Biomarkers of some pulmonary diseases in exhaled breath

Analysis of various biomarkers in exhaled breath allows completely non-invasive monitoring of inflammation and oxidative stress in the respiratory tract in inflammatory lung diseases, including asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), bronchiectasis and interstitial lung diseases. The technique is simple to perform, may be repeated frequently, and can be applied to children, including neonates, and patients with severe disease in whom more invasive procedures are not possible. Several volatile chemicals can be measured in the breath (nitric oxide, carbon monoxide, ammonia), and many non-volatile molecules (mediators, oxidation and nitration products, proteins) may be measured in exhaled breath condensate. Exhaled breath analysis may be used to quantify inflammation and oxidative stress in the respiratory tract, in differential diagnosis of airway disease and in the monitoring of therapy. Most progress has been made with exhaled nitric oxide (NO), which is increased in atopic asthma, is correlated with other inflammatory indices and is reduced by treatment with corticosteroids and antileukotrienes, but not (β₂-agonists. In contrast, exhaled NO is normal in COPD, reduced in CF and diagnostically low in primary ciliary dyskinesia. Exhaled carbon monoxide (CO) is increased in asthma, COPD and CF. Increased concentrations of 8-isoprostane, hydrogen peroxide, nitrite and 3-nitrotyrosine are found in exhaled breath condensate in inflammatory lung diseases. Furthermore, increased levels of lipid mediators are found in these diseases, with a differential pattern depending on the nature of the disease process. In the future it is likely that smaller and more sensitive analysers will extend the discriminatory value of exhaled breath analysis and that these techniques may be available to diagnose and monitor respiratory diseases in the general practice and home setting.     

Telomerase targeted oligonucleotide thio-phosphoramidates in T24-luc bladder cancer cells

Bladder carcinoma is the second most common genitourinary malignancy. Treatment options for bladder cancer include surgery, combined with chemotherapy, radiation, and/or immunotherapy. The adjuvant chemotherapy and immunotherapy regimen have been widely used in locally invasive as well as metastatic disease. The evaluation of new active agents with improved tolerability has been the focus of investigations over the past decade with minimal overall improvements in outcomes. Telomerase activity has been found in approximately 85-90% of all human tumors, but not in the majority of adjacent normal tissues. This suggests that telomerase may be an attractive target for the development of novel anticancer therapeutic agents. GRN163L is a lipid conjugated oligonucleotide N3' --> P5' thio-phosphoramidate, and is a potent telomerase RNA (hTR) template antagonist. In the present study, we show that the telomerase activity of T24-luc bladder cancer cells is inhibited by 1 microM GRN163L within 24 h of incubation. After two weeks of exposure to GRN163L, T24-luc cells became "clustered" whereas non-cancerous normal human uroepithelial cells were not morphologically affected. Moreover, in vitro GRN163L treated T24-luc bladder cancer cells entered G(0)/G(1) arrest following 2 weeks of continuous exposure and stopped dividing. Mismatch control compound had no effect on normal bladder epithelial cells or T24-luc cells. Additionally, a new generation of thio-phosphoramidate oligonucleotides were designed and tested in T24-luc cells and compared with GRN163L. The obtained results warrant further in vivo evaluation of GRN163L as a potential treatment for bladder cancer.     

Elucidating the site of action of oxalate in photosynthetic electron transport chain in spinach thylakoid membranes

The effects of oxalate on PS II and PS I photochemistry were studied. The results suggested that in chloride-deficient thylakoid membranes, oxalate inhibited activity of PS II as well as PS I. To our knowledge, this is the only anion so far known which inhibits both the photosystems. Measurements of fluorescence induction kinetics, YZ* decay, and S2 state multiline EPR signal suggested that oxalate inhibited PS II at the donor side most likely on the oxygen evolving complex. Measurements of re-reduction of P700+ signal in isolated PS I particles in oxalate-treated samples suggested a binding site of oxalate on the donor, as well as the acceptor side of PS I.     

Enantiomerically pure quaternary ammonium salts with a chiral alkyl chain N(CH3)(n-C3H7)2(sec-C4H9)I: synthesis and physical studies

A pair of enantiomerically pure quaternary ammonium salts with a chiral side chain, methyl-(R)-(1-methylpropyl)di(n-propyl)ammonium iodide 1 and methyl-(S)-(1-methylpropyl)di(n-propyl)ammonium iodide 2, and the related racemate, methyl-(rac)-(1-methylpropyl)di(n-propyl)ammonium iodide 3, were synthesized through a reductive alkylation procedure, starting from enantiomerically pure and, also, racemic forms of (rac)-(1-methylpropyl)amine. A spectroscopic chiroptical signature in solution was provided by the Raman optical activity spectra of compounds 1 and 2. The crystallographic structures of 1, 2, and 3 were examined by single crystal X-ray diffraction. 1 crystallizes in the tetragonal space group P4(3)2(1)2 (no. 96), a = b = 12.826 (2) A, c = 17.730 (2) A, V = 2916.9 (5) A(3), Z = 8, Flack coefficient 0.04 (2). 2 crystallizes in the tetragonal space group P4(1)2(1)2 (no. 92), a = b = 12.842 (1) A, c = 17.749 (2) A, V = 2927.0 (5) A(3), Z = 8, Flack coefficient 0.05 (2). The crystal structures and space groups for 1 and 2 are enantiomorphs and the crystallographic investigation confirmed the absolute configuration of the stereocenter in both compounds. 3 crystallizes in the monoclinic space group P2(1)/n(no. 14), a = 8.178 (1) A, b = 14.309 (2) A, c = 12.328 (2) A, beta = 96.811 (6) degrees, V = 1432.4 (2) A(3), Z = 4.     

Escape from HLA-B*08-restricted CD8 T cells by hepatitis C virus is associated with fitness costs

The inherent sequence diversity of the hepatitis C virus (HCV) represents a major hurdle for the adaptive immune system to control viral replication. Mutational escape within targeted CD8 epitopes during acute HCV infection has been well documented and is one possible mechanism for T-cell failure. HLA-B*08 was recently identified as one HLA class I allele associated with spontaneous clearance of HCV replication. Selection of escape mutations in the immunodominant HLA-B*08-restricted epitope HSKKKCDEL(1395-1403) was observed during acute infection. However, little is known about the impact of escape mutations in this epitope on viral replication capacity. Their previously reported reversion back toward the consensus residue in patients who do not possess the B*08 allele suggests that the consensus sequence in this epitope is advantageous for viral replication in the absence of immune pressure. The aim of this study was to determine the impact of mutational escape from this immunodominant epitope on viral replication. We analyzed it with a patient cohort with chronic HCV genotype 1b infection and in a single-source outbreak (genotype 1b). Sequence changes in this highly conserved region are rare and selected almost exclusively in the presence of the HLA-B*08 allele. When tested in the subgenomic replicon (Con1), the observed mutations reduce viral replication compared with the prototype sequence. The results provide direct evidence that escape mutations in this epitope are associated with fitness costs and that the antiviral effect of HLA-B*08-restricted T cells is sufficiently strong to force the virus to adopt a relatively unfavorable sequence.     

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

PSI-BLAST is an iterative program to search a database for proteins with distant similarity to a query sequence. We investigated over a dozen modifications to the methods used in PSI-BLAST, with the goal of improving accuracy in finding true positive matches. To evaluate performance we used a set of 103 queries for which the true positives in yeast had been annotated by human experts, and a popular measure of retrieval accuracy (ROC) that can be normalized to take on values between 0 (worst) and 1 (best). The modifications we consider novel improve the ROC score from 0.758 ± 0.005 to 0.895 ± 0.003. This does not include the benefits from four modifications we included in the ‘baseline’ version, even though they were not implemented in PSI-BLAST version 2.0. The improvement in accuracy was confirmed on a small second test set. This test involved analyzing three protein families with curated lists of true positives from the non-redundant protein database. The modification that accounts for the majority of the improvement is the use, for each database sequence, of a position-specific scoring system tuned to that sequence’s amino acid composition. The use of composition-based statistics is particularly beneficial for large-scale automated applications of PSI-BLAST.     

Accuracy of protein secondary structure determination from circular dichroism spectra based on immunoglobulin examples

Strong contribution of the aromatic amino acid side chain chromophores to the far-UV circular dichroism (CD) spectra substantially distorts a relatively weak CD signal originating from beta sheet, the main type of immunoglobulin secondary structure. In this study we compared the secondary structure calculated from the far-UV CD spectra with the X-ray data for three antibody Fab fragments. Calculations were performed with three different algorithms, using two sets of reference proteins. Low standard deviations between all six estimates indicate stable mathematical solutions. Despite pronounced differences in the shape and amplitude of the CD spectra, we found a strong correlation between CD and X-ray data in the secondary structure for every protein studied. The number and average length of the secondary structure elements estimated from the CD spectra closely resemble those of the X-ray data. Agreement between spectroscopic and crystallographic results demonstrates that modern methods of secondary structure calculation are resilient to distortions of the far-UV CD spectra of immunoglobulins caused by aromatic side chain chromophores.