Sequence and comparative analysis of the genome of HSV-1 strain McKrae

Ocular infection by HSV-1 strain McKrae is neurovirulent in both mice and rabbits and causes fatal encephalitis in approximately 50% of animals. In addition, it spontaneously reactivates with high frequency relative to other HSV-1 strains in rabbits. We sequenced the McKrae strain genome and compared its coding protein sequences with those of six other HSV-1 strains. Most of the 74 predicted protein sequences are conserved; only eleven are less than 98% conserved. Eight proteins were identified to be unique for McKrae based on sequence homology bit score ratio (BSR). These include five proteins showing significant variations (RL1, RS1, UL49A, US7, US11), two truncated proteins (UL36 and UL56) and one (US10) containing an extended open reading frame. The McKrae strain also has unique features in its ‘a’ sequence and non-coding sequences, such as LAT and miRNA. These data are indicative of strain variation but need further work to connect observed differences with phenotype effects.Keywords: DNA sequence comparison, High throughput DNA sequencing, Herpes viru

A white dwarf cooling age of 8 Gyr for NGC 6791 from physical separation processes

NGC 6791 is a well studied open cluster1 that it is so close to us that can be imaged down to very faint luminosities. The main sequence turn-off age (~8 Gyr) and the age derived from the termination of the white dwarf cooling sequence (~6 Gyr) are significantly different. One possible explanation is that as white dwarfs cool, one of the ashes of helium burning, 22Ne, sinks in the deep interior of these stars. At lower temperatures, white dwarfs are expected to crystallise and phase separation of the main constituents of the core of a typical white dwarf, 12C and 16O, is expected to occur. This sequence of events is expected to introduce significant delays in the cooling times, but has not hitherto been proven. Here we report that, as theoretically anticipated, physical separation processes occur in the cores of white dwarfs, solving the age discrepancy for NGC 6791.Comment: 3 pages, 2 figures, published in Natur

Evolutionary and pulsational properties of white dwarf stars

Abridged. White dwarf stars are the final evolutionary stage of the vast majority of stars, including our Sun. The study of white dwarfs has potential applications to different fields of astrophysics. In particular, they can be used as independent reliable cosmic clocks, and can also provide valuable information about the fundamental parameters of a wide variety of stellar populations, like our Galaxy and open and globular clusters. In addition, the high densities and temperatures characterizing white dwarfs allow to use these stars as cosmic laboratories for studying physical processes under extreme conditions that cannot be achieved in terrestrial laboratories. They can be used to constrain fundamental properties of elementary particles such as axions and neutrinos, and to study problems related to the variation of fundamental constants. In this work, we review the essentials of the physics of white dwarf stars. Special emphasis is placed on the physical processes that lead to the formation of white dwarfs as well as on the different energy sources and processes responsible for chemical abundance changes that occur along their evolution. Moreover, in the course of their lives, white dwarfs cross different pulsational instability strips. The existence of these instability strips provides astronomers with an unique opportunity to peer into their internal structure that would otherwise remain hidden from observers. We will show that this allows to measure with unprecedented precision the stellar masses and to infer their envelope thicknesses, to probe the core chemical stratification, and to detect rotation rates and magnetic fields. Consequently, in this work, we also review the pulsational properties of white dwarfs and the most recent applications of white dwarf asteroseismology.Comment: 85 pages, 28 figures. To be published in The Astronomy and Astrophysics Revie

The INSIG2 rs7566605 polymorphism is not associated with body mass index and breast cancer risk

Abstract Background The single nucleotide polymorphism rs7566605, located in the promoter of the INSIG2 gene, has been the subject of a strong scientific effort aimed to elucidate its possible association with body mass index (BMI). The first report showing that rs7566605 could be associated with body fatness was a genome-wide association study (GWAS) which used BMI as the primary phenotype. Many follow-up studies sought to validate the association of rs7566605 with various markers of obesity, with several publications reporting inconsistent findings. BMI is considered to be one of the measures of choice to evaluate body fatness and there is evidence that body fatness is related with an increased risk of breast cancer (BC). Methods we tested in a large-scale association study (3,973 women, including 1,269 invasive BC cases and 2,194 controls), nested within the EPIC cohort, the involvement of rs7566605 as predictor of BMI and BC risk. Results and Conclusions In this study we were not able to find any statistically significant association between this SNP and BMI, nor did we find any significant association between the SNP and an increased risk of breast cancer overall and by subgroups of age, or menopausal status.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Mediterranean dietary pattern and cancer risk in the EPIC cohort

Background: Although several studies have investigated the association of the Mediterranean diet with overall mortality or risk of specific cancers, data on overall cancer risk are sparse. Methods: We examined the association between adherence to Mediterranean dietary pattern and overall cancer risk using data from the European Prospective Investigation Into Cancer and nutrition, a multi-centre prospective cohort study including 142 605 men and 335 873. Adherence to Mediterranean diet was examined using a score (range: 0–9) considering the combined intake of fruits and nuts, vegetables, legumes, cereals, lipids, fish, dairy products, meat products, and alcohol. Association with cancer incidence was assessed through Cox regression modelling, controlling for potential confounders. Results: In all, 9669 incident cancers in men and 21 062 in women were identified. A lower overall cancer risk was found among individuals with greater adherence to Mediterranean diet (hazard ratio=0.96, 95% CI 0.95–0.98) for a two-point increment of the Mediterranean diet score. The apparent inverse association was stronger for smoking-related cancers than for cancers not known to be related to tobacco (P (heterogeneity)=0.008). In all, 4.7% of cancers among men and 2.4% in women would be avoided in this population if study subjects had a greater adherence to Mediterranean dietary pattern. Conclusion: Greater adherence to a Mediterranean dietary pattern could reduce overall cancer risk

The masses of PSR J1911-5958A and its white dwarf companion

We present spectroscopic and photometric observations of the optical counterpart to PSR J1911-5958A, a millisecond pulsar located towards the globular cluster NGC 6752. We measure radial velocities from the spectra and determine the systemic radial velocity of the binary and the radial-velocity amplitude of the white-dwarf orbit. Combined with the pulsar orbit obtained from radio timing, we infer a mass ratio of Mpsr/Mwd=7.36+-0.25. The spectrum of the counterpart is that of a hydrogen atmosphere, showing Balmer absorption lines upto H12, and we identify the counterpart as a helium-core white dwarf of spectral type DA5. Comparison of the spectra with hydrogen atmosphere models yield a temperature Teff=10090+-150 K and a surface gravity log g=6.44+-0.20 cm s^-2. Using mass-radius relations appropriate for low-mass helium-core white dwarfs, we infer the white-dwarf mass Mwd=0.18+-0.02 Msun and radius Rwd=0.043+-0.009 Rsun. Combined with the mass ratio, this constrains the pulsar mass to Mpsr=1.40^+0.16_-0.10 Msun. If we instead use the white-dwarf spectrum and the distance of NGC 6752 to determine the white-dwarf radius, we find Rwd=0.058+-0.004 Rsun. For the observed temperature, the mass-radius relations predict a white-dwarf mass of Mwd=0.175+-0.010 Msun, constraining the pulsar mass to Mpsr=1.34+-0.08 Msun. We find that the white-dwarf radius determined from the spectrum and the systemic radial velocity of the binary are only marginally consistent with the values that are expected if PSR J1911-5958A is associated with NGC 6752. We discuss possible causes to explain this inconsistency, but conclude that our observations do not conclusively confirm nor disprove the assocation of the pulsar binary with the globular cluster.Comment: 15 pages, 9 figures, accepted for publication in A&A. Some detailed discussions moved to appendices, extended discussion of photometry to refute variability claimed by other author

Animal foods, protein, calcium and prostate cancer risk: the European Prospective Investigation into Cancer and Nutrition

We examined consumption of animal foods, protein and calcium in relation to risk of prostate cancer among 142 251 men in the European Prospective Investigation into Cancer and Nutrition. Associations were examined using Cox regression, stratified by recruitment centre and adjusted for height, weight, education, marital status and energy intake. After an average of 8.7 years of follow-up, there were 2727 incident cases of prostate cancer, of which 1131 were known to be localised and 541 advanced-stage disease. A high intake of dairy protein was associated with an increased risk, with a hazard ratio for the top versus the bottom fifth of intake of 1.22 (95% confidence interval (CI): 1.07–1.41, Ptrend=0.02). After calibration to allow for measurement error, we estimated that a 35-g day−1 increase in consumption of dairy protein was associated with an increase in the risk of prostate cancer of 32% (95% CI: 1–72%, Ptrend=0.04). Calcium from dairy products was also positively associated with risk, but not calcium from other foods. The results support the hypothesis that a high intake of protein or calcium from dairy products may increase the risk for prostate cancer