Crystallization and resolution of the lipoxygenase of Pseudomonas aeruginosa 42A2 and phylogenetic study of the subfamilies of the lipoxygenases

Lipoxygenases are non-heme iron enzymes essential in eukaryotes, where they catalyze the formation of the fatty acid hydroperoxides that are required by a large diversity of biological and pathological processes. In prokaryotes, most of them totally lacking in polyunsaturated fatty acids, the possible biological roles oflipoxygenases have remained obscure. In this study, it is reported the crystallization of a lipoxygenase of Pseudomonas aeruginosa (Pa_LOX), the first from a prokaryote. High resolution data has been acquired which is expected to yield structural clues to the questions adressed. Besides, a preliminar phylogenetic analysis using 14 sequences has confirmed the existence of this subfamily of bacterial lipoxygenases, on one side, and a greater diversity than in the corresponding eukaryotic ones, on the other. Finally, an evolutionary study of bacteriallipoxygenases on the same set of lipoxygenases, show a selection pressure of a basically purifying or neutral character except for a single aminoacid, which would have been selected after a positive selection event.

Modeling the Emergence of Social Structure from a Phylogenetic Point of View

Based on provious (Hemelrijk 1998; Puga-González, Hildenbrant & Hemelrijk 2009), we have developed an agent-based model and software, called A-KinGDom, which allows us to simulate the emergence of the social structure in a group of non-human primates. The model includes dominance and affiliative interactions and incorporate s two main innovations (preliminary dominance interactions and a kinship factor), which allow us to define four different attack and affiliative strategies. In accordance with these strategies, we compared the data obtained under four simulation conditions with the results obtained in a provious study (Dolado & Beltran 2012) involving empirical observations of a captive group of mangabeys (Cercocebus torquatus)

On the preservation of combinatorial types for maps on trees

We study the preservation of the periodic orbits of an A-monotone tree map f:T→T in the class of all tree maps g:S→S having a cycle with the same pattern as A. We prove that there is a period-preserving injective map from the set of (almost all) periodic orbits of ƒ into the set of periodic orbits of each map in the class. Moreover, the relative positions of the corresponding orbits in the trees T and S (which need not be homeomorphic) are essentially preserved

Stratification of the severity of critically ill patients with classification trees

Background: Development of three classification trees (CT) based on the CART (Classification and Regression Trees), CHAID (Chi-Square Automatic Interaction Detection) and C4.5 methodologies for the calculation of probability of hospital mortality; the comparison of the results with the APACHE II, SAPS II and MPM II-24 scores, and with a model based on multiple logistic regression (LR). Methods: Retrospective study of 2864 patients. Random partition (70:30) into a Development Set (DS) n = 1808 and Validation Set (VS) n = 808. Their properties of discrimination are compared with the ROC curve (AUC CI 95%), Percent of correct classification (PCC CI 95%); and the calibration with the Calibration Curve and the Standardized Mortality Ratio (SMR CI 95%). Results: CTs are produced with a different selection of variables and decision rules: CART (5 variables and 8 decision rules), CHAID (7 variables and 15 rules) and C4.5 (6 variables and 10 rules). The common variables were: inotropic therapy, Glasgow, age, (A-a)O2 gradient and antecedent of chronic illness. In VS: all the models achieved acceptable discrimination with AUC above 0.7. CT: CART (0.75(0.71-0.81)), CHAID (0.76(0.72-0.79)) and C4.5 (0.76(0.73-0.80)). PCC: CART (72(69- 75)), CHAID (72(69-75)) and C4.5 (76(73-79)). Calibration (SMR) better in the CT: CART (1.04(0.95-1.31)), CHAID (1.06(0.97-1.15) and C4.5 (1.08(0.98-1.16)). Conclusion: With different methodologies of CTs, trees are generated with different selection of variables and decision rules. The CTs are easy to interpret, and they stratify the risk of hospital mortality. The CTs should be taken into account for the classification of the prognosis of critically ill patients.

The UlaG protein familly defines novel structural and functional motifs grafted on an ancient RNase fold

Background: Bacterial populations are highly successful at colonizing new habitats and adapting to changing environmental conditions, partly due to their capacity to evolve novel virulence and metabolic pathways in response to stress conditions and to shuffle them by horizontal gene transfer (HGT). A common theme in the evolution of new functions consists of gene duplication followed by functional divergence. UlaG, a unique manganese-dependent metallo-b-lactamase (MBL) enzyme involved in L-ascorbate metabolism by commensal and symbiotic enterobacteria, provides a model for the study of the emergence of new catalytic activities from the modification of an ancient fold. Furthermore, UlaG is the founding member of the so-called UlaG-like (UlaGL) protein family, a recently established and poorly characterized family comprising divalent (and perhaps trivalent)metal-binding MBLs that catalyze transformations on phosphorylated sugars and nucleotides. Results: Here we combined protein structure-guided and sequence-only molecular phylogenetic analyses to dissect the molecular evolution of UlaG and to study its phylogenomic distribution, its relatedness with present-day UlaGL protein sequences and functional conservation. Phylogenetic analyses indicate that UlaGL sequences are present in Bacteria and Archaea, with bona fide orthologs found mainly in mammalian and plant-associated Gramnegative and Gram-positive bacteria. The incongruence between the UlaGL tree and known species trees indicates exchange by HGT and suggests that the UlaGL-encoding genes provided a growth advantage under changing conditions. Our search for more distantly related protein sequences aided by structural homology has uncovered that UlaGL sequences have a common evolutionary origin with present-day RNA processing and metabolizing MBL enzymes widespread in Bacteria, Archaea, and Eukarya. This observation suggests an ancient origin for the UlaGL family within the broader trunk of the MBL superfamily by duplication, neofunctionalization and fixation. Conclusions: Our results suggest that the forerunner of UlaG was present as an RNA metabolizing enzyme in the last common ancestor, and that the modern descendants of that ancestral gene have a wide phylogenetic distribution and functional roles. We propose that the UlaGL family evolved new metabolic roles among bacterial and possibly archeal phyla in the setting of a close association with metazoans, such as in the mammalian gastrointestinal tract or in animal and plant pathogens, as well as in environmental settings. Accordingly, the major evolutionary forces shaping the UlaGL family include vertical inheritance and lineage-specific duplication and acquisition of novel metabolic functions, followed by HGT and numerous lineage-specific gene loss events.

Spatiotemporal variability in radial growth of trees in the Central Pyrenees: climatic and site influences.

To understand how tree growth has responded to recent climate warming, an understanding of the tree-climate-site complex is necessary. To achieve this, radial growth variability among 204 trees established before 1850 was studied in relation to both climatic and site factors. Seventeen forest stands were sampled in the Spanish Central Pyrenees. Three species were studied: Pinus uncinata, Abies alba, and Pinus sylvestris. For each tree, a ring-width residual chronology was built. All trees cross-dated well, indicating a common influence of the regional climate. For the 1952-1993 period, the radial growth of all species, especially P. uncinata, was positively correlated with warm Novembers during the year before ring formation and warm Mays of the year the annual ring formed. Differences in species-stand elevation modulated the growth-climate associations. Radial growth in P. uncinata at high elevation sites was reduced when May temperatures were colder and May precipitation more abundant. In the 20th century, two contrasting periods in radial growth were observed: one (1900-1949) with low frequency of narrow and wide rings, low mean annual sensitivity, and low common growth variation; and another (1950-1994) with the reverse characteristics. The increased variability in radial growth since the 1950s was observed for all species and sites, which suggests a climatic cause. The low shared variance among tree chronologies during the first half of the 20th century may result from a"relaxation" of the elevation gradient, allowing local site conditions to dominate macroclimatic influence. These temporal trends may be related to the recently reported increase of climatic variability and warmer conditions. This study emphasizes the need to carefully assess the relationships between radial growth and site conditions along ecological gradients to improve dendroclimatic reconstructions.

Phylogenetic relationships of the newly discovered sexual state of Talaromyces flavovirens, comb. nov.

Typical Talaromyces ascomata were observed on dry Quercus suber leaf litter amongst the characteristic synnemata of Penicillium aureocephalum, and they appear to represent the sexual state of the latter species. The species is a synonym of the older Lasioderma flavovirens, and we propose the new combination Talaromyces flavovirens. Lectotype and epitype specimens are designated for this name. The defining characters of the asexual state include yellow, short-stalked, mycetozoan-like synnemata with an unusual, almost closed terminal head of penicillate conidiophores intermixed with sinuous hyphae, and dark green conidia. Ascomata could not be induced in culture, but PCR amplifications of mating-type genes indicate the species is heterothallic. In nature, ascocarp initials appear to be antheridia coiled around clavate ascogonia, similar to those of T. flavus, and the thick-walled, spiny ascospores are also similar to those of T. flavus. ITS barcodes and β-tubulin sequences place T. flavovirens in a clade with T. apiculatus, T. flavus, T. funiculosus, T. galapagensis, T. pinophilus, T. macrosporus, and seven other species.