Alloy inhomogeneities in InAlAs strained layers grown by MBE

Transmission electron microscopy studies have been performed to characterize InxAl1−xAs layers grown by molecular beam epitaxy on (100) InP substrates. The first observations of compositional nonuniformities in strained InAlAs layers are reported. The coarse quasiperiodic structure present in each sample has been found to be dependent upon the growth parameters and the sample characteristics.

Fine speckle contrast in InGaAs/InP systems: Influence of layer thickness, missmatch, and growing temperature

This work is focused on the study of the fine speckle contrast present in planar view observations of matched and mismatched InGaAs layers grown by molecular beam epitaxy on InP substrates. Our results provide experimental evidence of the evolution of this fine structure with the mismatch, layer thickness, and growth temperature. The correlation of the influence of all these parameters on the appearance of the contrast modulation points to the development of the fine structure during the growth. Moreover, as growth proceeds, this structure shows a dynamic behavior which depends on the intrinsic layer substrate stress.

Activation of c-Jun in the nuclei of neurons of the CA-1 in thrombin preconditioning occurs via PAR-1.

Recently it has been shown that the c-Jun N-terminal kinase (JNK) plays a role in thrombin preconditioning (TPC) in vivo and in vitro. To investigate further the pathways involved in TPC, we performed an immunohistochemical study in hippocampal slice cultures. Here we show that the major target of JNK, the AP-1 transcription factor c-Jun, is activated by phosphorylation in the nuclei of neurons of the CA1 region by using phospho-specific antibodies against the two JNK phosphorylation sites. The activation is early and transient, peaking at 90 min and not present by 3 hr after low-dose thrombin administration. Treatment of cultures with a synthetic thrombin receptor agonist results in the same c-Jun activation profile and protection against subsequent OGD, both of which are prevented by specific JNK inhibitors, showing that thrombin signals through PAR-1 to JNK. By using an antibody against the Ser 73 phosphorylation site of c-Jun, we identify possible additional TPC substrates.

Improvement of the quality factor of RF integrated inductors by layout optimization

A systematic method to improve the quality (Q) factor of RF integrated inductors is presented in this paper. The proposed method is based on the layout optimization to minimize the series resistance of the inductor coil, taking into account both ohmic losses, due to conduction currents, and magnetically induced losses, due to eddy currents. The technique is particularly useful when applied to inductors in which the fabrication process includes integration substrate removal. However, it is also applicable to inductors on low-loss substrates. The method optimizes the width of the metal strip for each turn of the inductor coil, leading to a variable strip-width layout. The optimization procedure has been successfully applied to the design of square spiral inductors in a silicon-based multichip-module technology, complemented with silicon micromachining postprocessing. The obtained experimental results corroborate the validity of the proposed method. A Q factor of about 17 have been obtained for a 35-nH inductor at 1.5 GHz, with Q values higher than 40 predicted for a 20-nH inductor working at 3.5 GHz. The latter is up to a 60% better than the best results for a single strip-width inductor working at the same frequency.

Glucose transporters in the 21st Century.

The ability to take up and metabolize glucose at the cellular level is a property shared by the vast majority of existing organisms. Most mammalian cells import glucose by a process of facilitative diffusion mediated by members of the Glut (SLC2A) family of membrane transport proteins. Fourteen Glut proteins are expressed in the human and they include transporters for substrates other than glucose, including fructose, myoinositol, and urate. The primary physiological substrates for at least half of the 14 Glut proteins are either uncertain or unknown. The well-established glucose transporter isoforms, Gluts 1-4, are known to have distinct regulatory and/or kinetic properties that reflect their specific roles in cellular and whole body glucose homeostasis. Separate review articles on many of the Glut proteins have recently appeared in this journal. Here, we provide a very brief summary of the known properties of the 14 Glut proteins and suggest some avenues of future investigation in this area.

c-Jun N-terminal kinase binding domain-dependent phosphorylation of mitogen-activated protein kinase kinase 4 and mitogen-activated protein kinase kinase 7 and balancing cross-talk between c-Jun N-terminal kinase and extracellular signal-regulated kinase pathways in cortical neurons

The c-Jun N-terminal kinase (JNK) is a mitogen-activated protein kinase (MAPK) activated by stress-signals and involved in many different diseases. Previous results proved the powerful effect of the cell permeable peptide inhibitor d-JNKI1 (d-retro-inverso form of c-Jun N-terminal kinase-inhibitor) against neuronal death in CNS diseases, but the precise features of this neuroprotection remain unclear. We here performed cell-free and in vitro experiments for a deeper characterization of d-JNKI1 features in physiological conditions. This peptide works by preventing JNK interaction with its c-Jun N-terminal kinase-binding domain (JBD) dependent targets. We here focused on the two JNK upstream MAPKKs, mitogen-activated protein kinase kinase 4 (MKK4) and mitogen-activated protein kinase kinase 7 (MKK7), because they contain a JBD homology domain. We proved that d-JNKI1 prevents MKK4 and MKK7 activity in cell-free and in vitro experiments: these MAPKK could be considered not only activators but also substrates of JNK. This means that d-JNKI1 can interrupt downstream but also upstream events along the JNK cascade, highlighting a new remarkable feature of this peptide. We also showed the lack of any direct effect of the peptide on p38, MEK1, and extracellular signal-regulated kinase (ERK) in cell free, while in rat primary cortical neurons JNK inhibition activates the MEK1-ERK-Ets1/c-Fos cascade. JNK inhibition induces a compensatory effect and leads to ERK activation via MEK1, resulting in an activation of the survival pathway-(MEK1/ERK) as a consequence of the death pathway-(JNK) inhibition. This study should hold as an important step to clarify the strong neuroprotective effect of d-JNKI1.

Detection and measurement of paracaspase MALT1 activity.

The paracaspase MALT1 is a Cys-dependent, Arg-specific protease that plays an essential role in the activation and proliferation of lymphocytes during the immune response. Oncogenic activation of MALT1 is associated with the development of specific forms of B-cell lymphomas. Through specific cleavage of its substrates, MALT1 controls various aspects of lymphocyte activation, including the activation of transcriptional pathways, the stabilization of mRNAs, and an increase in cellular adhesion. In lymphocytes, the activity of MALT1 is tightly controlled by its inducible monoubiquitination, which promotes the dimerization of MALT1. Here, we describe both in vitro and in vivo assays that have been developed to assess MALT1 activity.

Chemical and physical properties of organic residues

Due to human activity, large amounts of organic residue are generated daily. Therefore, an adequate use in agricultural activities requires the characterization of the main properties. The chemical and physical characterization is important when planning the use and management of organic residue. In this study, chemical and physical properties of charcoal, coffee husk, pine-bark, cattle manure, chicken manure, coconut fiber, sewage sludge, peat, and vermiculite were determined. The following properties were analyzed: N-NH4+, N-N0(3)-, and total concentrations of N, P, S, K, Ca, Mg, Mn, Zn, Cu, and B, as well as pH, Electrical Conductivity (EC) and bulk density. Coffee husk, sewage sludge, chicken manure and cattle manure were generally richer in nutrients. The EC values of these residues were also the highest (0.08 - 40.6 dS m-1). Peat and sewage sludge had the highest bulky density. Sodium contents varied from 0 to 4.75 g kg-1, with the highest levels in chicken manure, cattle manure and sewage sludge. Great care must be taken when establishing proportions of organic residues in the production of substrates with coffee husk, cattle or chicken manure or sewage sludge in the calculation of the applied fertilizer quantity in crop fertilization programs.

Freezing of 4He and its liquid-solid interface from density functional theory

We show that, at high densities, fully variational solutions of solidlike types can be obtained from a density functional formalism originally designed for liquid 4He . Motivated by this finding, we propose an extension of the method that accurately describes the solid phase and the freezing transition of liquid 4He at zero temperature. The density profile of the interface between liquid and the (0001) surface of the 4He crystal is also investigated, and its surface energy evaluated. The interfacial tension is found to be in semiquantitative agreement with experiments and with other microscopic calculations. This opens the possibility to use unbiased density functional (DF) methods to study highly nonhomogeneous systems, like 4He interacting with strongly attractive impurities and/or substrates, or the nucleation of the solid phase in the metastable liquid.

Condensation of helium in nanoscopic alkali wedges at zero temperature

We present a complete calculation of the structure of liquid 4He confined to a concave nanoscopic wedge, as a function of the opening angle of the walls. This is achieved within a finite-range density functional formalism. The results here presented, restricted to alkali metal substrates, illustrate the change in meniscus shape from rather broad to narrow wedges on weak and strong alkali adsorbers, and we relate this change to the wetting behavior of helium on the corresponding planar substrate. As the wedge angle is varied, we find a sequence of stable states that, in the case of cesium, undergo one filling and one emptying transition at large and small openings, respectively. A computationally unambiguous criterion to determine the contact angle of 4He on cesium is also proposed.

Identification of GPx8 as a novel cellular substrate of the hepatitis C virus NS3-4A protease

Background: The hepatitis C virus (HCV) NS3-4A protease is not only an essential component of the viral replication complex and a prime target for antiviral intervention but also a key player in the persistence and pathogenesis of HCV. It cleaves and thereby inactivates two crucial adaptor proteins in viral RNA sensing and innate immunity (MAVS and TRIF) as well as a phosphatase involved in growth factor signaling (TC-PTP). The aim of this study was to identify novel cellular substrates of the NS3-4A protease and to investigate their role in the life cycle and pathogenesis of HCV. Methods: Cell lines inducibly expressing the NS3-4A protease were analyzed in basal as well as interferon- α -stimulated states by stable isotopic labeling using amino acids in cell culture (SILAC) coupled with protein separation and mass spectrometry. Candidates fulfilling strin- gent criteria for potential substrates or products of the NS3-4A protease were further investigated in different experimental sys- tems as well as in liver biopsies from patients with chronic hep- atitis C. Results: SILAC coupled with protein separation and mass spectrometry yielded > 5000 proteins of which 21 can- didates were selected for further analyses. These allowed us to identify GPx8, a membrane-associated peroxidase involved in disulfide bond formation in the endoplasmic reticulum, as a novel cellular substrate of the HCV NS3-4A protease. Cleavage occurs at cysteine in position 11, removing the cytosolic tip of GPx8, and was observed in different experimental systems as well as in liver biopsies from patients with chronic hepatitis C. Further functional studies, involving overexpression and RNA silencing, revealed that GPx8 is a proviral factor involved in viral particle production but not in HCV entry or RNA replica- tion. Conclusions: GPx8 is a proviral host factor cleaved by the HCV NS3-4A protease. Studies investigating the consequences of cleavage for GPx8 function are underway. The identification of novel cellular substrates of the HCV NS3-4A protease should yield new insights into the HCV life cycle and the pathogenesis of hepatitis C and may reveal novel angles for therapeutic inter- vention.

Promoter recognition and activation by the global response regulator CbrB in Pseudomonas aeruginosa.

In Pseudomonas aeruginosa, the CbrA/CbrB two-component system is instrumental in the maintenance of the carbon-nitrogen balance and for growth on carbon sources that are energetically less favorable than the preferred dicarboxylate substrates. The CbrA/CbrB system drives the expression of the small RNA CrcZ, which antagonizes the repressing effects of the catabolite repression control protein Crc, an RNA-binding protein. Dicarboxylates appear to cause carbon catabolite repression by inhibiting the activity of the CbrA/CbrB system, resulting in reduced crcZ expression. Here we have identified a conserved palindromic nucleotide sequence that is present in upstream activating sequences (UASs) of promoters under positive control by CbrB and σ(54) RNA polymerase, especially in the UAS of the crcZ promoter. Evidence for recognition of this palindromic sequence by CbrB was obtained in vivo from mutational analysis of the crcZ promoter and in vitro from electrophoretic mobility shift assays using crcZ promoter fragments and purified CbrB protein truncated at the N terminus. Integration host factor (IHF) was required for crcZ expression. CbrB also activated the lipA (lipase) promoter, albeit less effectively, apparently by interacting with a similar but less conserved palindromic sequence in the UAS of lipA. As expected, succinate caused CbrB-dependent catabolite repression of the lipA promoter. Based on these results and previously published data, a consensus CbrB recognition sequence is proposed. This sequence has similarity to the consensus NtrC recognition sequence, which is relevant for nitrogen control.

Dietary fat, lipogenesis and energy balance.

Today, there are still uncertainties about the role of exogenous fat on body fat regulation. Early models of energy utilization (for example, Kleiber's, early 20th century) failed to take into account the nature of substrate oxidized in the control of food intake, whereas more recent models (e.g., Flatt's model, end of 20th century) did. Excess body fat storage is ultimately a problem of chronic positive energy balance mediated by a poor control of energy intake or/and a blunted total energy expenditure. Excess fat storage can stem from exogenous fat and to a more limited extent by nonfat substrates precursors transformed into body fat, mostly from carbohydrates, a process known as de novo lipogenesis. When considered over periods of weeks, months or years, total fat balance is closely related to energy balance. Over periods of days, the net change in fat balance is quantitatively limited as compared to the size of endogenous fat storage. The issues discussed in this article primarily include the stimulation of de novo lipogenesis after acute or prolonged CHO overfeeding and whether de novo lipogenesis is a risk factor for obesity development.

Characterization of the expression, regulation and function of Sorting Nexin 9 and Sorting Nexin 18

Summary : Sorting nexin (SNX) family members play important roles in intracellular protein and membrane trafficking, The membrane-tubulating SNX9 protein has been shown to interact with multiple components of the endocytic machinery and to participate in clathrin-mediated endocytosis of cell surface receptors. It has not been investigated if SNX9 may also participate in other protein sorting pathways that involve vesicular transport, specifically the biogenesis of lysosome-related organelles (LROs). Closely related to SNX9 is SNXl8, whose function is largely unknown. In this work, we have characterized the expression of SNX9 and SNXl8 in LRO-containing cells and investigated their role in protein trafficking during the formation of LROs. Our results indicate that SNX9 and SNXl8 are not essential for the formation of LROs, nor for the sorting of melanosomal proteins. We investigated how the level of intracellular SNX9 protein is regulated and found that it is a substrate of the ubiquitin ligase Itch, a member of the NEDD4 family of E3 ubiquitin ligases. Itch ubiquitylates SNX9 and regulates SNX9 levels by enhancing its degradation. Using ? truncated proteins we found that the interaction with SNX9 is mediated by the proline-rich domain of Itch, a domain distinct from the conventional WW recognition domain, and the SH3 domain of SNX9. Interaction with the PRD of Itch is essential for SNX9 ubiquitylation and degradation. We further showed that Itch binding is not affected by tyrosine phosphorylation of SNX9. Using lentivector-mediated siRNA techniques, we found that Itch regulates the level of melanosomal proteins, while knock-down of SNX9 does not alter their level. Interestingly, we revealed that silencing of SNXIS affects the amount of the melanosomal protein Melan-A, but also of SNX9, and that SNXl8 can interact with SNX9. Taken together, our results highlight that the pool of substrates of NEDD4 family E3 ligases extends to proteins containing SH3 domains and provide insight into the potential functions of SNXI8. Résumé : Les membres de la famille des Sorting Nexins (SNX) jouent des rôles importants dans le trafic intracellulaire de protéines et membranes. Il a été démontré que la protéine SNX9, qui génère les tubules membranaires, interagit avec plusieurs composants de la machinerie d'endocytose et participe à l'endocytose des récepteurs de surface mediée par la clathrine. Aucune étude n'a investigué si SNX9 pourrait aussi participer à d'autres voies de trafic de protéines tel que le transport vésiculaire, et plus particulièrement la biogenèse des organites lysosomaux ("lysosome-related organelles", LR©s). SNXl8 est similaire à SNX9, mais sa fonction est largement inconnue. Dans ce travail, nous avons caractérisé l'expression de SNX9 et SNX18 dans des cellules contenants des LROs et investigué leur rôle dans le trafic de protéines pendant la formation des LROS. Nos résultats indiquent que SNX9 et SNXI8 ne sont essentiels ni pour la formation des LR©s, ni pour le trafic de protéines mélanosomales. Nous avons examiné la régulation du niveau intracellulaire de la protéine SNX9 et avons trouvé qu'elle est un substrat de l'ubiquitine ligase Itch, un membre de la famille NEDD4 des ubiquitine ligases E3. Itch ubiquitine SNX9 et régule les niveaux de SNX9 en augmentant sa dégradation. En utilisant des protéines mutées nous avons découvert que l'interaction avec SNX9 est médiée par le domaine riche en proline de Itch, qui est différent du domaine conventionnel de reconnaissance WW, et par le domaine SH3 de SNX9. L'interaction avec le domaine riche en proline de Itch est essentielle pour l'ubiquitination et la dégradation de SNX9. De plus, nous avons montré que cette liaison n'est pas affectée par la phosphorylation des résidus tyrosine de SNX9. En utilisant des vecteurs lentiviraux exprimant des siARN, nous avons trouvé que Itch régule les niveaux de protéines mélanosomales, alors que l'extinction de l'expression de SNX9 ne change pas leurs niveaux. En autre, nous avons révélé que la diminution de SNXl8 affecte le niveau de la protéine mélanosomale Melan-A et de SNX9, et aussi que SNXl8 peut interagir avec SNX9. En résumé, nos résultats démontrent que l'ensemble des substrats de la famille NEDD4 des ubiquitine ligases E3 s'élargit aux protéines contenant des domaines SH3 et ouvrent des perspectives sur les fonctions potentielles de SNXl8.

Comparison of the methane oxidation rate in four media

Landfill gas emissions are one of the main sources of anthropogenic methane (CH4), a major greenhouse gas. In this paper, an economically attractive alternative to minimize greenhouse gas emissions from municipal solid waste landfills was sought. This alternative consists in special biofilters as landfill covers with oxidative capacity in the presence of CH4. To improve the quality/cost ratio of the project, compost was chosen as one of the cover substrates and soil (Typic red yellow-silt-clay Podzolic) as the other. The performance of four substrates was studied in laboratory experiments: municipal solid waste (MSW) compost, soil, and two soil-compost at different proportions. This study aimed to evaluate the suitability and environmental compatibility as a means of CH4 oxidation in biofilters. Four biofilters were constructed in 60 cm PVC tubes with an internal diameter of 10 cm. Each filter contained 2.3 L of oxidizing substrate at the beginning of the experiment. The gas used was a mixture of CH4 and air introduced at the bottom of each biofilter, at a flow of 150 mL min-1, by a flow meter. One hundred days after the beginning of the experiment, the best biofilter was the MSW compost with an oxidation rate of 990 g m-3 day-1 , corresponding to an efficiency of 44 %. It can be concluded that the four substrates studied have satisfactory oxidative capacity, and the substrates can be used advantageously as cover substrate of MSW landfills.