Wheat Zapper: a flexible online tool for colinearity studies in grass genomes

In the course of evolution, the genomes of grasses have maintained an observable degree of gene order conservation. The information available for already sequenced genomes can be used to predict the gene order of nonsequenced species by means of comparative colinearity studies. The “Wheat Zapper” application presented here performs on-demand colinearity analysis between wheat, rice, Sorghum, and Brachypodium in a simple, time efficient, and flexible manner. This application was specifically designed to provide plant scientists with a set of tools, comprising not only synteny inference, but also automated primer design, intron/exon boundaries prediction, visual representation using the graphic tool Circos 0.53, and the possibility of downloading FASTA sequences for downstream applications. Quality of the “Wheat Zapper” prediction was confirmed against the genome of maize, with good correlation (r?>?0.83) observed between the gene order predicted on the basis of synteny and their actual position on the genome. Further, the accuracy of “Wheat Zapper” was calculated at 0.65 considering the “Genome Zipper” application as the “gold” standard. The differences between these two tools are amply discussed, making the point that “Wheat Zapper” is an accurate and reliable on-demand tool that is sure to benefit the cereal scientific community. The Wheat Zapper is available at http://wge.ndsu.nodak.edu/wheatzapper/.     

The A Allele of the rs1990760 Polymorphism in the IFIH1 Gene Is Associated with Protection for Arterial Hypertension in Type 1 Diabetic Patients and with Expression of This Gene in Human Mononuclear Cells

Background

The rs1990760 polymorphism of interferon induced with helicase C domain 1 (IFIH1) has been associated with type 1 diabetes mellitus (T1DM). Here, we investigated whether this polymorphism is associated with T1DM or its clinical characteristics in a Brazilian population, and if IFIH1 gene expression in mononuclear cells from T1DM patients differs according to the genotypes of this polymorphism. A meta-analysis was also conducted to evaluate if the rs1990760 polymorphism is associated with T1DM.

Methods

Frequencies of the rs1990760 polymorphism were analyzed in 527 T1DM patients and in 517 healthy subjects. IFIH1 gene expressions according to genotypes were measured in a sub-sample of 26 T1DM patients by quantitative real-time PCR.

Results

Our data show the association of the A allele with risk to T1DM under a dominant model of inheritance [odds ratio (OR) = 1.421, P = 0.037], adjusting for ethnicity. The meta-analysis revealed significant association between the rs199760A allele and risk for T1DM for all analyzed inheritance models. Surprisingly, T1DM patients carrying the A allele showed lower levels of systolic (P = 0.001) and diastolic (P = 1×10⁻¹⁰) blood pressures as compared to G/G carriers. Furthermore, the A/A genotype seems to be associated with protection to arterial hypertension (AH) after adjustment for covariates (OR = 0.339, P = 0.019). IFIH1 gene expression in mononuclear cells from 26 T1DM patients did not differ among genotypes (P = 0.274). Nevertheless, IFIH1 gene expression was increased in mononuclear cells from T1DM patients with AH as compared with T1DM patients without AH [6.7 (1.7–2.0) vs. 1.8 (1.3–7.1) arbitrary units; P = 0.036]. The association with blood pressures and AH was not observed in patients with type 2 diabetes mellitus.

Conclusions

Our results indicate that the rs1990760 polymorphism is associated with T1DM. Interestingly, the rs1990760 A allele seems to be associated with protection for AH in T1DM patients. Further studies are needed to confirm the association with AH.     

Angiovision: Aortic stent-graft placement by augmented angionavigation

The endovascular treatment of abdominal aortic aneurysm (EVAR - EndoVascular Aneurism Repair) has become an alternative therapy to conventional open surgery. The objective of Angiovision project was to contribute to the improvement of EVAR procedures in terms of accuracy and customization of the interventional strategy. Our approach was mainly based on the use of patient-specific data, computer-aided endovascular navigation and numerical simulation. We proposed a new FEM-based patient-specific simulation solution to estimate the deformations caused by the introduction of stiff endovascular devices. We developed and implemented an original endovascular navigation system to augment the intraoperative fluoroscopy with the visualization of deformed preoperative aorto-iliac structure, and related information concerning vessel wall (calcifications), as well as stent-graft virtual deployment. The proposed solution, that requires only lightweight computer equipment, can be used in a standard operating room in order to optimize device placement (from a single angle of incidence). Evaluation is currently under way.     

Soluble CD40 Ligand Stimulates the Pro-Angiogenic Function of Peripheral Blood Angiogenic Outgrowth Cells via Increased Release of Matrix Metalloproteinase-9

The role of endothelial progenitor cells in vascular repair is related to their incorporation at sites of vascular lesions, differentiation into endothelial cells, and release of various angiogenic factors specifically by a subset of early outgrowth endothelial progenitor cells (EOCs). It has been shown that patients suffering from cardiovascular disease exhibit increased levels of circulating and soluble CD40 ligand (sCD40L), which may influence the function of EOCs. We have previously shown that the inflammatory receptor CD40 is expressed on EOCs and its ligation with sCD40L impairs the anti-platelet function of EOCs. In the present study, we aimed at investigating the effect of sCD40L on the function of EOCs in endothelial repair. Human peripheral blood mononuclear cell-derived EOCs express CD40 and its adaptor proteins, the tumor necrosis factor receptor-associated factors; TRAF1, TRAF2 and TRAF3. Stimulation of EOCs with sCD40L increased the expression of TRAF1, binding of TRAF2 to CD40 and phosphorylation of p38 mitogen activated protein kinase (MAPK). In an in vitro wound healing assay, stimulation of EOCs with sCD40L increased the release of matrix metalloproteinase 9 (MMP-9) in a concentration-dependent manner and significantly enhanced the angiogenic potential of cultured human umbilical vein endothelial cells (HUVECs). Inhibition of p38 MAPK reversed sCD40L-induced MMP-9 release by EOCs, whereas inhibition of MMP-9 reversed their pro-angiogenic effect on HUVECs. This study reveals the existence of a CD40L/CD40/TRAF axis in EOCs and shows that sCD40L increases the pro-angiogenic function of EOCs on cultured HUVECs by inducing a significant increase in MMP-9 release via, at least, the p38 MAPK signaling pathway.     

Quantum Dot Based Heterostructures for Unassisted Photoelectrochemical Hydrogen Generation

TiO₂ hollow nanowires (HNWs) and nanoparticles (NPs) constitute promising architectures for QDs sensitized photoanodes for H₂ generation. We sensitize these structures with CdS/CdSe quantum dots by two different methods (chemical bath deposition, CBD and succesive ionic layer adsorption and reaction, SILAR) and evaluate the performance of these photoelectrodes. Remarkable photocurrents of 4 mA·cm and 8 mA·cm^?2 and hydrogen generation rates of 40 ml·cm^?2·day^?1 and 80 ml·cm^?2·day^?1 have been obtained in a three electrode configuration with sacrificial hole scavengers (Na₂S and Na₂SO₃), for HNWs and NPs respectively, which is confirmed through gas analysis. More importantly, autonomous generation of H₂ (20 ml·cm^?2·day^?1 corresponding to 2 mA·cm^?2 photocurrent) is obtained in a two electrode configuration at short circuit under 100 mW·cm^?2 illumination, clearly showing that these photoanodes can produce hydrogen without the assistance of any external bias. To the best of the authors' knowledge, this is the highest unbiased solar H₂ generation rate reported for these of QDs based heterostructures. Impedance spectroscopy measurements show similar electron density of trap states below the TiO₂ conduction band while the recombination resistance was higher for HNWs, consistently with the much lower surface area compared to NPs. However, the conductivity of both structures is similar, in spite of the one dimensional character of HNWs, which leaves some room for improvement of these nanowired structures. The effect of the QDs deposition method is also evaluated. Both structures show remarkable stability without any appreciable photocurrent loss after 0.5 hour of operation. The findings of this study constitute a relevant step towards the feasibility of hydrogen generation with wide bandgap semiconductors/quantum dots based heterostructures.     

Citrus Allergy from Pollen to Clinical Symptoms

Allergy to citrus fruits is often associated with pollinosis and sensitization to other plants due to a phenomenon of cross-reactivity. The aims of the present study were to highlight the cross-reactivity among citrus and the major allergenic pollens/fruits, throughout clinical and molecular investigations, and to evaluate the sensitization frequency to citrus fruits in a population of children and adults with pollinosis. We found a relevant percentage of sensitisation (39%) to citrus fruits in the patients recruited and in all of them the IgE-mediated mechanism has been confirmed by the positive response to the prick-to-prick test. RT-PCR experiments showed the expression of Cit s 1, Cit s 3 and a profilin isoform, already described in apple, also in Citrus clementine pollen. Data of multiple sequence alignments demonstrated that Citrus allergens shared high percentage identity values with other clinically relevant species (i.e. Triticum aestivum, Malus domestica), confirming the possible cross-allergenicity citrus/grasses and citrus/apple. Finally, a novelty of the present work has been the expression of two phospholipaseA2 isoforms (PLA2 α and β) in Citrus as well as in Triticum pollens; being PLA2 able to generate pro-inflammatory factors, this enzyme could participate in the activation of the allergenic inflammatory cascade.     

Schisandra henryi C. B. Clarke in vitro cultures: a promising tool for the production of lignans and phenolic compounds

Plant Cell, Tissue and Organ Culture (PCTOC) - We initiated and optimized in vitro culture conditions of the endemic Chinese plant species—Schisandra henryi C. B. Clarke. Different types of...     

Field and laboratory studies on the life-cycle, growth and feeding preference in the hairy snail Trochulus hispidus (L., 1758) (Gastropoda: Pulmonata: Hygromiidae)

For the first time the life cycle of the common land snail Trochulus hispidus was completely described in Central Europe (Poland). This is a semelparous species predominantly with an annual life cycle and the reproductive period lasting from April till October. The first young snails hatch in spring, grow rapidly in summer and reach ca. 4 whorls until winter. In spring of the next year they mature and reproduce. After that they die. There is hardly any growth from late autumn till early spring. The average proportional growth rate is ca. 0.3 whorl/month in the wild. The fastest growth is present in the youngest snails and then gradually decreases over the course of their age. Laboratory and field observations allowed for establishing the following life cycle parameters: eggs calcified, almost spherical, ca. 1.5 mm, laid in spring and summer in batches of between 1 and 47. Time to hatching is 6–24 days, hatching is asynchronous; newly-hatched snails have approximately 1.5 whorls. Analysis of food preferences revealed, that T. hispidus tends to restrict its diet during the life. Generally the youngest snails equally consumed leaves of all four tree species offered (Fraxinus excelsior, Acer pseudoplatanus, Tilia cordata and A. platanoides) whereas adults preferred F. excelsior over A. pseudoplatanus and A. platanoides.