Atrogin-1 and MuRF1 regulate cardiac MyBP-C levels via different mechanisms

Familial hypertrophic cardiomyopathy (FHC) is frequently caused by cardiac myosin-binding protein C (cMyBP-C) gene mutations, which should result in C-terminal truncated mutants. However, truncated mutants were not detected in myocardial tissue of FHC patients and were rapidly degraded by the ubiquitin-proteasome system (UPS) after gene transfer in cardiac myocytes. Since the diversity and specificity of UPS regulation lie in E3 ubiquitin ligases, we investigated whether the muscle-specific E3 ligases atrogin-1 or muscle ring finger protein-1 (MuRF1) mediate degradation of truncated cMyBP-C. Human wild-type (WT) and truncated (M7t, resulting from a human mutation) cMyBP-C species were co-immunoprecipitated with atrogin-1 after adenoviral overexpression in cardiac myocytes, and WT-cMyBP-C was identified as an interaction partner of MuRF1 by yeast two-hybrid screens. Overexpression of atrogin-1 in cardiac myocytes decreased the protein level of M7t-cMyBP-C by 80% and left WT-cMyBP-C level unaffected. This was rescued by proteasome inhibition. In contrast, overexpression of MuRF1 in cardiac myocytes not only reduced the protein level of WT- and M7t-cMyBP-C by > 60%, but also the level of myosin heavy chains (MHCs) by > 40%, which were not rescued by proteasome inhibition. Both exogenous cMyBP-C and endogenous MHC mRNA levels were markedly reduced by MuRF1 overexpression. Similar to cardiac myocytes, MuRF1-overexpressing (TG) mice exhibited 40% lower levels of MHC mRNAs and proteins. Protein levels of cMyBP-C were 29% higher in MuRF1 knockout and 34% lower in TG than in WT, without a corresponding change in mRNA levels. These data suggest that atrogin-1 specifically targets truncated M7t-cMyBP-C, but not WT-cMyBP-C, for proteasomal degradation and that MuRF1 indirectly reduces cMyBP-C levels by regulating the transcription of MHC.

Cell-cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris

RpfG is a paradigm for a class of widespread bacterial two-component regulators with a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase domain. In the plant pathogen Xanthomonas campestris pv. campestris (Xcc), a two-component system comprising RpfG and the complex sensor kinase RpfC is implicated in sensing and responding to the diffusible signaling factor (DSF), which is essential for cell-cell signaling. RpfF is involved in synthesizing DSF, and mutations of rpfF, rpfG, or rpfC lead to a coordinate reduction in the synthesis of virulence factors such as extracellular enzymes, biofilm structure, and motility. Using yeast two-hybrid analysis and fluorescence resonance energy transfer experiments in Xcc, we show that the physical interaction of RpfG with two proteins with diguanylate cyclase (GGDEF) domains controls a subset of RpfG-regulated virulence functions. RpfG interactions were abolished by alanine substitutions of the three residues of the conserved GYP motif in the HD-GYP domain. Changing the GYP motif or deletion of the two GGDEF-domain proteins reduced Xcc motility but not the synthesis of extracellular enzymes or biofilm formation. RpfG-GGDEF interactions are dynamic and depend on DSF signaling, being reduced in the rpfF mutant but restored by DSF addition. The results are consistent with a model in which DSF signal transduction controlling motility depends on a highly regulated, dynamic interaction of proteins that influence the localized expression of cyclic di-GMP.

Pseudomonas aeruginosa PA14 cupD transcription is activated by the RcsB response regulator, but repressed by its putative cognate sensor RcsC

The opportunistic pathogen Pseudomonas aeruginosa PA14 possesses four fimbrial cup clusters, which may confer the ability to adapt to different environments. cupD lies in the pathogenicity island PAPI-1 next to genes coding for a putative phosphorelay system composed of the hybrid histidine kinase RcsC and the response regulator RcsB. The main focus of this work was the regulation of cupD at the mRNA level. It was found that the HN-S-like protein MvaT does not exert a strong influence on cupD transcript levels, as it does for cupA. cupD transcription is higher in cultures grown at 28 degrees C, which agrees with a cupD mutant presenting attenuated virulence only in a plant model, but not in a mouse model of infection. Whereas an rcsC in-frame deletion mutant presented higher levels of cupD mRNA, rcsB deletion had the opposite effect. Accordingly, overexpression of RcsB increased the levels of cupD transcription, and promoted biofilm formation and the appearance of fimbriae. A single transcription start site was determined for cupD and transcription from this site was induced by RcsB. A motif similar to the enterobacterial RcsB/RcsA-binding site was detected adjacent to the -35 region, suggesting that this could be the RcsB-binding site. Comparison of P. aeruginosa and Escherichia coli Rcs may provide insights into how similar systems can be used by different bacteria to control gene expression and to adapt to various environmental conditions.

Quenching of Photoactivity in Phthalocyanine Copper(II)-Titanate Nanotube Hybrid Systems

Titanate nanotubes (TiNTs) were obtained by hydrothermal treatment of anatase powder in aqueous NaOH solution and then modified with 2,9,16,23-tertracarboxyl phthalocyanine copper(H) (CuPc). This hybrid organic inorganic nanoscopic system was characterized by X-ray diffraction, microscopy, and spectroscopy. Transmission electron microscopy (TEM) images of pure and modified TiNTs revealed multiwall structures with an average outer diameter of 9 nm and a length of several hundred nanometers. The tubular morphology of the TiNTs was covered with CuPc-film. The amount of CuPc adsorbed onto the TiNTs was quantified by electron paramagnetic resonance (EPR). Using the same technique and spin-trapping methodology, the photogeneration of reactive oxygen species (ROS) from the TiNTs was systematically investigated. A drastic quenching of photoactivity was observed in the CuPc/TiNT hybrid system. Electron transfer from excited CuPc states to the TiNT conduction band followed by electron recombination may be the cause of this quenching.

Local Structure and Photochromic Response in Ormosils Containing Dodecatungstophosphoric Acid

Two hybrid materials based on dodecatungstophosphoric acid (HPW) dispersed in ormosils modified with 3-aminopropiltrietoxysilane (APTS) or with N-(3-(trimethoxysilyl)-propyl)-ethylene-diamine (TSPEN) show reversible photochromic response induced by irradiation in the 200-390 nm UV range. A set of solid-state nuclear magnetic resonance (NMR) techniques was used to analyze the structural properties of the main components of these hybrids (the HPW polyanion, the inorganic matrix, and the organic functionalities). For the ormosils, the use of (29)Si NMR, {(1)H}-(29)Si cross-polarization, and {(1)H}-(29)Si HETCOR revealed a homogeneous distribution of silicon species Q ``, T(2), and T(3) for the APTS hybrid, contrasting with the separation of T(3) species in the TSPEN hybrid. The combination of (31)P NMR, {(1)H}-(31)P cross-polarization and (31)P-{(1)H} spin-echo double resonance (SEDOR) revealed the dispersion of the HPW ions in the ormosil, occupying sites with a high number of close protons (>50). Differences in the molecular dynamics at room temperature, inferred from SEDOR experiments, indicate a state of restricted mobility of the HPW ion and the surrounding molecular groups in the TSPEN hybrid. This behavior is consistent with the presence of more amino groups in the TSPEN, acting as chelating groups to the HPW ion. This hybrid, with the strong chelate interaction of the diamine group, shows the most intense photochromic response, in agreement with the charge transfer models proposed to explain the photochromic effect. Electronic reflectance spectroscopy in irradiated samples revealed the presence of one-electron and two-electron reduced polyanions. The one-electron reduced species could be detected also by (31)P NMR spectroscopy immediately after UV irradiation.

Free expanding cloud of cold atoms as an atomic standard: Ramsey fringes contrast

A compact frequency standard based on an expanding cold (133)CS cloud is under development in our laboratory. In a first experiment, Cs cold atoms were prepared by a magneto-optical trap in a vapor cell, and a microwave antenna was used to transmit the radiation for the clock transition. The signal obtained from fluorescence of the expanding cold atoms cloud is used to lock a microwave chain. In this way the overall system stability is evaluated. A theoretical model based on a two-level system interacting with the two microwave pulses enables interpretation for the observed features, especially the poor Ramsey fringes contrast. (C) 2008 Optical Society of America.

Dynamical models for computer viruses propagation

Nowadays, digital computer systems and networks are the main engineering tools, being used in planning, design, operation, and control of all sizes of building, transportation, machinery, business, and life maintaining devices. Consequently, computer viruses became one of the most important sources of uncertainty, contributing to decrease the reliability of vital activities. A lot of antivirus programs have been developed, but they are limited to detecting and removing infections, based on previous knowledge of the virus code. In spite of having good adaptation capability, these programs work just as vaccines against diseases and are not able to prevent new infections based on the network state. Here, a trial on modeling computer viruses propagation dynamics relates it to other notable events occurring in the network permitting to establish preventive policies in the network management. Data from three different viruses are collected in the Internet and two different identification techniques, autoregressive and Fourier analyses, are applied showing that it is possible to forecast the dynamics of a new virus propagation by using the data collected from other viruses that formerly infected the network. Copyright (c) 2008 J. R. C. Piqueira and F. B. Cesar. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.

Protecting a quantum state from environmental noise by an incompatible finite-time measurement

We show that measurements of finite duration performed on an open two-state system can protect the initial state from a phase-noisy environment, provided the measured observable does not commute with the perturbing interaction. When the measured observable commutes with the environmental interaction, the finite-duration measurement accelerates the rate of decoherence induced by the phase noise. For the description of the measurement of an observable that is incompatible with the interaction between system and environment, we have found an approximate analytical expression, valid at zero temperature and weak coupling with the measuring device. We have tested the validity of the analytical predictions against an exact numerical approach, based on the superoperator-splitting method, that confirms the protection of the initial state of the system. When the coupling between the system and the measuring apparatus increases beyond the range of validity of the analytical approximation, the initial state is still protected by the finite-time measurement, according with the exact numerical calculations.

Influence of organic shock loads in an ASBBR treating synthetic wastewater with different concentration levels

Safe application of the anaerobic sequencing biofilm batch reactor (ASBBR) still depends on deeper insight into its behavior when faced with common operational problems in wastewater treatments such as tolerance to abrupt variations in influent concentration, so called shock loads. To this end the current work shows the effect of organic shock loads on the performance of an ASBBR, with a useful volume of 5 L, containing 0.5-cm polyurethane cubes and operating at 30 degrees C with mechanical stirring of 500 rpm. In the assays 2 L of two types of synthetic wastewater were treated in 8-h cycles. Synthetic wastewater I was based on sucrose-amide-cellulose with concentration of 500 mg COD/L and synthetic wastewater II was based on volatile acids with concentration ranging from 500 to 2000 mg COD/L. Organic shock loads of 2-4 times the operation concentration were applied during one and two cycles. System efficiency was monitored before and after application of the perturbation. When operating with concentrations from 500 to 1000 mg COD/L and shock loads of 2-4 times the influent concentration during one or two cycles the system was able to regain stability after one cycle and the values of organic matter, total and intermediate volatile acids, bicarbonate alkalinity and pH were similar to those prior to the perturbations. At a concentration of 2000 mg COD/L the reactor appeared to be robust, regaining removal efficiencies similar to those prior to perturbation at shock loads twice the operation concentration lasting one cycle and stability was recovered after two cycles. However, for shock loads twice the operation concentration during two cycles and shock loads four times the operation concentration during one or two cycles filtered sample removal efficiency decreased to levels different from those prior to perturbation, on an average of 90-80%, approximately, yet the system managed to attain stability within two cycles after shock application. Therefore, this investigation envisions the potential of full scale application of this type of bioreactor which showed robustness to organic shock loads, despite discontinuous operation and the short times available for treating total wastewater volume. (c) 2007 Elsevier Ltd. All rights reserved.

Desalination of water by reverse osmosis using gravitational potential energy and wind energy

This paper proposes ail alternative configuration to conventional reverse osmosis (RO) desalination systems by incorporating the use of gravitational potential energy. The proposal suggests a model that can be viewed as the energy station of a RO desalination plant. Conventionally, RO plants use a high-pressure pump, powered by electricity or fossil fuel. The function of the pump is to send a flux of saline water to a group of semi-permeable membrane modules, capable of ""filtering"" the dissolved salts. In this proposed model, we intend to achieve a flux at the inlet of the membrane modules with a pressure high enough for the desalination process, without using, either electricity or fossil fuels. To do this we divised a hybrid system that uses both gravitational potential energy and wind energy. The technical viability of the alternative was theoretically proven by deductions based on physics and mathematics.

Comparison of oxygen mass transfer coefficient in simple and extractive fermentation systems

Aeration and agitation are important variables to ensure effective oxygen transfer rate during aerobic bioprocesses: therefore, the knowledge of the volumetric mass transfer coefficient (k(L)a) is required. In view of selecting the optimum oxygen requirements for extractive fermentation in aqueous two-phase system (ATPS), the k(L)a values in a typical ATPS medium were compared in this work with those in distilled water and in a simple fermentation medium. in the absence of biomass. Aeration and agitation were selected as the independent variables using a 2(2) full factorial design. Both variables showed statistically significant effects on k(L)a, and the highest values of this parameter in both media for simple fermentation (241 s(-1)) and extractive fermentation with ATPS (70.3 s(-1)) were observed at the highest levels of aeration (5 vvm) and agitation (1200 rpm). The k(L)a values were then used to establish mathematical correlations of this response as a function of the process variables. The exponents of the power number (N(3)D(2)) and superficial gas velocity (V(s)) determined in distilled water (alpha = 0.39 and beta = 0.47, respectively) were in reasonable agreement with the ones reported in the literature for several aqueous systems and close to those determined for a simple fermentation medium (alpha=0.38 and beta=0.41). On the other hand, as expected by the increased viscosity in the presence of polyethylene glycol, their values were remarkably higher in a typical medium for extractive fermentation (alpha=0.50 and beta=1.0). A reasonable agreement was found between the experimental data of k(L)a for the three selected systems and the values predicted by the theoretical models, under a wide range of operational conditions. (C) 2009 Elsevier B.V. All rights reserved.

Endoscopic Anatomy of the Pterygopalatine Fossa and the Transpterygoid Approach: Development of a Surgical Instruction Model

Introduction: The pterygopalatine fossa (PPF) is a narrow space located between the posterior wall of the antrum and the pterygoid plates. Surgical access to the PPF is difficult because of its protected position and its complex neurovascular anatomy. Endonasal approaches using rod lens endoscopes, however, provide better visualization of this area and are associated with less morbidity than external approaches. Our aim was to develop a simple anatomical model using cadaveric specimens injected with intravascular colored silicone to demonstrate the endoscopic anatomy of the PPF. This model could be used for surgical instruction of the transpterygoid approach. Methods: We dissected six PPF in three cadaveric specimens prepared with intravascular injection of colored material using two different injection techniques. An endoscopic endonasal approach, including a wide nasoantral window and removal of the posterior antrum wall, provided access to the PPF. Results: We produced our best anatomical model injecting colored silicone via the common carotid artery. We found that, using an endoscopic approach, a retrograde dissection of the sphenopalatine artery helped to identify the internal maxillary artery (IMA) and its branches. Neural structures were identified deeper to the vascular elements. Notable anatomical landmarks for the endoscopic surgeon are the vidian nerve and its canal that leads to the petrous portion of the internal carotid artery (ICA), and the foramen rotundum, and V2 that leads to Meckel`s cave in the middle cranial fossa. These two nerves, vidian and V2, are separated by a pyramidal shaped bone and its apex marks the ICA. Conclusion: Our anatomical model provides the means to learn the endoscopic anatomy of the PPF and may be used for the simulation of surgical techniques. An endoscopic endonasal approach provides adequate exposure to all anatomical structures within the PPF. These structures may be used as landmarks to identify and control deeper neurovascular structures. The significance is that an anatomical model facilitates learning the surgical anatomy and the acquisition of surgical skills. A dissection superficial to the vascular structures preserves the neural elements. These nerves and their bony foramina, such as the vidian nerve and V2, are critical anatomical landmarks to identify and control the ICA at the skull base.

The energy cycle and structural evolution of cyclones over southeastern South America in three case studies

In this paper, the Lorenz energy cycle over a limited area was applied for three cyclones with different origins and evolutions, where each of them was formed in an important cyclogenetic region near southeastern South America. The synoptic conditions and energetics were analyzed during each system`s life cycle and showed important relationships between their energy cycle and the evolution of their vertical structure. In the case of the weak baroclinic cyclone which formed on Brazil`s south-southeastern coast, the analysis showed that it originated through a midlevel cutoff low with contribution from barotropic instability. Its evolution would indicate potential transition to a hybrid system if the convective activity were stronger. The system that occurred in the La Plata River mouth had features of an oceanic bomb-type cyclogenesis and showed an important contribution from the available potential energy generation term through the latent heat release by the convection. Meanwhile, the system of the southern Argentina coast presented a classical baroclinic development of extratropical cyclogenesis in the energy cycle, from the wave amplification up to the final occlusion of the associated frontal system. These analyses revealed that the development of some cyclones that occur in eastern South America can present different mechanisms that are not related to the classical extratropical cyclogenesis.

Modelling the secular evolution of migrating planet pairs

The subject of this paper is the secular behaviour of a pair of planets evolving under dissipative forces. In particular, we investigate the case when dissipative forces affect the planetary semimajor axes and the planets move inwards/outwards the central star, in a process known as planet migration. To perform this investigation, we introduce fundamental concepts of conservative and dissipative dynamics of the three-body problem. Based on these concepts, we develop a qualitative model of the secular evolution of the migrating planetary pair. Our approach is based on the analysis of the energy and the orbital angular momentum exchange between the two-planet system and an external medium; thus no specific kind of dissipative forces is invoked. We show that, under the assumption that dissipation is weak and slow, the evolutionary routes of the migrating planets are traced by the Mode I and Mode II stationary solutions of the conservative secular problem. The ultimate convergence and the evolution of the system along one of these secular modes of motion are determined uniquely by the condition that the dissipation rate is sufficiently smaller than the proper secular frequency of the system. We show that it is possible to reassemble the starting configurations and the migration history of the systems on the basis of their final states and consequently to constrain the parameters of the physical processes involved.