Reproductive biology and species geographical distribution in the Melastomataceae: a survey based on New World taxa

Apomictic plants are less dependent on pollinator services and able to occupy more diverse habitats than sexual species. However, such assumptions are based on temperate species, and comparable evaluation for species-rich Neotropical taxa is lacking. In this context, the Melastomataceae is a predominantly Neotropical angiosperm family with many apomictic species, which is common in the Campos Rupestres, endemism-rich vegetation on rocky outcrops in central Brazil. In this study, the breeding system of some Campo Rupestre Melastomataceae was evaluated, and breeding system studies for New World species were surveyed to test the hypothesis that apomixis is associated with wide distributions, whilst sexual species have more restricted areas. The breeding systems of 20 Campo Rupestre Melastomataceae were studied using hand pollinations and pollen-tube growth analysis. In addition, breeding system information was compiled for 124 New World species of Melastomataceae with either wide (1000 km) or restricted distributions. Most (80 ) of the Campo Rupestre species studied were self-compatible. Self-incompatibility in Microlicia viminalis was associated with pollen-tube arrest in the style, as described for other Melastomataceae, but most self-incompatible species analysed showed pollen-tube growth to the ovary irrespective of pollination treatment. Apomictic species showed lower pollen viability and were less frequent among the Campo Rupestre plants. Among the New World species compiled, 43 were apomictic and 77 sexual (24 self-incompatible and 53 self-compatible). Most apomictic (86 ) and self-incompatible species (71 ) presented wide distributions, whilst restricted distributions predominate only among the self-compatible ones (53 ). Self-compatibility and dependence on biotic pollination were characteristic of Campo Rupestre and narrowly distributed New World Melastomataceae species, whilst apomictics are widely distributed. This is, to a certain extent, similar to the geographical parthenogenesis pattern of temperate apomictics.

A log-linear regression model for the beta-Birnbaum-Saunders distribution with censored data

The beta-Birnbaum-Saunders (Cordeiro and Lemonte, 2011) and Birnbaum-Saunders (Birnbaum and Saunders, 1969a) distributions have been used quite effectively to model failure times for materials subject to fatigue and lifetime data. We define the log-beta-Birnbaum-Saunders distribution by the logarithm of the beta-Birnbaum-Saunders distribution. Explicit expressions for its generating function and moments are derived. We propose a new log-beta-Birnbaum-Saunders regression model that can be applied to censored data and be used more effectively in survival analysis. We obtain the maximum likelihood estimates of the model parameters for censored data and investigate influence diagnostics. The new location-scale regression model is modified for the possibility that long-term survivors may be presented in the data. Its usefulness is illustrated by means of two real data sets. (C) 2011 Elsevier B.V. All rights reserved.

A Poisson mixed model with nonnormal random effect distribution

In this paper, we propose a random intercept Poisson model in which the random effect is assumed to follow a generalized log-gamma (GLG) distribution. This random effect accommodates (or captures) the overdispersion in the counts and induces within-cluster correlation. We derive the first two moments for the marginal distribution as well as the intraclass correlation. Even though numerical integration methods are, in general, required for deriving the marginal models, we obtain the multivariate negative binomial model from a particular parameter setting of the hierarchical model. An iterative process is derived for obtaining the maximum likelihood estimates for the parameters in the multivariate negative binomial model. Residual analysis is proposed and two applications with real data are given for illustration. (C) 2011 Elsevier B.V. All rights reserved.

Multivariate analyses of UV-Vis absorption spectral data from cachaca wood extracts: a model to classify aged Brazilian cachacas according to the wood species used

Multivariate analyses of UV-Vis spectral data from cachaca wood extracts provide a simple and robust model to classify aged Brazilian cachacas according to the wood species used in the maturation barrels. The model is based on inspection of 93 extracts of oak and different Brazilian wood species by a non-aged cachaca used as an extraction solvent. Application of PCA (Principal Components Analysis) and HCA (Hierarchical Cluster Analysis) leads to identification of 6 clusters of cachaca wood extracts (amburana, amendoim, balsamo, castanheira, jatoba, and oak). LDA (Linear Discriminant Analysis) affords classification of 10 different wood species used in the cachaca extracts (amburana, amendoim, balsamo, cabreuva-parda, canela-sassafras, castanheira, jatoba, jequitiba-rosa, louro-canela, and oak) with an accuracy ranging from 80% (amendoim and castanheira) to 100% (balsamo and jequitiba-rosa). The methodology provides a low-cost alternative to methods based on liquid chromatography and mass spectrometry to classify cachacas aged in barrels that are composed of different wood species.

On Equilibrium Distribution of a Reversible Growth Model

We study a probabilistic model of interacting spins indexed by elements of a finite subset of the d-dimensional integer lattice, da parts per thousand yen1. Conditions of time reversibility are examined. It is shown that the model equilibrium distribution converges to a limit distribution as the indexing set expands to the whole lattice. The occupied site percolation problem is solved for the limit distribution. Two models with similar dynamics are also discussed.

Cradoscrupocellaria, a new bryozoan genus for Scrupocellaria bertholletii (Audouin) and related species (Cheilostomata, Candidae): taxonomy, biodiversity and distribution

A new genus, Cradoscrupocellaria n. gen., is erected for Scrupocellaria bertholletii Audouin, 1826), reported as widespread in tropical and subtropical waters. Here we select a neotype of this species in order to establish its identity and distinguish it from morphologically similar species. We include redescriptions and figures of additional species now assigned to this new genus: Cradoscrupocellaria curacaoensis (Fransen, 1986) n. comb., Cradoscrupocellaria hirsuta (Jullien & Calvet, 1903) n. comb., and Cradoscrupocellaria macrorhyncha (Gautier, 1962) n. comb. Five additional species are assigned to the genus: Cradoscrupocellaria ellisi (Vieira & Spencer Jones, 2012) n. comb., Cradoscrupocellaria nanshaensis (Liu, 1991) n. comb., Cradoscrupocellaria reptans (Linnaeus, 1758) n. comb., Cradoscrupocellaria serrata (Waters, 1909) n. comb., and Cradoscrupocellaria tenuirostris (Osburn, 1950) n. comb. Eighteen new species are described: Cradoscrupocellaria aegyptiana n. sp., Cradoscrupocellaria arisaigensis n. sp., Cradoscrupocellaria atlantica n. sp., Cradoscrupocellaria calypso n. sp., Cradoscrupocellaria floridana n. sp., Cradoscrupocellaria galapagensis n. sp., Cradoscrupocellaria gautieri n. sp., Cradoscrupocellaria gorgonensis n. sp., Cradoscrupocellaria hastingsae n. sp., Cradoscrupocellaria insularis n. sp., Cradoscrupocellaria jamaicensis n. sp., Cradoscrupocellaria lagaaiji n. sp., Cradoscrupocellaria macrorhynchoides n. sp., Cradoscrupocellaria makua n. sp., Cradoscrupocellaria marcusorum n. sp., Cradoscrupocellaria normani n. sp., Cradoscrupocellaria odonoghuei n. sp., and Cradoscrupocellaria osburni n. sp.

Simulating short lived carbonaceous compounds with an atmospheric chemistry general circulation model

Ein neu entwickeltes globales Atmosphärenchemie- und Zirkulationsmodell (ECHAM5/MESSy1) wurde verwendet um die Chemie und den Transport von Ozonvorläufersubstanzen zu untersuchen, mit dem Schwerpunkt auf Nichtmethankohlenwasserstoffen. Zu diesem Zweck wurde das Modell durch den Vergleich der Ergebnisse mit Messungen verschiedenen Ursprungs umfangreich evaluiert. Die Analyse zeigt, daß das Modell die Verteilung von Ozon realistisch vorhersagt, und zwar sowohl die Menge als auch den Jahresgang. An der Tropopause gibt das Modell den Austausch zwischen Stratosphäre und Troposphäre ohne vorgeschriebene Flüsse oder Konzentrationen richtig wieder. Das Modell simuliert die Ozonvorläufersubstanzen mit verschiedener Qualität im Vergleich zu den Messungen. Obwohl die Alkane vom Modell gut wiedergeben werden, ergibt sich einige Abweichungen für die Alkene. Von den oxidierten Substanzen wird Formaldehyd (HCHO) richtig wiedergegeben, während die Korrelationen zwischen Beobachtungen und Modellergebnissen für Methanol (CH3OH) und Aceton (CH3COCH3) weitaus schlechter ausfallen. Um die Qualität des Modells im Bezug auf oxidierte Substanzen zu verbessern, wurden einige Sensitivitätsstudien durchgeführt. Diese Substanzen werden durch Emissionen/Deposition von/in den Ozean beeinflußt, und die Kenntnis über den Gasaustausch mit dem Ozean ist mit großen Unsicherheiten behaftet. Um die Ergebnisse des Modells ECHAM5/MESSy1 zu verbessern wurde das neue Submodell AIRSEA entwickelt und in die MESSy-Struktur integriert. Dieses Submodell berücksichtigt den Gasaustausch zwischen Ozean und Atmosphäre einschließlich der oxidierten Substanzen. AIRSEA, welches Informationen über die Flüssigphasenkonzentration des Gases im Oberflächenwasser des Ozeans benötigt wurde ausgiebig getestet. Die Anwendung des neuen Submodells verbessert geringfügig die Modellergebnisse für Aceton und Methanol, obwohl die Verwendung einer vorgeschriebenen Flüssigphasenkonzentration stark den Erfolg der Methode einschränkt, da Meßergebnisse nicht in ausreichendem Maße zu Verfügung stehen. Diese Arbeit vermittelt neue Einsichten über organische Substanzen. Sie stellt die Wichtigkeit der Kopplung zwischen Ozean und Atmosphäre für die Budgets vieler Gase heraus.

Mitochondrial inheritance and germ line determination in a bivalve species with Doubly Uniparental Inheritance (DUI)

Mitochondria are inherited maternally in most metazoans. However, in some bivalves, two mitochondrial lineages are present: one transmitted through eggs (F), the other through sperm (M). This is called Doubly Uniparental Inheritance (DUI). During male embryo development, spermatozoon mitochondria aggregate and end up in the primordial germ cells, while they are dispersed in female embryos. The molecular mechanisms of segregation patterns are still unknown. In the DUI species Ruditapes philippinarum, I examined sperm mitochondria distribution by MitoTracker, microtubule staining and TEM, and I localized germ line determinants with immunocytochemical analysis. I also analyzed the gonad transcriptome, searching for genes involved in reproduction and sex determination. Moreover, I analyzed an M-type specific open reading frame that could be responsible for maintenance/degradation of M mitochondria during embryo development. These transcripts were also localized in tissues using in situ hybridization. As in Mytilus, two distribution patterns of M mitochondria were detected in R. philippinarum, supporting that they are related to DUI. Moreover, the first division midbody concurs in positioning aggregated M mitochondria on the animal-vegetal axis of the male embryo: in organisms with spiral segmentation this zone is not involved in further cleavages, so aggregation is maintained. Moreover, sperm mitochondria reach the same embryonic area where germ plasm is transferred, suggesting their contribution in male germ line formation. The finding of reproduction and ubiquitination transcripts led to formulate a model in which ubiquitination genes stored in female oocytes during gametogenesis would activate sex-gene expression in the early embryonic developmental stages (preformation). Only gametogenetic cells were labeled by in situ hybridization, proving their specific transcription in developing gametes. Other than having a role in sex determination, some ubiquination factors could also be involved in mitochondrial inheritance, and their differential expression could be responsible for the different fate of sperm mitochondria in the two sexes.

Stochastic modeling of bacterial protein domains distribution to predict horizontal gene transfer

In questo elaborato, abbiamo tentato di modellizzare i processi che regolano la presenza dei domini proteici. I domini proteici studiati in questa tesi sono stati ottenuti dai genomi batterici disponibili nei data base pubblici (principalmente dal National Centre for Biotechnology Information: NCBI) tramite una procedura di simulazione computazionale. Ci siamo concentrati su organismi batterici in quanto in essi la presenza di geni trasmessi orizzontalmente, ossia che parte del materiale genetico non provenga dai genitori, e assodato che sia presente in una maggiore percentuale rispetto agli organismi più evoluti. Il modello usato si basa sui processi stocastici di nascita e morte, con l'aggiunta di un parametro di migrazione, usato anche nella descrizione dell'abbondanza relativa delle specie in ambito delle biodiversità ecologiche. Le relazioni tra i parametri, calcolati come migliori stime di una distribuzione binomiale negativa rinormalizzata e adattata agli istogrammi sperimentali, ci induce ad ipotizzare che le famiglie batteriche caratterizzate da un basso valore numerico del parametro di immigrazione abbiano contrastato questo deficit con un elevato valore del tasso di nascita. Al contrario, ipotizziamo che le famiglie con un tasso di nascita relativamente basso si siano adattate, e in conseguenza, mostrano un elevato valore del parametro di migrazione. Inoltre riteniamo che il parametro di migrazione sia direttamente proporzionale alla quantità di trasferimento genico orizzontale effettuato dalla famiglia batterica.

Mechanisms of species divergence through visual adaptation and sexual selection: Perspectives from a cichlid model system

The theory of ecological speciation suggests that assortative mating evolves most easily when mating preferences are;directly linked to ecological traits that are subject to divergent selection. Sensory adaptation can play a major role in this process,;because selective mating is often mediated by sexual signals: bright colours, complex song, pheromone blends and so on. When;divergent sensory adaptation affects the perception of such signals, mating patterns may change as an immediate consequence.;Alternatively, mating preferences can diverge as a result of indirect effects: assortative mating may be promoted by selection;against intermediate phenotypes that are maladapted to their (sensory) environment. For Lake Victoria cichlids, the visual environment;constitutes an important selective force that is heterogeneous across geographical and water depth gradients. We investigate;the direct and indirect effects of this heterogeneity on the evolution of female preferences for alternative male nuptial colours;(red and blue) in the genus Pundamilia. Here, we review the current evidence for divergent sensory drive in this system, extract;general principles, and discuss future perspectives

Cardiac sodium channel NaV1.5 distribution in myocytes via interacting proteins: the multiple pool model

The cardiac sodium current (INa) is responsible for the rapid depolarization of cardiac cells, thus allowing for their contraction. It is also involved in regulating the duration of the cardiac action potential (AP) and propagation of the impulse throughout the myocardium. Cardiac INa is generated by the voltage-gated Na(+) channel, NaV1.5, a 2016-residue protein which forms the pore of the channel. Over the past years, hundreds of mutations in SCN5A, the human gene coding for NaV1.5, have been linked to many cardiac electrical disorders, including the congenital and acquired long QT syndrome, Brugada syndrome, conduction slowing, sick sinus syndrome, atrial fibrillation, and dilated cardiomyopathy. Similar to many membrane proteins, NaV1.5 has been found to be regulated by several interacting proteins. In some cases, these different proteins, which reside in distinct membrane compartments (i.e. lateral membrane vs. intercalated disks), have been shown to interact with the same regulatory domain of NaV1.5, thus suggesting that several pools of NaV1.5 channels may co-exist in cardiac cells. The aim of this review article is to summarize the recent works that demonstrate its interaction with regulatory proteins and illustrate the model that the sodium channel NaV1.5 resides in distinct and different pools in cardiac cells. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction.

A Functional-Based Distribution Diagnostic for a Linear Model with Correlated Outcomes: Technical Report

Despite the widespread popularity of linear models for correlated outcomes (e.g. linear mixed modesl and time series models), distribution diagnostic methodology remains relatively underdeveloped in this context. In this paper we present an easy-to-implement approach that lends itself to graphical displays of model fit. Our approach involves multiplying the estimated marginal residual vector by the Cholesky decomposition of the inverse of the estimated marginal variance matrix. Linear functions or the resulting "rotated" residuals are used to construct an empirical cumulative distribution function (ECDF), whose stochastic limit is characterized. We describe a resampling technique that serves as a computationally efficient parametric bootstrap for generating representatives of the stochastic limit of the ECDF. Through functionals, such representatives are used to construct global tests for the hypothesis of normal margional errors. In addition, we demonstrate that the ECDF of the predicted random effects, as described by Lange and Ryan (1989), can be formulated as a special case of our approach. Thus, our method supports both omnibus and directed tests. Our method works well in a variety of circumstances, including models having independent units of sampling (clustered data) and models for which all observations are correlated (e.g., a single time series).