Cellular automaton model for molecular traffic jams

We consider the time evolution of an exactly solvable cellular automaton with random initial conditions both in the large-scale hydrodynamic limit and on the microscopic level. This model is a version of the totally asymmetric simple exclusion process with sublattice parallel update and thus may serve as a model for studying traffic jams in systems of self-driven particles. We study the emergence of shocks from the microscopic dynamics of the model. In particular, we introduce shock measures whose time evolution we can compute explicitly, both in the thermodynamic limit and for open boundaries where a boundary-induced phase transition driven by the motion of a shock occurs. The motion of the shock, which results from the collective dynamics of the exclusion particles, is a random walk with an internal degree of freedom that determines the jump direction. This type of hopping dynamics is reminiscent of some transport phenomena in biological systems.

Evidence of prognostic relevant expression profiles of heat-shock proteins and glucose-regulated proteins in oesophageal adenocarcinomas

A high percentage of oesophageal adenocarcinomas show an aggressive clinical behaviour with a significant resistance to chemotherapy. Heat-shock proteins (HSPs) and glucose-regulated proteins (GRPs) are molecular chaperones that play an important role in tumour biology. Recently, novel therapeutic approaches targeting HSP90/GRP94 have been introduced for treating cancer. We performed a comprehensive investigation of HSP and GRP expression including HSP27, phosphorylated (p)-HSP27((Ser15)), p-HSP27((Ser78)), p-HSP27((Ser82)), HSP60, HSP70, HSP90, GRP78 and GRP94 in 92 primary resected oesophageal adenocarcinomas by using reverse phase protein arrays (RPPA), immunohistochemistry (IHC) and real-time quantitative RT-PCR (qPCR). Results were correlated with pathologic features and survival. HSP/GRP protein and mRNA expression was detected in all tumours at various levels. Unsupervised hierarchical clustering showed two distinct groups of tumours with specific protein expression patterns: The hallmark of the first group was a high expression of p-HSP27((Ser15, Ser78, Ser82)) and low expression of GRP78, GRP94 and HSP60. The second group showed the inverse pattern with low p-HSP27 and high GRP78, GRP94 and HSP60 expression. The clinical outcome for patients from the first group was significantly improved compared to patients from the second group, both in univariate analysis (p = 0.015) and multivariate analysis (p = 0.029). Interestingly, these two groups could not be distinguished by immunohistochemistry or qPCR analysis. In summary, two distinct and prognostic relevant HSP/GRP protein expression patterns in adenocarcinomas of the oesophagus were detected by RPPA. Our approach may be helpful for identifying candidates for specific HSP/GRP-targeted therapies.

Influence of ageing, heat shock treatment and in vivo total antioxidant status on gene-expression profile and protein synthesis in human peripheral lymphocytes

Ageing results in a progressive, intrinsic and generalised imbalance of the control of regulatory systems. A key manifestation of this complex biological process includes the attenuation of the universal stress response. Here we provide the first global assessment of the ageing process as it affects the heat shock response, utilising human peripheral lymphocytes and cDNA microarray analysis. The genomic approach employed in our preliminary study was supplemented with a proteomic approach. In addition, the current study correlates the in vivo total antioxidant status with the age-related differential gene expression as well as the translational kinetics of heat shock proteins (hsps). Most of the genes encoding stress response proteins on the 4224 element microarray used in this study were significantly elevated after heat shock treatment of lymphocytes obtained from both young and old individuals albeit to a greater extent in the young. Cell signaling and signal transduction genes as well as some oxidoreductases showed varied response. Results from translational kinetics of induction of major hsps, from 0 to 24 It recovery period were broadly consistent with the differential expression of HSC 70 and HSP 40 genes. Total antioxidant levels in plasma from old individuals were found to be significantly lower by comparison with young, in agreement with the widely acknowledged role of oxidant homeostasis in the ageing process. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.

Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock

Background: Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profile of changes to the expression levels of genes coding for enzymes of the glycolytic pathway and some of its branches. The experimental determination of changes in gene expression profiles provides a descriptive picture of the adaptive response to stress. However, it does not explain why a particular profile is selected for any given response. Results: We used mathematical models and analysis of in silico gene expression profiles (GEPs) to understand how changes in gene expression correlate to an efficient response of yeast cells to heat shock. An exhaustive set of GEPs, matched with the corresponding set of enzyme activities, was simulated and analyzed. The effectiveness of each profile in the response to heat shock was evaluated according to relevant physiological and functional criteria. The small subset of GEPs that lead to effective physiological responses after heat shock was identified as the result of the tuning of several evolutionary criteria. The experimentally observed transcriptional changes in response to heat shock belong to this set and can be explained by quantitative design principles at the physiological level that ultimately constrain changes in gene expression. Conclusion: Our theoretical approach suggests a method for understanding the combined effect of changes in the expression of multiple genes on the activity of metabolic pathways, and consequently on the adaptation of cellular metabolism to heat shock. This method identifies quantitative design principles that facilitate understating the response of the cell to stress.

Modelling the line variations from the wind-wind shock emissions of WR 30a

The study of Wolf-Rayet stars plays an important role in evolutionary theories of massive stars. Among these objects, similar to 20 per cent are known to be in binary systems and can therefore be used for the mass determination of these stars. Most of these systems are not spatially resolved and spectral lines can be used to constrain the orbital parameters. However, part of the emission may originate in the interaction zone between the stellar winds, modifying the line profiles and thus challenging us to use different models to interpret them. In this work, we analysed the He II lambda 4686 angstrom + C IV lambda 4658 angstrom blended lines of WR 30a (WO4+O5) assuming that part of the emission originate in the wind-wind interaction zone. In fact, this line presents a quiescent base profile, attributed to the WO wind, and a superposed excess, which varies with the orbital phase along the 4.6-d period. Under these assumptions, we were able to fit the excess spectral line profile and central velocity for all phases, except for the longest wavelengths, where a spectral line with constant velocity seems to be present. The fit parameters provide the eccentricity and inclination of the binary orbit, from which it is possible to constrain the stellar masses.

Dimorphism, thermal tolerance, virulence and Heat shock protein 70 transcription in different isolates of Paracoccidioides brasiliensis

The mycelia-to-yeast (M-Y) transition, thermal tolerance and virulence profiles were evaluated for nine isolates of Paracoccidioides brasiliensis, including samples from two of the three recently discovered cryptic species, as well as their relation to the partial sequence and transcription of the hsp70 gene. The isolates Bt84 and T10 (from PS2 species) took more time to convert to yeast form and presented elongated yeast cells at 36 degrees C. Arthroconidia production was also observed during the M-Y transition for some isolates. Our data confirm that the hsp70 transcription may be associated with thermal tolerance, but this does not seem to be directly related to high virulence profiles. The partial sequencing of this gene allowed the separation of our isolates into two clusters that correspond to the two sympatric cryptic species occurring in an area hyperendemic for PCM (Botucatu, SP, Brazil).

Regulation of the heat shock response by thiol-reactive compounds in the yeast Saccharomyces cerevisiae

Cells govern their activities and modulate their interactions with the environment to achieve homeostasis. The heat shock response (HSR) is one of the most well studied fundamental cellular responses to environmental and physiological challenges, resulting in rapid synthesis of heat shock proteins (HSPs), which serve to protect cellular constituents from the deleterious effects of stress. In addition to its role in cytoprotection, the HSR also influences lifespan and is associated with a variety of human diseases including cancer, aging and neurodegenerative disorders. In most eukaryotes, the HSR is primarily mediated by the highly conserved transcription factor HSF1, which recognizes target hsp genes by binding to heat shock elements (HSEs) in their promoters. In recent years, significant efforts have been made to identify small molecules as potential pharmacological activators of HSF1 that could be used for therapeutic benefit in the treatment of human diseases relevant to protein conformation. However, the detailed mechanisms through which these molecules drive HSR activation remain unclear. In this work, I utilized the baker's yeast Saccharomyces cerevisiae as a model system to identify a group of thiol-reactive molecules including oxidants, transition metals and metalloids, and electrophiles, as potent activators of yeast Hsf1. Using an artificial HSE-lacZ reporter and the glucocorticoid receptor system (GR), these diverse thiol-reactive compounds are shown to activate Hsf1 and inhibit Hsp90 chaperone complex activity in a reciprocal, dose-dependent manner. To further understand whether cells sense these reactive compounds through accumulation of unfolded proteins, the proline analog azetidine-2-carboxylic acid (AZC) and protein cross-linker dithiobis(succinimidyl propionate) (DSP) were used to force misfolding of nascent polypeptides and existing cytosolic proteins, respectively. Both unfolding reagents display kinetic HSP induction profiles dissimilar to those generated by thiol-reactive compounds. Moreover, AZC treatment leads to significant cytotoxicity, which is not observed in the presence of the thiol-reactive compounds at the concentrations sufficient to induce Hsf1. Additionally, DSP treatment has little to no effect on Hsp90 functions. Together with the ultracentrifugation analysis of cell lysates that detected no insoluble protein aggregates, my data suggest that at concentrations sufficient to induce Hsf1, thiol-reactive compounds do not induce the HSR via a mechanism based on accumulation of unfolded cytosolic proteins. Another possibility is that thiol-reactive compounds may influence aspects of the protein quality control system such as the ubiquitin-proteasome system (UPS). To address this hypothesis, β-galactosidase reporter fusions were used as model substrates to demonstrate that thiol-reactive compounds do not inhibit ubiquitin activating enzymes (E1) or proteasome activity. Therefore, thiol-reactive compounds do not activate the HSR by inhibiting UPS-dependent protein degradation. I therefore hypothesized that these molecules may directly inactivate protein chaperones, known as repressors of Hsf1. To address this possibility, a thiol-reactive biotin probe was used to demonstrate in vitro that the yeast cytosolic Hsp70 Ssa1, which partners with Hsp90 to repress Hsf1, is specifically modified. Strikingly, mutation of conserved cysteine residues in Ssa1 renders cells insensitive to Hsf1 activation by cadmium and celastrol but not by heat shock. Conversely, substitution with the sulfinic acid and steric bulk mimic aspartic acid led to constitutive activation of Hsf1. Cysteine 303, located in the nucleotide-binding/ATPase domain of Ssa1, was shown to be modified in vivo by a model organic electrophile using Click chemistry technology, verifying that Ssa1 is a direct target for thiol-reactive compounds through adduct formation. Consistently, cadmium pretreatment promoted cells thermotolerance, which is abolished in cells carrying SSA1 cysteine mutant alleles. Taken together, these findings demonstrate that Hsp70 acts as a sensor to induce the cytoprotective heat shock response in response to environmental or endogenously produced thiol-reactive molecules and can discriminate between two distinct environmental stressors.

Improvement of Mechanical Properties and Life Extension of High Reliability Structural Components by Laser Shock Processing

Profiting by the increasing availability of laser sources delivering intensities above 109 W/cm2 with pulse energies in the range of several Joules and pulse widths in the range of nanoseconds, laser shock processing (LSP) is being consolidating as an effective technology for the improvement of surface mechanical and corrosion resistance properties of metals and is being developed as a practical process amenable to production engineering. The main acknowledged advantage of the laser shock processing technique consists on its capability of inducing a relatively deep compression residual stresses field into metallic alloy pieces allowing an improved mechanical behaviour, explicitly, the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Following a short description of the theoretical/computational and experimental methods developed by the authors for the predictive assessment and experimental implementation of LSP treatments, experimental results on the residual stress profiles and associated surface properties modification successfully reached in typical materials (specifically Al and Ti alloys) under different LSP irradiation conditions are presented. In particular, the analysis of the residual stress profiles obtained under different irradiation parameters and the evaluation of the corresponding induced surface properties as roughness and wear resistance are presented.

Laser Shock Processing: An Emerging Technique for the Enhancement of Surface Properties and Fatigue Life of High Strength Metal Alloys

Profiting by the increasing availability of laser sources delivering intensities above 10 9 W/cm 2 with pulse energies in the range of several Joules and pulse widths in the range of nanoseconds, laser shock processing (LSP) is being consolidating as an effective technology for the improvement of surface mechanical and corrosion resistance properties of metals and is being developed as a practical process amenable to production engineering. The main acknowledged advantage of the laser shock processing technique consists on its capability of inducing a relatively deep compression residual stresses field into metallic alloy pieces allowing an improved mechanical behaviour, explicitly, the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Following a short description of the theoretical/computational and experimental methods developed by the authors for the predictive assessment and experimental implementation of LSP treatments, experimental results on the residual stress profiles and associated surface properties modification successfully reached in typical materials (specifically steels and Al and Ti alloys) under different LSP irradiation conditions are presented

Mechanical properties enhancement of high reliability metallic materials by laser shock processing

Laser shock processing (LSP) is being increasingly applied as an effective technology for the improvement of metallic materials surface properties in different types of components as a means of enhancement of their corrosion and fatigue life behavior. As reported in previous contributions by the authors, a main effect resulting from the application of the LSP technique consists on the generation of relatively deep compression residual stresses field into metallic alloy pieces allowing an improved mechanical behaviour, explicitly the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Additional results accomplished by the authors in the line of practical development of the LSP technique at an experimental level (aiming its integral assessment from an interrelated theoretical and experimental point of view) are presented in this paper. Concretely, follow-on experimental results on the residual stress profiles and associated surface properties modification successfully reached in typical materials (especially Al and Ti alloys) under different LSP irradiation conditions are presented along with a practical correlated analysis on the protective character of the residual stress profiles obtained under different irradiation strategies and the evaluation of the corresponding induced properties as material specific volume reduction at the surface, microhardness and wear resistance. Additional remarks on the improved character of the LSP technique over the traditional “shot peening” technique in what concerns depth of induced compressive residual stresses fields are also made through the paper.

Effect of Thermal Treatments on the Mechanical Properties Enhancement of High Reliability Metallic Materials by Laser Shock Processing

Laser shock processing (LSP) is increasingly applied as an effective technology for the improvement of metallic materials mechanical properties in different types of components as a means of enhancement of their fatigue life behavior. As reported in previous contributions by the authors, a main effect resulting from the application of the LSP technique consists on the generation of relatively deep compression residual stresses fields into metallic components allowing an improved mechanical behaviour, explicitly the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Additional results accomplished by the authors in the line of practical development of the LSP technique at an experimental level (aiming its integral assessment from an interrelated theoretical and experimental point of view) are presented in this paper. Concretely, experimental results on the residual stress profiles and associated mechanical properties modification successfully reached in typical materials under different LSP irradiation conditions are presented. In this case, the specific behavior of a widely used material in high reliability components (especially in nuclear and biomedical applications) as AISI 316L is analyzed, the effect of possible “in-service” thermal conditions on the relaxation of the LSP effects being specifically characterized. I.

Induction of engineered residual stresses fields and enhancement of fatigue life of high reliability metallic components by laser shock processing

Laser shock processing (LSP) is being increasingly applied as an effective technology for the improvement of metallic materials mechanical and surface properties in different types of components as a means of enhancement of their corrosion and fatigue life behavior. As reported in previous contributions by the authors, a main effect resulting from the application of the LSP technique consists on the generation of relatively deep compression residual stresses field into metallic alloy pieces allowing an improved mechanical behaviour, explicitly the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Additional results accomplished by the authors in the line of practical development of the LSP technique at an experimental level (aiming its integral assessment from an interrelated theoretical and experimental point of view) are presented in this paper. Concretely, follow-on experimental results on the residual stress profiles and associated surface properties modification successfully reached in typical materials (especially Al and Ti alloys characteristic of high reliability components in the aerospace, nuclear and biomedical sectors) under different LSP irradiation conditions are presented along with a practical correlated analysis on the protective character of the residual stress profiles obtained under different irradiation strategies. Additional remarks on the improved character of the LSP technique over the traditional “shot peening” technique in what concerns depth of induced compressive residual stresses fields are also made through the paper

Effect of Thermal Treatments on the Mechanical Properties Enhancement of High Reliability Metallic Materials by Laser Shock Processing

Laser shock processing (LSP) is increasingly applied as an effective technology for the improvement of metallic materials mechanical properties in different types of components as a means of enhancement of their fatigue life behavior. As reported in previous contributions by the authors, a main effect resulting from the application of the LSP technique consists on the generation of relatively deep compression residual stresses fields into metallic components allowing an improved mechanical behaviour, explicitly the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Additional results accomplished by the authors in the line of practical development of the LSP technique at an experimental level (aiming its integral assessment from an interrelated theoretical and experimental point of view)are presented in this paper. Concretely, experimental results on the residual stress profiles and associated mechanical properties modification successfully reached in typical materials under different LSP irradiation conditions are presented. In this case, the specific behavior of a widely used material in high reliability components (especially in nuclear and biomedical applications) as AISI 316L is analyzed, the effect of possible “in-service” thermal conditions on the relaxation of the LSP effects being specifically characterized.

Induction of through-thickness compressive residual stress fields in thin Al2024-T351 plates by laser shock processing

Laser Shock Processing (LSP) has been demonstrated as an emerging technique for the induction of RS’s fields in subsurface layers of relatively thick specimens. However, the LSP treatment of relatively thin specimens brings, as an additional consequence, the possible bending in a process of laser shock forming. This effect poses a new class of problems regarding the attainment of specified RS’s depth profiles in the mentioned type of sheets, and, what can be more critical, an overall deformation of the treated component. The analysis of the problem of LSP treatment for induction of tentatively through-thickness RS’s fields for fatigue life enhancement in relatively thin sheets in a way compatible with reduced overall workpiece deformation due to spring-back self-equilibration is envisaged in this paper. The coupled theoretical-experimental predictive approach developed by the authors has been applied to the specification of LSP treatments for achievement of RS's fields tentatively able to retard crack propagation on normalized specimens. A convergence between numerical code results and experimental results coming from direct RS's measurement is presented as a first step for the treatment of the normalized specimens under optimized conditions and verification of the crack retardation properties virtually induced.

Characterization of heat shock protein-specific T cells in atherosclerosis

A role for infection and inflammation in atherogenesis is widely accepted. Arterial endothelium has been shown to express heat shock protein 60 (HSP60) and, since human (hHSP60) and bacterial (GroEL) HSP60s are highly conserved, the immune response to bacteria may result in cross-reactivity, leading to endothelial damage and thus contribute to the pathogenesis of atherosclerosis. In this study, GroEL-specific T-cell lines from peripheral blood and GroEL-, hHSP60-, and Porphyromonas gingivalis-specific T-cell lines from atherosclerotic plaques were established and characterized in terms of their cross-reactive proliferative responses, cytokine and chemokine profiles, and T-cell receptor (TCR) V beta expression by flow cytometry. The cross-reactivity of several lines was demonstrated. The cytokine profiles of the artery T-cell lines specific for GroEL, hHSP60, and P. gingivalis demonstrated Th2 phenotype predominance in the CD4 subset and Tc0 phenotype predominance in the CD8 subset. A higher proportion of CD4 cells were positive for interferon-inducible protein 10 and RANTES, with low percentages of cells positive for monocyte chemoattractant protein 1 and macrophage inflammatory protein la, whereas a high percentage of CD8 cells expressed all four chemokines. Finally, there was overexpression of the TCR V beta 5.2 family in all lines. These cytokine, chemokine, and V beta profiles are similar to those demonstrated previously for P. gingivalis-specific lines established from periodontal disease patients. These results support the hypothesis that in some patients cross-reactivity of the immune response to bacterial HSPs, including those of periodontal pathogens, with arterial endothelial cells expressing hHSP60 may explain the apparent association between atherosclerosis and periodontal infection.