A molecular linkage map for Drosophila mediopunctata confirms synteny with Drosophila melanogaster and suggests a region that controls the variation in the number of abdominal spots

The classic approach to gene discovery relies on the construction of linkage maps. We report the first molecular-based linkage map for Drosophila mediopunctata, a neotropical species of the tripunctata group. Eight hundred F2 individuals were genotyped at 49 microsatellite loci, resulting in a map that is approximate to 450 centimorgans long. Five linkage groups were detected, and the species' chromosomes were identified through cross-references to BLASTn searches and Muller elements. Strong synteny was observed when compared with the Drosophila melanogaster chromosome arms, but little conservation in the gene order was seen. The incorporation of morphological data corresponding to the number of central abdominal spots on the map was consistent with the expected location of a genomic region responsible for the phenotype on the second chromosome.

Feature-oriented regional modeling and simulations (FORMS) for the western South Atlantic: Southeastern Brazil region

The multi-scale synoptic circulation system in the southeastern Brazil (SEBRA) region is presented using a feature-oriented approach. Prevalent synoptic circulation structures, or ""features,"" are identified from previous observational studies. These features include the southward-flowing Brazil Current (BC), the eddies off Cabo Sao Tome (CST - 22 degrees S) and off Cabo Frio (CF - 23 degrees S), and the upwelling region off CF and CST. Their synoptic water-mass (T-S) structures are characterized and parameterized to develop temperature-salinity (T-S) feature models. Following [Gangopadhyay, A., Robinson, A.R., Haley, PJ., Leslie, W.J., Lozano, C.j., Bisagni, J., Yu, Z., 2003. Feature-oriented regional modeling and simulation (forms) in the gulf of maine and georges bank. Cont. Shelf Res. 23 (3-4), 317-353] methodology, a synoptic initialization scheme for feature-oriented regional modeling and simulation (FORMS) of the circulation in this region is then developed. First, the temperature and salinity feature-model profiles are placed on a regional circulation template and objectively analyzed with available background climatology in the deep region. These initialization fields are then used for dynamical simulations via the Princeton Ocean Model (POM). A few first applications of this methodology are presented in this paper. These include the BC meandering, the BC-eddy interaction and the meander-eddy-upwelling system (MEUS) simulations. Preliminary validation results include realistic wave-growth and eddy formation and sustained upwelling. Our future plan includes the application of these feature models with satellite, in-situ data and advanced data-assimilation schemes for nowcasting and forecasting the SEBRA region. (c) 2008 Elsevier Ltd. All rights reserved.

Production of Muons from Heavy Flavor Decays at Forward Rapidity in pp and Pb-Pb Collisions at root s(NN)=2.76 TeV

The ALICE Collaboration has measured the inclusive production of muons from heavy-flavor decays at forward rapidity, 2.5 < y < 4, in pp and Pb-Pb collisions at root s(NN) = 2.76 TeV. The p(t)-differential inclusive cross section of muons from heavy-flavor decays in pp collisions is compared to perturbative QCD calculations. The nuclear modification factor is studied as a function of p(t) and collision centrality. A weak suppression is measured in peripheral collisions. In the most central collisions, a suppression of a factor of about 3-4 is observed in 6 < p(t) < 10 GeV/c. The suppression shows no significant p(t) dependence.

Pion, Kaon, and Proton Production in Central Pb-Pb Collisions at root s(NN)=2.76 TeV

In this Letter we report the first results on pi(+/-), K-+/-, p, and (p) over bar production at midrapidity (vertical bar y vertical bar < 0.5) in central Pb-Pb collisions at root s(NN) = 2.76 TeV, measured by the ALICE experiment at the LHC. The p(T) distributions and yields are compared to previous results at root s(NN) = 200 GeV and expectations from hydrodynamic and thermal models. The spectral shapes indicate a strong increase of the radial flow velocity with root s(NN), which in hydrodynamic models is expected as a consequence of the increasing particle density. While the K/pi ratio is in line with predictions from the thermal model, the p/pi ratio is found to be lower by a factor of about 1.5. This deviation from thermal model expectations is still to be understood.

Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV

The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.

Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region

Abstract Background The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. Results We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. Conclusion The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

Validating NCAR-CCSM last glacial maximum sea surface temperature in the tropical and South Atlantic with proxy-data

Last Glacial Maximum simulated sea surface temperature from the Paleo-Climate version of the National Center for Atmospheric Research Coupled Climate Model (NCAR-CCSM) are compared with available reconstructions and data-based products in the tropical and south Atlantic region. Model results are compared to data proxies based on the Multiproxy Approach for the Reconstruction of the Glacial Ocean surface product (MARGO). Results show that the model sea surface temperature is not consistent with the proxy-data in all of the region of interest. Discrepancies are found in the eastern, equatorial and in the high-latitude South Atlantic. The model overestimates the cooling in the southern South Atlantic (near 50 degrees S) shown by the proxy-data. Near the equator, model and proxies are in better agreement. In the eastern part of the equatorial basin the model underestimates the cooling shown by all proxies. A northward shift in the position of the subtropical convergence zone in the simulation suggests a compression or/and an equatorward shift of the subtropical gyre at the surface, consistent with what is observed in the proxy reconstruction. (C) 2008 Elsevier B.V. All rights reserved

Biological, physical and chemical properties at the Subtropical Shelf Front Zone in the SW Atlantic Continental Shelf

The physical aspects of the Subtropical Shelf Front (STSF) for the Southwest Atlantic Continental Shelf were previously described. However, only scarce data on the biology of the front is available in the literature. The main goal of this paper is to describe the physical, chemical and biological properties of the STSF found in winter 2003 and summer 2004. A cross-section was established at the historically determined location of the STSF. Nine stations were sampled in winter and seven in summer. Each section included a series of conductivity-temperature-depth (CTD) stations where water samples from selected depths were filtered for nutrient determination. Surface samples were taken for chlorophyll a (Chl-a) determination and plankton net tows carried out above and below the pycnocline. Results revealed that winter was marked by an inner-shelf salinity front and that the STSF was located on the mid-shelf The low salinity waters in the inner-shelf indicated a strong influence of freshwater, with high silicate (72 mu M), suspended matter (45 mg l(-1)), phosphate (2.70 mu M) and low nitrate (1.0 mu M) levels. Total dissolved nitrogen was relatively high (22.98 mu M), probably due to the elevated levels of organic compound contribution close to the continental margin. Surface Chl-a concentration decreased from coastal well-mixed waters, where values up to 8.0 mg m(-3) were registered, to offshore waters. Towards the open ocean, high subsurface nutrients values were observed, probably associated to South Atlantic Central Waters (SACW). Zooplankton and ichthyoplankton abundance followed the same trend; three different groups associated to the inner-, mid- and outer-shelf region were identified. During summer, diluted waters extended over the shelf to join the STSF in the upper layer; the concentration of inorganic nutrients decreased in shallow waters; however, high values were observed between 40 and 60 m and in deep offshore waters. Surface Chl-a ranged 0.07-1.5 mg m(-3); winter levels were higher. Three groups of zoo and ichthyoplankton, separated by the STSF, were also identified. Results of the study performed suggest that the influence of freshwater was stronger during winter and that abundance distribution of Chl-a, copepods and ichthyoplankton was related to the Plata Plume Waters (PPW), rather than to the presence of the STSF. During summer, when the presence of freshwater decreases, plankton interactions seem to take place in the STSF. (C) 2008 Elsevier Ltd. All rights reserved.

Benthic foraminiferal distribution on the southeastern Brazilian shelf and upper slope

Foraminiferal data were obtained from 66 samples of box cores on the southeastern Brazilian upper margin (between 23.8A degrees-25.9A degrees S and 42.8A degrees-46.13A degrees W) to evaluate the benthic foraminiferal fauna distribution and its relation to some selected abiotic parameters. We focused on areas with different primary production regimes on the southern Brazilian margin, which is generally considered as an oligotrophic region. The total density (D), richness (R), mean diversity (H) over bar`, average living depth (ALD(X) ) and percentages of specimens of different microhabitats (epifauna, shallow infauna, intermediate infauna and deep infauna) were analyzed. The dominant species identified were Uvigerina spp., Globocassidulina subglobosa, Bulimina marginata, Adercotryma wrighti, Islandiella norcrossi, Rhizammina spp. and Brizalina sp.. We also established a set of mathematical functions for analyzing the vertical foraminiferal distribution patterns, providing a quantitative tool that allows correlating the microfaunal density distributions with abiotic factors. In general, the cores that fit with pure exponential decaying functions were related to the oligotrophic conditions prevalent on the Brazilian margin and to the flow of the Brazilian Current (BC). Different foraminiferal responses were identified in cores located in higher productivity zones, such as the northern and the southern region of the study area, where high percentages of infauna were encountered in these cores, and the functions used to fit these profiles differ appreciably from a pure exponential function, as a response of the significant living fauna in deeper layers of the sediment. One of the main factors supporting the different foraminiferal assemblage responses may be related to the differences in primary productivity of the water column and, consequently, in the estimated carbon flux to the sea floor. Nevertheless, also bottom water velocities, substrate type and water depth need to be considered.

Distribution and molecular characterization of hepatitis C virus (HCV) genotypes in patients with chronic infection from Pernambuco State, Brazil

Hepatitis C virus (HCV) is a public health problem throughout the world and 3% of the world population is infected with this virus. It is estimated that 3-4 millions individuals are being infected every year. It has been estimated that around 1.5% of Brazilian population is anti-HCV positive and the Northeast region showed the highest prevalence in Brazil. The aim of this study was to characterize HCV genotypes circulating in Pernambuco State (PE), Brazil, located in the Northeast region of the country. This study included 85 anti-HCV positive patients followed up between 2004 and 2011. For genotyping, a 380bp fragment of HCV RNA in the NS5B region was amplified by nested PCR. Phylogenetic analysis was conducted using Bayesian Markov chain Monte Carlo simulation (MCMC) using BEAST v.1.5.3. From 85 samples, 63 (74.1%) positive to NS5B fragment were successfully sequenced. Subtype 1b was the most prevalent in this population (42-66.7%), followed by 3a (16-25.4%), 1a (4-6.3%) and 2b (1-1.6%). Twelve (63.1%) and seven (36.9%) patients with HCV and schistosomiasis were infected with subtypes 1b and 3a, respectively. Brazil is a large country with many different population backgrounds; a large variation in the frequencies of HCV genotypes is predictable throughout its territory. This study reports HCV genotypes from Pernambuco State where subtype 1b was found to be the most prevalent. Phylogenetic analysis suggests the presence of the different HCV strains circulating within this population. (C) 2012 Elsevier B.V. All rights reserved.

Contribution of AT-, GC-, and methylated cytidine-rich DNA to chromatin composition in Malpighian tubule cell nuclei of Panstrongylus megistus (Hemiptera, Reduviidae)

The Malpighian tubule cell nuclei of male Panstrongylus megistus, a vector of Chagas disease, contain one chromocenter, which is composed solely of the Y chromosome. Considering that different chromosomes contribute to the composition of chromocenters in different triatomini species, the aim of this study was to determine the contribution of AT-, GC-, and methylated cytidine-rich DNA in the chromocenter as well as in euchromatin of Malpighian tubule cell nuclei of P. megistus in comparison with published data for Triatoma infestans. Staining with 4',6-diamidino-2-phenylindole/actinomycin D and chromomycin A(3)/distamycin, immunodetection of 5-methylcytidine and AgNOR test were used. The results revealed AT-rich/GC-poor DNA in the male chromocenter, but equally distributed AT and GC DNA sequences in male and female euchromatin, like in T. infestans. Accumulation of argyrophilic proteins encircling the chromocenter did not always correlate with that of GC-rich DNA. Methylated DNA identified by immunodetection was found sparsely distributed in the euchromatin of both sexes and at some points around the chromocenter edge, but it could not be considered responsible for chromatin condensation in the chromocenter, like in T. infestans. However, unlike in T. infestans, no correlation between the chromocenter AT-rich DNA and nucleolus organizing region (NOR) DNA was found in P. megistus. (c) 2011 Elsevier GmbH. All rights reserved.

Molecular Surveillance of the Newcastle Disease Virus in Domestic and Wild Birds on the North Eastern Coast and Amazon Biome of Brazil

Brazil is one of the world's largest countries with a rich diversity of wildlife, including resident and migratory wild birds, which may be natural reservoirs of the Newcastle disease virus (NDV). Because Brazil is a major global exporter of chicken meat, the emergence of such a disease may have a huge negative impact not only on the economy due to trade restrictions and embargoes, but also on the quality of life of the population. Samples were collected from 1,022 asymptomatic domestic and wild birds from the Brazilian coast and the Amazon region using tracheal/cloacal swabs and tested by RT-qPCR. The results showed 7 (0.7%) birds were positive for NDV. The positive samples were then isolated in embryonated chicken eggs and their matrix protein genes were partially sequenced, revealing a low-pathogenicity NDV. This study confirms the maintenance of the velogenic-NDV free status of Brazil.

A NEW GENUS AND SPECIES OF PHILOPTERIDAE (PHTHIRAPTERA: ISCHNOCERA) FROM THE TRUMPETERS (AVES: GRUIFORMES: PSOPHIIDAE)

A new chewing louse genus and species belonging to the Philopteridae, namely, Palmaellus inespectatus n. gen., n. sp., is described. The new genus is distinguished from the other ischnoceran genera hitherto described by its peculiar characters of the dorsal anterior head plate with 2 postero-lateral projections, pterothorax and abdomen with scarce chaetotaxy, male genitalia with simple mesomere and paramere lacking inner digitiform projection, and the genital region of female with postero-vulvar plates bearing setae. It is a parasite of the trumpeters, an avian family endemic to South America's Amazon Basin.

Measurement of event background fluctuations for charged particle jet reconstruction in Pb-Pb collisions at root s(NN)=2.76 TeV

The effect of event background fluctuations on charged particle jet reconstruction in Pb-Pb collisions at root s(NN) = 2.76 TeV has been measured with the ALICE experiment. The main sources of non-statistical fluctuations are characterized based purely on experimental data with an unbiased method, as well as by using single high p(t) particles and simulated jets embedded into real Pb-Pb events and reconstructed with the anti-k(t) jet finder. The influence of a low transverse momentum cut-off on particles used in the jet reconstruction is quantified by varying the minimum track p(t) between 0.15 GeV/c and 2 GeV/c. For embedded jets reconstructed from charged particles with p(t) > 0.15 GeV/c, the uncertainty in the reconstructed jet transverse momentum due to the heavy-ion background is measured to be 11.3 GeV/c (standard deviation) for the 10% most central Pb-Pb collisions, slightly larger than the value of 11.0 GeV/c measured using the unbiased method. For a higher particle transverse momentum threshold of 2 GeV/c, which will generate a stronger bias towards hard fragmentation in the jet finding process, the standard deviation of the fluctuations in the reconstructed jet transverse momentum is reduced to 4.8-5.0 GeV/c for the 10% most central events. A non-Gaussian tail of the momentum uncertainty is observed and its impact on the reconstructed jet spectrum is evaluated for varying particle momentum thresholds, by folding the measured fluctuations with steeply falling spectra.

Morphological and genetic variability in Hippolyte obliquimanus dana, 1852 (Decapoda, Caridea, Hippolytidae) from Brazil and the caribbean sea

Hippolyte obliquimanus is a marine shrimp reported from the Caribbean Sea and Brazil. The literature provides indications for morphological variation between populations from those regions and the species has a troubled taxonomic history. The aims of this study were to analyse morphological and genetic variation in the populations of H. obliquimanus from Brazil and the Caribbean Sea and to verify if those might support separation of H. obliquimanus into two or more species. This hypothesis was tested with the analysis of morphological and genetic data (mitochondrial gene 16S and the barcode region Cytochrome Oxidase I). The material analysed was obtained from samples and from loans of zoological collections. The rostrum as well as pereiopods 3, 4, and 5 were the adult morphological characters that showed variation, but this occurred in samples from both regions, Brazil and the Caribbean Sea. The sequences of the 16S gene were identical among all specimens analysed. There was, however, variation among the sequences of the barcoding gene COI (<2.0%); this divergence separated the specimens into two groups (Brazil versus the Caribbean) and these groups did not share haplotypes. In conclusion, specimens from the regions analysed showed both morphological and genetic variation, but these did not support the separation of H. obliquimanus into two or more species.