Performance of a new invariants method on homogeneous and nonhomogeneous quartet trees

An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several researchers (the initial idea due to Lake [1987] and Cavender and Felsenstein [1987]). However, the efficiency of methods based on invariants is still in doubt (Huelsenbeck 1995; Jin and Nei 1990). Probably because these methods only used few generators of the set of phylogenetic invariants. The method studied in this paper was first introduced in Casanellas et al. (2005) and it is the first method based on invariants that uses the "whole" set of generators for DNA data. The simulation studies performed in this paper prove that it is a very competitive and highly efficient phylogenetic reconstruction method, especially for nonhomogeneous models on phylogenetic trees.     

SPOC: A widely distributed domain associated with cancer,apoptosis and transcription

Background  

The Split ends (Spen) family are large proteins characterised by N-terminal RNA recognition motifs (RRMs) and a conserved SPOC (Spen paralog and ortholog C-terminal) domain. The aim of this study is to characterize the family at the sequence level.     

Ligninolytic activity of tropical rainforest basidiomycetes

A total of 116 strains of Brazilian tropical rainforest basidiomycetes were evaluated in terms of their ability to oxidize the dye rhemazol brilliant blue R (RBBR) and guaiacol. Laccase and peroxidase activities were detected by the drop test using solutions of α-naphthol and pyrogallol, respectively. RBBR and guaiacol oxidation occurred in 96.6 and 87.1% of the strains tested, respectively. One hundred strains oxidized both substrates. In the drop test, most strains presented laccase (96.6%) and peroxidase (92.2%) activity. The quick screening method used here can be useful to identify ligninolytic fungal strains to be used in various biotechnological applications. This revised version was published online in November 2006 with corrections to the Cover Date.     

Canopy height variation and environmental heterogeneity in the tropical dry forests of coastal Oaxaca,Mexico

Despite its importance for carbon storage and other ecosystem functions, the variation in vegetation canopy height is not yet well understood. We examined the relationship between this community attribute and environmental heterogeneity in a tropical dry forest of southern Mexico. We sampled vegetation in 15 sites along a 100‐km coastal stretch of Oaxaca State, and measured the heights of all woody plants (excluding lianas). The majority of the ca. 4000 individuals recorded concentrated in the 4–8 m height range. We defined three plant sets to describe overall community canopy height at each site: a set including all plants, a set made up by the tallest plants representing 10 percent of all individuals, and a set comprising the 10 tallest plants. For each site we computed maximum height and the mean and median heights of the three sets. Significant collinearity was observed between the seven resulting height variables, but null distributions constructed through bootstrap revealed their different behaviors as functions of species richness and density of individuals. Through linear modeling and a model selection procedure, we identified 21 models that best described the variation in canopy height variables. These models pointed out to soil (measured as PC1 of a principal component analysis performed on 10 soil variables), water stress, and elevation as the main drivers of canopy height variation in the region. In the event of increasing water stress resulting from global climate change, the studied tropical dry forests could become shorter and thus decrease their carbon storage potential.     

Chronic toxicity of methylparathion to the rotifer Brachionus calyciflorus fed on Nannochloris oculata and Chlorella pyrenoidosa

The effect of sublethal levels of methylparathion (0, 1, 3, 5, 7 mg l^–1) on the freshwater rotifer, Brachionus calyciflorus, during their entire life cycle was studied. Rotifers were fed on two species of unicellular algae: Nannochloris oculata and Chlorella pyrenoidosa; both algal concentrations were 5 × 10⁵ cell ml^–1.The parameters used to determine the toxicity of this compound were survival, fecundity, net reproductive rate (R)_o, generation time (T), intrinsic rate of natural increase (r), reproductive value (V _x/V_o) and life expectancy at hatching (eo). All the demographic parameters studied were affected by methyl-parathion exposure on rotifers fed on both species of algae, but the toxic effect was larger when animals were fed on Chlorella pyrenoidosa; in this case, animals showed a decreased in fertility and also a delayed first reproduction. Sublethal methylparathion levels produced a reduction in most of the parameters selected, especially after exposure to 7 mg l^–1, where the animals died before reproducing.     

Antimicrobial resistance and class I integrons in Salmonella enterica isolates from wild boars and Bísaro pigs

The antibiotic resistance phenotype and genotype and the integron type were characterized in 58 Salmonella enterica isolates recovered from Bísaro pigs and wild boars (20 S. Typhimurium, 17 S. Rissen, 14 S. Enteritidis and 7 S. Havana). Most S. Typhimurium isolates (15/20 of Bísaro pigs and wild boars) showed ampicillin, chloramphenicol, streptomycin, tetracycline, sulfonamide, and amoxicillin-clavulanic acid resistances. Of the 17 S. Rissen isolates of both origins, 13 were resistant to ampicillin, tetracycline and trimethoprim-sulfamethoxazole. Among the S. Enteritidis isolates of Bísaro pigs, eight were nalidixic acid-resistant and three were sulfonamide-resistant. The tet(A) or tet(G) genes were detected in most tetracycline-resistant isolates. The intI1 gene was identified in 72.5% of S. enterica isolates in which the conserved region 3' of class 1 integrons (qacEΔ1+sul1) was also amplified, whereas none had the intI2 gene. The dfrA12+orfF+aadA2 gene cassette arrangement was found in the variable region of class 1 integrons in 14 S. Rissen isolates. Fifteen S. Typhimurium isolates had two integrons with variable regions of 1000 and 1200 bp that harbored the aadA2 and blaPSE-1 gene cassettes, respectively. In these isolates the floR and tet(G) genes were also amplified, indicative of the genomic island 1 (SGI1). Salmonella Typhimurium and S. Rissen of animal origin frequently show a multi-antimicrobial resistant phenotype, which may have implications in public health.     

The calcium-binding C-terminal domain of Escherichia coli alpha-hemolysin is a major determinant in the surface-active properties of the protein

alpha-Hemolysin (HlyA) from Escherichia coli is a protein toxin (1024 amino acids) that targets eukaryotic cell membranes, causing loss of the permeability barrier. HlyA consists of two main regions, an N-terminal domain rich in amphipathic helices, and a C-terminal Ca(2+)-binding domain containing a Gly- and Asp-rich nonapeptide repeated in tandem 11-17 times. The latter is called the RTX domain and gives its name to the RTX protein family. It had been commonly assumed that membrane interaction occurred mainly if not exclusively through the amphipathic helix domain. However, we have cloned and expressed the C-terminal region of HlyA, containing the RTX domain plus a few stabilizing sequences, and found that it is a potent surface-active molecule. The isolated domain binds Ca(2+) with about the same affinity (apparent K(0.5) approximately 150 microM) as the parent protein HlyA, and Ca(2+) binding induces in turn a more compact folding with an increased proportion of beta-sheet structure. Both with and without Ca(2+) the C-terminal region of HlyA can interact with lipid monolayers spread at an air-water interface. However, the C-terminal domain by itself is devoid of membrane lytic properties. The present results can be interpreted in the light of our previous studies that involved in receptor binding a peptide in the C-terminal region of HlyA. We had also shown experimentally the distinction between reversible membrane adsorption and irreversible lytic insertion of the toxin. In this context, the present data allow us to propose that both major domains of HlyA are directly involved in membrane-toxin interaction, the nonapeptide repeat, calcium-binding RTX domain being responsible for the early stages of HlyA docking to the target membrane.     

Ripening in papaya fruit is altered by ACC oxidase cosuppression

Papaya (Carica papaya) is a very important crop in many tropical countries but it is highly susceptible to parasitic diseases, physiological disorders, mechanical damage and fruit overripening. Here we report a study on ACC oxidase cosuppression and its effects on papaya fruit ripening. Papaya ACC oxidase was isolated using PCR and embriogenic cells transformed by biolistic using the CaMV 35S promoter to drive the expression of the PCR fragment in sense orientation. Fifty transgenic lines were recovered and 20 of those were grown under field conditions. Southern analysis showed incorporation of the transgene in different copy numbers in the papaya genome. Fruits were evaluated in terms of texture (firmness), colour development, respiration and ethylene production. A sharp reduction in ethylene and CO2 production was detected, whereas softening and colour development of the peel were also altered. Overall, transgenic fruits showed a delay in ripening rate. A reduction in mRNA level for ACC oxidase in transgenic fruit was clearly detectable by northern blot. More studies are necessary before this technology can be used to extend the shelf life of papaya fruit.