beginning of the science of vaccines.     

A new proposal for multivariable modelling of time-varying effects in survival data based on fractional polynomial time-transformation

The Cox proportional hazards model has become the standard for the analysis of survival time data in cancer and other chronic diseases. In most studies, proportional hazards (PH) are assumed for covariate effects. With long-term follow-up, the PH assumption may be violated, leading to poor model fit. To accommodate non-PH effects, we introduce a new procedure, MFPT, an extension of the multivariable fractional polynomial (MFP) approach, to do the following: (1) select influential variables; (2) determine a sensible dose-response function for continuous variables; (3) investigate time-varying effects; (4) model such time-varying effects on a continuous scale. Assuming PH initially, we start with a detailed model-building step, including a search for possible non-linear functions for continuous covariates. Sometimes a variable with a strong short-term effect may appear weak or non-influential if 'averaged' over time under the PH assumption. To protect against omitting such variables, we repeat the analysis over a restricted time-interval. Any additional prognostic variables identified by this second analysis are added to create our final time-fixed multivariable model. Using a forward-selection algorithm we search for possible improvements in fit by adding time-varying covariates. The first part to create a final time-fixed model does not require the use of MFP. A model may be given from 'outside' or a different strategy may be preferred for this part. This broadens the scope of the time-varying part. To motivate and illustrate the methodology, we create prognostic models from a large database of patients with primary breast cancer. Non-linear time-fixed effects are found for progesterone receptor status and number of positive lymph nodes. Highly statistically significant time-varying effects are present for progesterone receptor status and tumour size.     

Evaluation of the Patient Acceptable Symptom State in a pooled analysis of two multicentre, randomised, double-blind, placebo-controlled studies evaluating lumiracoxib and celecoxib in patients with osteoarthritis

Patient Acceptable Symptom State (PASS) is an absolute threshold proposed for symptomatic variables in osteoarthritis (OA) to determine the point beyond which patients consider themselves well and, as such, are satisfied with treatment. Two large previously reported studies of knee OA have shown that both lumiracoxib and celecoxib were superior to placebo in terms of conventional outcome measures. To assess the clinical relevance of these results from the patient's perspective, the same data pooled from these two studies were analysed with respect to the PASS. In total, 3,235 patients were included in two multicentre, randomised, double-blind studies of identical design. Patients were randomly assigned to receive lumiracoxib 100 mg once daily (n = 811), lumiracoxib 100 mg once daily with an initial dose of lumiracoxib 200 mg once daily for the first 2 weeks (100 mg once daily with initial dose [n = 805]), celecoxib 200 mg once daily (n = 813), or placebo (n = 806) for 13 weeks. Treatments were compared with respect to the PASS criteria (for OA pain, patient's global assessment of disease activity, and the Western Ontario and McMaster Universities Osteoarthritis Index Likert version 3.1 [WOMAC LK 3.1] Function [difficulty in performing daily activities] subscale score). At week 13, 43.3%, 45.3%, and 42.2% of patients in the lumiracoxib 100 mg once daily, lumiracoxib 100 mg once daily with initial dose, and the celecoxib 200 mg once daily groups, respectively, considered their current states as satisfactory versus 35.5% in the placebo group. Similar results were observed for patient's global assessment of disease activity and WOMAC LK 3.1 Function subscale score. This post hoc analysis suggests that the statistical significance of the results observed with lumiracoxib or celecoxib compared with placebo using conventional outcome variables is complemented by clinical relevance to the patient. Trial registration numbers: NCT00366938 and NCT00367315.     

The Structure of the Cyprinid herpesvirus 3 ORF112-Zα·Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L,a Poxvirus Inhibitor of Interferon Response

In vertebrate species, the innate immune system down-regulates protein translation in response to viral infection through the action of the double-stranded RNA (dsRNA)-activated protein kinase (PKR). In some teleost species another protein kinase, Z-DNA-dependent protein kinase (PKZ), plays a similar role but instead of dsRNA binding domains, PKZ has Zα domains. These domains recognize the left-handed conformer of dsDNA and dsRNA known as Z-DNA/Z-RNA. Cyprinid herpesvirus 3 infects common and koi carp, which have PKZ, and encodes the ORF112 protein that itself bears a Zα domain, a putative competitive inhibitor of PKZ. Here we present the crystal structure of ORF112-Zα in complex with an 18-bp CpG DNA repeat, at 1.5 Å. We demonstrate that the bound DNA is in the left-handed conformation and identify key interactions for the specificity of ORF112. Localization of ORF112 protein in stress granules induced in Cyprinid herpesvirus 3-infected fish cells suggests a functional behavior similar to that of Zα domains of the interferon-regulated, nucleic acid surveillance proteins ADAR1 and DAI.     

Aromatic aldehyde and hydrazine activated peptide coated quantum dots for easy bioconjugation and live cell imaging

We present a robust scheme for preparation of semiconductor quantum dots (QDs) and cognate partners in a conjugation ready format. Our approach is based on bis-aryl hydrazone bond formation mediated by aromatic aldehyde and hydrazinonicotinate acetone hydrazone (HyNic) activated peptide coated quantum dots. We demonstrate controlled preparation of antibody--QD bioconjugates for specific targeting of endogenous epidermal growth factor receptors in breast cancer cells and for single QD tracking of transmembrane proteins via an extracellular epitope. The same approach was also used for optical mapping of RNA polymerases bound to combed genomic DNA in vitro.