Different Mechanisms Confer Gradual Control and Memory at Nutrient- and Stress-Regulated Genes in Yeast.

Cells respond to environmental stimuli by fine-tuned regulation of gene expression. Here we investigated the dose-dependent modulation of gene expression at high temporal resolution in response to nutrient and stress signals in yeast. The GAL1 activity in cell populations is modulated in a well-defined range of galactose concentrations, correlating with a dynamic change of histone remodeling and RNA polymerase II (RNAPII) association. This behavior is the result of a heterogeneous induction delay caused by decreasing inducer concentrations across the population. Chromatin remodeling appears to be the basis for the dynamic GAL1 expression, because mutants with impaired histone dynamics show severely truncated dose-response profiles. In contrast, the GRE2 promoter operates like a rapid off/on switch in response to increasing osmotic stress, with almost constant expression rates and exclusively temporal regulation of histone remodeling and RNAPII occupancy. The Gal3 inducer and the Hog1 mitogen-activated protein (MAP) kinase seem to determine the different dose-response strategies at the two promoters. Accordingly, GAL1 becomes highly sensitive and dose independent if previously stimulated because of residual Gal3 levels, whereas GRE2 expression diminishes upon repeated stimulation due to acquired stress resistance. Our analysis reveals important differences in the way dynamic signals create dose-sensitive gene expression outputs.

A computational model for defect prediction in shape castings based on the interaction of free surface flow, heat transfer, and solidification phenomena

High-integrity castings require sophisticated design and manufacturing procedures to ensure they are essentially macrodefect free. Unfortunately, an important class of such defects—macroporosity, misruns, and pipe shrinkage—are all functions of the interactions of free surface flow, heat transfer, and solidication in complex geometries. Because these defects arise as an interaction of the preceding continuum phenomena, genuinely predictive models of these defects must represent these interactions explicitly. This work describes an attempt to model the formation of macrodefects explicitly as a function of the interacting continuum phenomena in arbitrarily complex three-dimensional geometries. The computational approach exploits a compatible set of finite volume procedures extended to unstructured meshes. The implementation of the model is described together with its testing and a measure of validation. The model demonstrates the potential to predict reliably shrinkage macroporosity, misruns, and pipe shrinkage directly as a result of interactions among free-surface fluid flow, heat transfer, and solidification.

Design for reliability for wafer level system in package

This paper discusses the Design for Reliability modelling of several System-in-Package (SiP) structures developed by NXP and advanced on the basis of Wafer Level Packaging (WLP). Two different types of Wafer Level SiP (WLSiP) are presented and discussed. The main focus is on the modelling approach that has been adopted to investigate and analyse the board level reliability of the presented SiP configurations. Thermo-mechanical non-linear Finite Element Analysis (FEA) is used to analyse the effect of various package design parameters on the reliability of the structures and to identify design trends towards package optimisation. FEA is used also to gain knowledge on moulded wafer shrinkage and related issues during the wafer level fabrication. The paper provides a brief outline and demonstration of a design methodology for reliability driven design optimisation of SiP. The study emphasises the advantages of applying the methodology to address complex design problems where several requirements may exist and uncertainties and interactions between parameters in the design are common.

Probabilistic modeling of structural deterioration of reinforced concrete beams under saline environment corrosion

For existing reinforced concrete structures exposed to saline or marine conditions, there is an increasing engineering interest in their remaining safety and serviceability. A significant factor is the corrosion of steel reinforcement. At present there is little field experience and other data available. This limits the possibility for developing purely empirical models for strength and performance deterioration for use in structural safety and serviceability assessment. An alternative approach using theoretical concepts and probabilistic modeling is proposed herein. It is based on the evidence that the rate of diffusion of chlorides is influenced by internal damage to the concrete surrounding the reinforcement. This may be due to localized stresses resulting from external loading or through concrete shrinkage. Usually, the net effect is that the time to initiation of active corrosion is shortened, leading to greater localized corrosion and earlier reduction of ultimate capacity and structural stiffness. The proposed procedure is applied to an example beam and compared to experimental observations,including estimates of uncertainty in the remaining ultimate moment capacity and beam stiffness. Reasonably good agreement between the results of the proposed procedure and the experiment was found

1H NMR metabolomics reveals contrasting response by male and female mussels exposed to reduced seawater pH, increased temperature and a pathogen

Human activities are fundamentally altering the chemistry of the world's oceans. Ocean acidification (OA) is occurring against a background of warming and an increasing occurrence of disease outbreaks, posing a significant threat to marine organisms, communities, and ecosystems. In the current study, (1)H NMR spectroscopy was used to investigate the response of the blue mussel, Mytilus edulis, to a 90-day exposure to reduced seawater pH and increased temperature, followed by a subsequent pathogenic challenge. Analysis of the metabolome revealed significant differences between male and female organisms. Furthermore, males and females are shown to respond differently to environmental stress. While males were significantly affected by reduced seawater pH, increased temperature, and a bacterial challenge, it was only a reduction in seawater pH that impacted females. Despite impacting males and females differently, stressors seem to act via a generalized stress response impacting both energy metabolism and osmotic balance in both sexes. This study therefore has important implications for the interpretation of metabolomic data in mussels, as well as the impact of environmental stress in marine invertebrates in general.

A polysaccharide extracted from sphagnum moss as antifungal agent in archaeological conservation

On the basis of the well-known preservative properties of Sphagnum moss, a potential opportunity to use moss polysaccharides (Sphagnan) in art conservation was tested. Polysaccharides were extracted from the moss (S. palustre spp.) in the amount of 4.1% of the Sphagnum plant dry weight. All lignocelluloses were removed from this extract as a result of the treatment of the moss cellulose with sodium chlorite. The extracted polysaccharide possessed a strong acidic reaction (pH 2.8) and was soluble in water and organic solvents. The extract was tested on laboratory bacterial cultures by the disk-diffusion method. The antibacterial effect was demonstrated for E. coli and P. aeruginosa (both gram-negative) while Staphylococcus aurelus (gram-positive) was shown to be insensitive to Sphagnum polysaccharides. The antifungal effect of Sphagnum extract was tested by the disk-diffusion method on the spores of seventeen fungal species. These fungi were isolated from ethnographic museum objects and from archaeological objects excavated in the Arctic. Twelve of these isolates appeared susceptible to the extract. The inhibiting effect of the extract was also tested by the modified broth-dilution method on the most typical isolate (Aspergillus spp.). In this experiment, in one ml of the nutritious broth, 40µl of 3% solution of polysaccharides in water killed 10,000 fungal spores in 6 hours. The inhibiting effect was not connected to the acidity or osmotic effect of Sphagnum polysaccharides. As an example of the application of Sphagnum polysaccharides in art conservation, they were added as preservative agents to conservation waxes. After three weeks of exposure of microcrystalline wax to test fungi (Aspergillus spp.), 44% of wax was consumed. When, however, ~ 0.1% (w/w) of Sphagnum extract was mixed with wax, the weight loss of wax was only 4% in the same time interval. On the basis of this study it was concluded that Sphagnum moss and Sphagnum products can be recommended for use in art conservation as antifungal agents.

Alternative transcription factor sigma(B) is involved in regulation of biofilm expression in a Staphylococcus aureus mucosal isolate.

Rachid S, Ohlsen K, Wallner U, Hacker J, Hecker M, Ziebuhr W. Institut für Molekulare Infektionsbiologie, D-97070 Würzburg, Germany. Osmotic stress was found to induce biofilm formation in a Staphylococcus aureus mucosal isolate. Inactivation of a global regulator of the bacterial stress response, the alternative transcription factor sigma(B), resulted in a biofilm-negative phenotype and loss of salt-induced biofilm production. Complementation of the mutant strain with an expression plasmid encoding sigma(B) completely restored the wild-type phenotype. The combined data suggest a critical role of sigma(B) in S. aureus biofilm regulation under environmental stress conditions.

Thermodynamic Studies of Ionic Interactions in Aqueous Solutions of Imidazolium-Based Ionic Liquids [Emim][Br] and [Bmim][Cl]

Experimental measurements of density at different temperatures ranging from 293.15 to 313.15 K, the speed of sound and osmotic coefficients at 298.15 K for aqueous solution of 1-ethyl-3-methylimidazolium bromide ([Emim][Br]), and osmotic coefficients at 298.15 K for aqueous solutions of 1-butyl-3-methylimidazolium chloride ([Bmim][Cl]) in the dilute concentration region are taken. The data are used to obtain compressibilities, expansivity, apparent and limiting molar properties, internal pressure, activity, and activity coefficients for [Emim][Br] in aqueous solutions. Experimental activity coefficient data are compared with that obtained from Debye-Hückel and Pitzer models. The activity data are further used to obtain the hydration number and the osmotic second virial coefficients of ionic liquids. Partial molar entropies of [Bmim][Cl] are also obtained using the free-energy and enthalpy data. The distance of the closest approach of ions is estimated using the activity data for ILs in aqueous solutions and is compared with that of X-ray data analysis in the solid phase. The measured data show that the concentration dependence for aqueous solutions of [Emim][Br] can be accounted for in terms of the hydrophobic hydration of ions and that this IL exhibits Coulombic interactions as well as hydrophobic hydration for both the cations and anions. The small hydration numbers for the studied ILs indicate that the low charge density of cations and their hydrophobic nature is responsible for the formation of the water-structure-enforced ion pairs.

Phenotypic diversity amongst strains of Pleurotus sajor-caju: implications for cultivation in and environments

In arid regions, biodiversity and biomass are limited by water availability, and this problem has been compounded by desertification associated with global climate change. The saprotrophic macrofungi that are indigenous to hot subtropical and tropical regions, such as Pleurotus spp., can play key roles in water sequestration, nutrient cycling, human nutrition, and bioremediation of waste materials. We studied 15 strains of Pleurotus sajor-caju, a widespread and phenotypically-diverse species, to establish variability in growth response and primordium development over a range of stress parameters: osmotic potential (-0.5 to -5 MPa), temperature (5-40 degrees C) and pH (2-12). The initiation of primordia precedes basidiome production and therefore represents a key stage in bioremediation strategies and fungi-driven nutrient cycles. Primordia were produced at low pH (4-6), at suboptimal growth temperatures (<or =25 degrees C), and under moderate water stress (-0.5 to -3.5 MPa). Although the growth windows for different strains were similar, their maximum growth rates and the optimum conditions for growth varied. We discuss the phenotypic diversity of Pleurotus strains and discuss their potential for cultivation, bioremediation and ecological regeneration.

Analysis of malts by capillary electrophoresis

A range of malts, as well as their high- and low-molecular-mass fractions, has been examined by capillary electrophoresis in phosphate buffer, pH 2.5, and in carbonate buffer, pH 9.5, and the results have been compared with those for roasted barley and for caramels. The malts fall into two categories: (i) the lightly roasted malts, where the high-molecular-mass coloured fraction is negatively charged at pH 9.5 and positively charged at pH 2.5; and (ii) the highly roasted malts (and the roasted barley), where the high-molecular-mass fraction migrates close to the electro-osmotic flow at both pH 9.5 and 2.5, implying that it carries little or no charge. The former category shows migration patterns similar to Class III caramels, whereas the latter migrates differently from Class I, III and IV caramels as well as from the former. Capillary electrophoresis therefore has considerable potential for differentiating between malts and between malts and caramels and roasted barley. (C) 2002 Society of Chemical Industry.

The relationship between cement fatigue damage and implant surface finish in proximal femoral prostheses

The majority of cemented femoral hip replacements fail as a consequence of loosening. One design feature that may affect loosening rates is implant surface finish. To determine whether or not surface finish effects fatigue damage accumulation in a bone cement mantle, we developed an experimental model of the implanted proximal femur that allows visualisation of damage growth in the cement layer. Five matt surface and five polished surface stems were tested. Pre-load damage and damage after two million cycles was measured. Levels of pre-load (shrinkage) damage were the same for both matt and polished stems; furthermore damage for matt vs. polished stems was not significantly different after two million cycles. This was due to the large variability in damage accumulation rates. Finite element analysis showed that the stress is higher for the polished (assumed debonded) stem, and therefore we must conclude that either the magnitude of the stress increase is not enough to appreciably increase the damage accumulation rate or, alternatively, the polished stem does not debond immediately from the cement. Significantly (P = 0.05) more damage was initiated in the lateral cement compared to the medial cement for both kinds of surface finish. It was concluded that, despite the higher cement stresses with debonded stems, polished prostheses do not provoke the damage accumulation failure scenario. (C) 2003 IPEM. Published by Elsevier Ltd. All rights reserved.

Residual stress due to curing can initiate damage in porous bone cement: experimental and theoretical evidence

Residual stress due to shrinkage of polymethylmethacrylate bone cement after polymerisation is possibly one factor capable of initiating cracks in the mantle of cemented hip replacements. No relationship between residual stress and observed cracking of cement has yet been demonstrated. To investigate if any relationship exists, a physical model has been developed which allows direct observation of damage in the cement layer on the femoral side of total hip replacement. The model contains medial and lateral cement layers between a bony surface and a metal stem; the tubular nature of the cement mantle is ignored. Five specimens were prepared and examined for cracking using manual tracing of stained cracks, observed by transmission microscopy: cracks were located and measured using image analysis. A mathematical approach for the prediction of residual stress due to shrinkage was developed which uses the thermal history of the material to predict when stress-locking occurs, and estimates subsequent thermal stress. The residual stress distribution of the cement layer in the physical model was then calculated using finite element analysis. Results show maximum tensile stresses normal to the observed crack directions, suggesting a link between residual stress and preload cracking. The residual stress predicted depends strongly on the definition of the reference temperature for stress-locking. The highest residual stresses (4-7 MPa) are predicted for shrinkage from maximum temperature, in this case, magnitudes are sufficiently high to initiate cracks when the influence of stress raisers such as pores or interdigitation at the bone/cement interface are taken into account (up to 24 MPa when calculating stress around a pore according to the method of Harrigan and Harris (J. Biomech. 24(11) (1991) 1047-1058)). We conclude that the damage accumulation failure scenario begins before weight-bearing due to cracking induced by residual stress around pores or stress raisers. (C) 2002 Elsevier Science Ltd. All rights reserved.

The control of porosity at nano scale in resorcinol formaldehyde carbon aerogels

Organic aerogels were synthesized by sol–gel polymerization of resorcinol (R) with formaldehyde (F) catalyzed by sodium carbonate (C) followed by vacuum drying. The influence of the resorcinol/sodium carbonate ratio (R/C) on the porous structure of the resultant aerogels was investigated. The nitrogen adsorption–desorption measurements show that the aerogels possess a well developed porous structure and mesoporosity was found to increase with increasing the R/C ratio. Carbon aerogels were obtained by carbonization of RF aerogels. The carbonization temperature impacts the microstructure of the aerogels by pore transformations during carbonization probably due to the formation of micropores and shrinkage of the gel structure. The results showed that a temperature of 1073 Kis more effective in the development of the pore structure of the gel. Activated carbon aerogels were obtained from the CO2 activation of carbon aerogels. Activation results in an increase in the number of both micropores and mesopores, indicative of pore creation in the structure of the carbon. Activation at higher temperatures results in a higher degree of burn off and increases the pore volume and the surface area remarkably without change of the basic porous structure, pore size, and pore size distribution.

Hydrophobic substances induce water stress in microbial cells

Ubiquitous noxious hydrophobic substances, such as hydrocarbons, pesticides and diverse industrial chemicals, stress biological systems and thereby affect their ability to mediate biosphere functions like element and energy cycling vital to biosphere health. Such chemically diverse compounds may have distinct toxic activities for cellular systems; they may also share a common mechanism of stress induction mediated by their hydrophobicity. We hypothesized that the stressful effects of, and cellular adaptations to, hydrophobic stressors operate at the level of water : macromolecule interactions. Here, we present evidence that: (i) hydrocarbons reduce structural interactions within and between cellular macromolecules, (ii) organic compatible solutes-metabolites that protect against osmotic and chaotrope-induced stresses-ameliorate this effect, (iii) toxic hydrophobic substances induce a potent form of water stress in macromolecular and cellular systems, and (iv) the stress mechanism of, and cellular responses to, hydrophobic substances are remarkably similar to those associated with chaotrope-induced water stress. These findings suggest that it may be possible to devise new interventions for microbial processes in both natural environments and industrial reactors to expand microbial tolerance of hydrophobic substances, and hence the biotic windows for such processes.

Burkholderia cenocepacia requires RpoE for growth under stress conditions and delay of phagolysosomal fusion in macrophages

Burkholderia cenocepacia is an opportunistic pathogen causing serious infections in patients with cystic fibrosis. The widespread distribution of this bacterium in the environment suggests that it must adapt to stress to be able to survive. We identified in B. cenocepacia K56-2 a gene predicted to encode RpoE, the extra-cytoplasmic stress response regulator. The rpoE gene is the first gene of a predicted operon encoding proteins homologous to RseA, RseB, MucD and a protein of unknown function. The genomic organization and the co-transcription of these genes were confirmed by PCR and RT-PCR. The mucD and rpoE genes were mutated, giving rise to B. cenocepacia RSF24 and RSF25, respectively. While mutant RSF24 did not demonstrate any growth defects under the conditions tested, RSF25 was compromised for growth under temperature (44 degrees C) and osmotic stress (426 mM NaCl). Expression of RpoE in trans could complement the osmotic growth defect but exacerbated temperature sensitivity in both RSF25 and wild-type K56-2. Inactivation of rpoE altered the bacterial cell surface, as indicated by increased binding of the fluorescent dye calcofluor white and by an altered outer-membrane protein profile. These cell surface changes were restored by complementation with a plasmid encoding rpoE. Macrophage infections in which bacterial colocalization with fluorescent dextran was examined demonstrated that the rpoE mutant could not delay the fusion of B. cenocepacia-containing vacuoles with lysosomes, in contrast to the parental strain K56-2. These data show that B. cenocepacia rpoE is required for bacterial growth under certain stress conditions and for the ability of intracellular bacteria to delay phagolysosomal fusion in macrophages.