In Silico screening for functional candidates amongst hypothetical proteins

Background  

The definition of a hypothetical protein is a protein that is predicted to be expressed from an open reading frame, but for which there is no experimental evidence of translation. Hypothetical proteins constitute a substantial fraction of proteomes of human as well as of other eukaryotes. With the general belief that the majority of hypothetical proteins are the product of pseudogenes, it is essential to have a tool with the ability of pinpointing the minority of hypothetical proteins with a high probability of being expressed.     

Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution

Background  

Genome comparisons have made possible the reconstruction of the eutherian ancestral karyotype but also have the potential to provide new insights into the evolutionary inter-relationship of the different eutherian orders within the mammalian phylogenetic tree. Such comparisons can additionally reveal (i) the nature of the DNA sequences present within the evolutionary breakpoint regions and (ii) whether or not the evolutionary breakpoints occur randomly across the genome. Gene synteny analysis (E-painting) not only greatly reduces the complexity of comparative genome sequence analysis but also extends its evolutionary reach.     

Zinc transporter gene expression is regulated by pro-inflammatory cytokines: a potential role for zinc transporters in beta-cell apoptosis?

Background

Numerous studies have reported that age-induced increased parathyroid hormone plasma levels are associated with cognitive decline and dementia. Little is known about the correlation that may exist between neurological processing speed, cognition and bone density in cases of hyperparathyroidism. Thus, we decided to determine if parathyroid hormone levels correlate to processing speed and/or bone density.

Methods

The recruited subjects that met the inclusion criteria (n = 92, age-matched, age 18-90 years, mean = 58.85, SD = 15.47) were evaluated for plasma parathyroid hormone levels and these levels were statistically correlated with event-related P300 potentials. Groups were compared for age, bone density and P300 latency. One-tailed tests were used to ascertain the statistical significance of the correlations. The study groups were categorized and analyzed for differences of parathyroid hormone levels: parathyroid hormone levels <30 (n = 30, mean = 22.7 ± 5.6 SD) and PTH levels >30 (n = 62, mean = 62.4 ± 28.3 SD, p ≤ 02).

Results

Patients with parathyroid hormone levels <30 showed statistically significantly less P300 latency (P300 = 332.7 ± 4.8 SE) relative to those with parathyroid hormone levels >30, which demonstrated greater P300 latency (P300 = 345.7 ± 3.6 SE, p = .02). Participants with parathyroid hormone values <30 (n = 26) were found to have statistically significantly higher bone density (M = -1.25 ± .31 SE) than those with parathyroid hormone values >30 (n = 48, M = -1.85 ± .19 SE, p = .04).

Conclusion

Our findings of a statistically lower bone density and prolonged P300 in patients with high parathyroid hormone levels may suggest that increased parathyroid hormone levels coupled with prolonged P300 latency may become putative biological markers of both dementia and osteoporosis and warrant intensive investigation.     

Include or exclude? A review on the role and suitability of aquatic invertebrate neozoa as indicators in biological assessment with special respect to fresh and brackish European waters

This paper reviews published knowledge on how to deal with invasive species during biological quality assessments in European river systems for water management and assessments of ecological quality required, for example, by the European Water Frame Work Directive. The papers studied included international papers and some standards for water assessment. An overview of the current state of neozoa research showed that many different topics are treated, comprising biogeography and fauna records, species replacements and effectiveness of colonisation, life cycles, competition between native and invasive species, habitat quality and pathways of migration. Additionally, some papers have been published recently on the integration of neozoa in index-based assessment systems. Although the decline or increase of alien species populations and the corresponding impacts on indigenous populations were frequently observed, the mechanisms behind the invasions often remain hypothetical. In the reviewed papers, issues such as possible reasons for coexistence, tolerances, quality of habitat or water, life history traits and introduction of diseases were rarely covered. Few neozoa are sufficiently investigated to be categorised as indicators. After discussing the advantages and disadvantages of inclusion or exclusion, inclusion of invaders in assessments of both biodiversity (all species) and human impact (only species classified in their specific tolerance) is suggested. Further research is required to (1) update and assign ecological profiles of the non-indigenous species currently and (2) assess the effects of new invaders on native communities.     

Recombinantly produced hydrophobins from fungal analogues as highly surface-active performance proteins

Hydrophobins are available from natural resources only in milligram amounts. BASF succeeded in a recombinant production process, up-scaled to pilot plant production in kilogram scale. Strain and protein optimization by modulation of gene expression and generation of fusion proteins finally leads to two class I hydrophobins called H*Protein A and H*Protein B. By analytical ultracentrifugation, we confirm that the self-association of H*Proteins in solution is governed by their sequence, because oligomerization is induced by the same mechanisms (pH > 6, temperature ≫ 5°C, concentration > 0.2 mg/ml) as for the well-known native hydrophobins SC3 and HFB II. Additionally, we established the triggering of structure formation by bridging with divalent ions and the stabilization of dimers and tetramers by monovalent ions or surfactants. This interplay with surfactants can be exploited synergistically: The capacity for emulsification of a 300 ppm standard surfactant solution is boosted from 0 to 100% by the addition of a mere 1 ppm of our new hydrophobins, with H*Protein A and H*Protein B having specific application profiles. This astonishing performance is rationalized by the finding that the same minute admixtures enhance significantly the interfacial elastic modulus, thus stabilizing interfaces against coalescence and phase separation.     

Outcome measures in chronic obstructive pulmonary disease (COPD): strengths and limitations

Current methods for assessing clinical outcomes in COPD mainly rely on physiological tests combined with the use of questionnaires. The present review considers commonly used outcome measures such as lung function, health status, exercise capacity and physical activity, dyspnoea, exacerbations, the multi-dimensional BODE score, and mortality. Based on current published data, we provide a concise overview of the principles, strengths and weaknesses, and discuss open questions related to each methodology. Reviewed is the current set of markers for measuring clinically relevant outcomes with particular emphasis on their limitations and opportunities that should be recognized when assessing and interpreting their use in clinical trials of COPD.     

Indacaterol provides 24-hour bronchodilation in COPD: a placebo-controlled blinded comparison with tiotropium

Background

Indacaterol is a novel, inhaled, once-daily, ultra-long-acting β₂-agonist for the treatment of chronic obstructive pulmonary disease (COPD). This randomized, double-blind study compared the bronchodilator efficacy of indacaterol with that of placebo and tiotropium in patients with moderate-to-severe COPD.

Methods

In an incomplete-block, multi-dose, three-period, crossover design, patients received three of the following four treatments: indacaterol 150 μg, indacaterol 300 μg, tiotropium 18 μg and placebo, each once-daily for 14 days. Each treatment period was separated by a 14-day washout. Study drug was supplied daily by blinded, third party study personnel to maintain blinding of patients and investigators. The primary efficacy variable was trough forced expiratory volume in one second (FEV₁) at 24 h post-dose after 14 days. The study was powered to demonstrate non-inferiority of indacaterol to tiotropium for this variable.

Results

A total of 169 patients were randomized (mean age 65 years); 153 (90.5%) completed. Trough FEV₁ after 14 days with indacaterol 150 μg and 300 μg was statistically and clinically superior to placebo, with differences (95% CI) of 170 (120-220) and 150 (100-200) mL respectively (both p < 0.001). For this endpoint, both doses of indacaterol not only met the criterion for non-inferiority compared with tiotropium, but also achieved numerically higher values, with differences versus tiotropium of 40 and 30 mL for indacaterol 150 and 300 μg, respectively. At 5 min post-dose on Day 1, the mean FEV₁ for both indacaterol doses was significantly higher than placebo (by 120 and 130 mL for indacaterol 150 and 300 μg, respectively; p < 0.001) and tiotropium (by 80 mL for both doses; p < 0.001). Adverse events were reported by similar proportions of patients: 31.4%, 29.5%, 28.3% and 28.5% for indacaterol 150 μg and 300 μg, tiotropium and placebo treatments, respectively.

Conclusions

Once-daily indacaterol provided clinically and statistically significant 24-h bronchodilation. Indacaterol was at least as effective as tiotropium, with a faster onset of action (within 5 min) on the first day of dosing. Indacaterol should prove useful in patients with moderate-to-severe COPD, for whom treatment with one or more classes of long-acting bronchodilator is recommended.

Trial registration

ClinicalTrials.gov: {"type":"clinical-trial","attrs":{"text":"NCT00615459","term_id":"NCT00615459"}}NCT00615459, EudraCT number: 2007-004071-19     

Regional differences in prediction models of lung function in Germany

Background

Little is known about the influencing potential of specific characteristics on lung function in different populations. The aim of this analysis was to determine whether lung function determinants differ between subpopulations within Germany and whether prediction equations developed for one subpopulation are also adequate for another subpopulation.

Methods

Within three studies (KORA C, SHIP-I, ECRHS-I) in different areas of Germany 4059 adults performed lung function tests. The available data consisted of forced expiratory volume in one second, forced vital capacity and peak expiratory flow rate. For each study multivariate regression models were developed to predict lung function and Bland-Altman plots were established to evaluate the agreement between predicted and measured values.

Results

The final regression equations for FEV₁ and FVC showed adjusted r-square values between 0.65 and 0.75, and for PEF they were between 0.46 and 0.61. In all studies gender, age, height and pack-years were significant determinants, each with a similar effect size. Regarding other predictors there were some, although not statistically significant, differences between the studies. Bland-Altman plots indicated that the regression models for each individual study adequately predict medium (i.e. normal) but not extremely high or low lung function values in the whole study population.

Conclusions

Simple models with gender, age and height explain a substantial part of lung function variance whereas further determinants add less than 5% to the total explained r-squared, at least for FEV1 and FVC. Thus, for different adult subpopulations of Germany one simple model for each lung function measures is still sufficient.     

Cell wall α1-3glucans induce the aggregation of germinating conidia of Aspergillus fumigatus

The germination of Aspergillus fumigatus conidia can be divided into four stages: breaking of dormancy, isotropic swelling, establishment of cell polarity, and formation of a germ tube. Swelling of conidia is associated in liquid medium with a multi-cellular aggregation that produced large clumps of conidia. Conidial aggregation can be specifically prevented by the addition of α1-3glucanase. Swollen conidia specifically adhere to insoluble α1-3glucan chains. Electron microscopy studies showed that cell wall α1-3glucan chains became exposed at the cell surface during the swelling. These results demonstrate that cell wall α1-3glucans play an essential role in the aggregation between swollen conidia. Experiments with α1-3glucan coated latex beads show that α1-3glucan chains interacted between them without the requirement of any other cell wall component suggesting that biophysical properties of α1-3glucans are solely responsible for conidial aggregation.