The exceptionally high rate of spontaneous mutations in the polymerase delta proofreading exonuclease-deficient Saccharomyces cerevisiae strain starved for adenine

BACKGROUND: Mutagenesis induced in the yeast Saccharomyces cerevisiae by starvation for nutrilites is a well-documented phenomenon of an unknown mechanism. We have previously shown that the polymerase delta proofreading activity controls spontaneous mutagenesis in cells starved for histidine. To obtain further information, we compared the effect of adenine starvation on mutagenesis in wild-type cells and, in cells lacking the proofreading activity of polymerase delta (phenotype Exo(-), mutation pol3-01). RESULTS: Ade(+ )revertants accumulated at a very high rate on adenine-free plates so that their frequency on day 16 after plating was 1.5 × 10(-4 )for wild-type and 1.0 × 10(-2 )for the Exo(- )strain. In the Exo(- )strain, all revertants arising under adenine starvation are suppressors of the original mutation, most possessed additional nutritional requirements, and 50% of them were temperature sensitive. CONCLUSIONS: Adenine starvation is highly mutagenic in yeast. The deficiency in the polymerase delta proofreading activity in strains with the pol3-01 mutation leads to a further 66-fold increase of the rate of mutations. Our data suggest that adenine starvation induces genome-wide hyper-mutagenesis in the Exo(- )strain

Quantification of HIV-1 proviral DNA in patients with undetectable plasma viremia over long-term highly active antiretroviral therapy

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Early stages of solid state reactions: insights from micro-XRD and XAS

The mechanism of a solid state reaction in its early stages can be explored by investigating the time evolution of a model reactive system made of a thin layer of one reagent deposited onto a single crystal slab of the other reagent. Insights can be retrieved by comparing results at both local and long length scales obtained with films of different thicknesses and deposited onto different crystal orientations. In particular, reaction between ZnO and Al2O3has been chosen, as the spinel-forming reactions have been and still remain a model experimental system for investigating solid state reactions and because in the ZnO/Al2O3phase diagram, spinel is the only stable compound. The reaction initial steps have been investigated by using synchrotron X-ray diffraction, atomic force microscopy and X-ray absorption spectroscopy at the Zn-K edge starting from zincite films deposited onto (110)-, (012)-, (001)-oriented corundum single crystals [1,2]. The reaction eventually yields ZnAl2O4spinel but via a complex mechanism involving side and intermediate non-equilibrium compounds that do not appear in the equilibrium phase diagram of the pseudo-binary system. Spinel, when occurs, is polycrystalline at the end but initially forms with a few preferred orientations. Intermediate phases form before and in parallel with the growth of the spinel. Their number, composition, structure and kinetic role strongly depend on substrate orientation and film thickness. A more detailed understanding of the reactivity can be inferred by comparing EXAFS results to those of grazing incidence diffraction experiments of the films deposited on the (001) face of Al2O3and heat-treated at 10000C for different lengths of time. Information on the structure of the intermediate phases is given and results are discussed by comparing different films thickness to clarify the role of interfacial free energy and crystallographic orientation

The Complete mitochondrial genome of an 11,450-year-old Aurochsen (Bos primigenius) from Central Italy

Background: Bos primigenius, the aurochs, is the wild ancestor of modern cattle breeds and was formerly widespread across Eurasia and northern Africa. After a progressive decline, the species became extinct in 1627. The origin of modern taurine breeds in Europe is debated. Archaeological and early genetic evidence point to a single Near Eastern origin and a subsequent spread during the diffusion of herding and farming. More recent genetic data are instead compatible with local domestication events or at least some level of local introgression from the aurochs. Here we present the analysis of the complete mitochondrial genome of a pre-Neolithic Italian aurochs. Results: In this study, we applied a combined strategy employing both multiplex PCR amplifications and 454 pyrosequencing technology to sequence the complete mitochondrial genome of an 11,450-year-old aurochs specimen from Central Italy. Phylogenetic analysis of the aurochs mtDNA genome supports the conclusions from previous studies of short mtDNA fragments - namely that Italian aurochsen were genetically very similar to modern cattle breeds, but highly divergent from the North-Central European aurochsen. Conclusions: Complete mitochondrial genome sequences are now available for several modern cattle and two pre-Neolithic mtDNA genomes from very different geographic areas. These data suggest that previously identified sub-groups within the widespread modern cattle mitochondrial T clade are polyphyletic, and they support the hypothesis that modern European breeds have multiple geographic origins.Martina Lari, Ermanno Rizzi, Stefano Mona, Giorgio Corti, Giulio Catalano, Kefei Chen, Cristiano Vernesi, Greger Larson, Paolo Boscato, Gianluca De Bellis, Alan Cooper, David Caramelli and Giorgio Bertorell

Temporal changes in the epidemiology, management, and outcome from acute respiratory distress syndrome in European intensive care units: a comparison of two large cohorts

Background: Mortality rates for patients with ARDS remain high. We assessed temporal changes in the epidemiology and management of ARDS patients requiring invasive mechanical ventilation in European ICUs. We also investigated the association between ventilatory settings and outcome in these patients. Methods: This was a post hoc analysis of two cohorts of adult ICU patients admitted between May 1–15, 2002 (SOAP study, n = 3147), and May 8–18, 2012 (ICON audit, n = 4601 admitted to ICUs in the same 24 countries as the SOAP study). ARDS was defined retrospectively using the Berlin definitions. Values of tidal volume, PEEP, plateau pressure, and FiO2 corresponding to the most abnormal value of arterial PO2 were recorded prospectively every 24 h. In both studies, patients were followed for outcome until death, hospital discharge or for 60 days. Results: The frequency of ARDS requiring mechanical ventilation during the ICU stay was similar in SOAP and ICON (327[10.4%] vs. 494[10.7%], p = 0.793). The diagnosis of ARDS was established at a median of 3 (IQ: 1–7) days after admission in SOAP and 2 (1–6) days in ICON. Within 24 h of diagnosis, ARDS was mild in 244 (29.7%), moderate in 388 (47.3%), and severe in 189 (23.0%) patients. In patients with ARDS, tidal volumes were lower in the later (ICON) than in the earlier (SOAP) cohort. Plateau and driving pressures were also lower in ICON than in SOAP. ICU (134[41.1%] vs 179[36.9%]) and hospital (151[46.2%] vs 212[44.4%]) mortality rates in patients with ARDS were similar in SOAP and ICON. High plateau pressure (> 29 cmH2O) and driving pressure (> 14 cmH2O) on the first day of mechanical ventilation but not tidal volume (> 8 ml/kg predicted body weight [PBW]) were independently associated with a higher risk of in-hospital death. Conclusion: The frequency of and outcome from ARDS remained relatively stable between 2002 and 2012. Plateau pressure > 29 cmH2O and driving pressure > 14 cmH2O on the first day of mechanical ventilation but not tidal volume > 8 ml/kg PBW were independently associated with a higher risk of death. These data highlight the continued burden of ARDS and provide hypothesis-generating data for the design of future studies

Displacement field of a model slope from digital imaging and laser scanning

The paper deals with the behaviour of slopes subjected to increasing loads applied to the soil surface just behind the crest. To this end a new fully-automatic small scale 1g physical model has been recently built to reproduce a plain-strain state within a granular soil slope. Two relatively new measurement technologies, namely particle image velocimetry and reverse engineering were used to measure the relevant displacement field in the soil mass and at the slope face. The paper presents the physical model and testing procedure and discusses some preliminary test results