The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain

Small autonomously folding proteins are of interest as model systems to study protein folding, as the same molecule can be used for both experimental and computational approaches. The question remains as to how well these minimized peptide model systems represent larger native proteins. For example, is the core of a minimized protein tolerant to mutation like larger proteins are? Also, do minimized proteins use special strategies for specifying and stabilizing their folded structure? Here we examine these questions in the 35‐residue autonomously folding villin headpiece subdomain (VHP subdomain). Specifically, we focus on a cluster of three conserved phenylalanine (F) residues F47, F51, and F58, that form most of the hydrophobic core. These three residues are oriented such that they may provide stabilizing aromatic–aromatic interactions that could be critical for specifying the fold. Circular dichroism and 1D‐NMR spectroscopy show that point mutations that individually replace any of these three residues with leucine were destabilized, but retained the native VHP subdomain fold. In pair‐wise replacements, the double mutant that retains F58 can adopt the native fold, while the two double mutants that lack F58 cannot. The folding of the double mutant that retains F58 demonstrates that aromatic–aromatic interactions within the aromatic cluster are not essential for specifying the VHP subdomain fold. The ability of the VHP subdomain to tolerate mutations within its hydrophobic core indicates that the information specifying the three dimensional structure is distributed throughout the sequence, as observed in larger proteins. Thus, the VHP subdomain is a legitimate model for larger, native proteins.     

A potent and selective nonpeptide antagonist of CXCR2 inhibits acute and chronic models of arthritis in the rabbit

Much evidence implicates IL-8 as a major mediator of inflammation and joint destruction in rheumatoid arthritis. The effects of IL-8 and its related ligands are mediated via two receptors, CXCR1 and CXCR2. In the present study, we demonstrate that a potent and selective nonpeptide antagonist of human CXCR2 potently inhibits (125)I-labeled human IL-8 binding to, and human IL-8-induced calcium mobilization mediated by, rabbit CXCR2 (IC(50) = 40.5 and 7.7 nM, respectively), but not rabbit CXCR1 (IC(50) = >1000 and 2200 nM, respectively). These data suggest that the rabbit is an appropriate species in which to examine the anti-inflammatory effects of a human CXCR2-selective antagonist. In two acute models of arthritis in the rabbit induced by knee joint injection of human IL-8 or LPS, and a chronic Ag (OVA)-induced arthritis model, administration of the antagonist at 25 mg/kg by mouth twice a day significantly reduced synovial fluid neutrophils, monocytes, and lymphocytes. In addition, in the more robust LPS- and OVA-induced arthritis models, which were characterized by increased levels of proinflammatory mediators in the synovial fluid, TNF-alpha, IL-8, PGE(2), leukotriene B(4), and leukotriene C(4) levels were significantly reduced, as was erythrocyte sedimentation rate, possibly as a result of the observed decreases in serum TNF-alpha and IL-8 levels. In vitro, the antagonist potently inhibited human IL-8-induced chemotaxis of rabbit neutrophils (IC(50) = 0.75 nM), suggesting that inhibition of leukocyte migration into the knee joint is a likely mechanism by which the CXCR2 antagonist modulates disease.     

Identification of a new segment involved in cagA 3' region variation of Helicobacter pylori

The cagA 3' region shows marked variation among Helicobacter pylori strains. Two segments of 102 bp and 57 bp are reportedly responsible for this variation. We analysed the cagA 3' region in 70 H. pylori strains using polymerase chain reaction and sequencing. We found that another segment, namely beta segment, was also involved in the variation of this region. The beta segment was 105 bp long and located between the aforementioned two segments. Six genotypes were identified based on the structure of the cagA 3' region. No relationship was found between these genotypes and the clinical outcomes or vacA genotypes. The numbers of tyrosine phosphorylation sites within the cagA 3' region varied among strains, but this was not related to the cagA genotypes. Our data suggest that the cagA 3' region is significantly variable. It appears that the variation of the cagA 3' region might contribute to the modification of virulence.     

Does Helicobacter pylori eradication affect symptoms in nonulcer dyspepsia: a 5-year follow-up study

The role of Helicobacter pylori infection in nonulcer dyspepsia remains controversial. To date studies exploring the effect of H. pylori eradication on symptoms have reported conflicting results. Randomised control trials employing validated outcome measures have also been difficult to interpret because of several important issues such as the large placebo response seen in patients with nonulcer dyspepsia and both the natural variability in symptoms and symptom severity with time. The association of symptom improvement with resolution of gastritis has meant that the length of follow up employed in most studies has been insufficient. We report the findings of a randomised placebo controlled trial (n = 100), using a validated symptom questionnaire and 5 year follow up to determine the effect of H. pylori eradication on symptoms in nonulcer dyspepsia. In all 64 that were reviewed at 5 years there was a significant difference between patients who were H. pylori negative and those who remained positive with regard to complete symptom resolution, consumption of relevant medications and peptic ulcer disease development, in favour of active treatment. There was a trend for gradual symptom improvement over time irrespective of H. pylori status, which may reflect the natural history of this condition. For those who remained symptomatic at 5 years, there was no difference in symptom severity based on H. pylori status. The findings of this study support the use of H. pylori eradication in symptomatic patients with nonulcer dyspepsia both to induce symptom resolution and to prevent disease progression.     

Model misspecification and probabilistic tests of topology: evidence from empirical data sets

Probabilistic tests of topology offer a powerful means of evaluating competing phylogenetic hypotheses. The performance of the nonparametric Shimodaira-Hasegawa (SH) test, the parametric Swofford-Olsen-Waddell-Hillis (SOWH) test, and Bayesian posterior probabilities were explored for five data sets for which all the phylogenetic relationships are known with a very high degree of certainty. These results are consistent with previous simulation studies that have indicated a tendency for the SOWH test to be prone to generating Type 1 errors because of model misspecification coupled with branch length heterogeneity. These results also suggest that the SOWH test may accord overconfidence in the true topology when the null hypothesis is in fact correct. In contrast, the SH test was observed to be much more conservative, even under high substitution rates and branch length heterogeneity. For some of those data sets where the SOWH test proved misleading, the Bayesian posterior probabilities were also misleading. The results of all tests were strongly influenced by the exact substitution model assumptions. Simple models, especially those that assume rate homogeneity among sites, had a higher Type 1 error rate and were more likely to generate misleading posterior probabilities. For some of these data sets, the commonly used substitution models appear to be inadequate for estimating appropriate levels of uncertainty with the SOWH test and Bayesian methods. Reasons for the differences in statistical power between the two maximum likelihood tests are discussed and are contrasted with the Bayesian approach.     

Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera

We have applied Bayesian and maximum likelihood methods of phylogenetic estimation to data from four mitochondrial genes (COI, COII, 12S, and 16S) and a single nuclear gene (EF1alpha) from several genera of New Zealand, Australian, and New Caledonian cicada taxa. We specifically focused on the heterogeneity of phylogenetic signal among the different data partitions and the biogeographic origins of the New Zealand cicada fauna. The Bayesian analyses circumvent many of the problems associated with other statistical tests for comparing data partitions. We took an information-theoretic approach to model selection based on the Akaike Information Criterion (AIC). This approach indicated that there was considerable uncertainty in identifying the best-fit model for some of the partitions. Additionally, a large amount of uncertainty was associated with many parameter estimates from the substitution model. However, a sensitivity analysis on the combined dataset indicated that the model selection uncertainty had little effect on estimates of topology because these estimates were largely insensitive to changes in the assumed model. This outcome suggests strong signal in our data. Our analyses support a New Caledonian affiliation of the New Zealand cicada genera Maoricicada, Kikihia, and Rhodopsalta and Australian affinities for the genera Amphipsalta and Notopsalta. This result was surprising, given that previous cicada biologists suspected a close relationship between Amphipsalta, Notopsalta, and Rhodopsalta based on genitalic characters. Relationships among the closely related genera Maoricicada, Kikihia, and Rhodopsalta were poorly resolved, the mitochondrial data and the EF1alpha data favoring different arrangements within this clade.     

Red blood cell membrane essential fatty acid metabolism in early psychotic patients following antipsychotic drug treatment

A role of indices of oxidative stress, oxidative injury, and abnormal membrane phospholipid, specifically the phospholipid essential polyunsaturated fatty acids (EPUFAs) metabolism has been suggested based on studies in separate groups of patients with or without medication. The current study investigated the relationship between these biochemical measures in first-episode psychotic patients (N=16) at baseline and after 6 months of antipsychotic treatment (N=5 each with risperidone and olanzapine) and compared them to matched normal subjects. The indices of oxidative stress included: antioxidant enzymes; superoxide dismutase, glutathione peroxidase and catalase; and the oxidative injury as the levels of plasma lipid peroxides. The key membrane EPUFA's been; linolenic acid, arachidonic acid, nervonic acid, docosapentaenoic acid and docosahexaenoic acid. Furthermore, the changes in these biochemical measures were correlated with clinical symptomatology. Data indicated that, at baseline, reduced levels of antioxidant enzymes were associated with increased plasma lipid peroxides and reduced membrane EPUFAs, particularly omega-3 fatty acids. Furthermore, these biochemical measures normalized after 6 months of antipsychotic treatment. Parallel-improved psychopathology indicated that membrane EPUFA status might be partly affected by oxidative damage, which together may contribute to the pathophysiology and thereby, psychopathology of schizophrenia. These data also support the augmentation of antipsychotic treatment by supplementation with a combination of antioxidants and omega-3 fatty acids.