Ultrafast optical field-ionized gases-A laboratory platform for studying kinetic plasma instabilities.

Kinetic instabilities arising from anisotropic electron velocity distributions are ubiquitous in ionospheric, cosmic, and terrestrial plasmas, yet there are only a handful of experiments that purport to validate their theory. It is known that optical field ionization of atoms using ultrashort laser pulses can generate plasmas with known anisotropic electron velocity distributions. Here, we show that following the ionization but before collisions thermalize the electrons, the plasma undergoes two-stream, filamentation, and Weibel instabilities that isotropize the electron distributions. The polarization-dependent frequency and growth rates of these kinetic instabilities, measured using Thomson scattering of a probe laser, agree well with the kinetic theory and simulations. Thus, we have demonstrated an easily deployable laboratory platform for studying kinetic instabilities in plasmas.

Anomalous water expulsion from carbon-based rods at high humidity.

Three water adsorption-desorption mechanisms are common in inorganic materials: chemisorption, which can lead to the modification of the first coordination sphere; simple adsorption, which is reversible; and condensation, which is irreversible. Regardless of the sorption mechanism, all known materials exhibit an isotherm in which the quantity of water adsorbed increases with an increase in relative humidity. Here, we show that carbon-based rods can adsorb water at low humidity and spontaneously expel about half of the adsorbed water when the relative humidity exceeds a 50-80% threshold. The water expulsion is reversible, and is attributed to the interfacial forces between the confined rod surfaces. At wide rod spacings, a monolayer of water can form on the surface of the carbon-based rods, which subsequently leads to condensation in the confined space between adjacent rods. As the relative humidity increases, adjacent rods (confining surfaces) in the bundles are drawn closer together via capillary forces. At high relative humidity, and once the size of the confining surfaces has decreased to a critical length, a surface-induced evaporation phenomenon known as solvent cavitation occurs and water that had condensed inside the confined area is released as a vapour.

Demonstration of a positron beam-driven hollow channel plasma wakefield accelerator.

Plasma wakefield accelerators have been used to accelerate electron and positron particle beams with gradients that are orders of magnitude larger than those achieved in conventional accelerators. In addition to being accelerated by the plasma wakefield, the beam particles also experience strong transverse forces that may disrupt the beam quality. Hollow plasma channels have been proposed as a technique for generating accelerating fields without transverse forces. Here we demonstrate a method for creating an extended hollow plasma channel and measure the wakefields created by an ultrarelativistic positron beam as it propagates through the channel. The plasma channel is created by directing a high-intensity laser pulse with a spatially modulated profile into lithium vapour, which results in an annular region of ionization. A peak decelerating field of 230 MeV m(-1) is inferred from changes in the beam energy spectrum, in good agreement with theory and particle-in-cell simulations.

Gene expression changes caused by the p38 MAPK inhibitor dilmapimod in COPD patients: analysis of blood and sputum samples from a randomized, placebo-controlled clinical trial.

The p38 mitogen-activated protein kinase (MAPK) intracellular signaling pathway responds to a variety of extracellular stimuli, including cytokines, Toll-like receptor agonists, and components of cigarette smoke to influence the expression of proinflammatory mediators. Activation of p38 MAPK is increased within the lungs of chronic obstructive pulmonary disease (COPD) patients. In clinical trials, treatment of COPD patients with p38 MAPK inhibitors has been shown to reduce systemic inflammation plasma biomarkers C-reactive protein (CRP) and fibrinogen. As CRP and fibrinogen have been associated with poor clinical outcomes in COPD patients, such as mortality, exacerbation, and hospitalization, we analyzed gene expression data from COPD subjects treated with dilmapimod with the aim of understanding the effects of p38 MAPK inhibition on the inflammatory genome of immune cells within the systemic circulation. Whole blood and induced sputum samples were used to measure mRNA levels by gene array and PCR. Pathway and network analysis showed STAT1, MMP-9, CAV1, and IL-1ß as genes regulated by dilmapimod that could also influence fibrinogen levels, while only IL-1ß was identified as a gene regulated by dilmapimod that could influence CRP levels. This suggests that p38 MAPK inhibits specific inflammatory pathways, leading to to differential effects on CRP and fibrinogen levels in COPD patients.

Regulation of Wnt4 in chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is associated with persistent inflammation and oxidative stress in susceptible individuals. Using microarray analysis of bronchial biopsy samples from patients with COPD and controls, we identified Wnt4 as being up-regulated in COPD. Analysis of bronchial biopsy samples showed a very strong correlation between Wnt4 and IL8 gene expression, suggesting that Wnt4 plays a role in chronic lung inflammation. In vitro, Wnt4 induced proliferation and inflammation in human epithelial cells (BEAS-2B) and normal primary human bronchial epithelial cells in a concentration-dependent manner. This effect was enhanced in the presence of interleukin-1ß (IL-1ß) as a result of activation of the p38 and c-Jun NH2-terminal kinase mitogen-activated protein kinase pathways. Hydrogen peroxide, but not proinflammatory stimuli, up-regulated Wnt4 expression in epithelial cells. In monocytic THP-1 and primary airway smooth muscle cells, Wnt4 induced inflammation and enhanced the inflammatory response to lipopolysaccharide and IL-1ß but did not induce proliferation. In addition, these other cell types did not have enhanced Wnt4 expression in response to hydrogen peroxide. Our results indicate that airway epithelial activation, due to oxidative stress, may lead to Wnt4 induction. Wnt4, in turn, acts through the noncanonical pathway to activate epithelial cell remodeling and IL8 gene expression, leading to neutrophil infiltration and inflammation.

Behavior and target site selection of conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile.

The insertion sites of the conjugative transposon Tn916 in the anaerobic pathogen Clostridium difficile were determined using Illumina Solexa high-throughput DNA sequencing of Tn916 insertion libraries in two different clinical isolates: 630ΔE, an erythromycin-sensitive derivative of 630 (ribotype 012), and the ribotype 027 isolate R20291, which was responsible for a severe outbreak of C. difficile disease. A consensus 15-bp Tn916 insertion sequence was identified which was similar in both strains, although an extended consensus sequence was observed in R20291. A search of the C. difficile 630 genome showed that the Tn916 insertion motif was present 100,987 times, with approximately 63,000 of these motifs located in genes and 35,000 in intergenic regions. To test the usefulness of Tn916 as a mutagen, a functional screen allowed the isolation of a mutant. This mutant contained Tn916 inserted into a gene involved in flagellar biosynthesis.

Modification of the rat airway explant transcriptome by cigarette smoke.

Although a number of animal model studies have addressed changes in gene expression in the parenchyma and their relationship to emphysema, much less is known about the pathogenesis of cigarette smoke-induced small airway remodeling. In this study the authors exposed rat tracheal explants, a model of the airway wall, to whole smoke for 15 min, and then cultured the explants in air. The airway transcriptome was evaluated using RAE 230_2 gene chips. By 2 h after starting smoke exposure, expression levels of 502 genes were differentially expressed by more than 1.5 times (p < .01 or less) and by 24 h 1870 genes were significantly changed up or down. These included genes involved in antioxidant protection, epithelial defense and remodeling, inflammatory mediators and transcription factors, and a number of unexpected genes, including the matrix metalloproteinase (MMP)-12 inducer, tachykinin-1 (substance P). Pretreatment of the explants with 1 x 10(-7) M dexamethasone reduced the number of significantly changed genes by approximately 47% at 2 h and 68% at 24 h and in almost all instances reduced the magnitude of the smoke-induced changes. The authors conclude that even a very brief exposure to cigarette smoke can lead to rapid changes in the expression of a large number of genes in rat tracheal explants, and that these effects are directly mediated by smoke, without a need for exogenous inflammatory cells. Steroids, contrary to the usual belief, are able to ameliorate many of these changes, at least in this very acute model.

Inhibition of lipopolysaccharide-stimulated chronic obstructive pulmonary disease macrophage inflammatory gene expression by dexamethasone and the p38 mitogen-activated protein kinase inhibitor N-cyano-N'-(2-{[8-(2,6-difluorophenyl)-4-(4-fluoro-2-methylphenyl)-7-oxo-7,8-dihydropyrido[2,3-d] pyrimidin-2-yl]amino}ethyl)guanidine (SB706504).

p38 mitogen-activated protein kinase (MAPK) signaling is known to be increased in chronic obstructive pulmonary disease (COPD) macrophages. We have studied the effects of the p38 MAPK inhibitor N-cyano-N'-(2-{[8-(2,6-difluorophenyl)-4-(4-fluoro-2-methylphenyl)-7-oxo-7,8-dihydropyrido[2,3-d]-pyrimidin-2-yl]amino}ethyl)guanidine (SB706504) and dexamethasone on COPD macrophage inflammatory gene expression and protein secretion. We also studied the effects of combined SB706504 and dexamethasone treatment. Lipopolysaccharide (LPS)-stimulated monocyte derived macrophages (MDMs) and alveolar macrophages (AMs) were cultured with dexamethasone and/or SB706504. MDMs were used for gene array and protein studies, whereas tumor necrosis factor (TNF) alpha protein production was measured from AMs. SB706504 caused transcriptional inhibition of a range of cytokines and chemokines in COPD MDMs. The use of SB706504 combined with dexamethasone caused greater suppression of gene expression (-8.90) compared with SB706504 alone (-2.04) or dexamethasone (-3.39). Twenty-three genes were insensitive to the effects of both drugs, including interleukin (IL)-1beta, IL-18, and chemokine (CC motif) ligand (CCL) 5. In addition, the chromosome 4 chemokine cluster members, CXCL1, CXCL2, CXCL3, and CXCL8, were all glucocorticoid-resistant. SB706504 significantly inhibited LPS-stimulated TNFalpha production from COPD and smoker AMs, with near-maximal suppression caused by combination treatment with dexamethasone. We conclude that SB706504 targets a subset of inflammatory macrophage genes and when used with dexamethasone causes effective suppression of these genes. SB706504 and dexamethasone had no effect on the transcription of a subset of LPS-regulated genes, including IL-1beta, IL-18, and CCL5, which are all known to be involved in the pathogenesis of COPD.

Assessment of temporal variations of water quality in inland water bodies using atmospheric corrected satellite remotely sensed image data.

Although there have been many studies conducted on the use of satellite remote sensing for water quality monitoring and assessment in inland water bodies, relatively few studies have considered the problem of atmospheric intervention of the satellite signal. The problem is especially significant when using time series multi-spectral satellite data to monitor water quality surveillance in inland waters such as reservoirs, lakes, and dams because atmospheric effects constitute the majority of the at-satellite reflectance over water. For the assessment of temporal variations of water quality, the use of multi-date satellite images is required so atmospheric corrected image data must be determined. The aim of this study is to provide a simple way of monitoring and assessing temporal variations of water quality in a set of inland water bodies using an earth observation- based approach. The proposed methodology is based on the development of an image-based algorithm which consists of a selection of sampling area on the image (outlet), application of masking and convolution image processing filter, and application of the darkest pixel atmospheric correction. The proposed method has been applied in two different geographical areas, in UK and Cyprus. Mainly, the method has been applied to a series of eight archived Landsat-5 TM images acquired from March 1985 up to November 1985 of the Lower Thames Valley area in the West London (UK) consisting of large water treatment reservoirs. Finally, the method is further tested to the Kourris Dam in Cyprus. It has been found that atmospheric correction is essential in water quality assessment studies using satellite remotely sensed imagery since it improves significantly the water reflectance enabling effective water quality assessment to be made.

Cigarette smoke extract induced cytokine and chemokine gene expression changes in COPD macrophages.

Macrophages are key inflammatory cells in chronic obstructive pulmonary disease (COPD). The transcriptional regulation of inflammatory signalling pathways by cigarette smoke (CS) in COPD macrophages is not well understood. We have studied the effects of acute CS exposure on COPD macrophage cytokine, chemokine and signal transduction gene expression profiles. Monocyte derived macrophages (MDMs) from whole blood from patients with COPD (n=6) were stimulated with 1%, 10% and 25% CS extract (CSE) for 6h for microarray and quantitative polymerase chain reaction (Q-PCR) analysis. We observed a CSE dose dependant increase in the numbers of significantly regulated genes; 24, 340 and 627 genes at 1%, 10% and 25% CSE, respectively. IL-8 mRNA levels were up-regulated by 10% CSE (2.25-fold increase, 95% CI 1.28-4.00). In contrast a range of other cytokines and chemokines were down-regulated at both 10% and 25% CSE, including IL-1beta, -6, -10 and -18, chemokine ligands CCL-2, -3, -4, -5, -8, -15, -20 and CXCL-1, -2 and -10. Q-PCR and microarray data were highly correlated (r=0.95, p=0.0001). NF-kappaB component p50 and IkappaBalpha expression were suppressed by CSE, while there was up-regulation of the AP-1 components c-Jun, FOSL1 and FOSL2. Acute CSE exposure decreased macrophage inflammatory gene expression, with the exception of increased IL-8. There was diverse regulation of key inflammatory signal pathway genes. The effects of acute CS exposure appear to encompass both up-regulation of chemotaxis mechanisms through IL-8, but also down-regulation of innate immunity.

Use of gene expression profiling to identify a novel glucocorticoid sensitivity determining gene, BMPRII.

Wide variation in glucocorticoid (Gc) sensitivity exists between individuals which may influence susceptibility to, and treatment response of, inflammatory diseases. To determine a genetic fingerprint of Gc sensitivity 100 healthy human volunteers were polarized into the 10% most Gc-sensitive and 10% most Gc-resistant following a low dose dexamethasone (0.25 mg) suppression test. Gene expression profiling of primary lymphocytes identified the 98 most significantly Gc regulated genes. These genes were used to build a subnetwork of Gc signaling, with 54 genes mapping as nodes, and 6 non-Gc regulated genes inferred as signaling nodes. Twenty four of the 98 genes showed a difference in Gc response in vitro dependent on the Gc sensitivity of their donor individuals in vivo. A predictive model was built using both partial least squares discriminate analysis and support vector machines that predicted donor glucocorticoid sensitivity with 87% accuracy. Discriminating genes included bone morphogenetic protein receptor, type II (BMPRII). Transfection studies showed that BMPRII modulated Gc action. These studies reveal a broad base of gene expression that predicts Gc sensitivity and determine a Gc signaling network in human primary T lymphocytes. Furthermore, this combined gene profiling, and functional analysis approach has identified BMPRII as a modulator of Gc signaling.

Gene expression profiles in the rat streptococcal cell wall-induced arthritis model identified using microarray analysis.

Experimental arthritis models are considered valuable tools for delineating mechanisms of inflammation and autoimmune phenomena. Use of microarray-based methods represents a new and challenging approach that allows molecular dissection of complex autoimmune diseases such as arthritis. In order to characterize the temporal gene expression profile in joints from the reactivation model of streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rats, total RNA was extracted from ankle joints from naive, SCW injected, or phosphate buffered saline injected animals (time course study) and gene expression was analyzed using Affymetrix oligonucleotide microarray technology (RAE230A). After normalization and statistical analysis of data, 631 differentially expressed genes were sorted into clusters based on their levels and kinetics of expression using Spotfire profile search and K-mean cluster analysis. Microarray-based data for a subset of genes were validated using real-time PCR TaqMan analysis. Analysis of the microarray data identified 631 genes (441 upregulated and 190 downregulated) that were differentially expressed (Delta > 1.8, P < 0.01), showing specific levels and patterns of gene expression. The genes exhibiting the highest fold increase in expression on days -13.8, -13, or 3 were involved in chemotaxis, inflammatory response, cell adhesion and extracellular matrix remodelling. Transcriptome analysis identified 10 upregulated genes (Delta > 5), which have not previously been associated with arthritis pathology and are located in genomic regions associated with autoimmune disease. The majority of the downregulated genes were associated with metabolism, transport and regulation of muscle development. In conclusion, the present study describes the temporal expression of multiple disease-associated genes with potential pathophysiological roles in the reactivation model of SCW-induced arthritis in Lewis (LEW/N) rat. These findings improve our understanding of the molecular events that underlie the pathology in this animal model, which is potentially a valuable comparator to human rheumatoid arthritis (RA).

Assessment of cannabinoid induced gene changes: tolerance and neuroprotection.

The analysis of gene changes associated with exposure to cannabinoids is critical due to the multiple possible signaling pathways potentially affected by cannabinoid receptor activation. A comparison of altered gene profiles under two different conditions, one in vivo (chronic exposure to delta-9-THC) and the other in vitro (neuroprotection mediated by WIN55212-2), was made to determine whether it was possible to identify common genes that were affected. Up and down-regulated sets of genes are described. Genes affected in one or the other circumstance include alterations in a 14-3-3 regulator protein of PKC, CREB, BDNF and GABA receptor subunit proteins, as well as several genes associated with known cannabinoid receptor-coupled signaling pathways. Unexpectedly, several genes that were altered in both circumstances were associated with synaptic and membrane structure, motility and neuron growth. These included, neuronal cell adhesion molecule (NCAM), hyloronidan motility receptor, and myelin proteolipid protein. While the basis for involvement of these particular genes in cannabinoid receptor activated functional processes within the cell is still not well understood, awareness that significant numbers of genes and presumably proteins are changed following either acute or long-term exposure may provide new insight into their effects.