Light Regulation of Alternative Pre-mRNA Splicing in Plants.

Alternative splicing (AS) is a major post-transcriptional mechanism to enhance the diversity of proteome in response to environmental signals. Among the numerous external signals perceived by plants, light is the most crucial one. Plants utilize complex photoreceptor signaling networks to sense different light conditions and adjust their growth and development accordingly. Although light-mediated gene expression has been widely investigated, little is known regarding the mechanism of light affecting AS to modulate mRNA at the post-transcriptional level. In this minireview, we summarize current progresses on how light affects AS, and how sensory photoreceptors and retrograde signaling pathways may coordinately regulate AS of pre-mRNAs. In addition, we also discuss the possibility that AS of the mRNAs encoding photoreceptors may be involved in feedback control of AS. We hypothesize that light regulation of the expression and activity of splicing factors would be a major mechanism of light-mediated AS. The combination of genetic study and high-throughput analyses of AS and splicing complexes in response to light is likely to further advance our understanding of the molecular mechanisms underlying light control of AS and plant development

Dynamic Epistasis under Varying Environmental Perturbations

Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current knowledge for epistatic dynamics under multiple conditions is limited by the technological difficulties in experimentally screening epistatic relations among genes. We explored this issue by applying flux balance analysis to simulate epistatic landscapes under various environmental perturbations. Specifically, we looked at gene-gene epistatic interactions, where the mutations were assumed to occur in different genes. We predicted that epistasis tends to become more positive from glucose-abundant to nutrient-limiting conditions, indicating that selection might be less effective in removing deleterious mutations in the latter. We also observed a stable core of epistatic interactions in all tested conditions, as well as many epistatic interactions unique to each condition. Interestingly, genes in the stable epistatic interaction network are directly linked to most other genes whereas genes with condition-specific epistasis form a scale-free network. Furthermore, genes with stable epistasis tend to have similar evolutionary rates, whereas this co-evolving relationship does not hold for genes with condition-specific epistasis. Our findings provide a novel genome-wide picture about epistatic dynamics under environmental perturbations.Comment: 22 pages, 9 figure

Scaling dimension of fidelity susceptibility in quantum phase transitions

We analyze ground-state behaviors of fidelity susceptibility (FS) and show that the FS has its own distinct dimension instead of real system's dimension in general quantum phases. The scaling relation of the FS in quantum phase transitions (QPTs) is then established on more general grounds. Depending on whether the FS's dimensions of two neighboring quantum phases are the same or not, we are able to classify QPTs into two distinct types. For the latter type, the change in the FS's dimension is a characteristic that separates two phases. As a non-trivial application to the Kitaev honeycomb model, we find that the FS is proportional to $L^2\ln L$ in the gapless phase, while $L^2$ in the gapped phase. Therefore, the extra dimension of $\ln L$ can be used as a characteristic of the gapless phase.Comment: 4 pages, 1 figure, final version to appear in EP

Spin tunneling properties in mesoscopic magnets: effects of a magnetic field

The tunneling of a giant spin at excited levels is studied theoretically in mesoscopic magnets with a magnetic field at an arbitrary angle in the easy plane. Different structures of the tunneling barriers can be generated by the magnetocrystalline anisotropy, the magnitude and the orientation of the field. By calculating the nonvacuum instanton solution explicitly, we obtain the tunnel splittings and the tunneling rates for different angle ranges of the external magnetic field ($\theta_{H}=\pi/2$ and $\pi/2<\theta_{H}<\pi$). The temperature dependences of the decay rates are clearly shown for each case. It is found that the tunneling rate and the crossover temperature depend on the orientation of the external magnetic field. This feature can be tested with the use of existing experimental techniques.Comment: 27 pages, 4 figures, accepted by Euro. Phys. J.