Genomic exploration of the hemiascomycetous yeasts: 13. Pichia angusta

As part of a comparative genomics project on 13 hemiascomycetous yeasts, the Pichia angusta type strain was studied using a partial random sequencing strategy. With coverage of 0.5 genome equivalents, about 2500 novel protein-coding genes were identified, probably corresponding to more than half of the P. angusta protein-coding genes, 6% of which do not have homologs in Saccharomyces cerevisiae. Some of them contain one or two introns, on average three times shorter than those in S. cerevisiae. We also identified 28 tRNA genes, a few retrotransposons similar to Ty5 of S. cerevisiae, solo long terminal repeats, the whole ribosomal DNA cluster, and segments of mitochondrial DNA. The P. angusta sequences were deposited in EMBL under the accession numbers AL430961 to AL436044.     

Nitric oxide inhibits tyrosine hydroxylase of rat median eminence

Tyrosine hydroxylase (TH) is the rate-limiting enzyme in the biosynthesis of catecholamines. In a previous report we found that intracerebroventricular administration of nitric oxide (NO) generator sodium nitroprusside (SNP) to conscious male rats inhibited dose-dependently the TH activity of the median eminence (ME). In the present study we have tested the in vitro effects of SNP on TH activity, its possible mediator and action mechanism. Exposure of the ME TH to SNP (50, 100 and 500 microM) caused concentration-dependent inhibition of its enzyme activity. Addition of; reduced hemoglobin Hb (10 microM), a NO scavenger, superoxide dismutase SOD (1000 units/ml), a superoxide scavenger enzyme, or uric acid UA (300 microM), a peroxynitrite scavenger, did not affect the enzyme activity by themselves, but prevented the inhibitory effect of SNP 500 microM. However, the presence of methylene blue MB (100 microM), a guanylyl cyclase inhibitor, did not alter either basal enzyme activity or the inhibitory action of SNP 500 microM. These results suggest that this action of SNP on TH of the ME would be mediated by peroxynitrite generated by the reaction of NO with superoxide.     

The T29C polymorphism of the transforming growth factor-β1 (TGF-β1) gene is associated with genetic susceptibility to acute coronary syndrome in Mexican patients

Inflammation plays an essential role in the development and progression of atherosclerotic lesions, and plaque disruption. The TGF-β1 plays an important role in the anti-inflammatory process. The aim of the present study was to evaluate the role of TGF-β1 gene polymorphisms as susceptibility markers for acute coronary syndrome (ACS). Two polymorphisms (TGF-β -509T>C and TGF-β T29C) of the TGF-β gene were analyzed by 5' exonuclease TaqMan genotyping assays in a group of 426 patients with coronary acute syndrome and 551 healthy unrelated controls. A significant difference was observed in the distribution of TGF-β T29C polymorphism between ACS patients and healthy controls (P<10(-3)). According to the co-dominant model, individuals with the TGF-β 29 TT genotype have a 2.5-fold increased risk of developing ACS (P<10(-3)). Multiple logistic analysis showed that the largest risk factor for developing ACS was given by smoking habit, diabetes, hypertension, dyslipidemia, and the TGF-β1 29 TT genotype. The analysis of linkage disequilibrium showed one haplotype (TT) with increased frequency and one haplotype (CC) with decreased frequency in ACS patients when compared to healthy controls. The results suggest that TGF-β1 T29C gene polymorphism could be involved in the risk of developing ACS in Mexican individuals.     

Fluorescence resonance energy transfer-based technologies in the study of protein-protein interactions at the cell surface

Understanding of the molecular mechanisms of protein-protein interactions (PPIs) at the cell surface of living cells is fundamental to comprehend the functional meaning of a large number of cellular processes. Here we discuss how new methodological strategies derived from non-invasive fluorescence-based approaches (i.e. fluorescence resonance energy transfer, FRET) have been successfully developed to characterize plasma membrane PPIs. Importantly, these technologies alone - or in concert with complementary methods (i.e. SNAP-tag/TR-FRET, TIRF/FRET) - can become extremely powerful approaches for visualizing cell surface PPIs, even between more than two proteins and also in native tissues. Interestingly, these methods would also be relevant in drug discovery in order to develop new high-throughput screening approaches or to identify new therapeutic targets. Accordingly, herein we provide a thorough assessment on all biotechnological aspects, including strengths and weaknesses, of these fluorescence-based methodologies when applied in the study of PPIs occurring at the cell surface of living cells.     

Polyunsaturated fatty acids regulate Shiga toxin transport

Shiga toxin (Stx) is internalized by receptor-mediated endocytosis and transported retrogradely to the endoplasmic reticulum from where the enzymatically active part of the toxin is translocated to the cytosol. In this study, we have investigated the effect of polyunsaturated fatty acids (PUFA) on intoxication and retrograde transport of Stx. In HEp-2 cells, PUFA treatment inhibited Stx intoxication by a factor of 10. Moreover, both Stx internalization and endosome-to-Golgi transport were reduced by PUFA and these reductions can together explain the reduced toxicity. Also cholera toxin internalization was reduced by PUFA treatment. Finally, ricin and Pseudomonas exotoxin 1 cytotoxicity were not reduced by PUFA, demonstrating that PUFA do not cause a general block in retrograde transport to the endoplasmic reticulum. In conclusion, these results clearly demonstrate the importance of PUFA for Stx and cholera toxin trafficking.     

Multivariate and geometric morphometrics in the analysis of sexual dimorphism variation in Podarcis lizards

Podarcis bocagei and P. carbonelli are two closely related lacertid species, very similar morphologically and ecologically. We investigated sexual dimorphism patterns presented by both species in allopatry and in sympatry. Sexual size and shape dimorphism patterns were analyzed using both multivariate and geometric morphometric techniques. Multivariate morphometrics revealed a marked sexual dimorphism in both species--males being larger with more robust habitus and females presenting a longer trunk. General patterns of sexual size dimorphism are not modified in sympatry, although there is evidence for some morphological change in male head size. The application of geometric morphometrics offered a more detailed image of head shape and revealed that males present a more developed tympanic area than do females, while females have a more rounded head. Differences in the degree of sexual shape dimorphism were detected in sympatry, but no consistent patterns were observed. From the results of the study, and based on previous knowledge on the populations studied, we conclude that the morphological differences observed are probably not caused by exploitative competition between the species, but rather appear attributable to the modification of the relative influence of sexual and natural selection on both sexes.     

The efficiency of indicator groups for the conservation of amphibians in the Brazilian Atlantic Forest

The adequate selection of indicator groups of biodiversity is an important aspect of the systematic conservation planning. However, these assessments differ in the spatial scales, in the methods used and in the groups considered to accomplish this task, which generally produces contradictory results. The quantification of the spatial congruence between species richness and complementarity among different taxonomic groups is a fundamental step to identify potential indicator groups. Using a constructive approach, the main purposes of this study were to evaluate the performance and efficiency of eight potential indicator groups representing amphibian diversity in the Brazilian Atlantic Forest. Data on the geographic range of amphibian species that occur in the Brazilian Atlantic Forest were overlapped to the full geographic extent of the biome, which was divided into a regular equal‐area grid. Optimization routines based on the concept of complementarily were applied to verify the performance of each indicator group selected in relation to the representativeness of the amphibians in the Brazilian Atlantic Forest as a whole, which were solved by the algorithm “simulated annealing,” through the use of the software MARXAN. Some indicator groups were substantially more effective than others in regard to the representation of the taxonomic groups assessed, which was confirmed by the high significance of the data (F = 312.76; P < 0.01). Leiuperidae was considered as the best indicator group among the families analyzed, as it showed a good performance, representing 71% of amphibian species in the Brazilian Atlantic Forest (i.e., 290 species), which may be associated with the diffuse geographic distribution of their species. In this sense, this study promotes understanding of how the diversity standards of amphibians can be informative for systematic conservation planning on a regional scale.     

Phylogeographic and environmental correlates support the cryptic function of the zigzag pattern in a European viper

The predator–prey relationship is a strong agent of natural selection on phenotype, and two evolutionary strategies derived from this antagonistic interaction are crypsis and aposematism. Although usually considered as opposites, both strategies could be ascribed to the dark zigzag pattern of European vipers (Vipera). Experiments using plasticine models demonstrated its aposematic role, and no evidence had been found regarding a possible cryptic function. We examined the possibility of a cryptic role by measuring five characters related to the zigzag size and shape in 465 Vipera latastei specimens from the Iberian Peninsula to assess geographic variation in these characters. This species shows genetic substructuring resulting from population isolation and occurs in strong environmental gradients, which allows testing whether historic and/or environmental (adaptive) factors explain this variation. Spatial interpolation of zigzag characters identified two major Iberian groups: the Western and the Eastern. The Western group was characterised by a larger zigzag extension and higher number of dorsal marks; specimens within this group were in granitic grounds and areas with higher rainfall and lower solar radiation than those of the Eastern group. The correlation of the zigzag shape and size with lithology and climatic variables suggested that dorsal pattern variation is driven by: (1) its cryptic role, as detectability might be influenced by the degree of contrast between the target and background lithology, or (2) its thermal role, as the larger zigzag may allow for faster heating in Western Iberian regions with limited thermal opportunities. A log-linear analysis using dorsal pattern groups, genetic lineages and lithological classes, showed significant interactions among the three variables. These results suggest that dorsal pattern variation of V. latastei resulted from genetic (i.e. historic) as well as environmental (i.e. adaptive) factors, first by population isolation in geographic refuges and further by local adaptation to particular environments.     

The role of plasma IDO activity as a diagnostic marker of patients with colorectal cancer

High levels of indoleamine 2,3-dioxygenase (IDO) are involved in tumour escape mechanisms. The aim of this study is the evaluation of l-kynurenine of plasma as marker of diagnostic and prognostic in patients with colorectal cancer. The study included 78 patients with colorectal cancer, of whom 15 % were in stage I/II, 30 % in stage III, and 55 % in stage IV, and was compared with a control group of 70 healthy subjects. The receiver operating characteristic (ROC) curve analysis showed an area under the curve of 0.917, with a specificity of 100 % and with a sensitivity to detect cancer of the colon of 85.2 %, taking 1.83 μM as a cut-off point. The overall survival analysis also indicated that patients with low levels of l-kynurenine in plasma increased survival rate after 45 months of follow-up (P = 0.032). These results show that the plasma levels of l-kynurenine could be a good biomarker to differentiate individuals with colorectal cancer from healthy individuals.     

Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes

Background  

Chaperonin proteins are well known for the critical role they play in protein folding and in disease. However, the recent identification of three diverged chaperonin paralogs associated with the human Bardet-Biedl and McKusick-Kaufman Syndromes (BBS and MKKS, respectively) indicates that the eukaryotic chaperonin-gene family is larger and more differentiated than previously thought. The availability of complete genome sequences makes possible a definitive characterization of the complete set of chaperonin sequences in human and other species.