beta-arrestin-1 competitively inhibits insulin-induced ubiquitination and degradation of insulin receptor substrate 1.

beta-arrestin-1 is an adaptor protein that mediates agonist-dependent internalization and desensitization of G-protein-coupled receptors (GPCRs) and also participates in the process of heterologous desensitization between receptor tyrosine kinases and GPCR signaling. In the present study, we determined whether beta-arrestin-1 is involved in insulin-induced insulin receptor substrate 1 (IRS-1) degradation. Overexpression of wild-type (WT) beta-arrestin-1 attenuated insulin-induced degradation of IRS-1, leading to increased insulin signaling downstream of IRS-1. When endogenous beta-arrestin-1 was knocked down by transfection of beta-arrestin-1 small interfering RNA, insulin-induced IRS-1 degradation was enhanced. Insulin stimulated the association of IRS-1 and Mdm2, an E3 ubiquitin ligase, and this association was inhibited to overexpression of WT beta-arrestin-1, which led by decreased ubiquitin content of IRS-1, suggesting that both beta-arrestin-1 and IRS-1 competitively bind to Mdm2. In summary, we have found the following: (i) beta-arrestin-1 can alter insulin signaling by inhibiting insulin-induced proteasomal degradation of IRS-1; (ii) beta-arrestin-1 decreases the rate of ubiquitination of IRS-1 by competitively binding to endogenous Mdm2, an E3 ligase that can ubiquitinate IRS-1; (iii) dephosphorylation of S412 on beta-arrestin and the amino terminus of beta-arrestin-1 are required for this effect of beta-arrestin on IRS-1 degradation; and (iv) inhibition of beta-arrestin-1 leads to enhanced IRS-1 degradation and accentuated cellular insulin resistance.

The Trim39 ubiquitin ligase inhibits APC/CCdh1-mediated degradation of the Bax activator MOAP-1.

Proapoptotic Bcl-2 family members, such as Bax, promote release of cytochrome c from mitochondria, leading to caspase activation and cell death. It was previously reported that modulator of apoptosis protein 1 (MOAP-1), an enhancer of Bax activation induced by DNA damage, is stabilized by Trim39, a protein of unknown function. In this paper, we show that MOAP-1 is a novel substrate of the anaphase-promoting complex (APC/C(Cdh1)) ubiquitin ligase. The influence of Trim39 on MOAP-1 levels stems from the ability of Trim39 (a RING domain E3 ligase) to directly inhibit APC/C(Cdh1)-mediated protein ubiquitylation. Accordingly, small interfering ribonucleic acid-mediated knockdown of Cdh1 stabilized MOAP-1, thereby enhancing etoposide-induced Bax activation and apoptosis. These data identify Trim39 as a novel APC/C regulator and provide an unexpected link between the APC/C and apoptotic regulation via MOAP-1.

Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway.

PURPOSE: The endoplasmic reticulum-associated degradation pathway is responsible for the translocation of misfolded proteins across the endoplasmic reticulum membrane into the cytosol for subsequent degradation by the proteasome. To define the phenotype associated with a novel inherited disorder of cytosolic endoplasmic reticulum-associated degradation pathway dysfunction, we studied a series of eight patients with deficiency of N-glycanase 1. METHODS: Whole-genome, whole-exome, or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data. RESULTS: All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypolacrima or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele. CONCLUSION: NGLY1 deficiency is a novel autosomal recessive disorder of the endoplasmic reticulum-associated degradation pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a broader range of mutations are detected.

Conformational kinetics reveals affinities of protein conformational states.

Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.

The inoculum effect and band-pass bacterial response to periodic antibiotic treatment.

The inoculum effect (IE) refers to the decreasing efficacy of an antibiotic with increasing bacterial density. It represents a unique strategy of antibiotic tolerance and it can complicate design of effective antibiotic treatment of bacterial infections. To gain insight into this phenomenon, we have analyzed responses of a lab strain of Escherichia coli to antibiotics that target the ribosome. We show that the IE can be explained by bistable inhibition of bacterial growth. A critical requirement for this bistability is sufficiently fast degradation of ribosomes, which can result from antibiotic-induced heat-shock response. Furthermore, antibiotics that elicit the IE can lead to 'band-pass' response of bacterial growth to periodic antibiotic treatment: the treatment efficacy drastically diminishes at intermediate frequencies of treatment. Our proposed mechanism for the IE may be generally applicable to other bacterial species treated with antibiotics targeting the ribosomes.

Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators.

Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest sources of stochasticity is the binary noise that arises from the binding of a regulatory protein to a promoter in the chromosomal DNA. In this study, we focus on two minimal oscillators based on activator titration and repressor titration to understand the key parameters that are important for oscillations and for overcoming binary noise. We show that the rate of unbinding from the DNA, despite traditionally being considered a fast parameter, needs to be slow to broaden the space of oscillatory solutions. The addition of multiple, independent DNA binding sites further expands the oscillatory parameter space for the repressor-titration oscillator and lengthens the period of both oscillators. This effect is a combination of increased effective delay of the unbinding kinetics due to multiple binding sites and increased promoter ultrasensitivity that is specific for repression. We then use stochastic simulation to show that multiple binding sites increase the coherence of oscillations by mitigating the binary noise. Slow values of DNA unbinding rate are also effective in alleviating molecular noise due to the increased distance from the bifurcation point. Our work demonstrates how the number of DNA binding sites and slow unbinding kinetics, which are often omitted in biophysical models of gene circuits, can have a significant impact on the temporal and stochastic dynamics of genetic oscillators.

Optimal kinetics for quantification of antigen-induced cytokines in human peripheral blood mononuclear cells by real-time PCR and by ELISA.

Real-time polymerase chain reaction (PCR) has recently been described as a new tool to measure and accurately quantify mRNA levels. In this study, we have applied this technique to evaluate cytokine mRNA synthesis induced by antigenic stimulation with purified protein derivative (PPD) or heparin-binding haemagglutinin (HBHA) in human peripheral blood mononuclear cells (PBMC) from Mycobacterium tuberculosis-infected individuals. Whereas PPD and HBHA optimally induced IL-2 mRNA after respectively 8 and 16 to 24 h of in vitro stimulation, longer in vitro stimulation times were necessary for optimal induction of interferon-gamma (IFN-gamma) mRNA, respectively 16 to 24 h for PPD and 24 to 96 h for HBHA. IL-13 mRNA was optimally induced by in vitro stimulation after 16-48 h for PPD and after 48 to 96 h for HBHA. Comparison of antigen-induced Th1 and Th2 cytokines appears, therefore, valuable only if both cytokine types are analysed at their optimal time point of production, which, for a given cytokine, may differ for each antigen tested. Results obtained by real-time PCR for IFN-gamma and IL-13 mRNA correlated well with those obtained by measuring the cytokine concentrations in cell culture supernatants, provided they were high enough to be detected. We conclude that real-time PCR can be successfully applied to the quantification of antigen-induced cytokine mRNA and to the evaluation of the Th1/Th2 balance, only if the kinetics of cytokine mRNA appearance are taken into account and evaluated for each cytokine measured and each antigen analysed.

Negative hormonal control by the androgen DHT and antiestrogen EM-139 on cell cycle kinetics and proliferation in human breast cancer ZR-75-1 cells

info:eu-repo/semantics/submittedForPublication

The numerical simulation of noncharring thermal degradation and its application to the prediction of compartment fire development

In this paper we present some work concerned with the development and testing of a simple solid fuel combustion model incorporated within a Computational Fluid Dynamics (CFD) framework. The model is intended for use in engineering applications of fire field modeling and represents an extension of this technique to situations involving the combustion of solid fuels. The CFD model is coupled with a simple thermal pyrolysis model for combustible solid noncharring fuels, a six-flux radiation model and an eddy-dissipation model for gaseous combustion. The model is then used to simulate a series of small-scale room fire experiments in which the target solid fuel is polymethylmethacrylate. The numerical predictions produced by this coupled model are found to be in very good agreement with experimental data. Furthermore, numerical predictions of the relationship between the air entrained into the fire compartment and the ventilation factor produce a characteristic linear correlation with constant of proportionality 0.38 kg/sm5/12. The simulation results also suggest that the model is capable of predicting the onset of "flashover" type behavior within the fire compartment.

Computational modelling of particle degradation in dilute phase pneumatic conveyors

The aim of this paper is to develop a mathematical model with the ability to predict particle degradation during dilute phase pneumatic conveying. A numerical procedure, based on a matrix representation of degradation processes, is presented to determine the particle impact degradation propensity from a small number of particle single impact tests carried out in a new designed laboratory scale degradation tester. A complete model of particle degradation during dilute phase pneumatic conveying is then described, where the calculation of degradation propensity is coupled with a flow model of the solids and gas phases in the pipeline. Numerical results are presented for degradation of granulated sugar in an industrial scale pneumatic conveyor.

Numerical predictions of particle degradation in industrial-scale pneumatic conveyors

This paper presents an Eulerian-based numerical model of particle degradation in dilute-phase pneumatic conveying systems including bends of different angles. The model shows reasonable agreement with detailed measurements from a pilot-sized pneumatic conveying system and a much larger scale pneumatic conveyor. The potential of the model to predict degradation in a large-scale conveying system from an industrial plant is demonstrated. The importance of the effect of the bend angle on the damage imparted to the particles is discussed.

Computational model for prediction of particle degradation during dilute phase pneumatic conveying: the use of a laboratory scale degradation tester for the determination of degradation propensity

The overall objective of this work is to develop a computational model of particle degradation during dilute-phasepneumatic conveying. A key feature of such a model is the prediction of particle breakage due to particle–wall collisions in pipeline bends. This paper presents a method for calculating particle impact degradation propensity under a range of particle velocities and particle sizes. It is based on interpolation on impact data obtained in a new laboratory-scale degradation tester. The method is tested and validated against experimental results for degradation at 90± impact angle of a full-size distribution sample of granulated sugar. In a subsequent work, the calculation of degradation propensity is coupled with a ow model of the solids and gas phases in the pipeline.

Computational model for prediction of particle degradation during dilute-phase pneumatic conveying: modeling of dilute-phase pneumatic conveying

A complete model of particle impact degradation during dilute-phase pneumatic conveying is developed, which combines a degradation model, based on the experimental determination of breakage matrices, and a physical model of solids and gas flow in the pipeline. The solids flow in a straight pipe element is represented by a model consisting of two zones: a strand-type flow zone immediately downstream of a bend, followed by a fully suspended flow region after dispersion of the strand. The breakage matrices constructed from data on 90° angle single-impact tests are shown to give a good representation of the degradation occurring in a pipe bend of 90° angle. Numerical results are presented for degradation of granulated sugar in a large scale pneumatic conveyor.

Ag+- and Zn2+-exchange kinetics and antimicrobial properties of 11 angstrom tobermorites

Ag+- and Zn2+-exchanged zeolites zeolites and clays have been used as coatings and in composites to confer broad-spectrum antimicrobial properties on a range of technical and biomedical materials. 11 angstrom tobermorite is a bioactive layer lattice ion exchanger whose potential as a carrier for Ag+ and Zn2+ ions in antimicrobial formulations has not yet been explored. In view of this, batch Ag+- and Zn2+-exchange kinetics of two structurally distinct synthetic 11 angstrom tobermorites and their subsequent bactericidal action against Staphylococcus aureus and Pseudomonas aeruginosa are reported. During the exchange reactions, Ag+ ions were found to replace labile interlayer cations; whereas, Zn2+ ions also displaced structural Ca2+ ions from the tobermorite lattice. In spite of these different mechanisms, a simple pseudo-second-order model provided a suitable description of both exchange processes (R-2 >= 0.996). The Ag+- and Zn2+-exchanged tobermorite phases exhibited marked bacteriostatic effects against both bacteria, and accordingly, their potential for use as antimicrobial materials for in situ bone tissue regeneration is discussed. (C) 2008 Elsevier Ltd. All rights reserved.

Application of particle swarm optimisation to evaluation of polymer cure kinetics models

A particle swarm optimisation approach is used to determine the accuracy and experimental relevance of six disparate cure kinetics models. The cure processes of two commercially available thermosetting polymer materials utilised in microelectronics manufacturing applications have been studied using a differential scanning calorimetry system. Numerical models have been fitted to the experimental data using a particle swarm optimisation algorithm which enables the ultimate accuracy of each of the models to be determined. The particle swarm optimisation approach to model fitting proves to be relatively rapid and effective in determining the optimal coefficient set for the cure kinetics models. Results indicate that the singlestep autocatalytic model is able to represent the curing process more accurately than more complex model, with ultimate accuracy likely to be limited by inaccuracies in the processing of the experimental data.