Analysis of IL-12 p40 subunit gene and IFN-γ G5644A polymorphisms in Idiopathic Pulmonary Fibrosis

Background

Genes encoding cytokine mediators are prime candidates for genetic analysis in conditions with T-helper (Th) cell disease driven imbalance. Idiopathic Pulmonary Fibrosis (IPF) is a predominantly Th2 mediated disease associated with a paucity of interferon-gamma (IFN-γ). The paucity of IFN-γ may favor the development of progressive fibrosis in IPF. Interleukin-12 (IL-12) plays a key role in inducing IFN-γ production. The aim of the current study was to assess whether the 1188 (A/C) 3'UTR single nucleotide polymorphism (SNP) in the IL-12 p40 subunit gene which was recently found to be functional and the 5644 (G/A) 3' UTR SNP of the IFN-γ gene were associated with susceptibility to IPF.

Methods

We investigated the allelic distribution in these loci in UK white Caucasoid subjects comprising 73 patients with IPF and 157 healthy controls. The SNPs were determined using the polymerase chain reaction in association with sequence-specific primers incorporating mismatches at the 3'-end.

Results

Our results showed that these polymorphisms were distributed similarly in the IPF and control groups

Conclusion

We conclude that these two potentially important candidate gene single nucleotide polymorphisms are not associated with susceptibility to IPF.     

Genetic associations: false or true?

Genetic association studies for multigenetic diseases are like fishing for the truth in a sea of trillions of candidate analyses. Red herrings are unavoidably common, and bias might cause serious misconceptions. However, a sizeable proportion of identified genetic associations are probably true. Meta-analysis, a rigorous, comprehensive, quantitative synthesis of all the available data, might help us to separate the true from the false.     

Thyroid hormone and cardioprotection: Study of p38 MAPK and JNKs during ischaemia and at reperfusion in isolated rat heart

It has been recently shown that long-term thyroxine administration increases the tolerance of the heart to ischaemia. The present study investigated whether thyroxine induced cardioprotection involves alterations in the pattern of p38 mitogen activated protein kinase (p38MAPK) and c-Jun NH₂-terminal kinases (JNKs) activation during ischaemia-reperfusion. L-thyroxine (T4) was administered in Wistar rats (25 g/100 g/day, subcutaneously) for 2 weeks (THYR), while normal animals served as controls (NORM). NORM and THYR isolated rat hearts were perfused in Langendorff mode and subjected to 10 or 20 min of zero-flow global ischaemia only and also to 20 min of ischaemia followed by 10, 20 or 45 min of reperfusion. Postischaemic recovery of left ventricular developed pressure at 45 min of reperfusion was expressed as % of the initial value. Activation of p38 MAPK and JNKs was assessed at the different times of the experimental setting by standard Western blotting techniques using a dual phospho p38MAPK and phospho JNKs (p46/p54) antibodies. Activation of p38 MAPK was significantly attenuated during ischaemia and reperfusion in thyroxine treated hearts compared to normal hearts. JNKs were found to be activated only during the reperfusion period. The levels of phospho JNKs were found to be lower in thyroxine treated hearts as compared to untreated hearts, though not at a statistically significant level. Postischaemic functional recovery was higher in THYR as compared to NORM, p < 0.05. In summary, in hearts pretreated with thyroxine, p38 MAPK was attenuated during ischaemia and at reperfusion and this was associated with improved postischaemic recovery of function.     

Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood

Covalently closed circular RNA molecules (circRNAs) have recently emerged as a class of RNA isoforms with widespread and tissue specific expression across animals, oftentimes independent of the corresponding linear mRNAs. circRNAs are remarkably stable and sometimes highly expressed molecules. Here, we sequenced RNA in human peripheral whole blood to determine the potential of circRNAs as biomarkers in an easily accessible body fluid. We report the reproducible detection of thousands of circRNAs. Importantly, we observed that hundreds of circRNAs are much higher expressed than corresponding linear mRNAs. Thus, circRNA expression in human blood reveals and quantifies the activity of hundreds of coding genes not accessible by classical mRNA specific assays. Our findings suggest that circRNAs could be used as biomarker molecules in standard clinical blood samples.     

One Step forward: Benthic Pelagic Coupling and Indicators for Environmental Status

A large data set from the Eastern Mediterranean was analyzed to explore the relationship between seawater column variables and benthic community status. Our results showed a strong quantitative link between the seawater column variables (Chlorophyll a and Eutrophication Index) and various indicators describing benthic diversity and community composition. The percentage of benthic opportunistic species increased significantly in the stations with high trophic status of the seawater column and so did the strength of the coupling between values of seawater column and benthic indicators. The Eutrophication Index threshold level of 0.85, separating the “Bad and Poor” from “Moderate to High” conditions could serve as an acceptable critical value above which there is a readily observable change in benthic community composition.     

Testing generalized allometries in allocation modeling within an individual-based simulation framework

The allocation of carbohydrates from photosynthesis to various plant compartments is a key process in ecophysiology and consequently an important element in process-based ecosystem modeling. In this study, we tested generalized empirical equations in a widely applied partitioning concept based on compartment-specific biomass allometries. For an 88-year chronosequence of European beech (Fagus sylvatica L.) in Austria, we used the individual-based hybrid forest model PICUS v1.4 to compare simulations employing foliage biomass functions at different levels of generalization against runs with site-specific parameterization and observations. Sensitivities of the individual tree model were generally in line with the original stand-level partitioning concept and ecological process understanding. While stand-level leaf area increased with increasing allocation to foliage, net primary productivity showed no significant response due to saturated radiation interception in the dense chronosequence stands. Strong sensitivities were revealed at the individual tree level, where favoring allocation to the foliage compartment resulted in increasing asymmetry of competition and height–diameter relationships. Applying a generalized parameterization based on data from the full range of continental species distribution resulted in a significant overestimation of mean tree height and subsequently standing volume stock at the chronosequence. At a lower hierarchical level of generality, however, simulations with a representative regional parameterization performed satisfactorily compared to model runs using the site-specific allometry. In relation to common accuracy demands, e.g., in forest management decision support, the study suggests the rejection of a generic parameterization while corroborating the use of regional generalizations in ecosystem models.