Genetic analyses reveal a role for vitamin D insufficiency in HCV-associated hepatocellular carcinoma development

BACKGROUND: Vitamin D insufficiency has been associated with the occurrence of various types of cancer, but causal relationships remain elusive. We therefore aimed to determine the relationship between genetic determinants of vitamin D serum levels and the risk of developing hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC). METHODOLOGY/PRINCIPAL FINDINGS: Associations between CYP2R1, GC, and DHCR7 genotypes that are determinants of reduced 25-hydroxyvitamin D (25[OH]D3) serum levels and the risk of HCV-related HCC development were investigated for 1279 chronic hepatitis C patients with HCC and 4325 without HCC, respectively. The well-known associations between CYP2R1 (rs1993116, rs10741657), GC (rs2282679), and DHCR7 (rs7944926, rs12785878) genotypes and 25(OH)D3 serum levels were also apparent in patients with chronic hepatitis C. The same genotypes of these single nucleotide polymorphisms (SNPs) that are associated with reduced 25(OH)D3 serum levels were found to be associated with HCV-related HCC (P = 0.07 [OR = 1.13, 95% CI = 0.99-1.28] for CYP2R1, P = 0.007 [OR = 1.56, 95% CI = 1.12-2.15] for GC, P = 0.003 [OR = 1.42, 95% CI = 1.13-1.78] for DHCR7; ORs for risk genotypes). In contrast, no association between these genetic variations and liver fibrosis progression rate (P>0.2 for each SNP) or outcome of standard therapy with pegylated interferon-α and ribavirin (P>0.2 for each SNP) was observed, suggesting a specific influence of the genetic determinants of 25(OH)D3 serum levels on hepatocarcinogenesis. CONCLUSIONS/SIGNIFICANCE: Our data suggest a relatively weak but functionally relevant role for vitamin D in the prevention of HCV-related hepatocarcinogenesis.

Iron oxides in plinthic soils on sedimentary deposits in northeastern Brazil

This study was conducted to examine the distribution and nature of Fe oxides in plinthic soils on the sediments of Barreiras Group (in the state of Piauí) and Itapecuru Formation (in the state of Maranhão) in Northeastern Brazil. Four pedons were selected: a "plinthic, dystrophic, epieutrophic Gray Podzolic with low activity clay" and a "dystrophic Plinthosol with low activity clay" (both Plinthic Kandiustalfs) on the Barreiras sediments, as well as an "eutrophic Plinthosol with low activity clay" and an "allic Plinthosol with low activity clay" (both Plinthustalfs) on the Itapecuru sediments. Soil samples were fractionated into > 2 mm (pisoliths), water-stable aggregates (plinthite) and matrices; the aggregates and matrices were further fractionated into sand, silt and clay sizes. Dithionite extractable iron (Fe d) and aluminum (Al d), as well as oxalate extractable iron (Fe o), were determined for all fractions, and X-ray diffraction analyses were performed on the pisoliths. It was observed that the Plinthustalfs contain more iron oxides, exhibit more extensive plinthite development and have a greater potential for further plinthite development than the Kandiustalfs. The distribution of values for the Fe d indicates that plinthite formation and induration in all soils were accompanied by an enrichment of Fe oxides in all particle size fractions. This Fe segregation was accompanied by aggregation of particles leading to a greater degree of crystallinity, as indicated by analysis of the ratios of Al d:Fe d. Larger ratios of goethite to hematite, and relatively smaller amounts of silicates in the more mature pisoliths were revealed by X-ray diffraction analysis. Ratios of Al d:Fe d were larger in the Kandiustalfs than in the Plinthustalfs, and also larger than expected for Al-substituted Fe oxides. According to ratios of Al d:Fe d, Fe mobilization in all soils has likely occurred under reducing conditions, facilitated by organic matter on the soil surface.

Trophic dynamics in the northern Humboldt Current system: insights from stable isotopes and stomach content analyses

The northern Humboldt Current system (NHCS) off Peru is one of the most productive world marine regions. It represents less than 0.1% of the world ocean surface but presently sustains about 10% of the world fish catch, with the Peruvian anchovy or anchoveta Engraulis ringens as emblematic fish resource. Compared with other eastern boundary upwelling systems, the higher fish productivity of the NHCS cannot be explained by a corresponding higher primary productivity. On another hand, the NHCS is the region where El Niño, and climate variability in general, is most notable. Also, surface oxygenated waters overlie an intense and extremely shallow Oxygen Minimum Zone (OMZ). In this context, the main objective of this study is to better understand the trophic flows in the NHCS using both stomach content and stable isotope analyses. The study focuses on a variety of organisms from low trophic levels such as zooplankton to top predators (seabirds and fur seals). The approach combines both long-term and specific studies on emblematic species such as anchoveta, and sardine Sardinops sagax and a more inclusive analysis considering the 'global' food web in the recent years (2008 – 2012) using stable isotope analysis. Revisiting anchovy and sardine we show that whereas phytoplankton largely dominated anchoveta and sardine diets in terms of numerical abundance, the carbon content of prey items indicated that zooplankton was by far the most important dietary component. Indeed for anchovy euphausiids contributed 67.5% of dietary carbon, followed by copepods (26.3%). Selecting the largest prey, the euphausiids, provide an energetic advantage for anchoveta in its ecosystem where oxygen depletion imposes strong metabolic constrain to pelagic fish. Sardine feed on smaller zooplankton than do anchoveta, with sardine diet consisting of smaller copepods and fewer euphausiids than anchoveta diet. Hence, trophic competition between sardine and anchovy in the northern Humboldt Current system is minimized by their partitioning of the zooplankton food resource based on prey size, as has been reported in other systems. These results suggest an ecological role for pelagic fish that challenges previous understanding of their position in the foodweb (zooplanktophagous instead of phytophagous), the functioning and the trophic models of the NHCS. Finally to obtain a more comprehensive vision of the relative trophic position of NHCS main components we used stable isotope analyses. For that purpose we analyzed the δ13C and δ15N stable isotope values of thirteen taxonomic categories collected off Peru from 2008 - 2011, i.e., zooplankton, fish, squids and air-breathing top predators. The δ15N isotope signature was strongly impacted by the species, the body length and the latitude. Along the Peruvian coast, the OMZ get more intense and shallow south of ~7.5ºS impacting the baseline nitrogen stable isotopes. Employing a linear mixed-effects modelling approach taking into account the latitudinal and body length effects, we provide a new vision of the relative trophic position of key ecosystem components. Also we confirm stomach content-based results on anchoveta Engraulis ringens and highlight the potential remarkable importance of an often neglected ecosystem component, the squat lobster Pleuroncodes monodon. Indeed, our results support the hypothesis according to which this species forage to some extent on fish eggs and larvae and can thus predate on the first life stages of exploited species. However, the δ13C values of these two species suggest that anchoveta and squat lobster do not exactly share the same habitat. This would potentially reduce some direct competition and/or predation.

Analyses of six homologous proteins of Protochlamydia amoebophila UWE25 encoded by large GC-rich genes (lgr): a model of evolution and concatenation of leucine-rich repeats.

BACKGROUND: Along the chromosome of the obligate intracellular bacteria Protochlamydia amoebophila UWE25, we recently described a genomic island Pam100G. It contains a tra unit likely involved in conjugative DNA transfer and lgrE, a 5.6-kb gene similar to five others of P. amoebophila: lgrA to lgrD, lgrF. We describe here the structure, regulation and evolution of these proteins termed LGRs since encoded by "Large G+C-Rich" genes. RESULTS: No homologs to the whole protein sequence of LGRs were found in other organisms. Phylogenetic analyses suggest that serial duplications producing the six LGRs occurred relatively recently and nucleotide usage analyses show that lgrB, lgrE and lgrF were relocated on the chromosome. The C-terminal part of LGRs is homologous to Leucine-Rich Repeats domains (LRRs). Defined by a cumulative alignment score, the 5 to 18 concatenated octacosapeptidic (28-meric) LRRs of LGRs present all a predicted alpha-helix conformation. Their closest homologs are the 28-residue RI-like LRRs of mammalian NODs and the 24-meres of some Ralstonia and Legionella proteins. Interestingly, lgrE, which is present on Pam100G like the tra operon, exhibits Pfam domains related to DNA metabolism. CONCLUSION: Comparison of the LRRs, enable us to propose a parsimonious evolutionary scenario of these domains driven by adjacent concatenations of LRRs. Our model established on bacterial LRRs can be challenged in eucaryotic proteins carrying less conserved LRRs, such as NOD proteins and Toll-like receptors.

1st radiometric dating of a paleontologically dated Bathonian level from Georgia (USSR) - Use of the cathodoluminescence for selection of suitable plagioclases

Jurassic volcanic formations interlayered with (ammonite-bearing) sediments are common in the Caucasus area; this situation is of interest for the numerical calibration of the poorly documented Jurassic portion of the time scale. However, following petrographic study on thin sections no whole-rocks can be considered reliable geochronometers due to subsequent alteration; from about 20 samples, two were selected for plagioclase dating; one (V134) is probably early Kimmeridgian in age; the other (V136) is probably located in the Lower Bathonian stage according to diagnostic ammonites. Cathodoluminescence (CTL) study has shown that sample V136 was similar to usual volcanic feldspars (blue to green colour); however, the lack of CTL of the V134 plagioclase is a character common to diagenetic feldspars; consequently, in spite of a good optical preservation, this geo-chronometer cannot give an age representative of the time of emplacement of the lava flow. We have combined CTL observation with microprobe analysis in order to document the poorly known CTL behaviour of volcanic feldspars; cations Ti4+ and Fe2+ play a major role in the CTL colour of plagioclases and are able to document the growing history of these feldspars ; phenocrysts are initially rich in Fe2+ (core of the crystals, green in colour), then richer in Ti toward the exterior; microcrysts are even richer in Ti (blue to bright blue). We have also observed that natural CTL colour was modified resulting from acid ``cleaning'' of the separated feldspars : the initial blue or green colour tends to change to yellow or violet, respectively, after acid treatment probably due to oxydation of Fe2+ toward Fe3+. X-ray and microprobe analyses both indicated that plagioclases from sample V134 was near the sodic end member (albite) suggesting a diagenetic origin in this andesitic basalt; In contrast, sample V136 contains a calcic plagioclase of common composition for a doleritic basalt. The K-Ar conventional technique was applied as a preliminary tool for radiometric analysis. The Kimmeridgian Na-plagioclase sample gave a ``rejuvenated'' (85 Ma) apparent age which confirms a late genesis for the separated plagioclase phase; this interpretation is based on CTL observation, X-ray analysis, and microprobe analysis ; these techniques are able to distinguish samples which have been submitted to diagenetic alteration from those which have not. An age consistent with the stratigraphic location has been obtained from sample V136. This age of 161 +/- 3 (2-sigma) Ma, is the first one available from a sample palaeontologically located with reasonable precision within the mid Jurassic time.

Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses.

Nucleotide composition analyses of bacterial genomes such as cumulative GC skew highlight the atypical, strongly asymmetric architecture of the recently published chromosome of Idiomarina loihiensis L2TR, suggesting that an inversion of a 600-kb chromosomal segment occurred. The presence of 3.4-kb inverted repeated sequences at the borders of the putative rearrangement supports this hypothesis. Reverting in silico this segment restores (1) a symmetric chromosome architecture; (2) the co-orientation of transcription of all rRNA operons with DNA replication; and (3) a better conservation of gene order between this chromosome and other gamma-proteobacterial ones. Finally, long-range PCRs encompassing the ends of the 600-kb segment reveal the existence of the reverted configuration but not of the published one. This demonstrates how cumulative nucleotide-skew analyses can validate genome assemblies.

Cannabis and benzodiazepines as determinants of methadone trough plasma concentration variability in maintenance treatment: a transnational study.

PURPOSE: To assess tobacco, alcohol, cannabis and benzodiazepine use in methadone maintenance treatment (MMT) as potential sources of variability in methadone pharmacokinetics. METHODS: Trough plasma (R)- and (S)-methadone concentrations were measured on 77 Australian and 74 Swiss MMT patients with no additional medications other than benzodiazepines. Simple and multiple regression analyses were performed for the primary metric, plasma methadone concentration/dose. RESULTS: Cannabis and methadone dose were significantly associated with lower 24-h plasma (R)- and (S)-methadone concentrations/dose. The models containing these variables explained 14-16% and 17-25% of the variation in (R)- and (S)-methadone concentration/dose, respectively. Analysis of 61 patients using only CYP3A4 metabolised benzodiazepines showed this class to be associated with higher (R)-concentration/dose, which is consistent with a potential competitive inhibition of CYP3A4. CONCLUSION: Cannabis use and higher methadone doses in MMT could in part be a response to-or a cause of-more rapid methadone clearance. The effects of cannabis and benzodiazepines should be controlled for in future studies on methadone pharmacokinetics in MMT.

In vivo imaging of T cell delivery to tumors after adoptive transfer therapy.

Adoptive transfer therapy of in vitro-expanded tumor-specific cytolytic T lymphocytes (CTLs) can mediate objective cancer regression in patients. Yet, technical limitations hamper precise monitoring of posttherapy T cell responses. Here we show in a mouse model that fused single photon emission computed tomography and x-ray computed tomography allows quantitative whole-body imaging of (111)In-oxine-labeled CTLs at tumor sites. Assessment of CTL localization is rapid, noninvasive, three-dimensional, and can be repeated for longitudinal analyses. We compared the effects of lymphodepletion before adoptive transfer on CTL recruitment and report that combined treatment increased intratumoral delivery of CTLs and improved antitumor efficacy. Because (111)In-oxine is a Food and Drug Administration-approved clinical agent, and human SPECT-CT systems are available, this approach should be clinically translatable, insofar as it may assess the efficacy of immunization procedures in individual patients and lead to development of more effective therapies.

Détermination des vents extrêmes à l'aide d'analyses statistiques et de modélisations numériques dans une topographie accidentée en Suisse.

Les constructions en Suisse et en Europe doivent être dimensionnées pour subir sans dommages des vents extrêmes (rafales) avec une période de retour d'au moins 50 ans. Des analyses de Gumbel ont donc été effectuées sur des séries de mesures d'une vingtaine d'années à 67 endroits de la Suisse, afin de déterminer les vitesses extrêmes des vents pour différents courants régionaux. Elles ont abouti à de bons résultats pour la majorité des endroits. Mais ces vitesses extrêmes ne peuvent être extrapolées linéairement aux autres régions dans une topographie aussi accidentée que la Suisse. Un modèle numérique tridimensionnel des écoulements non hydrostatique a été expérimenté pour calculer les champs de vent extrêmes en Suisse avec une résolution horizontale de 2 km et une période de retour de 50 ans. Ces modélisations ont permis de reproduire de manière satisfaisante ces vents extrêmes pour l'ensemble du pays. Toutefois, elles sous-estiment leurs intensités sur les reliefs jurassiens et alpins, comparativement aux vallées alpines et au Plateau Suisse.

A numerical model for the gamma-ray emission of the microquasar LS 5039

The possible association between the microquasar LS 5039 and the EGRET source 3EG J1824-1514 suggests that microquasars could also be sources of high energy gamma-rays. In this paper, we explore, with a detailed numerical model, if this system can produce the emission detected by EGRET (>100 MeV) through inverse Compton (IC) scattering. Our numerical approach considers a population of relativistic electrons entrained in a cylindrical inhomogeneous jet, interacting with both the radiation and the magnetic fields, taking into account the Thomson and Klein-Nishina regimes of interaction. The computed spectrum reproduces the observed spectral characteristics at very high energy.

Microquasars as high energy gamma-ray sources

Galactic microquasars are certainly one of the most recent additions to the field of high energy astrophysics and have attracted increasing interest over the last decade. However, the high energy part of the spectrum of microquasars is the most poorly known, mainly due the lack of sensitive instrumentation in the past. Microquasars are now primary targets for all of the observatories working in the X-ray and gamma-ray domains. They also appear as the possible counterparts for some of the unidentified sources of high-energy gamma-rays detected by the experiment EGRET on board the satellite COMPTON-GRO. This paper provides a general review of the main observational results obtained up to now as well as a summary of the scenarios for production of high-energy gamma-rays at the present moment.

High-energy gamma-ray emission from microquasars: LS 5039 and LS I+61303

The possible associations between the microquasars LS 5039 and LS I +61 303 and the EGRET sources 3EG J1824-1514 and 3EG J0241+6103 suggest that microquasars could also be sources of high-energy gamma-rays. In this work, we present a detailed numerical inverse Compton (IC) model, based on a microquasar scenario, that reproduces the high-energy gamma-ray spectra and variability observed by EGRET for the mentioned sources. Our model considers a population of relativistic electrons entrained in a cylindrical inhomogeneous jet that interact through IC scattering with both the radiation and the magnetic fields.

Exploring the high frequency emission of radio loud X-ray binaries

We report millimetre-wave continuum observations of the X-ray binaries Cygnus X-3, SS 433, LSI+61 303, Cygnus X-1 and GRS 1915+105. The observations were carried out with the IRAM 30 m-antenna at 250 GHz (1.25 mm) from 1998 March 14 to March 20. These millimetre measurements are complemented with centimetre observations from the Ryle Telescope, at 15 GHz (2.0 cm) and from the Green Bank Interferometer at 2.25 and 8.3 GHz (13 and 3.6 cm). Both Cygnus X-3 and SS 433 underwent moderate flaring events during our observations, whose main spectral evolution properties are described and interpreted. A significant spectral steepening was observed in both sources during the flare decay, that is likely to be caused by adiabatic expansion, inverse Compton and synchrotron losses. Finally, we also report 250 GHz upper limits for three additional undetected X-ray binary stars: LSI+65 010, LSI+61 235 and X Per.

Search for very high energy gamma-ray emission from pulsar-pulsar wind nebula systems with the MAGIC telescope

The MAGIC collaboration has searched for high-energy gamma-ray emission of some of the most promising pulsar candidates above an energy threshold of 50 GeV, an energy not reachable up to now by other ground-based instruments. Neither pulsed nor steady gamma-ray emission has been observed at energies of 100 GeV from the classical radio pulsars PSR J0205+6449 and PSR J2229+6114 (and their nebulae 3C58 and Boomerang, respectively) and the millisecond pulsar PSR J0218+4232. Here, we present the flux upper limits for these sources and discuss their implications in the context of current model predictions.