Evidence for alteration of calpain/calpastatin system in PBMC of cystic fibrosis patients

We are here reporting that in peripheral blood mononuclear cells (PBMC) of patients homozygous for F508del-CFTR the calpain-calpastatin system undergoes a profound alteration. In fact, calpain basal activity, almost undetectable in control PBMC, becomes measurable at a significant extent in cells from cystic fibrosis (CF) patients, also due to a 40-60% decrease in both calpastatin protein and inhibitory activity. Constitutive protease activation in CF patients' cells induces a large accumulation of the mutated cystic fibrosis transmembrane conductance regulator (CFTR) in the 100kD+70kD split forms as well as a degradation of proteins associated to the CFTR complex. Specifically, the scaffolding protein Na(+)/H(+) exchanger 3 regulatory factor-1 (NHERF-1) is converted in two distinct fragments showing masses of 35kD and 20kD, being however the latter form the most represented one, thereby indicating that in CF-PBMC the CFTR complex undergoes a large disorganization. In conclusion, our observations are providing new information on the role of calpain in the regulation of plasma membrane ion conductance and provide additional evidence on the transition of this protease activity from a physiological to a pathological function.     

High Prevalence of Left Ventricle Diastolic Dysfunction in Severe COPD Associated with A Low Exercise Capacity: A Cross-Sectional Study

Background

A subclinical left ventricle diastolic dysfunction (LVDD) has been described in patients with chronic obstructive pulmonary disease (COPD).

Objectives

To evaluate the prevalence of LVDD in stable severe COPD patients, to analyze its relationship with exercise capacity and to look for its possible causes (lung hyperinflation, ventricular interdependence or inflammatory mechanisms).

Methods

We evaluated 106 consecutive outpatients with severe COPD (FEV₁ between 30–50%). Thirty-three (31%) were excluded because of previous heart disease. A pulmonary function test, a 6-minute walking test (6MWT), a Doppler echocardiography test, including diastolic dysfunction parameters, and an analysis of arterial blood gases, NT-proBNP and serum inflammatory markers (CRP, leucocytes), were performed in all patients.

Results

The prevalence of LVDD in severe stable COPD patients was 90% (80% type I, n=57, and 10% type II, n=7). A significant association between a lower E/A ratio (higher LVDD type I) and a lower exercise tolerance (6-minute walked distance (6MWD)) was found (r=0.29, p<0.05). The fully adjusted multivariable linear regression model demonstrated that a lower E/A ratio, a DLCO in the quartile 4^th and a higher tobacco consumption were associated with a lower 6MWD (76, 57 and 0.7 metres, respectively, p<0.05). A significant correlation between E/A ratio and PaO₂ was observed (r=0.26, p<0.05), but not with static lung hyperinflation, inflammation or right ventricle overload parameters.

Conclusion

In stable severe COPD patients, the prevalence of LVDD is high and this condition might contribute in their lower exercise tolerance. Hypoxemia could have a concomitant role in their pathogenesis.     

Cortical Depth Dependent Functional Responses in Humans at 7T: Improved Specificity with 3D GRASE

Ultra high fields (7T and above) allow functional imaging with high contrast-to-noise ratios and improved spatial resolution. This, along with improved hardware and imaging techniques, allow investigating columnar and laminar functional responses. Using gradient-echo (GE) (T2* weighted) based sequences, layer specific responses have been recorded from human (and animal) primary visual areas. However, their increased sensitivity to large surface veins potentially clouds detecting and interpreting layer specific responses. Conversely, spin-echo (SE) (T₂ weighted) sequences are less sensitive to large veins and have been used to map cortical columns in humans. T₂ weighted 3D GRASE with inner volume selection provides high isotropic resolution over extended volumes, overcoming some of the many technical limitations of conventional 2D SE-EPI, whereby making layer specific investigations feasible. Further, the demonstration of columnar level specificity with 3D GRASE, despite contributions from both stimulated echoes and conventional T₂ contrast, has made it an attractive alternative over 2D SE-EPI. Here, we assess the spatial specificity of cortical depth dependent 3D GRASE functional responses in human V1 and hMT by comparing it to GE responses. In doing so we demonstrate that 3D GRASE is less sensitive to contributions from large veins in superficial layers, while showing increased specificity (functional tuning) throughout the cortex compared to GE.     

Tenascin C Promiscuously Binds Growth Factors via Its Fifth Fibronectin Type III-Like Domain

Tenascin C (TNC) is an extracellular matrix protein that is upregulated during development as well as tissue remodeling. TNC is comprised of multiple independent folding domains, including 15 fibronectin type III-like (TNCIII) domains. The fifth TNCIII domain (TNCIII5) has previously been shown to bind heparin. Our group has shown that the heparin-binding fibronectin type III domains of fibronectin (FNIII), specifically FNIII12–14, possess affinity towards a large number of growth factors. Here, we show that TNCIII5 binds growth factors promiscuously and with high affinity. We produced recombinant fragments of TNC representing the first five TNCIII repeats (TNCIII1–5), as well as subdomains, including TNCIII5, to study interactions with various growth factors. Multiple growth factors of the platelet-derived growth factor (PDGF) family, the fibroblast growth factor (FGF) family, the transforming growth factor beta (TGF-β) superfamily, the insulin-like growth factor binding proteins (IGF-BPs), and neurotrophins were found to bind with high affinity to this region of TNC, specifically to TNCIII5. Surface plasmon resonance was performed to analyze the kinetics of binding of TNCIII1–5 with TGF-β1, PDGF-BB, NT-3, and FGF-2. The promiscuous yet high affinity of TNC for a wide array of growth factors, mediated mainly by TNCIII5, may play a role in multiple physiological and pathological processes involving TNC.     

Bias in Diet Determination: Incorporating Traditional Methods in Bayesian Mixing Models

There are not “universal methods” to determine diet composition of predators. Most traditional methods are biased because of their reliance on differential digestibility and the recovery of hard items. By relying on assimilated food, stable isotope and Bayesian mixing models (SIMMs) resolve many biases of traditional methods. SIMMs can incorporate prior information (i.e. proportional diet composition) that may improve the precision in the estimated dietary composition. However few studies have assessed the performance of traditional methods and SIMMs with and without informative priors to study the predators’ diets. Here we compare the diet compositions of the South American fur seal and sea lions obtained by scats analysis and by SIMMs-UP (uninformative priors) and assess whether informative priors (SIMMs-IP) from the scat analysis improved the estimated diet composition compared to SIMMs-UP. According to the SIMM-UP, while pelagic species dominated the fur seal’s diet the sea lion’s did not have a clear dominance of any prey. In contrast, SIMM-IP’s diets compositions were dominated by the same preys as in scat analyses. When prior information influenced SIMMs’ estimates, incorporating informative priors improved the precision in the estimated diet composition at the risk of inducing biases in the estimates. If preys isotopic data allow discriminating preys’ contributions to diets, informative priors should lead to more precise but unbiased estimated diet composition. Just as estimates of diet composition obtained from traditional methods are critically interpreted because of their biases, care must be exercised when interpreting diet composition obtained by SIMMs-IP. The best approach to obtain a near-complete view of predators’ diet composition should involve the simultaneous consideration of different sources of partial evidence (traditional methods, SIMM-UP and SIMM-IP) in the light of natural history of the predator species so as to reliably ascertain and weight the information yielded by each method.     

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analysis 1 of the most used preprocessing procedures is read trimming, which aims at removing low quality portions while preserving the longest high quality part of a NGS read. In the current work, we evaluate nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.     

Genetic Structure of Tibeto-Burman Populations of Bangladesh: Evaluating the Gene Flow along the Sides of Bay-of-Bengal

Human settlement and migrations along sides of Bay-of-Bengal have played a vital role in shaping the genetic landscape of Bangladesh, Eastern India and Southeast Asia. Bangladesh and Northeast India form the vital land bridge between the South and Southeast Asia. To reconstruct the population history of this region and to see whether this diverse region geographically acted as a corridor or barrier for human interaction between South Asia and Southeast Asia, we, for the first time analyzed high resolution uniparental (mtDNA and Y chromosome) and biparental autosomal genetic markers among aboriginal Bangladesh tribes currently speaking Tibeto-Burman language. All the three studied populations; Chakma, Marma and Tripura from Bangladesh showed strikingly high homogeneity among themselves and strong affinities to Northeast Indian Tibeto-Burman groups. However, they show substantially higher molecular diversity than Northeast Indian populations. Unlike Austroasiatic (Munda) speakers of India, we observed equal role of both males and females in shaping the Tibeto-Burman expansion in Southern Asia. Moreover, it is noteworthy that in admixture proportion, TB populations of Bangladesh carry substantially higher mainland Indian ancestry component than Northeast Indian Tibeto-Burmans. Largely similar expansion ages of two major paternal haplogroups (O2a and O3a3c), suggested that they arose before the differentiation of any language group and approximately at the same time. Contrary to the scenario proposed for colonization of Northeast India as male founder effect that occurred within the past 4,000 years, we suggest a significantly deep colonization of this region. Overall, our extensive analysis revealed that the population history of South Asian Tibeto-Burman speakers is more complex than it was suggested before.