Rational design of a bacterial transcriptional cascade for amplifying gene expression capacity

Cascade regulatory circuits have been described that control numerous cell processes, and may provide models for the design of artificial circuits with novel properties. Here we describe the design of a transcriptional regulatory cascade to amplify the cell response to a given signal. We used the salicylate-responsive activators of Pseudomonas putida NahR of the naphthalene degradation plasmid NAH7 and XylS2, a mutant regulator of the TOL plasmid for catabolism of m-xylene and their respective cognate promoters Psal and Pm. Control of the expression of xylS2 with the nahR/Psal system permitted either their selective activation with specific effectors for each protein or the simultaneous activation of both of them with salicylate. When cells face the common effector of the two regulators, both the increase in XylS2 concentration and the stimulation of its activity act synergistically on the Pm promoter, amplifying the gene expression capacity by at least one order of magnitude with respect to the individual systems. By changing the hierarchy of regulators, we showed that the specific features of the downstream regulator were crucial for the amplification effect. Directed changes in the effector profile of the regulators allowed the extension of the amplifying system to other molecular signals.

Prediction of protein deamidation rates from primary and three-dimensional structure

A method for the quantitative estimation of instability with respect to deamidation of the asparaginyl (Asn) residues in proteins is described. The procedure involves the observation of several simple aspects of the three-dimensional environment of each Asn residue in the protein and a calculation that includes these observations, the primary amino acid residue sequence, and the previously reported complete set of sequence-dependent rates of deamidation for Asn pentapeptides. This method is demonstrated and evaluated for 23 proteins in which 31 unstable and 167 stable Asn residues have been reported and for 7 unstable and 63 stable Asn residues that have been reported in 61 human hemoglobin variants. The relative importance of primary structure and three-dimensional structure in Asn deamidation is estimated.

Y chromosome short arm-Sxr recombination in XSxr/Y males causes deletion of Rbm and XY female sex reversal.

We earlier described three lines of sex-reversed XY female mice deleted for sequences believed close to the testes-determining gene (Sry) on the Y chromosome short arm (Yp). The original sex-reversed females appeared among the offspring of XY males that carried the Yp duplication Sxr on their X chromosome. Earlier cytogenetic observations had suggested that the deletions resulted from asymmetrical meiotic recombination between the Y and the homologous Sxr region, but no direct evidence for this hypothesis was available. We have now analyzed the offspring of XSxr/Y males carrying an evolutionarily divergent Mus musculus domesticus Y chromosome, which permits detection and characterization of such recombination events. This analysis has enabled the derivation of a recombination map of Yp and Sxr, also demonstrating the orientation of Yp with respect to the Y centromere. The mapping data have established that Rbm, the murine homologue of a gene family cloned from the human Y chromosome, lies between Sry and the centromere. Analysis of two additional XY female lines shows that asymmetrical Yp-Sxr recombination leading to XY female sex reversal results in deletion of Rbm sequences. The deletions bring Sry closer to Y centromere, consistent with the hypothesis that position-effect inactivation of Sry is the basis for the sex reversal.

Comparison of the defensive elicitation activity of cerato-populin and cerato-platanin: a structural model

Plants can defend themselves from potential pathogenic microorganisms relying on a complex interplay of signaling pathways: activation of the MAPK cascade, transcription of defense related genes, production of reactive oxygen species, nitric oxide and synthesis of other defensive compounds such as phytoalexins. These events are triggered by the recognition of pathogen’s effectors (effector-triggered immunity) or PAMPs (PAMP-triggered immunity). The Cerato Platanin Family (CPF) members are Cys-rich proteins secreted and localized on fungal cell walls, involved in several aspects of fungal development and pathogen-host interactions. Although more than hundred genes of the CPF have been identified and analyzed, the structural and functional characterization of the expressed proteins has been restricted only to few members of the family. Interestingly, those proteins have been shown to bind chitin with diverse affinity and after foliar treatment they elicit defensive mechanisms in host and non-host plants. This property turns cerato platanins into interesting candidates, worth to be studied to develop new fungal elicitors with applications in sustainable agriculture. This study focus on cerato-platanin (CP), core member of the family and on the orthologous cerato-populin (Pop1). The latter shows an identity of 62% and an overall homology of 73% with respect to CP. Both proteins are able to induce MAPKs phosphorylation, production of reactive oxygen species and nitric oxide, overexpression of defense’s related genes, programmed cell death and synthesis of phytoalexins. CP, however, when compared to Pop1, induces a faster response and, in some cases, a stronger activity on plane leaves. Aim of the present research is to verify if the dissimilarities observed in the defense elicitation activity of these proteins can be associated to their structural and dynamic features. Taking advantage of the available CP NMR structure, Pop1’s 3D one was obtained by homology modeling. Experimental residual dipolar couplings and 1H, 15N, 13C resonance assignments were used to validate the model. Previous works on CPF members, addressed the highly conserved random coil regions (loops b1-b2 and b2-b3) as sufficient and necessary to induce necrosis in plants’ leaves: that region was investigated in both Pop1 and CP. In the two proteins the loops differ, in their primary sequence, for few mutations and an insertion with a consequent diversification of the proteins’ electrostatic surface. A set of 2D and 3D NMR experiments was performed to characterize both the spatial arrangement and the dynamic features of the loops. NOE data revealed a more extended network of interactions between the loops in Pop1 than in CP. In addition, in Pop1 we identified a salt bridge Lys25/Asp52 and a strong hydrophobic interaction between Phe26/Trp53. These structural features were expected not only to affect the loops’ spatial arrangement, but also to reduce the degree of their conformational freedom. Relaxation data and the order parameter S2 indeed highlighted reduced flexibility, in particular for loop b1-b2 of Pop1. In vitro NMR experiments, where Pop1 and CP were titrated with oligosaccharides, supported the hypothesis that the loops structural and dynamic differences may be responsible for the different chitin-binding properties of the two proteins: CP selectively binds tetramers of chitin in a shallow groove on one side of the barrel defined by loops b1-b2, b2-b3 and b4-b5, Pop1, instead, interacts in a non-specific fashion with oligosaccharides. Because the region involved in chitin-binding is also responsible for the defense elicitation activity, possibly being recognized by plant's receptors, it is reasonable to expect that those structural and dynamic modifications may also justify the different extent of defense elicitation. To test that hypothesis, the initial steps of a protocol aimed to the identify a receptor for CP, in silico, are presented.

On the stability of Voronoi cells

Let T be a given subset of ℝ n , whose elements are called sites, and let s∈T. The Voronoi cell of s with respect to T consists of all points closer to s than to any other site. In many real applications, the position of some elements of T is uncertain due to either random external causes or to measurement errors. In this paper we analyze the effect on the Voronoi cell of small changes in s or in a given non-empty set P⊂T\{s}. Two types of perturbations of P are considered, one of them not increasing the cardinality of T. More in detail, the paper provides conditions for the corresponding Voronoi cell mappings to be closed, lower and upper semicontinuous. All the involved conditions are expressed in terms of the data.

Quand la réadaptation blesse? Éducateurs victimes de violence

Cette étude vise à comprendre le phénomène de la violence physique vécue par les éducateurs oeuvrant dans dix Centres Jeunesse (CJ) du Québec. Pour ce faire, un sondage de victimisation a été administré à 586 éducateurs en internat. En premier lieu, la prévalence de cette problématique sera établie. Par la suite, les facteurs individuels et environnementaux prédisposant aux agressions physiques seront identifiés. Des éducateurs sondés, 53,9 % rapportent avoir été victimes de violence physique au cours de la dernière année. Sur le plan individuel, être affecté par les manifestations agressives des clients et la fréquence des violences psychologiques subies augmentent les risques de victimisation physique. Quant au contexte, l’âge de la clientèle et le motif de l’intervention (basé sur la loi justifiant le placement) auprès de l’enfant ou de l’adolescent influencent l’occurrence des actes violents dirigés contre les éducateurs. Nos analyses montrent également que les violences physiques dont sont victimes les éducateurs affectent autant l’individu que l’institution. L’identification de facteurs permettant de prédire les risques de victimisation pourrait notamment servir à orienter les programmes de prévention de la violence dans les CJ, mais aussi à cibler les éducateurs les plus à risque afin de leur fournir un soutien adapté.

Geochemistry of Baltic Sea sediments and porewaters

Patterns of regeneration and burial of phosphorus (P) in the Baltic Sea are strongly dependent on redox conditions. Redox varies spatially along water depth gradients and temporally in response to the seasonal cycle and multidecadal hydrographic variability. Alongside the well-documented link between iron oxyhydroxide dissolution and release of P from Baltic Sea sediments, we show that preferential remineralization of P with respect to carbon (C) and nitrogen (N) during degradation of organic matter plays a key role in determining the surplus of bioavailable P in the water column. Preferential remineralization of P takes place both in the water column and upper sediments and its rate is shown to be redox-dependent, increasing as reducing conditions become more severe at greater water-depth in the deep basins. Existing Redfield-based biogeochemical models of the Baltic may therefore underestimate the imbalance between N and P availability for primary production, and hence the vulnerability of the Baltic to sustained eutrophication via the fixation of atmospheric N. However, burial of organic P is also shown to increase during multidecadal intervals of expanded hypoxia, due to higher net burial rates of organic matter around the margins of the deep basins. Such intervals may be characterized by basin-scale acceleration of all fluxes within the P cycle, including productivity, regeneration and burial, sustained by the relative accessibility of the water column P pool beneath a shallow halocline.

Theological views : comprising the substance of teachings during a ministry of thirty-five years, in New Orleans /

The existence and attributes of God -- The Bible -- Christian miracles -- Objections to the miracles of the New Testament answered -- Thoughts on the subject of sin -- The teachings of Scripture concerning punishment -- An examination of some of the erroneous interpretations of Scripture with respect to future retribution -- Exposition of Matthew 25:41 -- Parable of Dives and Lazarus -- The teachings of Jesus and his Apostles concerning the Resurrection and a future state -- On grace.

Treatment of dementia with neurotransmission modulation

The prevalence of dementia is growing in developed countries where elderly patients are increasing in numbers. Neurotransmission modulation is one approach to the treatment of dementia. Cholinergic precursors, anticholinesterases, nicotine receptor agonists and muscarinic M-2 receptor antagonists are agents that enhance cholinergic neurotransmission and that depend on having some intact cholinergic innervation to be effective in the treatment of dementia. The cholinergic precursor choline alfoscerate may be emerging as a potential useful drug in the treatment of dementia, with few adverse effects. Of the anticholinesterases, donepezil, in addition to having a similar efficacy to tacrine in mild-to-moderate Alzheimer's disease (AD), appears to have major advantages; its use is associated with lower drop-out rates in clinical trials, a lower incidence of cholinergic-like side effects and no liver toxicity. Rivastigmine is efficacious in the treatment in dementia with Lewy bodies, a condition in which the other anticholinesterases have not been tested extensively to date. Galantamine is an anticholinesterase and also acts as an allosteric potentiating modulator at nicotinic receptors to increase the release of acetylcholine. Pooled data from clinical trials of patients with mild-to-moderate AD suggest that the benefits and safety profile of galantamine are similar to those of the anticholinesterases. Selective nicotine receptor agonists are being developed that enhance cognitive performance without influencing autonomic and skeletal muscle function, but these have not yet entered clinical trial for dementia. Unlike the cholinergic enhancers, the M, receptor agonists do not depend upon intact cholinergic nerves but on intact M, receptors for their action, which are mainly preserved in AD and dementia with Lewy bodies. The M, receptor-selective agonists developed to date have shown limited efficacy in clinical trials and have a high incidence of side effects. A major recent advancement in the treatment of dementia is memantine, a non-competitive antagonist at NMDA receptors. Memantine is beneficial in the treatment of severe and moderate to-severe AD and may also be of some benefit in the treatment of mild-to-moderate vascular dementia. Drugs that modulate 5-HT, somatostatin and noradrenergic neurotransmission are also being considered for the treatment of dementia.

Matching conditional moments in PDF modelling of nonpremixed combustion

The rate of generation of fluctuations with respect to the scalar values conditioned on the mixture fraction, which significantly affects turbulent nonpremixed combustion processes, is examined. Simulation of the rate in a major mixing model is investigated and the derived equations can assist in selecting the model parameters so that the level of conditional fluctuations is better reproduced by the models. A more general formulation of the multiple mapping conditioning (MMC) model that distinguishes the reference and conditioning variables is suggested. This formulation can be viewed as a methodology of enforcing certain desired conditional properties onto conventional mixing models. Examples of constructing consistent MMC models with dissipation and velocity conditioning as well as of combining MMC with large eddy simulations (LES) are also provided. (c) 2005 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Stoichiometric and kinetic characterisation of Nitrobacter in mixed culture by decoupling the growth and energy generation processes

The growth, maintenance and lysis processes of Nitrobacter were characterised. A Nitrobacter culture was enriched in a sequencing batch reactor (SBR). Fluorescent in situ hybridisation showed that Nitrobacter constituted 73% of the bacterial population. Batch tests were carried out to measure the oxygen uptake rate and/or nitrite consumption rate when both nitrite and CO2 were in excess, and in the absence of either of these two substrates. The results obtained, along with the SBR performance data, allowed the determination of the maintenance coefficient and in situ cell lysis rate of Nitrobacter. Nitrobacter spends a significant amount of energy for maintenance, which varies considerably with the specific growth rate. At maximum growth, Nitrobacter consume nitrite at a rate of 0.042 mgN/mgCOD(biomass)center dot h for maintenance purposes, which increases more than threefold to 0.143 mgN/mgCOD(biomass)center dot h in the absence of growth. In the SBR, where Nitrobacter grew at 40% of its maximum growth rate, a maintenance coefficient of 0.113 mgN/mgCOD center dot h was found, resulting in 42% of the total amount of nitrite being consumed for maintenance. The above three maintenance coefficient values obtained at different growth rates appear to support the maintenance model proposed in Pirt (1982). The in situ lysis rate of Nitrobacter was determined to be 0.07/day under aerobic conditions at 22 C and pH 7.3. Further, the maximum specific growth rate of Nitrobacter was estimated to be 0.02/h (0.48/day). The affinity constant of Nitrobacter with respect to nitrite was determined to be 1.50 mgNO(2)(-)-N/L, independent of the presence or absence of CO2. (c) 2006 Wiley Periodicals, Inc.

Should an oral glucose tolerance test be performed routinely in all renal transplant recipients?

Posttransplantation diabetes (PTD) contributes to cardiovascular disease and graft loss in renal transplant recipients (RTR). Current recommendations advise fasting blood glucose (FBG) as the screening and diagnostic test of choice for PTD. This study sought to determine (1) the predictive power of FBG with respect to 2-h blood glucose (2HBG) and (2) the prevalence of PTD using FBG and 2HBG compared with that using FBG alone, in prevalent RTR. A total of 200 RTR (mean age 52 yr; 59% male; median transplant duration 6.6 yr) who were >6 mo posttransplantation and had no known history of diabetes were studied. Patients with FBG

Statistical mechanics of distribution networks

This thesis presents an analysis of the stability of complex distribution networks. We present a stability analysis against cascading failures. We propose a spin [binary] model, based on concepts of statistical mechanics. We test macroscopic properties of distribution networks with respect to various topological structures and distributions of microparameters. The equilibrium properties of the systems are obtained in a statistical mechanics framework by application of the replica method. We demonstrate the validity of our approach by comparing it with Monte Carlo simulations. We analyse the network properties in terms of phase diagrams and found both qualitative and quantitative dependence of the network properties on the network structure and macroparameters. The structure of the phase diagrams points at the existence of phase transition and the presence of stable and metastable states in the system. We also present an analysis of robustness against overloading in the distribution networks. We propose a model that describes a distribution process in a network. The model incorporates the currents between any connected hubs in the network, local constraints in the form of Kirchoff's law and a global optimizational criterion. The flow of currents in the system is driven by the consumption. We study two principal types of model: infinite and finite link capacity. The key properties are the distributions of currents in the system. We again use a statistical mechanics framework to describe the currents in the system in terms of macroscopic parameters. In order to obtain observable properties we apply the replica method. We are able to assess the criticality of the level of demand with respect to the available resources and the architecture of the network. Furthermore, the parts of the system, where critical currents may emerge, can be identified. This, in turn, provides us with the characteristic description of the spread of the overloading in the systems.

Efficient 2.87 μm fiber laser passively switched using a semiconductor saturable absorber mirror

A passively switched Ho3+, Pr3+ codoped fluoride fiber laser using a semiconductor saturable absorber mirror (SESAM) is demonstrated. Q-switching and partial mode-locking were observed with the output power produced at a slope efficiency of 24% with respect to the absorbed pump power. The partially mode-locked 2.87 µm pulses operated at a repetition rate of 27.1 MHz with an average power of 132 mW, pulse energy of 4.9 nJ, and pulse width of 24 ps.

A fast XPS study of sulphate promoted propene decomposition over Pt{111}

SO2 oxidation has been followed by Fast XPS over Pt{111}. Preadsorbed oxygen reduces the low temperature saturation coverage of SO2 with respect to the clean surface. Heating a mixed O2/SO2 adlayer results in efficient oxidation of both upright and flat-lying SO2 molecules to surface-bound SO4. Sulphate decomposes above room temperature liberating gas-phase SO2 and SO3. Propene adsorbs molecularly at 100 K over clean Pt{111} and dehydrogenates above 250 K to form a stable propylidyne adlayer, which in turn decomposes above 400 K to form graphitic carbon. Preadsorbed surface sulphate enhances the sticking probability of propene via formation of an alkyl-sulphate complex. Thermal decomposition of this complex accounts for low temperature propene combustion and is accompanied by atomic sulpur deposition. Propylidyne forms as on clean Pt but is less reactive undergoing partial oxidation above 450 K with residual surface oxygen.