Novel Primate-Specific Genes, RMEL 1, 2 and 3, with Highly Restricted Expression in Melanoma, Assessed by New Data Mining Tool

Melanoma is a highly aggressive and therapy resistant tumor for which the identification of specific markers and therapeutic targets is highly desirable. We describe here the development and use of a bioinformatic pipeline tool, made publicly available under the name of EST2TSE, for the in silico detection of candidate genes with tissue-specific expression. Using this tool we mined the human EST (Expressed Sequence Tag) database for sequences derived exclusively from melanoma. We found 29 UniGene clusters of multiple ESTs with the potential to predict novel genes with melanoma-specific expression. Using a diverse panel of human tissues and cell lines, we validated the expression of a subset of three previously uncharacterized genes (clusters Hs.295012, Hs.518391, and Hs.559350) to be highly restricted to melanoma/melanocytes and named them RMEL1, 2 and 3, respectively. Expression analysis in nevi, primary melanomas, and metastatic melanomas revealed RMEL1 as a novel melanocytic lineage-specific gene up-regulated during melanoma development. RMEL2 expression was restricted to melanoma tissues and glioblastoma. RMEL3 showed strong up-regulation in nevi and was lost in metastatic tumors. Interestingly, we found correlations of RMEL2 and RMEL3 expression with improved patient outcome, suggesting tumor and/or metastasis suppressor functions for these genes. The three genes are composed of multiple exons and map to 2q12.2, 1q25.3, and 5q11.2, respectively. They are well conserved throughout primates, but not other genomes, and were predicted as having no coding potential, although primate-conserved and human-specific short ORFs could be found. Hairpin RNA secondary structures were also predicted. Concluding, this work offers new melanoma-specific genes for future validation as prognostic markers or as targets for the development of therapeutic strategies to treat melanoma.

New Epidemiological Data on Brazilian Spotted Fever in an Endemic Area of the State of Sao Paulo, Brazil

The present work evaluated rickettsial infection in dogs and their ticks in an area endemic for Brazilian spotted fever (BSF) in the metropolitan area of Sao Paulo, Brazil, where the tick Amblyomma aureolatum was presumed to be the vector of the disease. Ticks were collected on dogs from 185 houses, encompassing single infestations by Rhipicephalus sanguineus, Amblyomma aureolatum, Amblyomma longirostre, or Amblyomma sp. in dogs from 60 (32.4%), 77 (41.6%), 2 (1.1%), and 25 (13.5%) houses, respectively; 19 (10.3%) houses had dogs with mixed infestations by R. sanguineus and A. aureolatum; 1 (0.5%) house had dogs with infestations by A. aureolatum and A. longirostre; and 1 (0.5%) house had dogs with infestations by R. sanguineus and Amblyomma sp. Overall, A. aureolatum was present in dogs from 97 (52.4%) houses, and R. sanguineus in dogs from 80 (43.2%) houses. A total of 287 ticks (130 A. aureolatum and 157 R. sanguineus) infesting dogs from 98 houses were selected for testing by polymerase chain reaction (PCR) targeting rickettsial genes. Overall, 3.1% of the A. aureolatum ticks were infected by Rickettsia bellii, and 1.3% of the R. sanguineus were infected by Ricketttsii rickettsii. For serology, we selected 23 dogs living in and in the vicinity of the house where the R. rickettsii-infected ticks were collected. The indirect fluorescent antibody (IFA) test detected antibodies reactive with R. rickettsii in sera from 16 (69.6%) dogs, with titers ranging from 256 to 32,768. It is established that Amblyomma aureolatum is a vector of R. rickettsii in the Sao Paulo metropolitan area, but our results highlight for the first time in Brazil, a possible role of R. sanguineus in the epidemiology of R. rickettsii, corroborating previous findings in Mexico and the United States, where R. sanguineus has been implicated in the transmission of R. rickettsii to humans.

DESCRIPTION OF ADULTS AND NYMPH, AND REDESCRIPTION OF THE LARVA, OF ORNITHODOROS MARINKELLEI (ACARI: ARGASIDAE), WITH DATA ON ITS PHYLOGENETIC POSITION

The argasid tick Ornithodoros marinkellei Kohls, Clifford, and Jones, 1969 was described 4 decades ago based on larval specimens collected from bats (Pteronotus spp.) in Colombia and Panama. Thereafter, larval O. marinkellei parasitizing bats were reported from Venezuela, Guyana, and Brazil. Herein, we describe the adults and nymph, and redescribe the larva of O. marinkellei based on specimens recently collected in the western Brazilian Amazon region. In contrast to all other known adult argasids, the idiosoma of both males and females of O. marinkellei is covered with sclerotized plaques. The idiosoma of the nymph of O. marinkellei is entirely micromamillated, and differs from the adults by the absence of plaques. The larva of O. marinkellei is morphologically similar to the larvae of the 2 other species belonging to the subgenus Subparmatus, i.e., Ornithodoros viguerasi Cooley and Kohls, 1941 and Ornithodoros mormoops Kohls, Clifford, and Jones, 1969. Because of the long and narrow dorsal plate, the larva of O. marinkellei is readily distinguished from O. viguerasi and O. mormoops. Comparison of our larvae from Brazil with O. marinkellei paratype specimens from Colombia confirmed their taxonomic identification. However, a few morphological differences, particularly in the size of the gnathosoma, were observed. Further studies are necessary to clarify whether O. marinkellei is a complex of different species, or a single species represented by morphologically polymorphic, and geographically distinct populations. Partial mitochondrial 16S rDNA gene sequences were generated for O. marinkellei specimens from Brazil, and compared with available homologous sequences in GenBank. Phylogenetic analyses revealed O. marinkellei to be distinct from the remaining argasid species available in GenBank, including other bat-associated tick species that are found in sympatry with O. marinkellei in the Neotropical region.

First stars XI. Chemical composition of the extremely metal-poor dwarfs in the binary CS 22876-032

Context. Unevolved metal-poor stars constitute a fossil record of the early Galaxy, and can provide invaluable information on the properties of the first generations of stars. Binary systems also provide direct information on the stellar masses of their member stars. Aims. The purpose of this investigation is a detailed abundance study of the double-lined spectroscopic binary CS 22876-032, which comprises the two most metal-poor dwarfs known. Methods. We used high-resolution, high-S/N ratio spectra from the UVES spectrograph at the ESO VLT telescope. Long-term radial-velocity measurements and broad-band photometry allowed us to determine improved orbital elements and stellar parameters for both components. We used OSMARCS 1D models and the TURBOSPECTRUM spectral synthesis code to determine the abundances of Li, O, Na, Mg, Al, Si, Ca, Sc, Ti, Cr, Mn, Fe, Co and Ni. We also used the (COBOLD)-B-5 model atmosphere code to compute the 3D abundance corrections, notably for Li and O. Results. We find a metallicity of [Fe/H] similar to -3.6 for both stars, using 1D models with 3D corrections of similar to -0.1 dex from averaged 3D models. We determine the oxygen abundance from the near-UV OH bands; the 3D corrections are large, -1 and -1.5 dex for the secondary and primary respectively, and yield [O/Fe] similar to 0.8, close to the high-quality results obtained from the [OI] 630 nm line in metal-poor giants. Other [alpha/Fe] ratios are consistent with those measured in other dwarfs and giants with similar [Fe/H], although Ca and Si are somewhat low ([X/Fe] less than or similar to 0). Other element ratios follow those of other halo stars. The Li abundance of the primary star is consistent with the Spite plateau, but the secondary shows a lower abundance; 3D corrections are small. Conclusions. The Li abundance in the primary star supports the extension of the Spite Plateau value at the lowest metallicities, without any decrease. The low abundance in the secondary star could be explained by endogenic Li depletion, due to its cooler temperature. If this is not the case, another, yet unknown mechanism may be causing increased scatter in A( Li) at the lowest metallicities.

Fast ray-tracing algorithm for circumstellar structures (FRACS) II. Disc parameters of the B[e] supergiant CPD-57 degrees 2874 from VLTI/MIDI data

Context. B[e] supergiants are luminous, massive post-main sequence stars exhibiting non-spherical winds, forbidden lines, and hot dust in a disc-like structure. The physical properties of their rich and complex circumstellar environment (CSE) are not well understood, partly because these CSE cannot be easily resolved at the large distances found for B[e] supergiants (typically greater than or similar to 1 kpc). Aims. From mid-IR spectro-interferometric observations obtained with VLTI/MIDI we seek to resolve and study the CSE of the Galactic B[e] supergiant CPD-57 degrees 2874. Methods. For a physical interpretation of the observables (visibilities and spectrum) we use our ray-tracing radiative transfer code (FRACS), which is optimised for thermal spectro-interferometric observations. Results. Thanks to the short computing time required by FRACS (<10 s per monochromatic model), best-fit parameters and uncertainties for several physical quantities of CPD-57 degrees 2874 were obtained, such as inner dust radius, relative flux contribution of the central source and of the dusty CSE, dust temperature profile, and disc inclination. Conclusions. The analysis of VLTI/MIDI data with FRACS allowed one of the first direct determinations of physical parameters of the dusty CSE of a B[e] supergiant based on interferometric data and using a full model-fitting approach. In a larger context, the study of B[e] supergiants is important for a deeper understanding of the complex structure and evolution of hot, massive stars.

SPITZER OBSERVATIONS OF A1763. II. CONSTRAINING THE NATURE OF ACTIVITY IN THE CLUSTER-FEEDING FILAMENT WITH VLA AND XMM-NEWTON DATA

The A1763 superstructure at z = 0.23 contains the first galaxy filament to be directly detected using mid-infrared observations. Our previous work has shown that the frequency of starbursting galaxies, as characterized by 24 mu m emission is much higher within the filament than at either the center of the rich galaxy cluster, or the field surrounding the system. New Very Large Array and XMM-Newton data are presented here. We use the radio and X-ray data to examine the fraction and location of active galaxies, both active galactic nuclei (AGNs) and starbursts (SBs). The radio far-infrared correlation, X-ray point source location, IRAC colors, and quasar positions are all used to gain an understanding of the presence of dominant AGNs. We find very few MIPS-selected galaxies that are clearly dominated by AGN activity. Most radio-selected members within the filament are SBs. Within the supercluster, three of eight spectroscopic members detected both in the radio and in the mid-infrared are radio-bright AGNs. They are found at or near the core of A1763. The five SBs are located further along the filament. We calculate the physical properties of the known wide angle tail (WAT) source which is the brightest cluster galaxy of A1763. A second double lobe source is found along the filament well outside of the virial radius of either cluster. The velocity offset of the WAT from the X-ray centroid and the bend of the WAT in the intracluster medium are both consistent with ram pressure stripping, indicative of streaming motions along the direction of the filament. We consider this as further evidence of the cluster-feeding nature of the galaxy filament.

Detection of high-velocity material from the wind-wind collision zone of Eta Carinae across the 2009.0 periastron passage

We report near-infrared spectroscopic observations of the Eta Carinae massive binary system during 2008-2009 using the CRIRES spectrograph mounted on the 8m UT 1 Very Large Telescope (VLT Antu). We detect a strong, broad absorption wing in He I lambda 10833 extending up to -1900 km s(-1) across the 2009.0 spectroscopic event. Analysis of archival Hubble Space Telescope/Space Telescope Imaging Spectrograph ultraviolet and optical data identifies a similar high-velocity absorption (up to -2100 km s(-1)) in the ultraviolet resonance lines of Si IV lambda lambda 1394, 1403 across the 2003.5 event. Ultraviolet resonance lines from low-ionization species, such as Si II lambda lambda 1527, 1533 and CII lambda lambda 1334, 1335, show absorption only up to -1200 km s(-1), indicating that the absorption with velocities -1200 to -2100 km s(-1) originates in a region markedly more rapidly moving and more ionized than the nominal wind of the primary star. Seeing-limited observations obtained at the 1.6m OPD/LNA telescope during the last four spectroscopic cycles of Eta Carinae (1989-2009) also show high-velocity absorption in He I lambda 10833 during periastron. Based on the large OPD/LNA dataset, we determine that material with velocities more negative than -900 km s(-1) is present in the phase range 0.976 <= phi <= 1.023 of the spectroscopic cycle, but absent in spectra taken at phi <= 0.947 and phi >= 1.049. Therefore, we constrain the duration of the high-velocity absorption to be 95 to 206 days (or 0.047 to 0.102 in phase). We propose that the high-velocity absorption component originates in shocked gas in the wind-wind collision zone, at distances of 15 to 45 AU in the line-of-sight to the primary star. With the aid of three-dimensional hydrodynamical simulations of the wind-wind collision zone, we find that the dense high-velocity gas is along the line-of-sight to the primary star only if the binary system is oriented in the sky such that the companion is behind the primary star during periastron, corresponding to a longitude of periastron of omega similar to 240 degrees-270 degrees. We study a possible tilt of the orbital plane relative to the Homunculus equatorial plane and conclude that our data are broadly consistent with orbital inclinations in the range i = 40 degrees-60 degrees.

HR Del REMNANT ANATOMY USING TWO-DIMENSIONAL SPECTRAL DATA AND THREE-DIMENSIONAL PHOTOIONIZATION SHELL MODELS

The HR Del nova remnant was observed with the IFU-GMOS at Gemini North. The spatially resolved spectral data cube was used in the kinematic, morphological, and abundance analysis of the ejecta. The line maps show a very clumpy shell with two main symmetric structures. The first one is the outer part of the shell seen in H alpha, which forms two rings projected in the sky plane. These ring structures correspond to a closed hourglass shape, first proposed by Harman & O'Brien. The equatorial emission enhancement is caused by the superimposed hourglass structures in the line of sight. The second structure seen only in the [O III] and [N II] maps is located along the polar directions inside the hourglass structure. Abundance gradients between the polar caps and equatorial region were not found. However, the outer part of the shell seems to be less abundant in oxygen and nitrogen than the inner regions. Detailed 2.5-dimensional photoionization modeling of the three-dimensional shell was performed using the mass distribution inferred from the observations and the presence of mass clumps. The resulting model grids are used to constrain the physical properties of the shell as well as the central ionizing source. A sequence of three-dimensional clumpy models including a disk-shaped ionization source is able to reproduce the ionization gradients between polar and equatorial regions of the shell. Differences between shell axial ratios in different lines can also be explained by aspherical illumination. A total shell mass of 9 x 10(-4) M(circle dot) is derived from these models. We estimate that 50%-70% of the shell mass is contained in neutral clumps with density contrast up to a factor of 30.

The young, tight, and low-mass binary TWA22AB: a new calibrator for evolutionary models? Orbit, spectral types, and temperature

Context. Tight binaries discovered in young, nearby associations are ideal targets for providing dynamical mass measurements to test the physics of evolutionary models at young ages and very low masses. Aims. We report the binarity of TWA22 for the first time. We aim at monitoring the orbit of this young and tight system to determine its total dynamical mass using an accurate distance determination. We also intend to characterize the physical properties (luminosity, effective temperature, and surface gravity) of each component based on near-infrared photometric and spectroscopic observations. Methods. We used the adaptive-optics assisted imager NACO to resolve the components, to monitor the complete orbit and to obtain the relative near-infrared photometry of TWA22 AB. The adaptive-optics assisted integral field spectrometer SINFONI was also used to obtain medium-resolution (R(lambda) = 1500-2000) spectra in JHK bands. Comparison with empirical and synthetic librairies were necessary for deriving the spectral type, the effective temperature, and the surface gravity for each component of the system. Results. Based on an accurate trigonometric distance (17.5 +/- 0.2 pc) determination, we infer a total dynamical mass of 220 +/- 21 M(Jup) for the system. From the complete set of spectra, we find an effective temperature T(eff) = 2900(-200)(+200) K for TWA22A and T(eff) = 2900(-100)(+200) for TWA22 B and surface gravities between 4.0 and 5.5 dex. From our photometry and an M6 +/- 1 spectral type for both components, we find luminosities of log(L/L(circle dot)) = -2.11 +/- 0.13 dex and log(L/L(circle dot)) = -2.30 +/- 0.16 dex for TWA22 A and B, respectively. By comparing these parameters with evolutionary models, we question the age and the multiplicity of this system. We also discuss a possible underestimation of the mass predicted by evolutionary models for young stars close to the substellar boundary.

Transiting exoplanets from the CoRoT space mission VIII. CoRoT-7b: the first super-Earth with measured radius

Aims. We report the discovery of very shallow (Delta F/F approximate to 3.4 x 10(-4)), periodic dips in the light curve of an active V = 11.7 G9V star observed by the CoRoT satellite, which we interpret as caused by a transiting companion. We describe the 3-colour CoRoT data and complementary ground-based observations that support the planetary nature of the companion. Methods. We used CoRoT colours information, good angular resolution ground-based photometric observations in- and out- of transit, adaptive optics imaging, near-infrared spectroscopy, and preliminary results from radial velocity measurements, to test the diluted eclipsing binary scenarios. The parameters of the host star were derived from optical spectra, which were then combined with the CoRoT light curve to derive parameters of the companion. Results. We examined all conceivable cases of false positives carefully, and all the tests support the planetary hypothesis. Blends with separation >0.40 '' or triple systems are almost excluded with a 8 x 10(-4) risk left. We conclude that, inasmuch we have been exhaustive, we have discovered a planetary companion, named CoRoT-7b, for which we derive a period of 0.853 59 +/- 3 x 10(-5) day and a radius of R(p) = 1.68 +/- 0.09 R(Earth). Analysis of preliminary radial velocity data yields an upper limit of 21 M(Earth) for the companion mass, supporting the finding. Conclusions. CoRoT-7b is very likely the first Super-Earth with a measured radius. This object illustrates what will probably become a common situation with missions such as Kepler, namely the need to establish the planetary origin of transits in the absence of a firm radial velocity detection and mass measurement. The composition of CoRoT-7b remains loosely constrained without a precise mass. A very high surface temperature on its irradiated face, approximate to 1800-2600 K at the substellar point, and a very low one, approximate to 50 K, on its dark face assuming no atmosphere, have been derived.

The CoRoT-7 planetary system: two orbiting super-Earths

We report on an intensive observational campaign carried out with HARPS at the 3.6 m telescope at La Silla on the star CoRoT-7. Additional simultaneous photometric measurements carried out with the Euler Swiss telescope have demonstrated that the observed radial velocity variations are dominated by rotational modulation from cool spots on the stellar surface. Several approaches were used to extract the radial velocity signal of the planet(s) from the stellar activity signal. First, a simple pre-whitening procedure was employed to find and subsequently remove periodic signals from the complex frequency structure of the radial velocity data. The dominant frequency in the power spectrum was found at 23 days, which corresponds to the rotation period of CoRoT-7. The 0.8535 day period of CoRoT-7b planetary candidate was detected with an amplitude of 3.3 m s(-1). Most other frequencies, some with amplitudes larger than the CoRoT-7b signal, are most likely associated with activity. A second approach used harmonic decomposition of the rotational period and up to the first three harmonics to filter out the activity signal from radial velocity variations caused by orbiting planets. After correcting the radial velocity data for activity, two periodic signals are detected: the CoRoT-7b transit period and a second one with a period of 3.69 days and an amplitude of 4 m s(-1). This second signal was also found in the pre-whitening analysis. We attribute the second signal to a second, more remote planet CoRoT-7c. The orbital solution of both planets is compatible with circular orbits. The mass of CoRoT-7b is 4.8 +/- 0.8 (M(circle plus)) and that of CoRoT-7c is 8.4 +/- 0.9 (M(circle plus)), assuming both planets are on coplanar orbits. We also investigated the false positive scenario of a blend by a faint stellar binary, and this may be rejected by the stability of the bisector on a nightly scale. According to their masses both planets belong to the super-Earth planet category. The average density of CoRoT-7b is rho = 5.6 +/- 1.3 g cm(-3), similar to the Earth. The CoRoT-7 planetary system provides us with the first insight into the physical nature of short period super-Earth planets recently detected by radial velocity surveys. These planets may be denser than Neptune and therefore likely made of rocks like the Earth, or a mix of water ice and rocks.

The B0.5IVe CoRoT target HD 49330 I. Photometric analysis from CoRoT data

Context. Be stars undergo outbursts producing a circumstellar disk from the ejected material. The beating of non-radial pulsations has been put forward as a possible mechanism of ejection. Aims. We analyze the pulsational behavior of the early B0.5IVe star HD 49330 observed during the first CoRoT long run towards the Galactical anticenter (LRA1). This Be star is located close to the lower edge of the beta Cephei instability strip in the HR diagram and showed a 0.03 mag outburst during the CoRoT observations. It is thus an ideal case for testing the aforementioned hypothesis. Methods. We analyze the CoRoT light curve of HD 49330 using Fourier methods and non-linear least square fitting. Results. In this star, we find pulsation modes typical of beta Cep stars (p modes) and SPB stars (g modes) with amplitude variations along the run directly correlated with the outburst. These results provide new clues about the origin of the Be phenomenon as well as strong constraints on the seismic modelling of Be stars.

The BRAzilian Seismographic Integrated Systems (BRASIS): infrastructure and data management

In geophysics and seismology, raw data need to be processed to generate useful information that can be turned into knowledge by researchers. The number of sensors that are acquiring raw data is increasing rapidly. Without good data management systems, more time can be spent in querying and preparing datasets for analyses than in acquiring raw data. Also, a lot of good quality data acquired at great effort can be lost forever if they are not correctly stored. Local and international cooperation will probably be reduced, and a lot of data will never become scientific knowledge. For this reason, the Seismological Laboratory of the Institute of Astronomy, Geophysics and Atmospheric Sciences at the University of Sao Paulo (IAG-USP) has concentrated fully on its data management system. This report describes the efforts of the IAG-USP to set up a seismology data management system to facilitate local and international cooperation.

Kinematic constraints to the transition redshift from supernovae type Ia union data

The kinematic approach to cosmological tests provides direct evidence to the present accelerating stage of the Universe that does not depend on the validity of general relativity, as well as on the matter-energy content of the Universe. In this context, we consider here a linear two-parameter expansion for the decelerating parameter, q(z)=q(0)+q(1)z, where q(0) and q(1) are arbitrary constants to be constrained by the union supernovae data. By assuming a flat Universe we find that the best fit to the pair of free parameters is (q(0),q(1))=(-0.73,1.5) whereas the transition redshift is z(t)=0.49(-0.07)(+0.14)(1 sigma) +0.54-0.12(2 sigma). This kinematic result is in agreement with some independent analyses and more easily accommodates many dynamical flat models (like Lambda CDM).

The taxonomic status of the endangered thin-spined porcupine, Chaetomys subspinosus (Olfers, 1818), based on molecular and karyologic data

Background: The thin-spined porcupine, also known as the bristle-spined rat, Chaetomys subspinosus (Olfers, 1818), the only member of its genus, figures among Brazilian endangered species. In addition to being threatened, it is poorly known, and even its taxonomic status at the family level has long been controversial. The genus Chaetomys was originally regarded as a porcupine in the family Erethizontidae, but some authors classified it as a spiny-rat in the family Echimyidae. Although the dispute seems to be settled in favor of the erethizontid advocates, further discussion of its affinities should be based on a phylogenetic framework. In the present study, we used nucleotide-sequence data from the complete mitochondrial cytochrome b gene and karyotypic information to address this issue. Our molecular analyses included one individual of Chaetomys subspinosus from the state of Bahia in northeastern Brazil, and other hystricognaths. Results: All topologies recovered in our molecular phylogenetic analyses strongly supported Chaetomys subspinosus as a sister clade of the erethizontids. Cytogenetically, Chaetomys subspinosus showed 2n = 52 and FN = 76. Although the sexual pair could not be identified, we assumed that the X chromosome is biarmed. The karyotype included 13 large to medium metacentric and submetacentric chromosome pairs, one small subtelocentric pair, and 12 small acrocentric pairs. The subtelocentric pair 14 had a terminal secondary constriction in the short arm, corresponding to the nucleolar organizer region (Ag-NOR), similar to the erethizontid Sphiggurus villosus, 2n = 42 and FN = 76, and different from the echimyids, in which the secondary constriction is interstitial. Conclusion: Both molecular phylogenies and karyotypical evidence indicated that Chaetomys is closely related to the Erethizontidae rather than to the Echimyidae, although in a basal position relative to the rest of the Erethizontidae. The high levels of molecular and morphological divergence suggest that Chaetomys belongs to an early radiation of the Erethizontidae that may have occurred in the Early Miocene, and should be assigned to its own subfamily, the Chaetomyinae.