isomiR2Function: An integrated workflow for identifying MicroRNA variants in plants

© 2017 Yang, Sablok, Qiao, Nie and Wen. In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking. In the present research, we present isomiR2Function, a standalone easily deployable tool that allows for the robust and high-throughput discovery of templated and non-templated isomiRs. Additionally, isomiR2Function allows for identification of differentially expressed isomiRs and in parallel target prediction based on both transcripts or PARE-Seq either using Targetfinder or Cleaveland. isomiR2Function allows for the functional enrichment of the detected targets using TopGO package. Benchmarking of isomiR2Function revealed highly accurate prediction and classification of isomiRs as compared to the previously developed isomiR prediction tools. Additionally, the downstream implementation of additional features allows isomiR2Function to be classified as a single standalone tool for isomiR profiling from discovery to functional roles. All in all, isomiR2Function allows the streamline processing of the miRNA-seq for the identification and characterization of isomiRs with minimal efforts. isomiR2Function can be accessed through: https://gi thub.com/347033139/isomiR2Function

Topological quantum phase transition in an extended Kitaev spin model

We study the quantum phase transition between Abelian and non-Abelian phases in an extended Kitaev spin model on the honeycomb lattice, where the periodic boundary condition is applied by placing the lattice on a torus. Our analytical results show that this spin model exhibits a continuous quantum phase transition. Also, we reveal the relationship between bipartite entanglement and the ground-state energy. Our approach directly shows that both the entanglement and the ground-state energy can be used to characterize the topological quantum phase transition in the extended Kitaev spin model.Comment: 9 Pages, 4 figure

Levinson's theorem for the Schr\"{o}dinger equation in two dimensions

Levinson's theorem for the Schr\"{o}dinger equation with a cylindrically symmetric potential in two dimensions is re-established by the Sturm-Liouville theorem. The critical case, where the Schr\"{o}dinger equation has a finite zero-energy solution, is analyzed in detail. It is shown that, in comparison with Levinson's theorem in non-critical case, the half bound state for $P$ wave, in which the wave function for the zero-energy solution does not decay fast enough at infinity to be square integrable, will cause the phase shift of $P$ wave at zero energy to increase an additional $\pi$.Comment: Latex 11 pages, no figure and accepted by P.R.A (in August); Email: [email protected], [email protected]

Implementing topological quantum manipulation with superconducting circuits

A two-component fermion model with conventional two-body interactions was recently shown to have anyonic excitations. We here propose a scheme to physically implement this model by transforming each chain of two two-component fermions to the two capacitively coupled chains of superconducting devices. In particular, we elaborate how to achieve the wanted operations to create and manipulate the topological quantum states, providing an experimentally feasible scenario to access the topological memory and to build the anyonic interferometry.Comment: 4 pages with 3 figures; V2: published version with minor updation

Landau-Zener-Stuckelberg interference in a multi-anticrossing system

We propose a universal analytical method to study the dynamics of a multi-anticrossing system subject to driving by one single large-amplitude triangle pulse, within its time scales smaller than the dephasing time. Our approach can explain the main features of the Landau-Zener-Stuckelberg interference patterns recently observed in a tripartite system [Nature Communications 1:51 (2010)]. In particular, we focus on the effects of the size of anticrossings on interference and compare the calculated interference patterns with numerical simulations. In addition, Fourier transform of the patterns can extract information on the energy level spectrum.Comment: 6 pages, 5 figure

Tropical forest restoration: Fast resilience of plant biomass contrasts with slow recovery of stable soil C stocks

Due to intensifying human disturbance, over half of the world's tropical forests are reforested or afforested secondary forests or plantations. Understanding the resilience of carbon (C) stocks in these forests, and estimating the extent to which they can provide equivalent carbon (C) sequestration and stabilization to the old growth forest they replace, is critical for the global C balance. In this study, we combined estimates of biomass C stocks with a detailed assessment of soil C pools in bare land, Eucalyptus plantation, secondary forest and natural old-growth forest after over 50 years of forest restoration in a degraded tropical region of South China. We used isotope studies, density fractionation and physical fractionation to determine the age and stability of soil C pools at different soil depths. After 52 years, the secondary forests had equivalent biomass C stocks to natural forest, whereas soil C stocks were still much higher in natural forest (97.42 t/ha) than in secondary forest (58.75 t/ha) or Eucalyptus plantation (38.99 t/ha) and lowest in bare land (19.9 t/ha). Analysis of δ13C values revealed that most of the C in the soil surface horizons in the secondary forest was new C, with a limited increase of more recalcitrant old C, and limited accumulation of C in deeper soil horizons. However, occlusion of C in microaggregates in the surface soil layer was similar across forested sites, which suggests that there is great potential for additional soil C sequestration and stabilization in the secondary forest and Eucalyptus plantation. Collectively, our results demonstrate that reforestation on degraded tropical land can restore biomass C and surface soil C stocks within a few decades, but much longer recovery times are needed to restore recalcitrant C pools and C stocks at depth. Repeated harvesting and disturbance in rotation plantations had a substantial negative impact on the recovery of soil C stocks. We suggest that current calculations of soil C in secondary tropical forests (e.g. IPCC Guidelines for National Greenhouse Gas Inventories) could overestimate soil C sequestration and stabilization levels in secondary forests and plantations