Etiologic diagnosis of lower respiratory tract bacterial infections using sputum samples and quantitative loop-mediated isothermal amplification

Etiologic diagnoses of lower respiratory tract infections (LRTI) have been relying primarily on bacterial cultures that often fail to return useful results in time. Although DNA-based assays are more sensitive than bacterial cultures in detecting pathogens, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. Here we report a nationwide cohort study on 2986 suspected LRTI patients across P. R. China. We compared the performance of a DNA-based assay qLAMP (quantitative Loop-mediated isothermal AMPlification) with that of standard bacterial cultures in detecting a panel of eight common respiratory bacterial pathogens from sputum samples. Our qLAMP assay detects the panel of pathogens in 1047(69.28%) patients from 1533 qualified patients at the end. We found that the bacterial titer quantified based on qLAMP is a predictor of probability that the bacterium in the sample can be detected in culture assay. The relatedness of the two assays fits a logistic regression curve. We used a piecewise linear function to define breakpoints where latent pathogen abruptly change its competitive relationship with others in the panel. These breakpoints, where pathogens start to propagate abnormally, are used as cutoffs to eliminate the influence of contaminations from normal flora. With help of the cutoffs derived from statistical analysis, we are able to identify causative pathogens in 750 (48.92%) patients from qualified patients. In conclusion, qLAMP is a reliable method in quantifying bacterial titer. Despite the fact that there are always latent bacteria contaminated in sputum samples, we can identify causative pathogens based on cutoffs derived from statistical analysis of competitive relationship. TRIAL REGISTRATION: ClinicalTrials.gov NCT00567827.     

Insulators, long-range interactions, and genome function

Insulators are DNA-protein complexes that can mediate interactions in cis or trans between different regions of the genome. Although originally defined on the basis of their ability to block enhancer-promoter communication or to serve as barriers against the spreading of heterochromatin in reporter systems, recent information suggests that their function is more nuanced and depends on the nature of the sequences brought together by contacts between specific insulator sites. Here we provide an overview of new evidence that has uncovered a wide range of functions for these sequences in addition to their two classical roles.     

The Effect of Sulfur on the Composition of Arbuscular Mycorrhizal Fungal Communities During the Pod-Setting Stage of Different Soybean Cultivars

This study sought to investigate the effect of sulfur levels on changes in the fungal community composition of arbuscular mycorrhizae (AM) at the pod-setting stage and the relationship between the amount of applied sulfur and AM fungal diversity in different soybean cultivars. The objective of the research was to determine the optimal sulfur application level for different soybean cultivars and to improve soybean yield and quality from the perspective of AM fungal diversity. Three soybean cultivars, Heinong 44, Heinong 48, and Heinong 37, were selected as study materials. In addition to 0.033?g each of N, P₂O₅ and K₂O per kg of soil, 0, 0.02, 0.04, or 0.06?g of elemental sulfur was applied to each kg of soil for the four treatment groups, S1, S2, S3, and S4, respectively. The AM fungal community structure was analyzed in the soil and root of different soybean cultivars using the PCR-DGGE technology. The results indicated a significant effect of sulfur on the AM fungal community structure in the roots and rhizospheric soil of different soybean cultivars. The three soybean cultivars in group S2 exhibited the highest diversity in AM fungus. Significant changes in the dominant fungal species were observed in the DGGE fingerprints of each sample, and Glomus, Funneliformis, Rhizophagus, and Claroideoglomus fungi were the dominant species of AM fungus in the roots and soil of soybean. The application of an appropriate amount of sulfur improved the diversity of AM fungi in roots and rhizospheric soil of different soybean cultivars.     

A Vesicular Stomatitis Virus-Based Vaccine Carrying Zika Virus Capsid Protein Protects Mice from Viral Infection

<正>Dear Editor,Zika virus (ZIKV) is a mosquito-borne virus that belongs to the Flavivirus family along with dengue virus (DENV),yellow fever virus, West Nile virus, and Japanese encephalitis virus (Ming et al. 2016). ZIKV is a singlestranded positive-sense RNA virus encoding three structural proteins, including nucleocapsid protein C, prM/M,envelope glycoprotein E, and seven non-structural proteins.Since 2015, over 70 countries and territories had reported     

淫羊藿总黄酮通过TGF-β1/Smad3信号通路改善自然衰老大鼠肾脏组织纤维化

为探讨淫羊藿总黄酮(TFE)对自然衰老大鼠肾脏纤维化的影响及其可能的作用机制,将18月龄SD大鼠随机分为自然衰老组、淫羊藿总黄酮低(10 mg/kg)、高(40 mg/kg)剂量组,另取2月龄SD大鼠作为青年对照组,给药4个月。通过HE染色和Masson染色观察肾脏组织形态及胶原纤维含量,生化酶法检测肾脏组织SOD活力和MDA含量,免疫组化法检测αSMA的蛋白表达水平,实时定量PCR和Western blot技术检测TGF-β1和Smad3的mRNA及蛋白表达水平。结果显示,TFE(低、高剂量)可改善衰老SD大鼠肾脏组织形态,减少胶原纤维,提升肾脏组织SOD活力(P<0.05),降低MDA含量(P<0.05),并降低肾脏组织中αSMA蛋白表达(P<0.05),同时显著下调TGF-β1及Smad3的mRNA和蛋白表达(P<0.05)。淫羊藿总黄酮可改善自然衰老大鼠肾脏纤维化,其机制可能与其抑制TGFβ1/Smad3信号通路传导有关。     

Variations analysis of NLGN3 and NLGN4X gene in Chinese autism patients

Autism is a neurodevelopmental disorder clinically characterized by impairment of social interaction, deficits in verbal communication, as well as stereotypic and repetitive behaviors. Several studies have implicated that abnormal synaptogenesis was involved in the incidence of autism. Neuroligins are postsynaptic cell adhesion molecules and interacted with neurexins to regulate the fine balance between excitation and inhibition of synapses. Recently, mutation analysis, cellular and mice models hinted neuroligin mutations probably affected synapse maturation and function. In this study, four missense variations [p.G426S (NLGN3), p.G84R (NLGN4X), p.Q162 K (NLGN4X) and p.A283T (NLGN4X)] in four different unrelated patients have been identified by PCR and direct sequencing. These four missense variations were absent in the 453 controls and have not been reported in 1000 Genomes Project. Bioinformatic analysis of the four missense variations revealed that p.G84R and p.A283T were “Probably Damaging”. The variations may cause abnormal synaptic homeostasis and therefore trigger the patients more predisposed to autism. By case–control analysis, we identified the common SNPs (rs3747333 and rs3747334) in the NLGN4X gene significantly associated with risk for autism [p = 5.09E-005; OR 4.685 (95 % CI 2.073–10.592)]. Our data provided a further evidence for the involvement of NLGN3 and NLGN4X gene in the pathogenesis of autism in Chinese population.     

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in the Arabidopsis thaliana lineage.     

抑癌基因DLC-1的研究进展

DLC-1(肝癌缺失基因1)是近年来被发现的一种重要的抑癌基因,目前研究发现其在多种肿瘤的发生、发展过程中产生了重要的作用。随着基因技术及分子生物技术的飞速发展,关于DLC-1基因以及与之相关的上、下游靶基因,DLC-1基因的甲基化修饰及其相互作用的信号传导通路的研究将更深入、更彻底、更清楚。通过构建肿瘤动物实验模型,我们可以对人类各种肿瘤进行去甲基化药物治疗,分析实验结果,综合评估治疗指征,为临床上对肿瘤的治疗提供理论基础及实践指导。相信在不久的将来,针对DLC-1基因在肿瘤分子生物学研究有望成为多种肿瘤诊断、治疗的突破。     

Role of the mitochondrial pathway in serum deprivation-induced apoptosis of rat endplate cells

The apoptosis of cartilage endplates (CEPs), acting as an initiating factor, plays a vital role in the pathogenesis of intervertebral disc degenerative diseases, the underlying molecular mechanism of the apoptotic process in CEPs is still not clear. The present study aimed to investigate the mechanism of CEP cell apoptosis. We found that low levels of fetal bovine serum (FBS) can induce cell apoptosis. Serum deprivation led to high expression levels of caspase-9, caspase-3, PARP, cytochrome-c and Bax. Flow cytometric analysis showed that inhibition of the intrinsic pathway by a caspase-9 inhibitor (z-LEHD-fmk) significantly suppressed serum deprivation-induced apoptosis. However, a caspase-8 inhibitor (z-IETD-fmk) did not reduce apoptotic cell death. These data suggest that serum deprivation induces apoptosis in rat CEP cells via the activation of the intrinsic apoptotic pathway. The efficacy of a caspase-9 inhibitor in attenuating or preventing apoptosis of serum deprivation-induced disc cell apoptosis suggests that targeting the intrinsic apoptotic pathway may be used as a potential therapy for the treatment of disc degeneration.