BreakTrans: uncovering the genomic architecture of gene fusions

Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance for personalized cancer diagnosis and targeted therapy. We present a tool, BreakTrans, that systematically maps predicted gene fusions to structural rearrangements. Thus, BreakTrans not only validates both types of predictions, but also provides mechanistic interpretations. BreakTrans effectively validates known fusions and discovers novel events in a breast cancer cell line. Applying BreakTrans to 43 breast cancer samples in The Cancer Genome Atlas identifies 90 genomically validated gene fusions. BreakTrans is available at http://bioinformatics.mdanderson.org/main/BreakTrans     

Surfactin-Induced Apoptosis Through ROS–ERS–Ca2+-ERK Pathways in HepG2 Cells

Although surfactin is able to inhibit cancer cell proliferation and to induce cancer cell apoptosis, the molecular mechanism responsible for this process remain elusive. In this study, the signaling network underlying the apoptosis of human hepatoma (HepG2) cells induced by surfactin was investigated. It is found that the reaction oxygen species (ROS) production and intracellular calcium ([Ca²⁺]_i) accumulation are both induced HepG2 cells apoptosis. The [Ca²⁺]_i exaltation was partly depended on the Ca²⁺ release from inositol 1,4,5-trisphosphate (IP3) and ryanodine (Ry) receptors channels, which both triggered endoplasmic reticulum stress (ERS). The results showed that surfactin induced the ROS production and ROS production led to ERS. The occurrence of ERS increased the [Ca²⁺]_i level and the processes associated with blocking extracellular signal-regulated kinase (ERK) pathway. According to a comprehensive review of all the evidence, it is concluded that surfactin induces apoptosis of HepG2 cells through a ROS–ERS–Ca²⁺ mediated ERK pathway.     

CRM1 Is a Cellular Target of Curcumin: New Insights for the Myriad of Biological Effects of an Ancient Spice

Curcumin is the major constituent of turmeric plant, an ancient spice widely used in Indian cuisine and traditional herbal medicine. Recently, the potential medical use of curcumin as anti‐cancer and anti‐inflammatory agent has set off an upsurge in research into the mechanism for its broad biological effects. We showed that CRM1, an important nuclear exportin, is a cellular target of curcumin by serious experimental and theoretical investigation. Using a nuclear export functional assay, we observed a clear and rapid shift of cargo proteins from a cytoplasmic localization to the nucleus when treated with curcumin or its structural analogue dibenzylideneacetone (DBA). We demonstrated that curcumin could specifically target the conserved Cys⁵²⁸ of CRM1 through mass spectrometric analysis and in vivo experiments. Furthermore, computational modeling has revealed that curcumin could be correctly docked into the hydrophobic pocket of CRM1 judged from shape complementarity and putative molecular interactions. The Michael acceptor moiety on curcumin is within the appropriate distance to enable Michael reaction with Cys residue of CRM1. More importantly, we showed that nuclear retention of FOXO1 could be observed in the presence of Leptomycin B (LMB) or curcumin whereas in cells expressing the CRM1‐Cys⁵²⁸ mutant, only a cytoplasmic localization was observed. The inhibition of nuclear traffic by curcumin may account for its myriad of biological effects, particularly for its therapeutic properties in cancer and inflammatory diseases. Our findings may have important implications for further clinical investigation of curcumin .     

Enhanced resistance to sclerotinia stem rot in transgenic soybean that overexpresses a wheat oxalate oxidase

Sclerotinia stem rot (SSR), caused by the oxalate-secreting necrotrophic fungal pathogen Sclerotinia sclerotiorum, is one of the devastating diseases that causes significant yield loss in soybean (Glycine max). Until now, effective control of the pathogen is greatly limited by a lack of strong resistance in available commercial soybean cultivars. In this study, transgenic soybean plants overexpressing an oxalic acid (OA)-degrading oxalate oxidase gene OXO from wheat were generated and evaluated for their resistance to S. sclerotiorum. Integration and expression of the transgene were confirmed by Southern and western blot analyses. As compared with non-transformed (NT) control plants, the transgenic lines with increased oxalate oxidase activity displayed significantly reduced lesion sizes, i.e., by 58.71–82.73% reduction of lesion length in a detached stem assay (T₃ and T₄ generations) and 76.67–82.0% reduction of lesion area in a detached leaf assay (T₄ generation). The transgenic plants also showed increased tolerance to the externally applied OA (60 mM) relative to the NT controls. Consecutive resistance evaluation further confirmed an enhanced and stable resistance to S. sclerotiorum in the T₃ and T₄ transgenic lines. Similarly, decreased OA content and increased hydrogen peroxide (H₂O₂) levels were also observed in the transgenic leaves after S. sclerotiorum inoculation. Quantitative real-time polymerase chain reaction analysis revealed that the expression level of OXO reached a peak at 1 h and 4 h after inoculation with S. sclerotiorum. In parallel, a significant up-regulation of the hypersensitive response-related genes GmNPR1-1, GmNPR1-2, GmSGT1, and GmRAR occurred, eventually induced by increased release of H₂O₂ at the infection sites. Interestingly, other defense-related genes such as salicylic acid-dependent genes (GmPR1, GmPR2, GmPR3, GmPR5, GmPR12 and GmPAL), and ethylene/jasmonic acid-dependent genes (GmAOS, GmPPO) also exhibited higher expression levels in the transgenic plants than in the NT controls. Our results demonstrated that overexpression of OXO enhances SSR resistance by degrading OA secreted by S. sclerotiorum and increasing H₂O₂ levels, and eliciting defense responses mediated by multiple signaling pathways.

     

微生物1,3-1,4-β-葡聚糖酶蛋白质改造及工业应用研究进展

1,3-1,4-β-葡聚糖酶(E.C.3.2.1.73)是一种重要的工业用酶,其可以通过特异性切割毗邻β-1,3-糖苷键的β-1,4-糖苷键将β-葡聚糖或地衣多糖降解为纤维三糖和纤维四糖。微生物β-葡聚糖酶属于糖苷水解酶家族16,其三维结构为卷心蛋糕状的逆向β-片层结构。文中综述了近些年来β-葡聚糖酶在工业上的应用情况及酶蛋白质工程改造的研究进展,并对其研究前景进行了展望。     

An Efficient Separator with Low Li‐Ion Diffusion Energy Barrier Resolving Feeble Conductivity for Practical Lithium–Sulfur Batteries

Due to unprecedented features including high‐energy density, low cost, and light weight, lithium–sulfur batteries have been proposed as a promising successor of lithium‐ion batteries. However, unresolved detrimental low Li‐ion transport rates in traditional carbon materials lead to large energy barrier in high sulfur loading batteries, which prevents the lithium–sulfur batteries from commercialization. In this report, to overcome the challenge of increasing both the cycling stability and areal capacity, a metallic oxide composite (NiCo₂O₄@rGO) is designed to enable a robust separator with low energy barrier for Li‐ion diffusion and simultaneously provide abundant active sites for the catalytic conversion of the polar polysulfides. With a high sulfur‐loading of 6 mg cm^?2 and low sulfur/electrolyte ratio of 10, the assembled batteries deliver an initial capacity of 5.04 mAh cm^?2 as well as capacity retention of 92% after 400 cycles. The metallic oxide composite NiCo₂O₄@rGO/PP separator with low Li‐ion diffusion energy barrier opens up the opportunity for lithium–sulfur batteries to achieve long‐cycle, cost‐effective operation toward wide applications in electric vehicles and electronic devices.     

Phenotypic Characteristics and Fatty Acid Composition of Seeds from Different Herbaceous Peony Species Native to China

Herbaceous peony has been widely cultivated in China due to its substantial ornamental and medicinal value. In the present study, the phenotypic characteristics, total fatty acid (FA) content, and nine FA compositions of herbaceous peony seeds from 14 populations belonging to six species and one subspecies were determined by normal test and gas chromatography/mass spectrometry (GC/MS). The results showed that the phenotypic characteristics of seeds varied dramatically among species. The concentrations of five major FAs in seed oils were as follows: linoleic acid (173.95–236.51 μg/mg), linolenic acid (227.82–302.71 μg/mg), oleic acid (135.32–208.81 μg/mg), stearic acid (6.52–11.7 μg/mg), and palmitic acid (30.67–47.64 μg/mg). Correlation analysis demonstrated that oleic acid had the highest partial correlation coefficient with total FAs and might be applied to develop a model of phenotypic characteristics. FAs were significantly influenced by the following environmental factors: latitude, elevation, and annual average temperature. Based on the FA levels in the seed oils, clustering analysis divided 14 populations into two clusters. It was found that the average contents of oleic acid, linoleic acid, and total FAs in cluster I (147.16 μg/mg, 200.31 μg/mg, and 671.24 μg/mg, respectively) were significantly lower than those in cluster II (196.65 μg/mg, 220.16 μg/mg, and 741.78 μg/mg, respectively). Cluster I was perfectly consistent with subsect. Foliolatae, while cluster II was in good agreement with subsect. Dissectifoliae. Therefore, the FA composition of wild herbaceous peony seed oil might be used as a chemotaxonomic marker.     

Molecular Modelling reveals the inhibition mechanism and structure–activity relationship of curcumin and its analogues to Staphylococcal aureus Sortase A

Previous studies found that the activity of Sortase A, a bacterial surface protein from Staphylococcus aureus, was inhibited by curcumin and its analogues. To explore this inhibitory mechanism, Sortase A and its inhibitors in complex systems were studied by molecular docking, molecular modelling, binding energy decomposition calculation and steered molecular dynamics simulations. Energy decomposition analysis indicated that PRO-163, LEU-169, GLN-172, ILE-182 and ILE-199 are key residues in Sortase A-inhibitor complexes. Furthermore, interactions between the methoxyl group on the benzene ring in the conjugated molecule (curcumin, demethoxycurcumin, bisdemethoxycurcumin) and VAL-168, LEU-169 and GLN-172 induce the inhibitory activity based on the energy decomposition and distance analyses between the whole residues and inhibitors. However, because of its coiled structure, the non-conjugated molecule, tetrahydrocurcumin, with key residues in the binding sites of Sortase A, interacted weakly with SrtA, leading to the loss of inhibitory activity. Based on these results, the methoxyl group on the benzene ring in the conjugated molecule largely influenced the inhibitory activity of the Sortase A inhibitors.     

Moderate- and Low-Dose of Atorvastatin Alleviate Cognition Impairment Induced by High-Fat Diet via Sirt1 Activation

Neurochemical Research - Mounting evidences have demonstrated that diet-induced obesity is associated with cognition impairment via increasing oxidative stress and inflammation in the brain....