Phylogeography of the common vampire bat (Desmodus rotundus): Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

Background: The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA) marker and two nuclear markers (RAG2 and DRB) to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat. Results: Five reciprocally monophyletic clades were evident in the mitochondrial gene tree, and in most cases with high bootstrap support: Central America (CA), Amazon and Cerrado (AMC), Pantanal (PAN), Northern Atlantic Forest (NAF) and Southern Atlantic Forest (SAF). The Atlantic forest clades formed a monophyletic clade with high bootstrap support, creating an east/west division for this species in South America. On the one hand, all coalescent and non-coalescent estimates point to a Pleistocene time of divergence between the clades. On the other hand, the nuclear markers showed extensive sharing of haplotypes between distant localities, a result compatible with male-biased gene flow. In order to test if the disparity between the mitochondrial and nuclear markers was due to the difference in mutation rate and effective size, we performed a coalescent simulation to examine the feasibility that, given the time of separation between the observed lineages, even with a gene flow rate close to zero, there would not be reciprocal monophyly for a neutral nuclear marker. We used the observed values of theta and an estimated mutation rate for the nuclear marker gene to perform 1000 iterations of the simulation. The results of this simulation were inconclusive: the number of iterations with and without reciprocal monophyly of one or more clades are similar. Conclusions: We therefore conclude that the pattern exhibited by the common vampire bat, with marked geographical structure for a mitochondrial marker and no phylogeographic structure for nuclear markers is compatible with a historical scenario of complete isolation of refuge-like populations during the Pleistocene. The results on demographic history on this species is compatible with the Carnaval-Moritz model of Pleistocene vicariance, with demographic expansions in the southern Atlantic forest.FAPESP grants number 03/01583 -3 and 04/08682-4CAPES grant number BEX4687/06-

Determinação de doses de micronutrientes a serem aplicadas via sementes à cultura do feijão (Phaseolus vulgaris L.).

O presente trabalho teve como objetivo estudar a aplicação dos micronutrientes Boro (na forma de ácido bórico - H3BO3), Molibdênio (na forma de molibidato de sódio - Na2MoO4) e Cobalto (na forma de sulfato de cobalto - CoSO4) em sementes de feijão, através do processo de recobrimento

Comparação entre diferentes formas de fornecer micronutrientes às sementes de feijão.

O presente trabalho teve como objetivo comparar diferentes formas de aplicação dos micronutrientes: Boro (B), Cobalto (Co) e Molibdênio (Mo) em sementes de feijão. As formas de aplicação avaliadas foram: recobrimento de sementes em leito de jorro, recobrimento em sacos plásticos e o fornecimento via sulco

Metagenomics in Polluted Aquatic Environments

Metagenomics is defined as the culture-independent genomic analysis of biological assemblages providing access to the whole set of genes and genomes from a sample. It encompasses a variety of techniques that are based on (i) total DNA extraction from samples followed by PCR amplification of specific genes, (ii) library construction or amplification and sequencing of the whole genetic material. These methodologies have successfully been applied in studies of composition, dynamics, and functions of microbial communities in a variety of ecosystems including those subjected to anthropogenic modifications (Gilbert & Dupont, 2011). Culture independent methods allow the analysis of a set of metabolic genes from microbial communities, which can be used to determine how environmental conditions such as pollution can shape community composition and the diversity of genes associated with biogeochemical cycles such as those of carbon, nitrogen, and phosphorus (Singh et al., 2009). This approach is also useful for the discovery of novel environmental microorganisms and genes, with important applications for biotechnology, medicine, and bioremediation (Cardoso et al., 2011). This applicability has resulted in a recent sharp increase in studies focusing in the metagenomic analysis of polluted sites. Their aim is to characterize microbial communities from a diverse set of environments such as freshwater, marine sediments, open ocean, pelagic ecosystems, soil, and host-associated communities. An example of these initiatives is the Global Ocean Sampling Expedition (GOS), which assessed the genetic diversity of marine microbial communities around the Earth. Since 2003, an enormous amount of data has been generated by GOS helping scientists to reveal the microbial diversity and also allowing them to better understand microbial phylogeny and ecology (Gilbert & Dupont, 2011)

Systems involving hydrogenated and fluorinated chains: Volumetric properties of Perfluoroalkanes and Perfluoroalkylalkane Surfactants

As part of a combined experimental and theoretical study of the thermodynamic properties of perfluoroalkylalkanes (PFAAs), the liquid density of perfluorobutylpentane (F4H5), perfluorobutylhexane (F4H6), and perfluorobutyloctane (F4H8) was measured as a function of temperature from 278.15 to 353.15 K and from atmospheric pressure to 70 MPa. The liquid densities of n-perfluoropentane, n-perfluorohexane, n-perfluorooctane, and n-perfluorononane were also measured at room pressure over the same temperature range. The PVT behavior of the PFAAs was also studied using the SAFT-VR equation of state. The PFAA molecules were modeled as heterosegmented diblock chains, using different parameters for the alkyl and perfluoroalkyl segments, that were developed in earlier work. Through this simple approach, we are able to predict the thermodynamic behavior of the perfluoroalkylalkanes, without fitting to any experimental data for the systems being studied. Molecular dynamics simulations have also been performed and used to calculate the densities of the perfluoroalkylalkanes studied

Comparative genomics allowed the identification of drug targets against human fungal pathogens

<p>Abstract</p> <p>Background</p> <p>The prevalence of invasive fungal infections (IFIs) has increased steadily worldwide in the last few decades. Particularly, there has been a global rise in the number of infections among immunosuppressed people. These patients present severe clinical forms of the infections, which are commonly fatal, and they are more susceptible to opportunistic fungal infections than non-immunocompromised people. IFIs have historically been associated with high morbidity and mortality, partly because of the limitations of available antifungal therapies, including side effects, toxicities, drug interactions and antifungal resistance. Thus, the search for alternative therapies and/or the development of more specific drugs is a challenge that needs to be met. Genomics has created new ways of examining genes, which open new strategies for drug development and control of human diseases.</p> <p>Results</p> <p><it>In silico </it>analyses and manual mining selected initially 57 potential drug targets, based on 55 genes experimentally confirmed as essential for <it>Candida albicans </it>or <it>Aspergillus fumigatus </it>and other 2 genes (<it>kre2 </it>and <it>erg6</it>) relevant for fungal survival within the host. Orthologs for those 57 potential targets were also identified in eight human fungal pathogens (<it>C. albicans</it>, <it>A. fumigatus</it>, <it>Blastomyces dermatitidis</it>, <it>Paracoccidioides brasiliensis</it>, <it>Paracoccidioides lutzii, Coccidioides immitis</it>, <it>Cryptococcus neoformans </it>and <it>Histoplasma capsulatum</it>). Of those, 10 genes were present in all pathogenic fungi analyzed and absent in the human genome. We focused on four candidates: <it>trr1 </it>that encodes for thioredoxin reductase, <it>rim8 </it>that encodes for a protein involved in the proteolytic activation of a transcriptional factor in response to alkaline pH, <it>kre2 </it>that encodes for α-1,2-mannosyltransferase and <it>erg6 </it>that encodes for Δ(24)-sterol C-methyltransferase.</p> <p>Conclusions</p> <p>Our data show that the comparative genomics analysis of eight fungal pathogens enabled the identification of four new potential drug targets. The preferred profile for fungal targets includes proteins conserved among fungi, but absent in the human genome. These characteristics potentially minimize toxic side effects exerted by pharmacological inhibition of the cellular targets. From this first step of post-genomic analysis, we obtained information relevant to future new drug development.</p

Multiply charged naphthalene and its C10H8 isomers: bonding, spectroscopy and implications in AGN environments

Naphthalene (C10H8) is the simplest polycyclic aromatic hydrocarbon (PAH) and an important component in a series of astrochemical reactions involving hydrocarbons. Its molecular charge state affects the stability of its isomeric structures, which is specially relevant in ionised astrophysical environments. We thus perform an extensive computational search for low-energy molecular structures of neutral, singly, and multiply charged naphthalene and its isomers with charge states +q = 0-4 and investigate their geometric properties and bonding situations. We find that isomerisation reactions should be frequent for higher charged states and that open chains dominate their low-energy structures. We compute both the scaled-harmonic and anharmonic infrared spectra of selected low-energy species and provide the calculated scaling factors for the naphthalene neutral, cation, and dication global minima. All simulated spectra reproduce satisfactorily the experimental data and, thus, are adequate for aiding observations. Moreover, the potential presence of these species in the emission spectra of the circumnuclear regions of active galactic nuclei (AGNs), with high energetic X-ray photon fluxes, is explored using the experimental value of the naphthalene photodissociation cross-section, \sigma_{ph-d}, to determine its half-life, t_{1/2}, at a photon energy of 2.5 keV in a set of relevant sources. Finally, we show that the computed IR bands of the triply and quadruply charged species are able to reproduce some features of the selected AGN sources.Comment: Accepted for publication in the Monthly Notices of the Royal Astronomical Society. 15 pages, 7 pages, supplementary information available onlin

First Description of KPC-2-Producing Klebsiella oxytoca in Brazil

The present work reports the detection of the first case of nosocomial Klebsiella oxytoca producing class A carbapenemase KPC-2 in Brazil. the isolate KPN106 carried a 65-kb IncW-type plasmid that harbors the bla(KPC) gene and Tn4401b. Moreover, we detected the presence of a class 1 integron containing a new allele, arr-8, followed by a 5'-truncated dhfrIIIc gene. in view of the recent results, we emphasize the high variability of the bacterial and genetic hosts of this resistance determinant.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)FACEPEPFA/UPEUniv Pernambuco, Inst Ciencias Biol, Lab Resistencia Microbiana, Recife, PE, BrazilUniv Fed Pernambuco, Dept Genet, Lab Genet Microrganismos, Recife, PE, BrazilUniversidade Federal de São Paulo, Lab Alerta, São Paulo, BrazilCPqAM Fiocruz, Ctr Pesquisa Aggeu Magalhaes, Recife, PE, BrazilUniversidade Federal de São Paulo, Lab Alerta, São Paulo, BrazilWeb of Scienc

ESTs from a wild Arachis species for gene discovery and marker development

BACKGROUND: Due to its origin, peanut has a very narrow genetic background. Wild relatives can be a source of genetic variability for cultivated peanut. In this study, the transcriptome of the wild species Arachis stenosperma accession V10309 was analyzed. RESULTS: ESTs were produced from four cDNA libraries of RNAs extracted from leaves and roots of A. stenosperma. Randomly selected cDNA clones were sequenced to generate 8,785 ESTs, of which 6,264 (71.3%) had high quality, with 3,500 clusters: 963 contigs and 2537 singlets. Only 55.9% matched homologous sequences of known genes. ESTs were classified into 23 different categories according to putative protein functions. Numerous sequences related to disease resistance, drought tolerance and human health were identified. Two hundred and six microsatellites were found and markers have been developed for 188 of these. The microsatellite profile was analyzed and compared to other transcribed and genomic sequence data. CONCLUSION: This is, to date, the first report on the analysis of transcriptome of a wild relative of peanut. The ESTs produced in this study are a valuable resource for gene discovery, the characterization of new wild alleles, and for marker development. The ESTs were released in the [GenBank:EH041934 to EH048197]