sTarPicker: A Method for Efficient Prediction of Bacterial sRNA Targets Based on a Two-Step Model for Hybridization

Bacterial sRNAs are a class of small regulatory RNAs involved in regulation of expression of a variety of genes. Most sRNAs act in trans via base-pairing with target mRNAs, leading to repression or activation of translation or mRNA degradation. To date, more than 1,000 sRNAs have been identified. However, direct targets have been identified for only approximately 50 of these sRNAs. Computational predictions can provide candidates for target validation, thereby increasing the speed of sRNA target identification. Although several methods have been developed, target prediction for bacterial sRNAs remains challenging.Here, we propose a novel method for sRNA target prediction, termed sTarPicker, which was based on a two-step model for hybridization between an sRNA and an mRNA target. This method first selects stable duplexes after screening all possible duplexes between the sRNA and the potential mRNA target. Next, hybridization between the sRNA and the target is extended to span the entire binding site. Finally, quantitative predictions are produced with an ensemble classifier generated using machine-learning methods. In calculations to determine the hybridization energies of seed regions and binding regions, both thermodynamic stability and site accessibility of the sRNAs and targets were considered. Comparisons with the existing methods showed that sTarPicker performed best in both performance of target prediction and accuracy of the predicted binding sites.sTarPicker can predict bacterial sRNA targets with higher efficiency and determine the exact locations of the interactions with a higher accuracy than competing programs. sTarPicker is available at http://ccb.bmi.ac.cn/starpicker/

Biomineral Amorphous Lasers through Light-Scattering Surfaces Assembled by Electrospun Fiber Templates

New materials aim at exploiting the great control of living organisms over molecular architectures and minerals. Optical biomimetics has been widely developed by microengineering, leading to photonic components with order resembling those found in plants and animals. These systems, however, are realized by complicated and adverse processes. Here we show how biomineralization might enable the one-step generation of components for amorphous photonics, in which light is made to travel through disordered scattering systems, and particularly of active devices such as random lasers, by using electrospun fiber templates. The amount of bio-enzymatically produced silica is related to light-scattering capacity and the resulting organosilica surfaces exhibit a transport mean free path for light as low as 3 micron, and lasing with linewidth below 0.2 nm. The resulting, complex optical material is characterized and modelled to elucidate scattered fields and lasing performance. Tightly-controlled nanofabrication of direct biological inspiration establishes a new concept for the additive manufacturing of engineered light-diffusing materials and photonic components, not addressed by existing technologies.Comment: 37 pages, 11 figure

Scaling behavior of low-temperature orthorhombic domains in the prototypical high-temperature superconductor La₁.₈₇₅ Ba₀.₁₂₅ CuO₄

Structural symmetry breaking and recovery in condensed-matter systems are closely related to exotic physical properties such as superconductivity (SC), magnetism, spin density waves, and charge density waves (CDWs). The interplay between different order parameters is intricate and often subject to intense debate, as in the case of CDW order and superconductivity. In La₁.₈₇₅ Ba₀.₁₂₅ CuO

Anisotropy of antiferromagnetic domains in a spin-orbit Mott insulator

The temperature-dependent behavior of magnetic domains plays an essential role in the magnetic properties of materials, leading to widespread applications. However, experimental methods to access the three-dimensional (3D) magnetic domain structures are very limited, especially for antiferromagnets. Over the past decades, the spin-orbit Mott insulator iridate Formula Presented has attracted particular attention because of its interesting magnetic structure and analogy to superconducting cuprates. Here, we apply resonant x-ray magnetic Bragg coherent diffraction imaging to track the real-space 3D evolution of antiferromagnetic ordering inside a Formula Presented single crystal as a function of temperature, finding that the antiferromagnetic domain shows anisotropic changes. The anisotropy of the domain shape reveals the underlying anisotropy of the antiferromagnetic coupling strength within Formula Presented. These results demonstrate the high potential significance of 3D domain imaging in magnetism research

Conformational dynamics in TRPV1 channels reported by an encoded coumarin amino acid

TRPV1 channels support the detection of noxious and nociceptive input. Currently available functional and structural data suggest that TRPV1 channels have two gates within their permeation pathway: one formed by a 0bundle-crossing0 at the intracellular entrance and a second constriction at the selectivity filter. To describe conformational changes associated with channel gating, the fluorescent non-canonical amino acid coumarin-tyrosine was genetically encoded at Y671, a residue proximal to the selectivity filter. Total internal reflection fluorescence microscopy was performed to image the conformational dynamics of the channels in live cells. Photon counts and optical fluctuations from coumarin encoded within TRPV1 tetramers correlates with channel activation by capsaicin, providing an optical marker of conformational dynamics at the selectivity filter. In agreement with the fluorescence data, molecular dynamics simulations display alternating solvent exposure of Y671 in the closed and open states. Overall, the data point to a dynamic selectivity filter that may serve as a gate for permeation

YAP and TAZ maintain PROX1 expression in the developing lymphatic and lymphovenous valves in response to VEGF-C signaling

Lymphatic vasculature is an integral part of digestive, immune and circulatory systems. The homeobox transcription factor PROX1 is necessary for the development of lymphatic vessels, lymphatic valves (LVs) and lymphovenous valves (LVVs). We and others previously reported a feedback loop between PROX1 and vascular endothelial growth factor-C (VEGF-C) signaling. PROX1 promotes the expression of the VEGF-C receptor VEGFR3 in lymphatic endothelial cells (LECs). In turn, VEGF-C signaling maintains PROX1 expression in LECs. However, the mechanisms of PROX1/VEGF-C feedback loop remain poorly understood. Whether VEGF-C signaling is necessary for LV and LVV development is also unknown. Here, we report for the first time that VEGF-C signaling is necessary for valve morphogenesis. We have also discovered that the transcriptional co-activators YAP and TAZ are required to maintain PROX1 expression in LVs and LVVs in response to VEGF-C signaling. Deletion o