678 research outputs found
Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus
BACKGROUND: The integrity of DNA molecules is fundamental for maintaining life. The DNA repair proteins protect organisms against genetic damage, by removal of DNA lesions or helping to tolerate them. DNA repair genes are best known from the gamma-proteobacterium Escherichia coli, which is the most understood bacterial model. However, genome sequencing raises questions regarding uniformity and ubiquity of these DNA repair genes and pathways, reinforcing the need for identifying genes and proteins, which may respond to DNA damage in other bacteria. RESULTS: In this study, we employed a bioinformatic approach, to analyse and describe the open reading frames potentially related to DNA repair from the genome of the alpha-proteobacterium Caulobacter crescentus. This was performed by comparison with known DNA repair related genes found in public databases. As expected, although C. crescentus and E. coli bacteria belong to separate phylogenetic groups, many of their DNA repair genes are very similar. However, some important DNA repair genes are absent in the C. crescentus genome and other interesting functionally related gene duplications are present, which do not occur in E. coli. These include DNA ligases, exonuclease III (xthA), endonuclease III (nth), O(6)-methylguanine-DNA methyltransferase (ada gene), photolyase-like genes, and uracil-DNA-glycosylases. On the other hand, the genes imuA and imuB, which are involved in DNA damage induced mutagenesis, have recently been described in C. crescentus, but are absent in E. coli. Particularly interesting are the potential atypical phylogeny of one of the photolyase genes in alpha-proteobacteria, indicating an origin by horizontal transfer, and the duplication of the Ada orthologs, which have diverse structural configurations, including one that is still unique for C. crescentus. CONCLUSION: The absence and the presence of certain genes are discussed and predictions are made considering the particular aspects of the C. crescentus among other known DNA repair pathways. The observed differences enlarge what is known for DNA repair in the Bacterial world, and provide a useful framework for further experimental studies in this organism
The singlet scalar as FIMP dark matter
The singlet scalar model is a minimal extension of the Standard Model that
can explain the dark matter. We point out that in this model the dark matter
constraint can be satisfied not only in the already considered WIMP regime but
also, for much smaller couplings, in the Feebly Interacting Massive Particle
(FIMP) regime. In it, dark matter particles are slowly produced in the early
Universe but are never abundant enough to reach thermal equilibrium or
annihilate among themselves. This alternative framework is as simple and
predictive as the WIMP scenario but it gives rise to a completely different
dark matter phenomenology. After reviewing the calculation of the dark matter
relic density in the FIMP regime, we study in detail the evolution of the dark
matter abundance in the early Universe and the predicted relic density as a
function of the parameters of the model. A new dark matter compatible region of
the singlet model is identified, featuring couplings of order 10^-11 to 10^-12
for singlet masses in the GeV to TeV range. As a consequence, no signals at
direct or indirect detection experiments are expected. The relevance of this
new viable region for the correct interpretation of recent experimental bounds
is emphasized.Comment: 12 pages, 6 figure
Should physical activity recommendations be ethnicity-specific? Evidence from a cross-sectional study of south Asian and European men
Background
Expert bodies and health organisations recommend that adults undertake at least 150 min.week−1 of moderate-intensity physical activity (MPA). However, the underpinning data largely emanate from studies of populations of European descent. It is unclear whether this level of activity is appropriate for other ethnic groups, particularly South Asians, who have increased cardio-metabolic disease risk compared to Europeans. The aim of this study was to explore the level of MPA required in South Asians to confer a similar cardio-metabolic risk profile to that observed in Europeans undertaking the currently recommended MPA level of 150 min.week−1.<p></p>
Methods
Seventy-five South Asian and 83 European men, aged 40–70, without cardiovascular disease or diabetes had fasted blood taken, blood pressure measured, physical activity assessed objectively (using accelerometry), and anthropometric measures made. Factor analysis was used to summarise measured risk biomarkers into underlying latent ‘factors’ for glycaemia, insulin resistance, lipid metabolism, blood pressure, and overall cardio-metabolic risk. Age-adjusted regression models were used to determine the equivalent level of MPA (in bouts of ≥10 minutes) in South Asians needed to elicit the same value in each factor as Europeans undertaking 150 min.week−1 MPA.<p></p>
Findings
For all factors, except blood pressure, equivalent MPA values in South Asians were significantly higher than 150 min.week−1; the equivalent MPA value for the overall cardio-metabolic risk factor was 266 (95% CI 185-347) min.week−1.<p></p>
Conclusions
South Asian men may need to undertake greater levels of MPA than Europeans to exhibit a similar cardio-metabolic risk profile, suggesting that a conceptual case can be made for ethnicity-specific physical activity guidance. Further study is needed to extend these findings to women and to replicate them prospectively in a larger cohort.<p></p>
Zero Sound in Strange Metallic Holography
One way to model the strange metal phase of certain materials is via a
holographic description in terms of probe D-branes in a Lifshitz spacetime,
characterised by a dynamical exponent z. The background geometry is dual to a
strongly-interacting quantum critical theory while the probe D-branes are dual
to a finite density of charge carriers that can exhibit the characteristic
properties of strange metals. We compute holographically the low-frequency and
low-momentum form of the charge density and current retarded Green's functions
in these systems for massless charge carriers. The results reveal a
quasi-particle excitation when z<2, which in analogy with Landau Fermi liquids
we call zero sound. The real part of the dispersion relation depends on
momentum k linearly, while the imaginary part goes as k^2/z. When z is greater
than or equal to 2 the zero sound is not a well-defined quasi-particle. We also
compute the frequency-dependent conductivity in arbitrary spacetime dimensions.
Using that as a measure of the charge current spectral function, we find that
the zero sound appears only when the spectral function consists of a single
delta function at zero frequency.Comment: 20 pages, v2 minor corrections, extended discussion in sections 5 and
6, added one footnote and four references, version published in JHE
Kahler Moduli Inflation Revisited
We perform a detailed numerical analysis of inflationary solutions in Kahler
moduli of type IIB flux compactifications. We show that there are inflationary
solutions even when all the fields play an important role in the overall shape
of the scalar potential. Moreover, there exists a direction of attraction for
the inflationary trajectories that correspond to the constant volume direction.
This basin of attraction enables the system to have an island of stability in
the set of initial conditions. We provide explicit examples of these
trajectories, compute the corresponding tilt of the density perturbations power
spectrum and show that they provide a robust prediction of n_s approximately
0.96 for 60 e-folds of inflation.Comment: 27 pages, 9 figure
Analysing the technical efficiency of the Spanish Football League First Division with a random frontier model
Chern-Simons diffusion rate in a holographic Yang-Mills theory
Using holography, we compute the Chern-Simons diffusion rate of 4d gauge
theories constructed by wrapping D4-branes on a circle. In the model with
antiperiodic boundary conditions for fermions, we find that it scales like
in the high-temperature phase. With periodic fermions, this scaling
persists at low temperatures. The scaling is reminiscent of 6d hydrodynamic
behavior even at temperatures small compared to compactification scales of the
M5-branes from which the D4-branes descend. We offer a holographic explanation
of this behavior by adding a new entry to the known map between D4 and M5
hydrodynamics, and suggest a field theory explanation based on "deconstruction"
or "fractionization".Comment: 13 pages, misstatement in published version about low temperature
phase removed, main results unaffecte
Detection and phylogenetic analysis of Orf virus from sheep in Brazil: a case report
<p>Abstract</p> <p>Background</p> <p><it>Orf virus </it>(ORFV), the prototype of the genus <it>Parapoxvirus </it>(PPV), is the etiological agent of contagious ecthyma, a severe exanthematic dermatitis that afflicts domestic and wild small ruminants. Although South American ORFV outbreaks have occurred and diagnosed there are no South American PPV major membrane glycoprotein B2L gene nucleotide sequences available.</p> <p>Case presentation</p> <p>an outbreak of ovine contagious ecthyma in Midwest Brazil was investigated. The diagnosis was based on clinical examinations and molecular biology techniques. The molecular characterization of the virus was done using PCR amplification, cloning and DNA sequencing of the B2L gene. The phylogenetic analysis demonstrated a high degree of identity with ORFV strains, and the isolate was closest to the ORFV-India 82/04 isolate. Another Brazilian ORFV isolate, NE1, was sequenced for comparative analysis and also showed a high degree of identity with an Asian ORFV strain.</p> <p>Conclusion</p> <p>Distinct ORFV strains are circulating in Brazil. This is the first report on the phylogenetic analysis of an ORFV in South America.</p
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