A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.      

Microbiological assay of carnitine

A method for carnitine assay has been devised by the growth response of the yeast Torulopsis bovina. As little as 0.0005 μg/ml of l (?) carnitine could be assayed by this method. Free carnitine was assayed in several biological materials together with the carnitine present as soluble esters. Lipid-bound carnitine was precipitated by trichloroacetic acid and assayed independently. Average recovery of added carnitine in the free-carnitine assays was 95%. In lipid-bound carnitine assays, recovery of added carnitine ranged from 76.2 to 95%. Treatment of materials for the microbiological assays included separation in ion-exchange resins and alkaline or acid hydrolyses. Materials containing negligible amounts of carnitine esters could be assayed directly without further treatment.     

Nod1 participates in the innate immune response to Pseudomonas aeruginosa

The mammalian innate immune system recognizes pathogen-associated molecular patterns through pathogen recognition receptors. Nod1 has been described recently as a cytosolic receptor that detects specifically diaminopimelate-containing muropeptides from Gram-negative bacteria peptidoglycan. In the present study we investigated the potential role of Nod1 in the innate immune response against the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that Nod1 detects the P. aeruginosa peptidoglycan leading to NF-kappaB activation and that this activity is diminished in epithelial cells expressing a dominant-negative Nod1 construct or in mouse embryonic fibroblasts from Nod1 knock-out mice infected with P. aeruginosa. Finally, we demonstrate that the cytokine secretion kinetics and bacterial killing are altered in Nod1-deficient cells infected with P. aeruginosa in the early stages of infection.     

Biology,ecology and biogeography of the South American silver croaker,an important Neotropical fish species in South America

The South American silver croaker is a popular fish that has recently received substantial attention from scientists, mainly due to its importance as source of animal protein and as a key fisheries species. However, little is known about the conditions that explain its historical and current spatial distribution, both in its native habitat and where it is a successful invasive species. The aim of the present study was to explore the ecological information available for this species, to then critically examine ecological theories related to the conditions underpinning its success. To this end, an exhaustive literature search was conducted with the immediate aim of investigating whether the success of South American silver croaker was driven by species-climate or species–human interactions. The non-native populations were found to occupy climate niche spaces different from those observed in their native ranges. In addition, it was clear that humans played a role in facilitating the large-scale dispersion of silver croaker, and assisted as agents of impact driving the observed current and, probably, the future spatial distribution, which we can predict from our data and from the pattern of propagule pressure. Overall, the current biogeography of this species illustrates how the construction of dams, along with the introduction and stocking of non-native species, overfishing and other human activities can alter fish populations and assemblages. Such processes can reduce native species, increase the abundance and distribution of invasive species, as well as cause changes in life-history traits and genetic variability, all with long-term socioeconomic consequences.     

Widespread and ancient distribution of a noncanonical genetic code in diplomonads

Recently, a group of diplomonads has been found to use a genetic code in which TAA and TAG encode glutamine rather than termination. To survey the distribution of this characteristic in diplomonads, we sought to identify TAA and TAG codons at positions where glutamine is expected in genes for alpha-tubulin, elongation factor-1 alpha, and the gamma subunit of eukaryotic translation initiation factor-2. These sequences show that the variant genetic code is utilized by almost all diplomonads, with the genus Giardia alone using the universal genetic code. Comparative phylogenetic analysis reveals that the switch to this genetic code took place very early in the evolution of diplomonads and was likely a single event. Termination signals and downstream untranslated regions were also cloned from three Hexamita genes. In all three of these genes, the predicted TGA termination codon was found at the expected position. Interestingly, the untranslated regions of these genes are high in AT. This is incongruent with the coding regions, which are comparatively GC-rich.      

Synthesis, in vitro and in vivo biological evaluation,COX-1/2 inhibition and molecular docking study of indole-N-acylhydrazone derivatives

The objective of this work was to obtain and evaluate anti-inflammatory in vitro, in vivo and in silico potential of novel indole-N-acylhydrazone derivatives. In total, 10 new compounds (3a–j) were synthesized in satisfactory yields, through a condensation reaction in a single synthesis step. In the lymphoproliferation assay, using mice splenocytes, 3a and 3b showed inhibition of lymphocyte proliferation of 62.7% (±3.5) and 50.7% (±2), respectively, while dexamethasone presented an inhibition of 74.6% (±2.4). Moreover, compound 3b induced higher Th2 cytokines production in mice splenocytes cultures. The results for COX inhibition assays showed that compound 3b is a selective COX-2 inhibitor, but with less potency when compared to celecoxib, and compound 3a not presented selectivity towards COX-2. The molecular docking results suggest compounds 3a and 3b interact with the active site of COX-2 in similar conformations, but not with the active site of COX-1, and this may be the main reason to the COX-2 selectivity of compound 3b. In vivo carrageenan-induced paw edema assays were adopted for the confirmation of the anti-inflammatory activity. Compound 3b showed better results in suppressing edema at all tested concentrations and was able to induce an edema inhibition of 100% after 5?h of carrageenan injection at the 30?mg?kg^?1 dosage, corroborating with the COX inhibition and lymphoproliferation results. I addition to our experimental results, in silico analysis suggest that compounds 3a and 3b present a well-balanced profile between pharmacodynamics and pharmacokinetics. Thus, our preliminary results revealed the potentiality of a new COX-2 selective derivative in the modulation of the inflammatory process.     

Trophic ecology and persistence of invasive silver carp Hypophthalmichthys molitrix in an oligotrophic South African impoundment

The alien invasive silver carp Hypophthalmichthys molitrix established a self-sustaining feral population in an oligotrophic impoundment, Flag Boshielo Dam, in South Africa. The ability of this population to persist in a dam with low algal biomass (median annual suspended chlorophyll a = 0.08 µg l^?1), and limited access to rivers considered large enough for successful spawning, has implications for their invasive potential in other systems. Stomach content and stable isotope analysis were used to assess the trophic ecology of H. molitrix, which was then compared with indigenous Mozambique tilapia Oreochromis mossambicus, on a seasonal basis during 2011. Hypophthalmichthys molitrix are generalist filter feeders, with a diet consisting primarily of sediment, vegetative detritus, dinoflagellates and diatoms. The dominance of sediments in their stomachs suggests occasional benthic scavenging. However, H. molitrix occupied a higher trophic level (TL = 2.8) than expected, suggesting that this population subsidised their diet with an unidentified dietary constituent, characterised by enriched nitrogen values. Although the stomach contents indicated dietary overlap between H. molitrix and O. mossambicus, stable isotopes revealed fine-scale resource partitioning, despite both species occupying the same trophic level. Nonetheless, the persistence of this feral H. molitrix population in an oligotrophic impoundment highlights their phenotypic plasticity.     

Extracting information from imaging cytometry: a review

The extraction of statistically meaningful quantitative information from microscopy images is increasingly important for modern biological research. Obtaining accurate, quantitative information from biological specimens, however, is a complex process that requires optimization of several parameters. One must consider the number of probes, fluorescent channels required, type of plate to be used, number of fields to be acquired and optimal resolution for image acquisition. The extraction of information from images is dependent on and can be aided greatly by careful consideration of the factors involved in the image acquisition process. I summarize here the general principles behind the imaging and software technology that is used to quantify images and highlight particular issues of concern for critically applying image quantitation techniques for research.     

A Stochastic Dynamic Methodology (StDM) to simulate the effects of fire on vegetation and bird communities in Pinus pinaster stands

Worldwide forests have been impacted by broad-scale anthropogenic pressures, such as fire and logging, leading to the disruption of the structure and functioning of these systems. The present paper examined the applicability of a holistic Stochastic Dynamic Methodology (StDM) in predicting the tendencies of passerine bird communities in maritime pine (Pinus pinaster) stands as a response to the changes induced by fire occurrence. The StDM is a sequential modelling process developed in order to predict the ecological status of changed ecosystems, from which management strategies can be designed. The case of the pine stands of central Portugal was used to test the StDM performance in the scope of the wildfire problems. The datasets used in the dynamic model construction included the main gradients of environmental and biological characteristics of the studied maritime pine stands over space and time. The ecological integrity of the pine stands can be partly assessed by the observation of the occurrence of passerine indicators. The dynamic model developed was preceded by a conventional multivariate statistical procedure performed to discriminate the significant relationships between conceptually isolated key-components of the studied ecosystems. The final model provided some basis to analyse the responses of selected passerine indicators to fire scenarios that characterize the region. In this context, the simulation results are encouraging since they seem to demonstrate the StDM reliability in capturing the passerine community dynamics by predicting the behavioural pattern of indicators roughly associated with their structural and functional composition and habitat main characteristics.