MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies

MamMiBase, the mammalian mitochondrial genome database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that are useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, which are also given by MamMiBase. A simple phylogenetic tree (neighbor-joining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks. AVAILABILITY: MamMiBase is available at http://www.mammibase.lncc.br     

Viruses, prokaryotes and DNA in the sediments of a deep-hypersaline anoxic basin (DHAB) of the Mediterranean Sea

Viral and prokaryote abundance were investigated in a deep-hypersaline anoxic basin of the Eastern Mediterranean Sea (DHAB Atalante basin at c. 3000 m depth). This system was compared with two nearby deep-sea sites characterized by oxic conditions. Viral abundance and virus to prokaryote abundance ratio in hypersaline anoxic sediments displayed values close to those reported in oxic sites. The analysis of vertical profiles of viral abundance in the Atalante basin revealed the lack of significant changes with depth in the sediment, suggesting that benthic viruses in these anoxic and hypersaline conditions are preserved or resistant to decay. The anoxic basin displayed also very high concentrations of labile organic components (proteins and lipids) and extracellular DNA. These findings suggest that the DHAB sediments represent a reservoir for long-term preservation of benthic viruses and nucleic acids.     

An ectophosphatase activity in Cryptococcus neoformans

There is increasing evidence in the literature showing that fungal pathogens express biologically active ectoenzymes. The expression of surface phosphatases at the cell surface of Cryptococcus neoformans, the etiologic agent of cryptococcosis, was evaluated in the present study. Different isolates of C. neoformans express ectophosphatase activity, which is not influenced by capsule size or serotype. The cryptococcal enzyme is an acid phosphatase, inhibited by classic inhibitors of ectophosphatases, including ammonium molybdate and sodium salts of fluoride and orthovanadate. Only the inhibition of enzyme activity caused by sodium orthovanadate has been shown to be irreversible. The cryptococcal ectoenzyme is also inhibited by Zn2+ and inorganic phosphate, the final product of reactions catalyzed by phosphatases. The ectophosphatase from C. neoformans efficiently releases phosphate groups from different phosphorylated amino acids, giving a higher rate of phosphate removal when phosphothreonine is used as a substrate. Yeast cells with irreversibly inhibited ectophosphatases are less capable of adhering to animal epithelial cells than fungi fully expressing enzyme activity, suggesting that ectoenzyme expression can contribute to the pathogenesis of C. neoformans.     

Synthesis, stability and reactivity of palladium(0) olefin complexes bearing labile or hemi-labile ancillary ligands and electron-poor olefins

An overview of the general features of electron-poor olefin stabilized palladium(0) complexes bearing labile and hemi-labile ancillary ligands is presented. In particular, we have summarized the synthetic methodologies, the ligands commonly used, and the characterization of such complexes. The behavior of these species in solution is also described with particular attention to their fluxional rearrangements and reactivity. Thus, olefin exchange reactions are described and a comprehensive order of coordinative capability of the most widely used electron-poor alkenes is presented. The reactions of the title complexes dealing with olefin isomerization, oxidative addition, and formation of palladacyclopentadiene derivatives are eventually reported together with their main structural characteristics.     

Recovery of the pubic symphysis on primiparous young and multiparous senescent mice at postpartum

It has been observed that parturition has a significant effect on female skeletal architecture and that age alters musculoskeletal tissues and their functions. We therefore hypothesized that multiparity affects the recovery of the pubic symphysis in senescent mice at postpartum and the morphology of the interpubic tissues. The pubic symphysis of primiparous young, virgin senescent (VS) and multiparous senescent (MS) Swiss mice was examined by light microscopy, transmission electron microscopy, morphometric analysis and immunohistochemistry. The mouse pubic symphysis was remodeled during the first pregnancy: the cellular phenotype and morphology changed to ensure a structurally safe birth canal, followed by recovery of the interpubic articulation after birth. The morphology of the pubic symphysis in the VS group was maintained in a state similar to that observed in virgin young mice. In contrast, MS mice exhibited an interpubic ligament characterized by extended fibrocyte-like cells, an opened interpubic articulation gap, compacted and thin collagen fibrils and scarce galectin-3-positive cells. Thus, we found that the cellular and extracellular characteristics of the pubic symphysis were altered by multiparity in senescent mice. These particular tissue characteristics of the MS group might be associated with an impaired recovery process at postpartum. Thus, a better understanding of the alterations that occur in the birth canal, including the pubic symphysis, due to multiparity in reproductively aged mice may contribute to our comprehension of the biological mechanisms that modify the skeleton and pelvic ligaments and even play a role in the murine model of pelvic organ prolapse.     

Feeding ecology and prey preferences of a piscivorous fish in the Lagoa do Peixe National Park, a Biosphere Reserve in Southern Brazil

We investigated the diet, feeding strategy, size-related dietary shifts and prey preferences of South American Hoplias aff. malabaricus in an internationally recognized but poorly investigated Biosphere Reserve in southern Brazil. Fish were caught between April 2008 and March 2009 using a variety of fishing gear. The analysis of 113 individuals revealed a diet essentially composed of fish (16 species), particularly characid species (9). The diet became more diverse and contained larger fish prey with increasing predator size. Feeding strategy analysis revealed a clear specialization towards the consumption of fish. However, individuals did not prey upon particular prey species, instead opportunistically consuming many different fish species, which could be a strategy to avoid intraspecific competition. Characid species were the most important prey, followed by poecillids. A multi-gear sampling of the ichthyofauna revealed that these prey species were the most abundant (Characidae: 61.3%, Poeciliidae 18.8%) of the 14 fish families occurring at the study site, suggesting that the predator exploits the most abundant fish resources available rather than the rarer fish prey. These findings suggest that potential top-down controls exerted by H. aff. malabaricus in this system follow specific food web pathways that seem to be mediated by the abundance of prey resources.     

Genome sequences of the ethanol-tolerant Lactobacillus vini strains LMG 23202T and JP7.8.9

We report on the genome sequences of Lactobacillus vini type strain LMG 23202(T) (DSM 20605) (isolated from fermenting grape musts in Spain) and the industrial strain L. vini JP7.8.9 (isolated from a bioethanol plant in northeast Brazil). All contigs were assembled using gsAssembler, and genes were predicted and annotated using Rapid Annotation using Subsystem Technology (RAST). The identified genome sequence of LMG 23202(T) had 2.201.333 bp, 37.6% G+C, and 1,833 genes, whereas the identified genome sequence of JP7.8.9 had 2.301.037 bp, 37.8% G+C, and 1,739 genes. The gene repertoire of the species L. vini offers promising opportunities for biotechnological applications.     

Structuring of bacterioplankton diversity in a large tropical bay

Structuring of bacterioplanktonic populations and factors that determine the structuring of specific niche partitions have been demonstrated only for a limited number of colder water environments. In order to better understand the physical chemical and biological parameters that may influence bacterioplankton diversity and abundance, we examined their productivity, abundance and diversity in the second largest Brazilian tropical bay (Guanabara Bay, GB), as well as seawater physical chemical and biological parameters of GB. The inner bay location with higher nutrient input favored higher microbial (including vibrio) growth. Metagenomic analysis revealed a predominance of Gammaproteobacteria in this location, while GB locations with lower nutrient concentration favored Alphaproteobacteria and Flavobacteria. According to the subsystems (SEED) functional analysis, GB has a distinctive metabolic signature, comprising a higher number of sequences in the metabolism of phosphorus and aromatic compounds and a lower number of sequences in the photosynthesis subsystem. The apparent phosphorus limitation appears to influence the GB metagenomic signature of the three locations. Phosphorus is also one of the main factors determining changes in the abundance of planktonic vibrios, suggesting that nutrient limitation can be observed at community (metagenomic) and population levels (total prokaryote and vibrio counts).     

Separation of clavulanic acid from fermented broth of amino acids by an aqueous two-phase system and ion-exchange adsorption

The clavulanic acid is a substance which inhibits the β-lactamases used with penicillins for therapeutic treatment. After the fermentation, by-products of low molecular weight such as amino acids lysine, histidine, proline and tyrosine are present in the fermented broth. To remove these impurities the techniques of extraction by an aqueous two-phase system of 17% polyethylene glycol molecular weight 600 and 15% potassium phosphate were used for a partial purification. A subsequent ion-exchange adsorption was used for the recuperation of the clavulanic acid of the top phase and purification getting a concentration factor of 2 and purification of 100% in relation to the amino acids lysine, histidine, proline and tyrosine.     

Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data

The health of the coral reefs of the Abrolhos Bank (Southwestern Atlantic) was characterized with a holistic approach using measurements of four ecosystem components: (i) inorganic and organic nutrient concentrations, [1] fish biomass, [1] macroalgal and coral cover and (iv) microbial community composition and abundance. The possible benefits of protection from fishing were particularly evaluated by comparing sites with varying levels of protection. Two reefs within the well-enforced no-take area of the National Marine Park of Abrolhos (Parcel dos Abrolhos and California) were compared with two unprotected coastal reefs (Sebasti?o Gomes and Pedra de Leste) and one legally protected but poorly enforced coastal reef (the "paper park" of Timbebas Reef). The fish biomass was lower and the fleshy macroalgal cover was higher in the unprotected reefs compared with the protected areas. The unprotected and protected reefs had similar seawater chemistry. Lower vibrio CFU counts were observed in the fully protected area of California Reef. Metagenome analysis showed that the unprotected reefs had a higher abundance of archaeal and viral sequences and more bacterial pathogens, while the protected reefs had a higher abundance of genes related to photosynthesis. Similar to other reef systems in the world, there was evidence that reductions in the biomass of herbivorous fishes and the consequent increase in macroalgal cover in the Abrolhos Bank may be affecting microbial diversity and abundance. Through the integration of different types of ecological data, the present study showed that protection from fishing may lead to greater reef health. The data presented herein suggest that protected coral reefs have higher microbial diversity, with the most degraded reef (Sebasti?o Gomes) showing a marked reduction in microbial species richness. It is concluded that ecological conditions in unprotected reefs may promote the growth and rapid evolution of opportunistic microbial pathogens.