Early changes in apoplast composition associated with defence and disease in interactions between Phaseolus vulgaris and the halo blight pathogen Pseudomonas syringae pv. phaseolicola

The apoplast is the arena in which endophytic pathogens such as Pseudomonas syringae grow and interact with plant cells. Using metabolomic and ion analysis techniques, this study shows how the composition of Phaseolus vulgaris leaf apoplastic fluid changes during the first six hours of compatible and incompatible interactions with two strains of Pseudomonas syringae pv. phaseolicola (Pph) that differ in the presence of the genomic island PPHGI-1. Leaf inoculation with the avirulent island-carrying strain Pph 1302A elicited effector-triggered immunity (ETI) and resulted in specific changes in apoplast composition, including increases in conductivity, pH, citrate, γ-aminobutyrate (GABA) and K+, that are linked to the onset of plant defence responses. Other apoplastic changes, including increases in Ca2+, Fe2/3+ Mg2+, sucrose, β-cyanoalanine and several amino acids, occurred to a relatively similar extent in interactions with both Pph 1302A and the virulent, island-less strain Pph RJ3. Metabolic footprinting experiments established that Pph preferentially metabolizes malate, glucose and glutamate, but excludes certain other abundant apoplastic metabolites, including citrate and GABA, until preferred metabolites are depleted. These results demonstrate that Pph is well-adapted to the leaf apoplast metabolic environment and that loss of PPHGI-1 enables Pph to avoid changes in apoplast composition linked to plant defences.

The Xanthomonas citri effector protein PthA interacts with citrus proteins involved in nuclear transport, protein folding and ubiquitination associated with DNA repair

P>Xanthomonas axonopodis pv. citri utilizes the type III effector protein PthA to modulate host transcription to promote citrus canker. PthA proteins belong to the AvrBs3/PthA family and carry a domain comprising tandem repeats of 34 amino acids that mediates protein-protein and protein-DNA interactions. We show here that variants of PthAs from a single bacterial strain localize to the nucleus of plant cells and form homo- and heterodimers through the association of their repeat regions. We hypothesize that the PthA variants might also interact with distinct host targets. Here, in addition to the interaction with alpha-importin, known to mediate the nuclear import of AvrBs3, we describe new interactions of PthAs with citrus proteins involved in protein folding and K63-linked ubiquitination. PthAs 2 and 3 preferentially interact with a citrus cyclophilin (Cyp) and with TDX, a tetratricopeptide domain-containing thioredoxin. In addition, PthAs 2 and 3, but not 1 and 4, interact with the ubiquitin-conjugating enzyme complex formed by Ubc13 and ubiquitin-conjugating enzyme variant (Uev), required for K63-linked ubiquitination and DNA repair. We show that Cyp, TDX and Uev interact with each other, and that Cyp and Uev localize to the nucleus of plant cells. Furthermore, the citrus Ubc13 and Uev proteins complement the DNA repair phenotype of the yeast Delta ubc13 and Delta mms2/uev1a mutants, strongly indicating that they are also involved in K63-linked ubiquitination and DNA repair. Notably, PthA 2 affects the growth of yeast cells in the presence of a DNA damage agent, suggesting that it inhibits K63-linked ubiquitination required for DNA repair.

Prior residence and body size influence interactions between black sea urchins

Body size and prior residence can modulate agonistic interaction in several animal species, but scientists know little about these relationships in echinoderms. In this study, we tested the effects of these traits on interactions in the black sea urchin (Echinometra lucunter). After a sea urchin was isolated for 24-h in a glass tank to establish prior residence, we introduced an intruder animal adjacent to the resident in the tank and observed interactions for 30 min. The intruder animal was larger, smaller, or size-matched to the resident. We found body size and prior residence concomitantly modulated interactions among black sea urchins, with prior residence as the major determinant. Black sea urchins mainly exhibited opponent inspection and fleeing responses during interaction to avoid fights, especially when a fight could be seriously disadvantageous (small intruder vs. large resident). (C) 2008 Elsevier B.V. All rights reserved.

Autonomic control of cardiorespiratory interactions in fish, amphibians and reptiles

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Unusual interactions binding iron tetrasulfonated phthalocyanine and poly(allylamine hydrochloride) in layer-by-layer films

Molecular-level interactions are found to bind iron tetrasulfonated phthalocyanine (FeTsPc) and the polyelectrolyte poly(allylamine hydrochloride) (PAH) in electroactive layer-by-layer (LBL) films. These interactions have been identified by comparing Fourier transform infrared (FTIR) and Raman spectroscopy data from bulk samples of FeTsPc and PAH with those from FeTsPc/PAH LBL films. of particular importance were the SO3- -NH3 interactions that we believe to bind PAH and FeTsPc and the interactions between unprotonated amine groups of PAH and the coordinating metal of the phthalocyanine. The multilayer formation was monitored via UV-vis spectroscopy by measuring the increase in the Q band of FeTsPc at 676 nm. Film thickness estimated with profilometry was ca. I I Angstrom per bilayer for films adsorbed on glass. Reflection absorption infrared spectroscopy (RAIRS) revealed an anisotropy in the LBL film adsorbed on gold with FeTsPc molecules oriented perpendicularly to the substrate plane. Cyclic voltammograms showed reproducible pairs of oxidation-reduction peaks at 1.07 and 0.81 V, respectively, for a 50-bilayer PAH/FeTsPc film at 50 mV/s (vs Ag/Ag+). The peak shape and current dependence on the scan rate suggest that the process is a diffusion controlled charge transport. In the presence of dopamine, the electroactivity of FeTsPc/PAH LBL films vanishes due to a passivation effect. Dopamine activity is not detected either because the interaction between Fe atoms and NH2 groups prevents dopamine molecules from coordinating with the Fe atoms.

Prediction of Oncogenic Interactions and Cancer-Related Signaling Networks Based on Network Topology

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mathematical modeling and analysis of the particle interactions in the direct filtration using the colloidal theory

This work used the colloidal theory to describe forces and energy interactions of colloidal complexes in the water and those formed during filtration run in direct filtration. Many interactions of particle energy profiles between colloidal surfaces for three geometries are presented here in: spherical, plate and cylindrical; and four surface interactions arrangements: two cylinders, two spheres, two plates and a sphere and a plate. Two different situations were analyzed, before and after electrostatic destabilization by action of the alum sulfate as coagulant in water studies samples prepared with kaolin. In the case were used mathematical modeling by extended DLVO theory (from the names: Derjarguin-Landau-Verwey-Overbeek) or XDLVO, which include traditional approach of the electric double layer (EDL), surfaces attraction forces or London-van der Waals (LvdW), esteric forces and hydrophobic forces, additionally considering another forces in colloidal system, like molecular repulsion or Born Repulsion and Acid-Base (AB) chemical function forces from Lewis.

Galaxy interactions I. Major and minor mergers

Aims. We study galaxy pair samples selected from the Sloan Digital Sky Survey (SDSS-DR7) and we perform an analysis of minor and major mergers with the aim of investigating the dependence of galaxy properties on interactions. Methods. We build a galaxy pair catalog requiring r(p) < 25 kpc h(-1) and Delta V < 350 km s(-1) within redshift z < 0.1. By visual inspection of SDSS images we remove false identifications and we classify the interactions into three categories: pairs undergoing merging, M; pairs with evident tidal features, T; and non disturbed, N. We also divide the pair sample into minor and major interactions according to the luminosity ratio of the galaxy members. We study star formation activity through colors, the 4000 angstrom break, and star formation rates. Results. We find that similar to 10% of the pairs are classified as M. These systems show an excess of young stellar populations as inferred from the D-n(4000) spectral index, colors, and star formation rates of the member galaxies, an effect which we argue is directly related to the ongoing merging process. We find similar to 30% of the pairs exhibiting tidal features (T pairs) with member galaxies showing evidence of old stellar populations. This can be associated either to the disruptive effect of some tidal interactions, or to the longer time-scale of morphological disturbance with respect to the bursts of the tidal induced star formation. Regardless of the color distribution, we find a prominent blue peak in the strongest mergers, while pairs with tidal signs under a minor merger show a strong red peak. Therefore, our results show that galaxy interactions are important in driving the evolution of galaxy bimodality. By adding stellar masses and star formation rates of the two members of the pairs, we explore the global efficiency of star formation of the pairs as a whole. We find that, at a given total stellar mass, major mergers are significantly more efficient (a factor approximate to 2) in forming new stars, with respect to both minor mergers or a control sample of non-interacting galaxies. We conclude that the characteristics of the interactions and the ratio of luminosity galaxy pair members involved in a merger are important parameters in setting galaxy properties.

Structure and dynamics of supramolecular assemblies studied by advanced solid-state NMR spectroscopy

Ziel der vorliegenden Arbeit ist die Aufklärung von Struktur und Dynamik komplexer supramolekularer Systeme mittels Festkörper NMR Spektroskopie. Die Untersuchung von pi-pi Wechselwirkungen, welche einen entscheidenden Einfluss auf die strukturellen und dynamischen Eigenschaften supra- molekularer Systeme haben, hilft dabei, die Selbst- organisationsprozesse dieser komplexen Materialien besser zu verstehen. Mit dipolaren 1H-1H and 1H-13C Wiedereinkopplungs NMR Methoden unter schnellem MAS können sowohl 1H chemische Verschiebungen als auch dipolare 1H-1H und 1H-13C Kopplungen untersucht werden, ohne dass eine Isotopenmarkierung erforderlich ist. So erhält man detaillierte Informationen über die Struktur und die Beweglichkeit einzelner Molekül- segmente. In Verbindung mit sogenannten nucleus independent chemical shift (NICS) maps (berechnet mit ab-initio Methoden) lassen sich Abstände von Protonen relativ zu pi-Elektronensystemen bestimmen und so Strukturvorschläge ableiten. Mit Hilfe von homo- und heteronuklearen dipolaren Rotationsseitenbandenmustern könnenaußerdem Ordnungs- parameter für verschiedene Molekülsegmente bestimmt werden. Die auf diese Weise gewonnenen Informationen über die strukturellen und dynamischen Eigenschaften supramolekularer Systeme tragen dazu bei, strukturbestimmende Molekül- einheiten und Hauptordnungsphänomene zu identifizieren sowie lokale Wechselwirkungen zu quantifizieren, um so den Vorgang der Selbstorganisation besser zu verstehen.

Contribution of Non-Covalent Interactions and Electronic Effects on the Conformational Landscape and Tautomeric Equilibria of Molecules and Molecular Complexes: Structural and Dynamical Data from Rotational Spectroscopy

This thesis concerns the study of complex conformational surfaces and tautomeric equilibria of molecules and molecular complexes by quantum chemical methods and rotational spectroscopy techniques. In particular, the focus of this research is on the effects of substitution and noncovalent interactions in determining the energies and geometries of different conformers, tautomers or molecular complexes. The Free-Jet Absorption Millimeter Wave spectroscopy and the Pulsed-Jet Fourier Transform Microwave spectroscopy have been applied to perform these studies and the obtained results showcase the suitability of these techniques for the study of conformational surfaces and intermolecular interactions. The series of investigations of selected medium-size molecules and complexes have shown how different instrumental setups can be used to obtain a variety of results on molecular properties. The systems studied, include molecules of biological interest such as anethole and molecules of astrophysical interest such as N-methylaminoethanol. Moreover halogenation effects have been investigated on halogen substituted tautomeric systems (5-chlorohydroxypyridine and 6-chlorohydroxypyridine), where it has shown that the position of the inserted halogen atom affects the prototropic equilibrium. As for fluorination effects, interesting results have been achieved investigating some small complexes where a molecule of water is used as a probe to reveal the changes on the electrostatic potential of different fluorinated compounds: 2-fluoropyridine, 3-fluoropyridine and penta-fluoropyridine. While in the case of the molecular complex between water and 2-fluoropyridine and 3-fluoropyridine the geometry of the complex with one water molecule is analogous to that of pyridine with the water molecule linked to the pyridine nitrogen, the case of pentafluoropyridine reveals the effect of perfluorination and the water oxygen points towards the positive center of the pyridine ring. Additional molecular adducts with a molecule of water have been analyzed (benzylamine-water and acrylic acid-water) in order to reveal the stabilizing driving forces that characterize these complexes.

A unifying approach for haplotype analysis of quantitative traits in family-based association studies: Testing and estimating gene-environment interactions with complex exposure variables

We propose robust and e±cient tests and estimators for gene-environment/gene-drug interactions in family-based association studies. The methodology is designed for studies in which haplotypes, quantitative pheno- types and complex exposure/treatment variables are analyzed. Using causal inference methodology, we derive family-based association tests and estimators for the genetic main effects and the interactions. The tests and estimators are robust against population admixture and strati¯cation without requiring adjustment for confounding variables. We illustrate the practical relevance of our approach by an application to a COPD study. The data analysis suggests a gene-environment interaction between a SNP in the Serpine gene and smok- ing status/pack years of smoking that reduces the FEV1 volume by about 0.02 liter per pack year of smoking. Simulation studies show that the pro- posed methodology is su±ciently powered for realistic sample sizes and that it provides valid tests and effect size estimators in the presence of admixture and stratification.

Plant-microbe-herbivore interactions in invasive and non-invasive alien plant species

1. Plants interact with many organisms, such as microbes and herbivores, and these interactions are likely to affect the establishment and spread of plants. In the context of plant invasions, mycorrhizal fungi and constitutive and induced resistance of plants against herbivores have received attention independently of each other. However, plants are frequently involved in complex multi-trophic interactions, which might differ between invasive and non-invasive alien plants. 2. In a multi-species comparative experiment, we aimed to improve our understanding of plant traits associated with invasiveness. We tested whether eight invasive alien plant species use the mycorrhizal symbiosis in a more beneficial way, and have higher levels of constitutive or induced resistance against two generalist bioassay herbivores, than nine non-invasive alien species. We further assessed whether the presence of mycorrhizal fungi altered the resistance of the plant species, and whether this differed between invasive and non-invasive alien species. 3. While invasive species produced more biomass, they did not differ in their biomass response to mycorrhizal fungi from non-invasive alien species. Invasive species also did not have higher levels of constitutive or induced resistance against the two generalist herbivores. Mycorrhizal fungi greatly affected the resistance of our plant species, however, this was also unrelated to whether the alien species were invasive or not. 4. Our study confirms the previous findings that invasive species generally grow faster and produce more biomass than non-invasive alien species. We further show that alien plant species used a variety of defence strategies, and also varied in their interactions with mycorrhizal fungi. These multi-trophic interactions were not consistently related to invasiveness of the alien plant species. 5. We suggest that awareness of the fact that alien plant species are involved in multi-trophic interactions might lead to a more complete understanding of the factors contributing to a plant's success.

The importance of biotic interactions and local adaptation for plant response to environmental changes: field evidence along an elevational gradient

Predicting the response of species to environmental changes is a great and on-going challenge for ecologists, and this requires a more in-depth understanding of the importance of biotic interactions and the population structuration in the landscape. Using a reciprocal transplantation experiment, we tested the response of five species to an elevational gradient. This was combined to a neighbour removal treatment to test the importance of local adaptation and biotic interactions. The trait studied was performance measured as survival and biomass. Species response varied along the elevational gradient, but with no consistent pattern. Performance of species was influenced by environmental conditions occurring locally at each site, as well as by positive or negative effects of the surrounding vegetation. Indeed, we observed a shift from competition for biomass to facilitation for survival as a response to the increase in environmental stress occurring in the different sites. Unlike previous studies pointing out an increase of stress along the elevation gradient, our results supported a stress gradient related to water availability, which was not strictly parallel to the elevational gradient. For three of our species, we observed a greater biomass production for the population coming from the site where the species was dominant (central population) compared to population sampled at the limit of the distribution (marginal population). Nevertheless, we did not observe any pattern of local adaptation that could indicate adaptation of populations to a particular habitat. Altogether, our results highlighted the great ability of plant species to cope with environmental changes, with no local adaptation and great variability in response to local conditions. Our study confirms the importance of taking into account biotic interactions and population structure occurring at local scale in the prediction of communities’ responses to global environmental changes.

Learning Analytics and Interactions in Virtual Learning Environments. A Comparative Study of Typologies and their Relationship with Academic Performance

Analysis of learning data (learning analytics) is a new research field with high growth potential. The main objective of Learning analytics is the analysis of data (interactions being the basic data unit) generated in virtual learning environments, in order to maximize the outcomes of the learning process; however, a consensus has not been reached yet on which interactions must be measured and what is their influence on learning outcomes. This research is grounded on the study of e-learning interaction typologies and their relationship with students? academic performance, by means of a comparative study between different interaction typologies (based on the agents involved, frequency of use and participation mode). The main conclusions are a) that classifications based on agents offer a better explanation of academic performance; and b) that each of the three typologies are able to explain academic performance in terms of some of their components (student-teacher and student-student interactions, evaluating students interactions and active interactions, respectively), with the other components being nonrelevant.