On the shoulder of giants: Mitogenome recovery from non-targeted genome projects for phylogenetic inference and molecular evolution studies

The advent of high-throughput sequencing technologies (HTS) has generated an unprecedented amount of genomic and transcriptomic information. A vast amount of these data is not even used in targeted projects but is made available in public repositories. Previous studies have demonstrated that HTS data constitute a valuable resource to recover mitogenomic information, which is most relevant for studies of non-model and undersampled taxa. The spider family Dysderidae exemplifies well this situation: It is a highly diverse group, exceptionally well-suited for evolutionary and ecological research, but with a sparse mitogenomic record. In this study, we used public and in-house HTS data to assemble and annotate at no cost 13 complete and 6 partial Dysderidae mitogenomes, as well as 34 partial mitogenomes belonging to other taxa within the Synspermiata clade, to which Dysderidae belongs. The mitogenomic information was further used to interrogate on a diverse array of evolutionary questions posed by the family. Phylogenetic inference clarified the evolutionary scenario of the colonization of the Canary Islands by the genus Dysdera, supporting two independent colonizations from the continent. Synteny analyses indicated that gene organization at the mitogenomic level is overall conserved within Dysderidae, the only exceptions being two cave-dwelling species, each of them with a unique putative transposition not described before in spiders. Finally, tRNA secondary structure reconstruction confirmed that the extreme compaction of tRNA is conserved across the family, suggesting that its origin could be traced back to approximately 100 million years ago (Mya). Altogether, this study demonstrates the potential of publicly available HTS data to conduct low-cost evolutionary research at different biological levels

Challenges and Technical Requirements for Integration of Renewable Energy Sources in Cuban Electric System

The decision of the Cuban Government to massively introduce Renewable Energy Sources (RES) as a way to change the energy matrix, and in particular, the electricity matrix, is presented as an opportunity to introduce not only sources of energy friendly with the environment, but also make the contributions that, without limiting the development of the country, respond to the UN Millennium Development Goals (UNMDG). However, the large-scale use of RESs in an electrical system such as Cuba, isolated and not interconnected to other systems, can have a group of challenges that must be taken into consideration when it is exploited, since it does not incorporate only new technologies, some of which depend on weather conditions such as solar, wind and hydro technology for the production of electricity, but allow us to think about the introduction of emerging technologies that can increase the penetration of RES in the electrical system and introduce new management concepts, both territorially and nationally. The present work reflects on this, from some experiences that have been analyzed in different research works carried out at CIPEL, plus other International experiences

Endothelial Progenitor Cells as a Potential Biomarker in Interstitial Lung Disease Associated with Rheumatoid Arthritis

Interstitial lung disease (ILD) increases morbidity and mortality in patients with rheumatoid arthritis (RA). Although the pathogenesis of ILD associated with RA (RA-ILD(+)) remains poorly defined, vascular tissue is crucial in lung physiology. In this context, endothelial progenitor cells (EPC) are involved in endothelial tissue repair. However, little is known about their implication in RA-ILD(+). Accordingly, we aimed to investigate the potential role of EPC related to endothelial damage in RA-ILD(+). EPC quantification in peripheral blood from 80 individuals (20 RA-ILD(+) patients, 25 RA-ILD(-) patients, 21 idiopathic pulmonary fibrosis (IPF) patients, and 14 healthy controls) was performed by flow cytometry. EPC were considered as CD34(+), CD45(low), CD309(+) and CD133(+). A significant increase in EPC frequency in RA-ILD(+) patients, as well as in RA-ILD(-) and IPF patients, was found when compared with controls (p < 0.001, p = 0.02 and p < 0.001, respectively). RA-ILD(+) patients exhibited a higher EPC frequency than the RA-ILD(-) ones (p = 0.003), but lower than IPF patients (p < 0.001). Our results suggest that EPC increase may represent a reparative compensatory mechanism in patients with RA-ILD(+). The degree of EPC frequency may help to identify the presence of ILD in RA patients and to discriminate RA-ILD(+) from IPF

Global behavior of cosmological dynamics with interacting Veneziano ghost

In this paper, we shall study the dynamical behavior of the universe accelerated by the so called Veneziano ghost dark energy component locally and globally by using the linearization and nullcline method developed in this paper. The energy density is generalized to be proportional to the Hawking temperature defined on the trapping horizon instead of Hubble horizon of the Friedmann-Robertson-Walker (FRW) universe. We also give a prediction of the fate of the universe and present the bifurcation phenomenon of the dynamical system of the universe. It seems that the universe could be dominated by dark energy at present in some region of the parameter space.Comment: 8 pages, 7 figures, accepted for publication in JHE

Statefinder diagnosis and the interacting ghost model of dark energy

A new model of dark energy namely "ghost dark energy model" has recently been suggested to interpret the positive acceleration of cosmic expansion. The energy density of ghost dark energy is proportional to the hubble parameter. In this paper we perform the statefinder diagnostic tool for this model both in flat and non-flat universe. We discuss the dependency of the evolutionary trajectories in $s-r$ and $q-r$ planes on the interaction parameter between dark matter and dark energy as well as the spatial curvature parameter of the universe. Eventually, in the light of SNe+BAO+OHD+CMB observational data, we plot the evolutionary trajectories in $s-r$ and $q-r$ planes for the best fit values of the cosmological parameters and compare the interacting ghost model with other dynamical dark energy models. We show that the evolutionary trajectory of ghost dark energy in statefinder diagram is similar to holographic dark energy model. It has been shown that the statefinder location of $\Lambda$CDM is in good agreement with observation and therefore the dark energy models whose current statefinder values are far from the $\Lambda$CDM point can be ruled out.Comment: 23 pages, 6 figure

QCD ghost f(T)-gravity model

Within the framework of modified teleparallel gravity, we reconstruct a f(T) model corresponding to the QCD ghost dark energy scenario. For a spatially flat FRW universe containing only the pressureless matter, we obtain the time evolution of the torsion scalar T (or the Hubble parameter). Then, we calculate the effective torsion equation of state parameter of the QCD ghost f(T)-gravity model as well as the deceleration parameter of the universe. Furthermore, we fit the model parameters by using the latest observational data including SNeIa, CMB and BAO data. We also check the viability of our model using a cosmographic analysis approach. Moreover, we investigate the validity of the generalized second law (GSL) of gravitational thermodynamics for our model. Finally, we point out the growth rate of matter density perturbation. We conclude that in QCD ghost f(T)-gravity model, the universe begins a matter dominated phase and approaches a de Sitter regime at late times, as expected. Also this model is consistent with current data, passes the cosmographic test, satisfies the GSL and fits the data of the growth factor well as the LCDM model.Comment: 19 pages, 9 figures, 2 tables. arXiv admin note: substantial text overlap with arXiv:1111.726

Self-interacting holographic dark energy

We investigate a spatially flat Friedmann-Robertson-Walker (FRW) universe where dark matter exchanges energy with a self-interacting holographic dark energy (SIHDE). Using the $\chi^2$--statistical method on the Hubble function, we obtain a critical redshift that seems to be consistent with both BAO and CMB data. We calculate the theoretical distance modulus for confronting with the observational data of SNe Ia for small redshift $z\leq 0.1$ and large redshift $0.1 \leq z\leq 1.5$. The model gets accelerate faster than the $\Lambda$CDM one and it can be a good candidate to alleviate the coincidence problem. We also examine the age crisis at high redshift associated with the old quasar APM 08279+5255.Comment: 9 pages, 5 figures. Title and motivation changed. Statistical analysis improved. Accepted for publication in Modern Physics Letters A (2012). arXiv admin note: text overlap with arXiv:1012.0883 by other author

Phylogenomics of Unusual Histone H2A Variants in Bdelloid Rotifers

Rotifers of Class Bdelloidea are remarkable in having evolved for millions of years, apparently without males and meiosis. In addition, they are unusually resistant to desiccation and ionizing radiation and are able to repair hundreds of radiation-induced DNA double-strand breaks per genome with little effect on viability or reproduction. Because specific histone H2A variants are involved in DSB repair and certain meiotic processes in other eukaryotes, we investigated the histone H2A genes and proteins of two bdelloid species. Genomic libraries were built and probed to identify histone H2A genes in Adineta vaga and Philodina roseola, species representing two different bdelloid families. The expressed H2A proteins were visualized on SDS-PAGE gels and identified by tandem mass spectrometry. We find that neither the core histone H2A, present in nearly all other eukaryotes, nor the H2AX variant, a ubiquitous component of the eukaryotic DSB repair machinery, are present in bdelloid rotifers. Instead, they are replaced by unusual histone H2A variants of higher mass. In contrast, a species of rotifer belonging to the facultatively sexual, desiccation- and radiation-intolerant sister class of bdelloid rotifers, the monogononts, contains a canonical core histone H2A and appears to lack the bdelloid H2A variant genes. Applying phylogenetic tools, we demonstrate that the bdelloid-specific H2A variants arose as distinct lineages from canonical H2A separate from those leading to the H2AX and H2AZ variants. The replacement of core H2A and H2AX in bdelloid rotifers by previously uncharacterized H2A variants with extended carboxy-terminal tails is further evidence for evolutionary diversity within this class of histone H2A genes and may represent adaptation to unusual features specific to bdelloid rotifers

Search for squarks and gluinos in events with isolated leptons, jets and missing transverse momentum at s√=8 TeV with the ATLAS detector

The results of a search for supersymmetry in final states containing at least one isolated lepton (electron or muon), jets and large missing transverse momentum with the ATLAS detector at the Large Hadron Collider are reported. The search is based on proton-proton collision data at a centre-of-mass energy s√=8 TeV collected in 2012, corresponding to an integrated luminosity of 20 fb−1. No significant excess above the Standard Model expectation is observed. Limits are set on supersymmetric particle masses for various supersymmetric models. Depending on the model, the search excludes gluino masses up to 1.32 TeV and squark masses up to 840 GeV. Limits are also set on the parameters of a minimal universal extra dimension model, excluding a compactification radius of 1/R c = 950 GeV for a cut-off scale times radius (ΛR c) of approximately 30

Evidence for the Higgs-boson Yukawa coupling to tau leptons with the ATLAS detector

Results of a search for H → τ τ decays are presented, based on the full set of proton-proton collision data recorded by the ATLAS experiment at the LHC during 2011 and 2012. The data correspond to integrated luminosities of 4.5 fb−1 and 20.3 fb−1 at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV respectively. All combinations of leptonic (τ → `νν¯ with ` = e, µ) and hadronic (τ → hadrons ν) tau decays are considered. An excess of events over the expected background from other Standard Model processes is found with an observed (expected) significance of 4.5 (3.4) standard deviations. This excess provides evidence for the direct coupling of the recently discovered Higgs boson to fermions. The measured signal strength, normalised to the Standard Model expectation, of µ = 1.43 +0.43 −0.37 is consistent with the predicted Yukawa coupling strength in the Standard Model