AtPIN: Arabidopsis thaliana Protein Interaction Network

Background: Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. Description: All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C(3)) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening. Conclusions: AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.

Increased Endothelial Cell-Leukocyte Interaction in Murine Schistosomiasis: Possible Priming of Endothelial Cells by the Disease

Background and Aims: Schistosomiasis is an intravascular parasitic disease associated with inflammation. Endothelial cells control leukocyte transmigration and vascular permeability being modulated by pro-inflammatory mediators. Recent data have shown that endothelial cells primed in vivo in the course of a disease keep the information in culture. Herein, we evaluated the impact of schistosomiasis on endothelial cell-regulated events in vivo and in vitro. Methodology and Principal Findings: The experimental groups consisted of Schistosoma mansoni-infected and age-matched control mice. In vivo infection caused a marked influx of leukocytes and an increased protein leakage in the peritoneal cavity, characterizing an inflamed vascular and cellular profile. In vitro leukocyte-mesenteric endothelial cell adhesion was higher in cultured cells from infected mice as compared to controls, either in the basal condition or after treatment with the pro-inflammatory cytokine tumor necrosis factor (TNF). Nitric oxide (NO) donation reduced leukocyte adhesion to endothelial cells from control and infected groups; however, in the later group the effect was more pronounced, probably due to a reduced NO production. Inhibition of control endothelial NO synthase (eNOS) increased leukocyte adhesion to a level similar to the one observed in the infected group. Besides, the adhesion of control leukocytes to endothelial cells from infected animals is similar to the result of infected animals, confirming that schistosomiasis alters endothelial cells function. Furthermore, NO production as well as the expression of eNOS were reduced in cultured endothelial cells from infected animals. On the other hand, the expression of its repressor protein, namely caveolin-1, was similar in both control and infected groups. Conclusion/Significance: Schistosomiasis increases vascular permeability and endothelial cell-leukocyte interaction in vivo and in vitro. These effects are partially explained by a reduced eNOS expression. In addition, our data show that the disease primes endothelial cells in vivo, which keep the acquired phenotype in culture.

Interaction and behavior of virgin and physogastric queens in three Meliponini species (Hymenoptera, Apidae)

We studied the behavior of virgin queens of the stingless bee species Schwarziana quadripunctata, Paratrigona lineata and Tetragona clavipes, investigating internal nest activities, including the cell provisioning and oviposition process. We made direct observation of queen behavior, with the aid of video filming. Forty-four virgin queens of S. quadripunctata were observed; one was larger and more attractive than the others. Miniature queens were more abundant than normal-size queens; both were found in prison chambers. Agonistic behavior between virgin and physogastric queens of P. lineata was observed during attempts at queen supersedure. After the disappearance of the physogastric queen and the appearance of a virgin queen in T. clavipes nests, the brood cells were sealed with pollen alone, but no egg. In all three species, the presence of one or more virgin queens appeared to make the colonies nervous, even though constant production of virgin queens is vital to the survival of the colony and is part of the colony cycle in these bees.

Electrochemical Evidence of Strong Electronic Interaction of PtRu on Carbon Nanotubes with High Density of Defects

We show that carbon nanotubes (CNTs) with high density of defects can present a strong electronic interaction with nanoparticles of Pt-Ru with average particle size of 3.5 +/- 0.8 nm. Depending on the Pt-Ru loading on the CNTs, CO and methanol oxidation reactions suggest there is a charge transfer between Pt-Ru that in turn provokes a decrease in the electronic interaction taking place between Ru and Pt in the PtRu alloy. The CO stripping potentials were observed at about 0.65 and 0.5 V for Pt-Ru/CNT electrodes with Pt-Ru loadings of 10 and 20, and 30 wt %, respectively. (C) 2008 The Electrochemical Society. [DOI: 10.1149/1.2990222] All rights reserved.

Qualitative Analysis of the Interdisciplinary Interaction between Data Analysis Specialists and Novice Clinical Researchers

Background: The inherent complexity of statistical methods and clinical phenomena compel researchers with diverse domains of expertise to work in interdisciplinary teams, where none of them have a complete knowledge in their counterpart's field. As a result, knowledge exchange may often be characterized by miscommunication leading to misinterpretation, ultimately resulting in errors in research and even clinical practice. Though communication has a central role in interdisciplinary collaboration and since miscommunication can have a negative impact on research processes, to the best of our knowledge, no study has yet explored how data analysis specialists and clinical researchers communicate over time. Methods/Principal Findings: We conducted qualitative analysis of encounters between clinical researchers and data analysis specialists (epidemiologist, clinical epidemiologist, and data mining specialist). These encounters were recorded and systematically analyzed using a grounded theory methodology for extraction of emerging themes, followed by data triangulation and analysis of negative cases for validation. A policy analysis was then performed using a system dynamics methodology looking for potential interventions to improve this process. Four major emerging themes were found. Definitions using lay language were frequently employed as a way to bridge the language gap between the specialties. Thought experiments presented a series of ""what if'' situations that helped clarify how the method or information from the other field would behave, if exposed to alternative situations, ultimately aiding in explaining their main objective. Metaphors and analogies were used to translate concepts across fields, from the unfamiliar to the familiar. Prolepsis was used to anticipate study outcomes, thus helping specialists understand the current context based on an understanding of their final goal. Conclusion/Significance: The communication between clinical researchers and data analysis specialists presents multiple challenges that can lead to errors.

Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions

Background: Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. Methodology: We develop a procedure to incorporate prey availability data into Bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates. Conclusions: Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.

Signature of the interaction between dark energy and dark matter in observations

We investigate the effect of an interaction between dark energy and dark matter upon the dynamics of galaxy clusters. This effect is computed through the Layser-Irvine equation, which describes how an astrophysical system reaches virial equilibrium and was modified to include the dark interactions. Using observational data from almost 100 purportedly relaxed galaxy clusters we put constraints on the strength of the couplings in the dark sector. We compare our results with those from other observations and find that a positive (in the sense of energy flow from dark energy to dark matter) nonvanishing interaction is consistent with the data within several standard deviations.

Signals for new spin-1 resonances in electroweak gauge boson pair production at the LHC

The mechanism of electroweak symmetry breaking ( EWSB) will be directly scrutinized soon at the CERN Large Hadron Collider. We analyze the LHC potential to look for new vector bosons associated with the EWSB sector, presenting a possible model independent approach to search for these new spin-1 resonances. We show that the analyses of the processes pp -> l(+)l(1-)E(T), l +/- jjE(T), l(1 +/-)l(+)l(-)E(T), l(+/-)jjE(T), and l(+)l(-) jj (with l, l' = e or mu and j = jet) have a large reach at the LHC and can lead to the discovery or exclusion of many EWSB scenarios such as Higgsless models.

Field theory model for dark matter and dark energy in interaction

We propose a field theory model for dark energy and dark matter in interaction. Comparing the classical solutions of the field equations with the observations of the CMB shift parameter, baryonic acoustic oscillations, lookback time, and the Gold supernovae sample, we observe a possible interaction between dark sectors with energy decay from dark energy into dark matter. The observed interaction provides an alleviation to the coincidence problem.

Strongly coupled fourth generation at the LHC

We study extensions of the standard model with a strongly coupled fourth generation. This occurs in models where electroweak symmetry breaking is triggered by the condensation of at least some of the fourth-generation fermions. With focus on the phenomenology at the LHC, we study the pair production of fourth-generation down quarks, D(4). We consider the typical masses that could be associated with a strongly coupled fermion sector, in the range (300-600) GeV. We show that the production and successive decay of these heavy quarks into final states with same-sign dileptons, trileptons, and four leptons can be easily seen above background with relatively low luminosity. On the other hand, in order to confirm the presence of a new strong interaction responsible for fourth-generation condensation, we study its contribution to D(4) pair production, and the potential to separate it from standard QCD-induced heavy quark production. We show that this separation might require large amounts of data. This is true even if it is assumed that the new interaction is mediated by a massive colored vector boson, since its strong coupling to the fourth generation renders its width of the order of its mass. We conclude that, although this class of models can be falsified at early stages of the LHC running, its confirmation would require high integrated luminosities.

Determination of the spin of new resonances in electroweak gauge boson pair production at the LHC

The appearance of spin-1 resonances associated with the electroweak symmetry breaking sector is expected in many extensions of the standard model. We analyze the CERN Large Hadron Collider potential to probe the spin of possible new charged and neutral vector resonances through the purely leptonic processes pp -> Z' -> l(+) l'(-) E(T), and pp -> W' -> l'(+/-) l(+) l(-) E(T), with l, l' = e or mu. We perform a model-independent analysis and demonstrate that the spin of the new states can be determined with 99% C. L. in a large fraction of the parameter space where these resonances can be observed with 100 fb(-1). We show that the best sensitivity to the spin is obtained by directly studying correlations between the final state leptons, without the need of reconstructing the events in their center-of-mass frames.

Testing the interaction between dark energy and dark matter via the latest observations

Cosmological analyses based on currently available observations are unable to rule out a sizeable coupling between dark energy and dark matter. However, the signature of the coupling is not easy to grasp, since the coupling is degenerate with other cosmological parameters, such as the dark energy equation of state and the dark matter abundance. We discuss possible ways to break such degeneracy. Based on the perturbation formalism, we carry out the global fitting by using the latest observational data and get a tight constraint on the interaction between dark sectors. We find that the appropriate interaction can alleviate the coincidence problem.

New strongly coupled sector at the Tevatron and the LHC

We examine the possibility that a new strong interaction is accessible to the Tevatron and the LHC. In an effective theory approach, we consider a scenario with a new color-octet interaction with strong couplings to the top quark, as well as the presence of a strongly coupled fourth generation which could be responsible for electroweak symmetry breaking. We apply several constraints, including the ones from flavor physics. We study the phenomenology of the resulting parameter space at the Tevatron, focusing on the forward-backward asymmetry in top pair production, as well as in the production of the fourth-generation quarks. We show that if the excess in the top production asymmetry is indeed the result of this new interaction, the Tevatron could see the first hints of the strongly coupled fourth-generation quarks. Finally, we show that the LHC with root s = 7 TeV and 1 fb(-1) integrated luminosity should observe the production of fourth-generation quarks at a level at least 1 order of magnitude above the QCD prediction for the production of these states.

Effect of weak dipolar interaction on the magnetic properties of Ni nanoparticles assembly analyzed with different protocols

The effect of weak dipolar interactions (DIs) between Ni nanoparticles (NPs) in samples with different Ni concentrations was investigated by performing a detailed characterization of their structural and magnetic properties. From the determination of several physical parameters of Ni NP assemblies, it was found that the ac and dc magnetic susceptibility measurements are valuable for identifying the DIs between NPs while hysteresis loops measurements showed to be very insensitive, provided that the strength of the DI field is much smaller than the maximum coercive field. Therefore, the sensitivity of the observed static and dynamical magnetic properties to the effect of weak DI depends on the measurement protocols used. (C) 2011 American Institute of Physics. [doi:10.1063/1.3556767]

Casimir interaction between a perfect conductor and graphene described by the Dirac model

We adopt the Dirac model for graphene and calculate the Casimir interaction energy between a plane suspended graphene sample and a parallel plane perfect conductor. This is done in two ways. First, we use the quantum-field-theory approach and evaluate the leading-order diagram in a theory with 2+1-dimensional fermions interacting with 3+1-dimensional photons. Next, we consider an effective theory for the electromagnetic field with matching conditions induced by quantum quasiparticles in graphene. The first approach turns out to be the leading order in the coupling constant of the second one. The Casimir interaction for this system appears to be rather weak. It exhibits a strong dependence on the mass of the quasiparticles in graphene.