Convergence of discrete duality finite volume schemes for the cardiac bidomain model

We prove convergence of discrete duality finite volume (DDFV) schemes on distorted meshes for a class of simplified macroscopic bidomain models of the electrical activity in the heart. Both time-implicit and linearised time-implicit schemes are treated. A short description is given of the 3D DDFV meshes and of some of the associated discrete calculus tools. Several numerical tests are presented

On a two-sidedly degenerate chemotaxis model with volume-filling effect

We consider a fully parabolic model for chemotaxis with volume-filling effect and a nonlinear diffusion that degenerates in a two-sided fashion. We address the questions of existence of weak solutions and of their regularity by using, respectively, a regularization method and the technique of intrinsic scaling.Outstanding Young Investigators Award from the Research Council of Norway; (J. M. Urbano) CMUC/FCT, Project POCI/MAT/57546/200

H¹-PERTURBATIONS OF SMOOTH SOLUTIONS FOR A WEAKLY DISSIPATIVE HYPERELASTIC-ROD WAVE EQUATION

We consider a weakly dissipative hyperelastic-rod wave equation (or weakly dissipative Camassa-Holm equation) describing nonlinear dispersive dissipative waves in compressible hyperelastic rods. By fixed a smooth solution, we establish the existence of a strongly continuous semigroup of global weak solutions for any initial perturbation from $H^1({\mathbb R})$. In particular, the supersonic solitary shock waves [8] are included in the analysis

HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression

The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT (HWS) affects organ growth and the timing of floral organ abscission. The loss-of-function hws-1 mutant exhibits fused sepals and increased organ size. To understand the molecular mechanisms of HWS during plant development, we mutagenized hws-1 seeds with ethylmethylsulphonate (EMS) and screened for mutations suppressing hws-1 associated phenotypes. We isolated the shs1/hws-1 (suppressor of hws-1) mutant in which hws-1 sepal fusion phenotype was suppressed. The shs1/hws-1 mutant carries a G→A nucleotide substitution in the MIR164 binding site of CUP-SHAPED COTYLEDON 1 (CUC1) mRNA. CUC1 and CUP-SHAPED COTYLEDON 2 (CUC2) transcript levels were altered in shs1, renamed cuc1-1D, and in hws-1 mutant. Genetic interaction analyses using single, double and triple mutants of cuc1-1D, cuc2-1D (a CUC2 mutant similar to cuc1-1D), and hws-1, demonstrate that HWS, CUC1 and CUC2 act together to control floral organ number. Loss of function of HWS is associated with larger petal size due to alterations in cell proliferation and mitotic growth, a role shared with the CUC1 gene

HAWAIIAN SKIRT, and F-box gene from Arabidopsis, is a new player in the microRNA pathway

F-box proteins belong to a multi-protein E3 ubiquitin ligase complex (SCF) that target proteins for degradation via the proteasome.We demonstrated that HAWAIIAN SKIRT(HWS), an Arabidopsis ubiquitin protein ligase (SCFHWS), regulates organ growth, flower development and timing of abscission. Mutants of this gene (hws-1) are pleiotropic and the most obvious phenotype is the fusion of its floral organs, a phenotype shared with the cuc1/cuc2 double mutants and over-expressing lines of MIR164B. To understand the molecular mechanisms of HWS during plant development, an ethylmethylsulphonate mutagenized population of hws-1 seeds was generated and screened for mutations suppressing the hws-1 sepal fusion. We isolated shs-1/hws-1, shs-2/hws-1, and shs-3/hws-1, (suppressor of hws-1) mutants. Mapping analyses shown that shs1 is mutated in the miRNA164 binding site of CUPSHAPED COTYLEDON1 (CUC1) mRNA; while shs-2 and shs-3 are novel alleles of the plant homolog of Exporting-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Consequently, we renamed them cuc1-1D, hst23 and hst24, respectively. We demonstrated that transcript levels of CUC1 and CUPSHAPED COTYLEDON 2 (CUC2), and MIR164 change in cuc1-1D and in hws-1 mutants; analyses revealed a role for HWS in cell proliferation and control of floral organ number. Additional genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway were performed and double mutants obtained shown restoration of the hws-1 sepal fusion phenotype. Our data propose HWS as a new regulator in miRNA pathway and reveal a role for HWS to control floral organ number and cell proliferation

Suffusion susceptibility characterization by triaxial erodimeter and statistical analysis

Suffusion process corresponds to the coupled processes of detachment-transport-filtration of the soil’s fine fraction within the voids between the coarse fraction. Because of the great length of earth structures and because of the heterogeneities of soils, it is very difficult to characterize the suffusion susceptibility of soils all along the earth structures. So, a statistical analysis can be performed in order to optimize the experimental campaign. By using a specific triaxial erodimeter, an experimental program was setup to study suffusion susceptibility of thirty two specimens. The suffusion susceptibility is determined by the erosion resistance index. Ten physical parameters are determined and a statistical analysis is performed in order to identify the main parameters for a correlation with erosion resistance index. The multivariate statistical analysis leads to an expression of the erosion resistance index as a function of eight physical parameters, and by distinguishing the gap-graded and widely-graded soils, another new correlation is obtained with five physical parameters

Protein–protein interactions as a proxy to monitor conformational changes and activation states of the tomato resistance protein I-2

Plant resistance proteins (R) are involved in pathogen recognition and subsequent initiation of defence responses. Their activity is regulated by inter- and intramolecular interactions. In a yeast two-hybrid screen two clones (I2I-1 and I2I-2) specifically interacting with I-2, a Fusarium oxysporum f. sp. lycopersici resistance protein of the CC-NB-LRR family, were identified. Sequence analysis revealed that I2I-1 belongs to the Formin gene family (SlFormin) whereas I2I-2 has homology to translin-associated protein X (SlTrax). SlFormin required only the N-terminal CC I-2 domain for binding, whereas SlTrax required both I-2 CC and part of the NB-ARC domain. Tomato plants stably silenced for these interactors were not compromised in I-2-mediated disease resistance. When extended or mutated forms of I-2 were used as baits, distinct and often opposite, interaction patterns with the two interactors were observed. These interaction patterns correlated with the proposed activation state of I-2 implying that active and inactive R proteins adopt distinct conformations. It is concluded that the yeast two hybrid system can be used as a proxy to monitor these different conformational states

AGO1 and AGO2 Act Redundantly in miR408-Mediated Plantacyanin Regulation

Background: In Arabidopsis, AGO1 and AGO2 associate with small RNAs that exhibit a Uridine and an Adenosine at their 59 end, respectively. Because most plant miRNAs have a 59U, AGO1 plays many essential roles in miRNA-mediated regulation of development and stress responses. In contrast, AGO2 has only been implicated in antibacterial defense in association with miR393*, which has a 59A. AGO2 also participates in antiviral defense in association with viral siRNAs. Principal Findings: This study reveals that miR408, which has a 59A, regulates its target Plantacyanin through either AGO1 or AGO2. Indeed, neither ago1 nor ago2 single mutations abolish miR408-mediated regulation of Plantacyanin. Only an ago1 ago2 double mutant appears compromised in miR408-mediated regulation of Plantacyanin, suggesting that AGO1 and AGO2 have redundant roles in this regulation. Moreover, the nature of the 59 nucleotide of miR408 does not appear essential for its regulatory role because both a wildtype 59A-MIR408 and a mutant 59U-MIR408 gene complement a mir408 mutant. Conclusions/Significance: These results suggest that miR408 associates with both AGO1 and AGO2 based on criteria that differ from the 59 end rule, reminiscent of miR390-AGO7 and miR165/166-AGO10 associations, which are not based on the nature of the 59 nucleotide

Identification of Mendel's White Flower Character

BACKGROUND: The genetic regulation of flower color has been widely studied, notably as a character used by Mendel and his predecessors in the study of inheritance in pea. METHODOLOGY/PRINCIPAL FINDINGS: We used the genome sequence of model legumes, together with their known synteny to the pea genome to identify candidate genes for the A and A2 loci in pea. We then used a combination of genetic mapping, fast neutron mutant analysis, allelic diversity, transcript quantification and transient expression complementation studies to confirm the identity of the candidates. CONCLUSIONS/SIGNIFICANCE: We have identified the pea genes A and A2. A is the factor determining anthocyanin pigmentation in pea that was used by Gregor Mendel 150 years ago in his study of inheritance. The A gene encodes a bHLH transcription factor. The white flowered mutant allele most likely used by Mendel is a simple G to A transition in a splice donor site that leads to a mis-spliced mRNA with a premature stop codon, and we have identified a second rare mutant allele. The A2 gene encodes a WD40 protein that is part of an evolutionarily conserved regulatory complex

A putative antiviral role of plant cytidine deaminases

[EN] Background: A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade. Host cytidine deaminases (e.g., APOBEC3 proteins) edit viral genomes, giving rise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis. By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity. To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation. The model plant Arabidopsis thaliana genome encodes nine cytidine deaminases (AtCDAs), raising the question of whether deamination is an antiviral mechanism in plants as well. Methods: Here we tested the effects of expression of AtCDAs on the pararetrovirus Cauliflower mosaic virus (CaMV). Two different experiments were carried out. First, we transiently overexpressed each one of the nine A. thaliana AtCDA genes in Nicotiana bigelovii plants infected with CaMV, and characterized the resulting mutational spectra, comparing them with those generated under normal conditions. Secondly, we created A. thaliana transgenic plants expressing an artificial microRNA designed to knock-out the expression of up to six AtCDA genes. This and control plants were then infected with CaMV. Virus accumulation and mutational spectra where characterized in both types of plants. Results: We have shown that the A. thaliana AtCDA1 gene product exerts a mutagenic activity, significantly increasing the number of G to A mutations in vivo, with a concomitant reduction in the amount of CaMV genomes accumulated. Furthermore, the magnitude of this mutagenic effect on CaMV accumulation is positively correlated with the level of AtCDA1 mRNA expression in the plant. Conclusions: Our results suggest that deamination of viral genomes may also work as an antiviral mechanism in plants.This work was supported by the former Spanish Ministerio de Ciencia e Innovación-FEDER grant BFU2009-06993 to SFE. JMC was supported by the CSIC JAE-doc program/Fondo Social Europeo. AG-P was supported by a grant for Scientific and Technical Activities and by grant P10-CVI-65651, both from Junta de Andalucía.Martín, S.; Cuevas, J.; Grande-Perez, A.; Elena Fito, SF. (2017). A putative antiviral role of plant cytidine deaminases. F1000Research. 1-14. https://doi.org/10.12688/f1000research.11111.2S11