Shifting patterns of natural variation in the nuclear genome of caenorhabditis elegans

<p>Abstract</p> <p>Background</p> <p>Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode <it>Caenorhabditis elegans </it>(CB4856 and CB4858) and the reference genome (N2).</p> <p>Results</p> <p>The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.</p> <p>In both CB4856 and CB4858, based on a measure of the strength of selection (k_a/k_s), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, k_a/k_svalues are smaller in the autosomes than in the X chromosome. In addition, in CB4858, k_a/k_svalues differ between chromosomes.</p> <p>Conclusions</p> <p>The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the k_a/k_sratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.</p

Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide inC. elegans

Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses. Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation between systems that monitor temperature, O₂ and CO₂. CO₂ is less aversive to animals acclimated to 15°C than those grown at 22°C. This difference requires the AFD neurons, which respond to both temperature and CO₂ changes. CO₂ evokes distinct AFD Ca²⁺ responses in animals acclimated at 15°C or 22°C. Mutants defective in synaptic transmission can reprogram AFD CO₂ responses according to temperature experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely sensitive to CO₂. Surprisingly, gradients of 0.01% CO₂/second evoke very different Ca²⁺ responses from gradients of 0.04% CO₂/second. Ambient O₂ provides further contextual modulation of CO₂ avoidance. At 21% O₂ tonic signalling from the O₂-sensing neuron URX inhibits CO₂ avoidance. This inhibition can be graded according to O₂ levels. In a natural wild isolate, a switch from 21% to 19% O₂ is sufficient to convert CO₂ from a neutral to an aversive cue. This sharp tuning is conferred partly by the neuroglobin GLB-5. The modulatory effects of O₂ on CO₂ avoidance involve the RIA interneurons, which are post-synaptic to URX and exhibit CO₂-evoked Ca²⁺ responses. Ambient O₂ and acclimation temperature act combinatorially to modulate CO₂ responsiveness. Our work highlights the integrated architecture of homeostatic responses in C. elegans

Clinical utility of telavancin for treatment of hospital-acquired pneumonia: focus on non-ventilator-associated pneumonia

Ethan Rubinstein,1 Martin E Stryjewski,2 Steven L Barriere31University of Manitoba, Winnipeg, MB, Canada; 2Department of Medicine, Section of Infectious Diseases, Centro de Educaci&oacute;n M&eacute;dica e Investigaciones Cl&iacute;nicas (CEMIC), Buenos Aires, Argentina; 3Theravance, Inc., South San Francisco, CA, USA Background: Hospital-acquired pneumonia (HAP) is the most common health care-associated infection contributing to death. Studies have indicated that there may be differences in the causative pathogens and outcomes of ventilator-associated pneumonia (VAP) and non-ventilator-associated pneumonia (NV-HAP). However, with limited NV-HAP-specific data available, treatment is generally based on data from studies of VAP. The Phase 3 Assessment of Telavancin for Treatment of Hospital-Acquired Pneumonia (ATTAIN) studies were two double-blind randomized controlled trials that demonstrated the non-inferiority of telavancin to vancomycin for treatment of Gram-positive HAP. We conducted a post hoc subgroup analysis of patients enrolled in the ATTAIN studies who had NV-HAP. Methods: Data from the two ATTAIN studies were pooled, and patients with NV-HAP were analyzed. The all-treated (AT) population consisted of all randomized patients who received &ge;1 dose of study medication, and the clinically evaluable (CE) population consisted of AT patients who were protocol-adherent or who died on or after study day 3, where death was attributable to the HAP episode under study. The primary endpoint was clinical response (cure, failure, or indeterminate) at the follow-up/test of cure visit, conducted 7&ndash;14 days after the end of therapy. Results: A total of 1,076 patients (71.6% of overall ATTAIN AT population) had NV-HAP (533 and 543 patients in the telavancin and vancomycin treatment groups, respectively). Clinical cure rates in the CE population were similar for patients with NV-HAP treated with telavancin and vancomycin (83.1% [201/242] and 84.1% [233/277], respectively). In patients with methicillin-resistant Staphylococcus aureus isolated at baseline, cure rates in the CE population were 74.8% (77/103) for telavancin and 79.3% (96/121) for vancomycin. The incidence of adverse events, serious adverse events, and deaths in patients with NV-HAP was similar whether patients received telavancin or vancomycin. Conclusion: This post hoc subgroup analysis of the ATTAIN studies demonstrated similar cure rates for telavancin and vancomycin for treatment of NV-HAP. Keywords: nosocomial pneumonia, Staphylococcus aureus, methicillin-resistant Staphylococcus aureu