Improving transmembrane protein consensus topology prediction using inter-helical interaction

Alpha helix transmembrane proteins (αTMPs) represent roughly 30% of all open reading frames (ORFs) in a typical genome and are involved in many critical biological processes. Due to the special physicochemical properties, it is hard to crystallize and obtain high resolution structures experimentally, thus, sequence-based topology prediction is highly desirable for the study of transmembrane proteins (TMPs), both in structure prediction and function prediction. Various model-based topology prediction methods have been developed, but the accuracy of those individual predictors remain poor due to the limitation of the methods or the features they used. Thus, the consensus topology prediction method becomes practical for high accuracy applications by combining the advances of the individual predictors. Here, based on the observation that inter-helical interactions are commonly found within the transmembrane helixes (TMHs) and strongly indicate the existence of them, we present a novel consensus topology prediction method for αTMPs, CNTOP, which incorporates four top leading individual topology predictors, and further improves the prediction accuracy by using the predicted inter-helical interactions. The method achieved 87% prediction accuracy based on a benchmark dataset and 78% accuracy based on a non-redundant dataset which is composed of polytopic αTMPs. Our method derives the highest topology accuracy than any other individual predictors and consensus predictors, at the same time, the TMHs are more accurately predicted in their length and locations, where both the false positives (FPs) and the false negatives (FNs) decreased dramatically. The CNTOP is available at: http://ccst.jlu.edu.cn/JCSB/cntop/CNTOP.html.     

Sodium (±)‐5‐bromo‐2‐(α‐hydroxypentyl) benzoate ameliorates pressure overload‐induced cardiac hypertrophy and dysfunction through inhibiting autophagy

Sodium (±)‐5‐bromo‐2‐(a‐hydroxypentyl) benzoate (generic name: brozopine, BZP) has been reported to protect against stroke‐induced brain injury and was approved for Phase II clinical trials for treatment of stroke‐related brain damage by the China Food and Drug Administration (CFDA). However, the role of BZP in cardiac diseases, especially in pressure overload‐induced cardiac hypertrophy and heart failure, remains to be investigated. In the present study, angiotensin II stimulation and transverse aortic constriction were employed to induce cardiomyocyte hypertrophy in vitro and in vivo, respectively, prior to the assessment of myocardial cell autophagy. We observed that BZP administration ameliorated cardiomyocyte hypertrophy and excessive autophagic activity. Further results indicated that AMP‐activated protein kinase (AMPK)‐mediated activation of the mammalian target of rapamycin (mTOR) pathway likely played a role in regulation of autophagy by BZP after Ang II stimulation. The activation of AMPK with metformin reversed the BZP‐induced suppression of autophagy. Finally, for the first time, we demonstrated that BZP could protect the heart from pressure overload‐induced hypertrophy and dysfunction, and this effect is associated with its inhibition of maladaptive cardiomyocyte autophagy through the AMPK‐mTOR signalling pathway. These findings indicated that BZP may serve as a promising compound for treatment of pressure overload‐induced cardiac remodelling and heart failure.     

Halogen Engineering for Operationally Stable Perovskite Solar Cells via Sequential Deposition

The performance of perovskite solar cells (PSCs) relies on the synthesis method and chemical composition of the perovskite materials. So far, PSCs that have adopted two‐step sequential deposited perovskite with the state‐of‐art composition (FAPbI₃)_1?x(MAPbBr₃)_x (x < 0.05) have achieved record power conversion efficiency (PCE), while their one‐step antisolvent dripping counterparts with typical composition Cs_0.05FA_0.81MA_0.14Pb(I_0.85Br_0.15)₃ with more bromine have exhibited much better long‐term operational stability. Thus, halogen engineering that aims to elevate bromine content in sequential deposited perovskite film would push operational stability of PSCs toward that of antisolvent dripping deposited perovskite materials. Here, a Br‐rich seeding growth method is devised and perovskite seed solution with high bromine content is introduced into a PbI₂ precursor, leading to bromine incorporation in the resulting perovskite film. Photovoltaic devices fabricated by Br‐rich seeding growth method exhibit a PCE of 21.5%, similar to 21.6% for PSCs having lower bromine content. Whereas, the operational stability of PSCs with higher bromine content is significantly enhanced, with over 80% of initial PCE retained after 500 h tracking at maximum power point under 1‐sun illumination. This work highlights the vital importance of halogen composition for the operational stability of PSCs, and introduces an effective way to incorporate bromine into mixed‐cation‐halide perovskite film via sequential deposition method.     

Changes of Endogenous Hormone Contents During Floral Bud and Vegetative Bud Differentiation in Thin Cell Layer Culture of Cichorium intybus L. Explant

The sectioned thin cell layers (TCL) of flower stalk of Cichorium intybus L. were cultured in MS medium supplemented with NAA and BA or IAA and BA where floral and vegetative buds were developed from the explant. Endogenous IAA, DHZ+DHZR, iPA increased significantly during the floral bud formation, while Z+ZR remained changed. The levels of cytokinins, DHZ +DHZR, iPA, and Z-f-ZR all increased significantly during the vegetative bud formation, however IAA level was reduced during the first 7 days of culture and increased to two-thirds of initial values on the day when the bud primordia were formed. The results suggested that the initiation of floral buds was associated with a high IAA/CTK ratio, whereas the induction of vegetative bud differentiation was related to a low IAA/CTK ratio.     

SNP-based pool genotyping and haplotype analysis accelerate fine-mapping of the wheat genomic region containing stripe rust resistance gene <Emphasis Type="Italic">Yr26</Emphasis>

Key message

NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding.

Abstract

Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China. Large DNA and RNA super-pools were genotyped by Wheat SNP Array and sequenced by Illumina HiSeq, respectively. Hundreds of thousands of SNPs were identified and then filtered by multiple filtering criteria. Among selected SNPs, over 900 were found within an overlapping interval of less than 30 Mb as the Yr26 candidate genomic region in the centromeric region of chromosome arm 1BL. The 235 chromosome-specific SNPs were converted into KASP assays to validate the Yr26 interval in different genetic populations. Using a high-resolution mapping population (>?30,000 gametes), we confined Yr26 to a 0.003-cM interval. The Yr26 target region was anchored to the common wheat IWGSC RefSeq v1.0 and wild emmer WEWSeq v.1.0 sequences, from which 488 and 454 kb fragments were obtained. Several candidate genes were identified in the target genomic region, but there was no typical resistance gene in either genome region. Haplotype analysis identified specific SNPs linked to Yr26 and developed robust and breeder-friendly KASP markers. This integration strategy can be applied to accelerate generating many markers closely linked to target genes/QTL for a trait of interest in wheat and other polyploid species.

     

Association of myostatin deficiency with collagen related disease-umbilical hernia and tippy toe standing in pigs

Transgenic Research - Herein, we investigate the high incidence of umbilical hernia and tippy-toe standing and their underlying changes in gene expression and proliferation in myostatin knockout...