Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses

G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5'-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NF\u3baB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5'-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place

Atmospheric effects on extensive air showers observed with the Surface Detector of the Pierre Auger Observatory

Atmospheric parameters, such as pressure (P), temperature (T) and density, affect the development of extensive air showers initiated by energetic cosmic rays. We have studied the impact of atmospheric variations on extensive air showers by means of the surface detector of the Pierre Auger Observatory. The rate of events shows a ~10% seasonal modulation and ~2% diurnal one. We find that the observed behaviour is explained by a model including the effects associated with the variations of pressure and density. The former affects the longitudinal development of air showers while the latter influences the Moliere radius and hence the lateral distribution of the shower particles. The model is validated with full simulations of extensive air showers using atmospheric profiles measured at the site of the Pierre Auger Observatory.Comment: 24 pages, 9 figures, accepted for publication in Astroparticle Physic

The Pierre Auger Observatory III: Other Astrophysical Observations

Astrophysical observations of ultra-high-energy cosmic rays with the Pierre Auger ObservatoryComment: Contributions to the 32nd International Cosmic Ray Conference, Beijing, China, August 201

Low recurrence rate of a two-layered closure repair for primary and recurrent midline incisional hernia without mesh

Background: Incisional hernia is a serious complication after abdominal surgery and occurs in 11-23% of laparotomies. Repair can be done, for instance, with a direct suture technique, but recurrence rates are high. Recent literature advises the use of mesh repair. In contrast to this development, we studied the use of a direct suture repair in a separate layer technique. The objective of this retrospective observational study is to assess the outcomes (recurrences and complications) of a two-layered open closure repair for primary and recurrent midline incisional hernia without the use of mesh. Methods: In an observational retrospective cohort study, we analysed the hospital and outpatient records of 77 consecutive patients who underwent surgery for a primary or recurrent incisional hernia between 1st May 2002 and 8th November 2006. The repair consisted of separate continuous suturing of the anterior and posterior fascia, including the rectus muscle, after extensive intra-abdominal adhesiolysis. Results: Forty-one men (53.2%) and 36 women (46.8%) underwent surgery. Sixty-three operations (81.8%) were primary repairs and 14 (18.2%) were repairs for a recurrent incisional hernia. Of the 66 patients, on physical examination, three had a recurrence (4.5%) after an average follow-up of 2.6 years. The 30-day postoperative mortality was 1.1%. Wound infection was seen in five patients (6.5%). Conclusions: A two-layered suture repair for primary and recurrent incisional hernia repair without mesh with extensive adhesiolysis was associated with a recurrence rate comparable to mesh repair and had an acceptable complication rate

Highlights from the Pierre Auger Observatory

The Pierre Auger Observatory is the world's largest cosmic ray observatory. Our current exposure reaches nearly 40,000 km$^2$ str and provides us with an unprecedented quality data set. The performance and stability of the detectors and their enhancements are described. Data analyses have led to a number of major breakthroughs. Among these we discuss the energy spectrum and the searches for large-scale anisotropies. We present analyses of our X$_{max}$ data and show how it can be interpreted in terms of mass composition. We also describe some new analyses that extract mass sensitive parameters from the 100% duty cycle SD data. A coherent interpretation of all these recent results opens new directions. The consequences regarding the cosmic ray composition and the properties of UHECR sources are briefly discussed.Comment: 9 pages, 12 figures, talk given at the 33rd International Cosmic Ray Conference, Rio de Janeiro 201

Update on the correlation of the highest energy cosmic rays with nearby extragalactic matter

Data collected by the Pierre Auger Observatory through 31 August 2007 showed evidence for anisotropy in the arrival directions of cosmic rays above the Greisen-Zatsepin-Kuz'min energy threshold, \nobreak{$6\times 10^{19}$eV}. The anisotropy was measured by the fraction of arrival directions that are less than $3.1^\circ$ from the position of an active galactic nucleus within 75 Mpc (using the V\'eron-Cetty and V\'eron $12^{\rm th}$ catalog). An updated measurement of this fraction is reported here using the arrival directions of cosmic rays recorded above the same energy threshold through 31 December 2009. The number of arrival directions has increased from 27 to 69, allowing a more precise measurement. The correlating fraction is $(38^{+7}_{-6})$, compared with $21$ expected for isotropic cosmic rays. This is down from the early estimate of $(69^{+11}_{-13})$. The enlarged set of arrival directions is examined also in relation to other populations of nearby extragalactic objects: galaxies in the 2 Microns All Sky Survey and active galactic nuclei detected in hard X-rays by the Swift Burst Alert Telescope. A celestial region around the position of the radiogalaxy Cen A has the largest excess of arrival directions relative to isotropic expectations. The 2-point autocorrelation function is shown for the enlarged set of arrival directions and compared to the isotropic expectation.Comment: Accepted for publication in Astroparticle Physics on 31 August 201

A search for point sources of EeV photons

Measurements of air showers made using the hybrid technique developed with the fluorescence and surface detectors of the Pierre Auger Observatory allow a sensitive search for point sources of EeV photons anywhere in the exposed sky. A multivariate analysis reduces the background of hadronic cosmic rays. The search is sensitive to a declination band from -85{\deg} to +20{\deg}, in an energy range from 10^17.3 eV to 10^18.5 eV. No photon point source has been detected. An upper limit on the photon flux has been derived for every direction. The mean value of the energy flux limit that results from this, assuming a photon spectral index of -2, is 0.06 eV cm^-2 s^-1, and no celestial direction exceeds 0.25 eV cm^-2 s^-1. These upper limits constrain scenarios in which EeV cosmic ray protons are emitted by non-transient sources in the Galaxy.Comment: 28 pages, 10 figures, accepted for publication in The Astrophysical Journa

Integrated use of residues from olive mill and winery for lipase production by solid state fermentation with Aspergillus sp

Two phase olive mill waste (TPOMW) is presently the major waste produced by the olive mill industry. This waste has potential to be used as substrate for solid state fermentation (SSF) despite of its high concentration of phenolic compounds and low nitrogen content. In this work, it is demonstrated that mixtures of TPOMW with winery wastes support the production of lipase by Aspergillus spp. By agar plate screening, Aspergillus niger MUM 03.58, Aspergillus ibericus MUM 03.49 and Aspergillus uvarum MUM 08.01 were chosen for lipase production by SSF. Plackett-Burman experimental design was employed to evaluate the effect of substrate composition and time on lipase production. The highest amounts of lipase were produced by A. ibericus on a mixture of TPOMW, urea and exhausted grape mark (EGM). Urea was found to be the most influent factor for the lipase production. Further optimization of lipase production by A. ibericus using a full factorial design (32) conducted to optimal conditions of substrate composition (0.073 g urea/g and 25% of EGM) achieving 18.67 U/g of lipolytic activity.Jose Manuel Salgado is grateful for Postdoctoral fellowship (EX-2010-0402) of Education Ministry of Spanish Government. Luis Abrunhosa was supported by the grant SFRH/BPD/43922/2008 from Fundacao para a Ciencia e Tecnologia-FCT, Portugal. Authors thank Fundacao para a Ciencia e a Tecnologia (FCT) for financial support through the project FCT Pest-OE/EQB/LA0023/2011

Catalytic Tri-reforming of Biomass-Derived Syngas to Produce Desired H2:CO Ratios for Fuel Applications

This study focuses on upgrading biomass derived syngas for the synthesis of liquid fuels using Fischer-Tropsch synthesis (FTS). The process includes novel gasification of biomass via a tri-reforming process which involves a synergetic combination of CO2 reforming, steam reforming, and partial oxidation of methane. Typical biomass-derived syngas H2:CO is 1:1 and contains tars that deactivate FT catalyst. This innovation allows for cost-effective one-step production of syngas in the required H2:CO of 2:1 with reduction of tars for use in the FTS. To maximize the performance of the tri-reforming catalyst, an attempt to control oxygen mobility, thermal stability, dispersion of metal, resistance to coke formation, and strength of metal interaction with support is investigated by varying catalyst synthesis parameters. These synthesis variables include Ce and Zr mixed oxide support ratios, amount Mg and Ni loading, and the preparation of the catalyst. Reaction conditions were also varied to determine the influences reaction temperature, gas composition, and GHSV have on the catalyst performance. Testing under controlled reaction conditions and the use of several catalyst characterization techniques (BET, XRD, TPR, XAFS, SEM-EDS, XPS) were employed to better explain the effects of the synthesis parameters. Applications of the resulting data were used to design proof of concept solar powered BTL plant. This paper highlights the performance of the tri-reforming catalyst under various reaction conditions and explains results using catalyst characterization