Genome-wide analysis of alternative splicing events in Hordeum vulgare: highlighting retention of intron-based splicing and its possible function through network analysis

In this study, using homology mapping of assembled expressed sequence tags against the genomic data, we identified alternative splicing events in barley. Results demonstrated that intron retention is frequently associated with specific abiotic stresses. Network analysis resulted in discovery of some specific sub-networks between miRNAs and transcription factors in genes with high number of alternative splicing, such as cross talk between SPL2, SPL10 and SPL11 regulated by miR156 and miR157 families. To confirm the alternative splicing events, elongation factor protein (MLOC_3412) was selected followed by experimental verification of the predicted splice variants by Semi quantitative Reverse Transcription PCR (qRT-PCR). Our novel integrative approach opens a new avenue for functional annotation of alternative splicing through regulatory-based network discovery.Bahman Panahi, Seyed Abolghasem Mohammadi, Reyhaneh Ebrahimi Khaksefidi, Jalil Fallah Mehrabadi, Esmaeil Ebrahimi

Unilateral interactions in granular packings: A model for the anisotropy modulus

Unilateral interparticle interactions have an effect on the elastic response of granular materials due to the opening and closing of contacts during quasi-static shear deformations. A simplified model is presented, for which constitutive relations can be derived. For biaxial deformations the elastic behavior in this model involves three independent elastic moduli: bulk, shear, and anisotropy modulus. The bulk and the shear modulus, when scaled by the contact density, are independent of the deformation. However, the magnitude of the anisotropy modulus is proportional to the ratio between shear and volumetric strain. Sufficiently far from the jamming transition, when corrections due to non-affine motion become weak, the theoretical predictions are qualitatively in agreement with simulation results.Comment: 6 pages, 5 figure

The closest elastic tensor of arbitrary symmetry to an elasticity tensor of lower symmetry

The closest tensors of higher symmetry classes are derived in explicit form for a given elasticity tensor of arbitrary symmetry. The mathematical problem is to minimize the elastic length or distance between the given tensor and the closest elasticity tensor of the specified symmetry. Solutions are presented for three distance functions, with particular attention to the Riemannian and log-Euclidean distances. These yield solutions that are invariant under inversion, i.e., the same whether elastic stiffness or compliance are considered. The Frobenius distance function, which corresponds to common notions of Euclidean length, is not invariant although it is simple to apply using projection operators. A complete description of the Euclidean projection method is presented. The three metrics are considered at a level of detail far greater than heretofore, as we develop the general framework to best fit a given set of moduli onto higher elastic symmetries. The procedures for finding the closest elasticity tensor are illustrated by application to a set of 21 moduli with no underlying symmetry.Comment: 48 pages, 1 figur

Stress distribution and the fragility of supercooled melts

We formulate a minimal ansatz for local stress distribution in a solid that includes the possibility of strongly anharmonic short-length motions. We discover a broken-symmetry metastable phase that exhibits an aperiodic, frozen-in stress distribution. This aperiodic metastable phase is characterized by many distinct, nearly degenerate configurations. The activated transitions between the configurations are mapped onto the dynamics of a long range classical Heisenberg model with 6-component spins and anisotropic couplings. We argue the metastable phase corresponds to a deeply supercooled non-polymeric, non-metallic liquid, and further establish an order parameter for the glass-to-crystal transition. The spin model itself exhibits a continuous range of behaviors between two limits corresponding to frozen-in shear and uniform compression/dilation respectively. The two regimes are separated by a continuous transition controlled by the anisotropy in the spin-spin interaction, which is directly related to the Poisson ratio $\sigma$ of the material. The latter ratio and the ultra-violet cutoff of the theory determine the liquid configurational entropy. Our results suggest that liquid's fragility depends on the Poisson ratio in a non-monotonic way. The present ansatz provides a microscopic framework for computing the configurational entropy and relaxational spectrum of specific substances.Comment: 11 pages, 5 figures, Final version published in J Phys Chem