Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small- and intermediate-size homozygous variants (1-50 kb) including insertions, deletions, inversions and their precise breakpoints, and in contrast to other methods, can resolve complex rearrangements. In total, we identified 277,243 SVs ranging in length from 1-23 kb. Validation using computational and experimental methods suggests that we achieve overall <6% false-positive rate and <10% false-negative rate in genomic regions that can be assembled, which outperforms other methods. Analysis of the SVs in the genomes of 106 individuals sequenced as part of the 1000 Genomes Project suggests that SVs account for a greater fraction of the diversity between individuals than do single-nucleotide polymorphisms (SNPs). These findings demonstrate that whole-genome de novo assembly is a feasible approach to deriving more comprehensive maps of genetic variation.     

Dimethoate,fenvalerate and their mixture affects Hylyphantes graminicola (Araneae: Linyphiidae) adults and their unexposed offspring

• 1 Mixtures of organophosphorus and pyrethroid insecticides are widely used to combat resistance in agricultural pests, although few studies have been conducted on the effects of pesticide mixtures on beneficial nontarget organisms.
• 2 In the present study, we exposed adult females (F₀) of Hylyphantes graminicola (Araneae: Linyphiidae) to fenvalerate, dimethoate and their commercially available 1 : 1 mixture (by mass). We investigated the acute toxicity of these pesticides to the exposed adults, as well as sublethal effects on reproduction and acetylcholinesterase and carboxylesterase activity. We also studied the effects of parental exposure on the size, development and enzyme activity of unexposed offspring.
• 3 All three formulations were acutely toxic to H. graminicola, with synergism between dimethoate and fenvalerate leading to greater toxicity in the 1 : 1 mixture than for the two insecticides alone. The sublethal effects of direct pesticide exposure were a reduction in acetylcholinesterase and carboxylesterase activity and a reduction in the number of egg sacs produced by exposed spiders relative to the control spiders. The unexposed offspring of the fenvalerate and mixture exposed spiders were smaller and took longer to mature than the control spiders. Offspring of all exposed spiders also had significantly reduced carboxylesterase activity relative to control spiders.
• 4 We concluded that the effects of parental exposure on the offspring were likely to increase their susceptibility to future pesticide exposures, and reduce the capacity of this spider to serve as a pest control agent.

     

子宫颈糜烂病毒病因的探讨

491份宫颈拭子病毒分离结果表明:糜烂宫颈单纯疱疹病毒(HSV)分离阳性率(30.8％)是正常宫颈(2.6％)的11.8倍,用人干扰素治疗一个疗程后,病毒分离率下降至疗前的1/4.36例糜烂宫颈活体组织DNA分子杂交表明,乳头瘤病毒16型(HPV-16)阳性者占52.8和,HPV-18占17.9％,HPV-6B占28.1％,HPV-11占7.7％,251例宫颈糜烂患者经人(?)D型基因工程干扰素双盲对比治疗后,总有效率达93.8％,显效率达60％,分析临床疗效与HSV分离率的变化表明,临床有效病例中有35％(49/140)在治疗后病毒阴转,有57％在疗前疗后均未分离出HSV,有5％在疗前疗后保持阳性不变,有2.9％疗前阴性,疗后阳性,上述结果表明,HSV和HPV与慢性宫颈炎有一定关系。     

ku70 and ku80 null mutants improve the gene targeting frequency in Monascus ruber M7

Normally, gene targeting by homologous recombination occurs rarely during a transformation process since non-homologous recombination is predominant in filamentous fungi. In our previous researches, the average gene replacement frequency (GRF) in Monascus ruber M7 was as low as 15 %. To develop a highly efficient gene targeting system for M. ruber M7, two M. ruber M7 null mutants of ku70 (MrΔku70) and ku80 (MrΔku80) were constructed which had no apparent defects in the development including vegetative growth, colony phenotype, microscopic morphology and spore yield compared with M. ruber M7. In addition, the production of some significant secondary metabolites such as pigments and citrinin had no differences between the two disruptants and the wild-type strain. Further results revealed that the GRFs of triA (encoding a putative acetyltransferase) were 42.2 % and 61.5 % in the MrΔku70 and MrΔku80 strains, respectively, while it was only about 20 % in M. ruber M7. Furthermore, GRFs of these two disruptants at other loci (the pigE, fmdS genes in MrΔku70 and the ku70 gene in MrΔku80) were investigated, and the results indicated that GRFs in the MrΔku70 strain and the MrΔku80 strain were doubled and tripled compared with that in M. ruber M7, respectively. Therefore, the ku70 and ku80 null mutants of M. ruber M7, especially the ku80-deleted strain, will be excellent hosts for efficient gene targeting.     

Capsaicin induces apoptosis in human osteosarcoma cells through AMPK-dependent and AMPK-independent signaling pathways

Recent studies have focused on the anti-tumor activity of capsaicin. However, the potential effects of capsaicin in osteosarcoma cells and the underlying mechanisms are not fully understood. In the current study, we observed that capsaicin-induced growth inhibition and apoptosis in cultured osteosarcoma cells (U2OS and MG63), which were associated with a significant AMP-activated protein kinase (AMPK) activation. AMPK inhibition by compound C or RNA interference suppressed capsaicin-induced cytotoxicity, while AMPK activators (AICAR and A769662) promoted osteosarcoma cell death. For the mechanism study, we found that AMPK activation was required for capsaicin-induced mTORC1 (mTOR complex 1) inhibition, B cell lymphoma 2 (Bcl-2) downregulation and Bax upregulation in MG63 cells. Capsaicin administration induced p53 activation, mitochondrial translocation and Bcl-2 killer association, such effects were dependent on AMPK activation. Interestingly, we observed a significant pro-apoptotic c-Jun NH2-terminal kinases activation by capsaicin in MG63 cells, which appeared to be AMPK independent. In conclusion, capsaicin possessed strong efficacy against human osteosarcoma cells. Molecular studies revealed that capsaicin activated AMPK-dependent and AMPK-independent signalings to mediate cell apoptosis. The results of this study should have significant translational relevance in managing this deadly malignancy.     

A novel ultrasensitive bioluminescent receptor-binding assay of INSL3 through chemical conjugation with nanoluciferase

Insulin-like peptide 3 (INSL3) is a reproduction-related peptide hormone belonging to the insulin/relaxin superfamily, which mediates testicular descent in the male fetus, suppresses male germ cell apoptosis and promotes oocyte maturation in adults by activating the relaxin family peptide receptor 2 (RXFP2). To establish an ultrasensitive receptor-binding assay for INSL3−RXFP2 interaction studies, in the present work we labeled a recombinant INSL3 peptide with a newly developed nanoluciferase (NanoLuc) reporter through a convenient chemical conjugation approach, including the introduction of an active disulfide bond to INSL3 by chemical modification and engineering of a 6× His-Cys-NanoLuc carrying a unique exposed cysteine at the N-terminus. The bioluminescent NanoLuc-conjugated INSL3 retained high binding affinity with the target receptor RXFP2 (K_d = 2.0 ± 0.1 nM, n = 3) and was able to sensitively monitor the receptor-binding of a variety of ligands, representing a novel ultrasensitive tracer for non-radioactive receptor-binding assays. Our present chemical conjugation approach could readily be adapted for conjugation of NanoLuc with other proteins, even other macrobiomolecules, for various highly sensitive bioluminescent assays.     

TRAIP modulates the IGFBP3/AKT pathway to enhance the invasion and proliferation of osteosarcoma by promoting KANK1 degradation

Osteosarcoma is one of the most common primary malignancies in bones and is characterized by high metastatic rates. Circulating tumor cells (CTCs) derived from solid tumors can give rise to metastatic lesions, increasing the risk of death in patients with cancer. Here, we used bioinformatics tools to compare the gene expression between CTCs and metastatic lesions in osteosarcoma to identify novel molecular mechanisms underlying osteosarcoma metastasis. We identified TRAIP as a key differentially expressed gene with prognostic significance in osteosarcoma. We demonstrated that TRAIP regulated the proliferation and invasion of osteosarcoma cells. In addition, we found that TRAIP promoted KANK1 polyubiquitination and subsequent degradation, downregulating IGFBP3 and activating the AKT pathway in osteosarcoma cells. These results support the critical role of the TRAIP/KANK1/IGFBP3/AKT signaling axis in osteosarcoma progression and suggest that TRAIP may represent a promising therapeutic target for osteosarcoma.Subject terms: Bone cancer, Oncogenes