Coding potential of the products of alternative splicing in human

Background: Analysis of the human genome has revealed that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized genes. A number of these transcripts are alternatively spliced forms of known protein coding genes; however, it is becoming clear that many of them do not necessarily correspond to a functional protein. Results: In this study we analyze alternative splicing isoforms of human gene products that are unambiguously identified by mass spectrometry and compare their properties with those of isoforms of the same genes for which no peptide was found in publicly available mass spectrometry datasets. We analyze them in detail for the presence of uninterrupted functional domains, active sites as well as the plausibility of their predicted structure. We report how well each of these strategies and their combination can correctly identify translated isoforms and derive a lower limit for their specificity, that is, their ability to correctly identify non-translated products. Conclusions: The most effective strategy for correctly identifying translated products relies on the conservation of active sites, but it can only be applied to a small fraction of isoforms, while a reasonably high coverage, sensitivity and specificity can be achieved by analyzing the presence of non-truncated functional domains. Combining the latter with an assessment of the plausibility of the modeled structure of the isoform increases both coverage and specificity with a moderate cost in terms of sensitivity

Preliminary studies for a possible use of Doppier Signals in the analysis of systolic time intervals of fetal heart

Peer Reviewe

Analysis of the effect of LRP-1 silencing on the invasive potential of cancer cells by nanomechanical probing and adhesion force measurements using atomic force microscopy

Low-density lipoprotein receptor-related protein 1 (LRP-1) can internalize proteases involved in cancer progression and is thus considered a promising therapeutic target. However, it has been demonstrated that LRP-1 is also able to regulate the endocytosis of membrane-anchored proteins. Thus, strategies that target LRP-1 to modulate proteolysis could also affect adhesion and cytoskeleton dynamics. Here, we investigated the effect of LRP-1 silencing on parameters reflecting cancer cells’ invasiveness by atomic force microscopy (AFM). The results show that LRP-1 silencing induces changes in the cells’ adhesion behavior,particularly the dynamics of cell attachment. Clear alterations in morphology, such as more pronounced stress fibers and increased spreading, leading to increased area and circularity, were also observed. The determination of the cells’ mechanical properties by AFM showed that these differences are correlated with an increase in Young’s modulus. Moreover, the measurements show an overall decrease in cell motility and modifications of directional persistence. An overall increase in the adhesion force between the LRP-1-silenced cells and a gelatin-coated bead was also observed. Ultimately, our AFM-based force spectroscopy data, recorded using an antibody directed against the β1 integrin subunit,provide evidence that LRP-1 silencing modifies the rupture force distribution. Together, our results show that techniques traditionally used for the investigation of cancer cells can be coupled with AFM to gain access to complementary phenotypic parameters that can help discriminate between specific phenotypes associated with different degrees of invasivenes

Two Aspergillus species, A. flavus and A. fumigatus - a comparative study of their conidial surface properties and immunological reactivities

International audienceThough belonging to the Aspergillus genus, Aspergillus fumigatus is the major causative agent of fatal invasive aspergillosis, the systemic infection in immunocompromised, while A. flavus causes keratitis, a superficial health hazardous infection in immunocompetent individuals. In the present study, we have been exploring these two Aspergillus species in understanding differences in their preferred sites of infection. Structurally, there was a difference in their conidial sizes. A. fumigatus conidia were uniformly labelled by calcofluor white, negative for FITC conjugated Concanavalin-A or wheat-germ agglutinin labelling, while A. flavus conidia showed heterogenous labelling. The A. fumigatus conidia surface was covered by a uniform rodlet layer whereas A. flavus conidia showed heterogeneity; some conidia showing rodlet layer, but others with additional amorphous structure. A. flavus conidial cell wall contained significantly higher amount of chitin and lower amount of glucan in the alkali-insoluble fraction compared to A. fumigatus conidial cell wall. Whereas, in the mycelial morphotype, the A. flavus cell wall showed a significantly lower amount of glucan in cell wall and higher amounts of chitin and galactosamine containing polysaccharide in the alkali-insoluble fraction. A. fumigatus condia failed to activate human monocyte derived macrophages, dendritic cells and isolated neutrophils, but A. flavus conidia were immuno-stimulatory in their effect. Interestingly, though macrophages secreted both pro- and anti-inflammatory cytokines, dendritic cells and neutrophils secreted only IL-8 upon A. flavus conidial interaction. These observations may reason for their preferred mode and thus the site of infectio