Exhaled breath condensate pH as a biomarker of COPD severity in ex-smokers

Endogenous airway acidification, as assessed by exhaled breath condensate (EBC) pH, is present in patients with stable COPD. The aim of this study was to measure EBC pH levels in a large cohort of COPD patients and to evaluate associations with functional parameters according to their smoking status.EBC was collected from 161 patients with stable COPD and 112 controls (current and ex-smokers). EBC pH was measured after Argon deaeration and all subjects underwent pulmonary function testing.EBC pH was lower in COPD patients compared to controls [7.21 (7.02, 7.44) vs. 7.50 (7.40, 7.66); p < 0.001] and ex-smokers with COPD had lower EBC pH compared to current smokers [7.16 (6.89, 7.36) vs 7.24 (7.09, 7.54), p = 0.03]. In ex-smokers with COPD, EBC pH was lower in patients with GOLD stage III and IV compared to patients with stage I disease (p = 0.026 and 0.004 respectively). No differences were observed among current smokers with different disease severity. EBC pH levels in ex-smokers were associated with static hyperinflation (as expressed by IC/TLC ratio), air trapping (as expressed by RV/TLC ratio) and diffusing capacity for carbon monoxide, whereas no associations were observed in current smokers.Endogenous airway acidification is related to disease severity and to parameters expressing hyperinflation and air trapping in ex-smokers with COPD. The possible role of EBC pH in COPD needs to be further evaluated in longitudinal studies.     

Multi-membership gene regulation in pathway based microarray analysis

Background

Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway.

Results

We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency.

Conclusions

We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.     

Muscle intermediate filaments and their links to membranes and membranous organelles

Intermediate filaments (IFs) play a key role in the integration of structure and function of striated muscle, primarily by mediating mechanochemical links between the contractile apparatus and mitochondria, myonuclei, the sarcolemma and potentially the vesicle trafficking apparatus. Linkage of all these membranous structures to the contractile apparatus, mainly through the Z-disks, supports the integration and coordination of growth and energy demands of the working myocyte, not only with force transmission, but also with de novo gene expression, energy production and efficient protein and lipid trafficking and targeting. Desmin, the most abundant and intensively studied muscle intermediate filament protein, is linked to proper costamere organization, myoblast and stem cell fusion and differentiation, nuclear shape and positioning, as well as mitochondrial shape, structure, positioning and function. Similar links have been established for lysosomes and lysosome-related organelles, consistent with the presence of widespread links between IFs and membranous structures and the regulation of their fusion, morphology and stabilization necessary for cell survival.     

α1‐adrenergic stimulation mediates Ca2+‐dependent inositol phosphate formation through the α1B‐like adrenoceptor subtype in adult rat cardiac myocytes

We studied the effects of increased Ca²⁺ influx on α₁‐adrenoceptor‐stimulated InsP formation in adult rat cardiac myocytes. We further examined if such effects could be mediated through a specific α₁‐adrenoceptor subtype. [³H]InsP responses to adrenaline were dependent on extracellular Ca²⁺ concentration, from 0.1 μM to 2 mM, and were completely blocked by Ca²⁺ removal. However, in cardiac myocytes preloaded with BAPTA, a highly selective calcium chelating agent, Ca²⁺ concentrations higher than 1 μM had no effect on adrenaline‐stimulated [³H]InsP formation. Taken together these results suggest that [³H]InsP formation induced by α₁‐adrenergic stimulation is in part mediated by increased Ca²⁺ influx. Consistent with this, ionomycin, a calcium ionophore, stimulated [³H]InsP formation. This response was additive with the response to adrenaline stimulation implying that different signaling mechanisms may be involved. In cardiac myocytes treated with the α_1B‐adrenoceptor alkylating agent, CEC, [³H]InsP formation remained unaffected by increased Ca²⁺ concentrations, a pattern similar to that observed when intracellular Ca²⁺ was chelated with BAPTA. In contrast, addition of the α_1A‐subtype antagonist, 5′‐methyl urapidil, did not affect the Ca²⁺ dependence of [³H]InsP formation. Neither nifedipine, a voltage‐dependent Ca²⁺ channel blocker nor the inorganic Ca²⁺ channel blockers, Ni²⁺ and Co²⁺, had any effect on adrenaline stimulated [³H]InsP, at concentrations that inhibit Ca²⁺ channels. The results suggest that in adult rat cardiac myocytes, in addition to G protein‐mediated response, α₁‐adrenergic‐stimulated [³H]InsP formation is activated by increased Ca²⁺ influx mediated by the α_1B‐subtype. J. Cell. Biochem. 84: 201–210, 2002. © 2001 Wiley‐Liss, Inc.     

Metabolism of polyamines and oxidative stress in the brain of cholestatic rats

In a recently published article in “Amino Acids” it was shown that obstructive jaundice of 9 days’ duration in rats induces significant alterations of polyamines’ metabolism in the brain, which might play an important pathogenetic role in cholestatic brain injury. The authors proposed that alterations of polyamines in cholestatic brain might induce neuronal toxicity through a mechanism that implicates the production of reactive oxygen species and oxidative stress, although this parameter was not evaluated in their study. This hypothesis is supported by our recent findings on brain oxidative status in rats with obstructive jaundice of 10 days’ duration. Potential interrelations of the two studies’ findings are discussed in this commentary.     

Analysis of selected kinematic and physiological performance determinants during incremental testing in elite swimmers

This study examined the relationships between selected kinematic and physiological parameters and their influence on performance during incremental exercise in elite swimmers competing at the international level. Eleven men and ten women (all specialized in 200-m events) performed an incremental 7 x 200-m test in their specialized stroke. Stroke rate (SR), stroke length (SL), velocity (V), and blood lactate concentration (BLa) were measured for each 200 m. In addition to the cross-sectional group design, the longitudinal performance of a male swimmer was evaluated by 4 tests during a period of 20 weeks. Stroke rate increased and SL decreased with V, regardless of the age, stroke, or gender of the swimmer. Statistically significant correlations were found between SR and V (p < 0.01; r = 0.66 to 0.99), SR and SL (p < 0.01; r = -0.78 to -0.99), SL and V (except for women's freestyle and breaststroke) (p < 0.01; r = -0.67 to -0.98), and BLa and V (p < 0.01; r = 0.7 to 0.96). Changes in SR and SL were not affected by changes in BLa. Similar velocities were produced with different combinations of SR and SL. The fastest times reached in the test were generally slower than expected, and the performance in the test was not associated with competition performance. The case study revealed similar results to those of the group. The test used in this study was informative with respect to identifying the most economical and effective stroke kinematics combination for slow to submaximal velocities. It is possible that the swimming speeds were not maximal in the final 200-m swim because of cumulative fatigue, which is a major limitation for assessing race pace. An additional test that produces velocities similar to those used in competitions would be more useful for the purpose of providing optimal kinematic information specific to racing speeds, which would facilitate performance improvement through regular monitoring in training.     

Retrovirus-associated heparan sulfate mediates immobilization and gene transfer on recombinant fibronectin

Recombinant retroviruses have been shown to bind to fibronectin (FN) and increase the efficiency of gene transfer to a variety of cell types. Despite recent work to optimize gene transfer on recombinant FN, the mechanism of retrovirus binding to FN and the interactions of target cells with the bound virus remain elusive. We investigated the roles of virus surface glycoprotein (gp70), cell-conditioned medium, and proteoglycans in mediating retrovirus binding to FN. We also examined the role of Polybrene (PB) in these interactions. We found that gp70 is not involved in retrovirus binding to FN. Immobilization of the virus, however, does not overcome its receptor requirement, and gp70 is still needed for successful gene transfer. Our results clearly show that retrovirus binds FN through virus-associated heparan sulfate (HS) and that binding is necessary for transduction without PB. Two distinct modes of gene transfer occur depending on PB: (i) in the presence of PB, retrovirus interacts directly with the target cells; and (ii) in the absence of PB, retrovirus binds to FN and target cells interact with the immobilized virus. PB may promote the former mode by interacting with the virus HS and reducing the negative charge of the viral particles. Interestingly, the latter mode is more efficient, leading to significantly enhanced gene transfer. A better understanding of these interactions may provide insight into virus-cell interactions and lead to a more rational design of transduction protocols.     

Determination of cathepsin B expression may offer additional prognostic information for ovarian cancer patients

The lysosomal cysteine proteinase cathepsin B has been implicated in the progression of various human tumors including ovarian cancer. Included in this study were 63 patients with epithelial ovarian carcinoma. Follow-up information (median follow-up period 7 years) was available for all patients, among whom 42 (66.7%) had relapsed and 32 (50.8%) had died. The immunohistochemistry method was adopted for the detection of cathepsin B using paraffin embedded specimens. Results were compared to clinico-pathological data. Statistical analysis showed cathepsin B expression to be significantly associated with the stage of disease, debulking success and interestingly, with progesterone receptors. It was also inversely related to progression-free survival (PFS) and overall survival (OS). Accordingly, cathepsin B can be regarded as unfavorable and as an independent tumor marker for progression-free survival and overall survival in ovarian cancer patients with long follow-up.     

First record of Alicia mirabilis (Anthozoa: Actiniaria) from the Aegean Sea and density assessment with distance sampling in a site of high abundance

The occurrence of the actiniarian Alicia mirabilis in the Aegean Sea is documented for the first time from five sites in the Saronikos Gulf. The density of A. mirabilis was assessed in one site (Lychnari bay) with line transects (underwater distance sampling with SCUBA). Its density ranged between 0 and 4.3 individuals are^-1 (1 are=100 m²) with a mean of 1.1±0.5 individuals are^-1. The species was found in a variety of substrates (sandy bottoms, weeds, seagrass beds, rocks, litter) and its distribution was aggregated. Distance sampling was an efficient way to estimate the density of A. mirabillis and is proposed as a good choice for density estimations of actiniarians and other benthic fauna.