Role of cell-to-cell variability in activating a positive feedback antiviral response in human dendritic cells

In the first few hours following Newcastle disease viral infection of human monocyte-derived dendritic cells, the induction of IFNB1 is extremely low and the secreted type I interferon response is below the limits of ELISA assay. However, many interferon-induced genes are activated at this time, for example DDX58 (RIGI), which in response to viral RNA induces IFNB1. We investigated whether the early induction of IFNBI in only a small percentage of infected cells leads to low level IFN secretion that then induces IFN-responsive genes in all cells. We developed an agent-based mathematical model to explore the IFNBI and DDX58 temporal dynamics. Simulations showed that a small number of early responder cells provide a mechanism for efficient and controlled activation of the DDX58-IFNBI positive feedback loop. The model predicted distributions of single cell responses that were confirmed by single cell mRNA measurements. The results suggest that large cell-to-cell variation plays an important role in the early innate immune response, and that the variability is essential for the efficient activation of the IFNB1 based feedback loop.     

Comparison of Insect Gut Cellulase and Xylanase Activity Across Different Insect Species with Distinct Food Sources

Insect guts represent unique natural biocatalyst systems for biocatalyst discovery and biomass deconstruction mechanism studies. In order to guide the further research for enzyme discovery and biodiversity analysis, we carried out comprehensive xylanase and cellulase activity assays for the gut contents of three insect species representing different orders and food sources. The three insect species are grasshopper (Acrididae sp.), woodborer (Cerambycidae spp.), and silkworm (Bombyx mori) to represent the wood-consuming, grass-consuming, and leaf-consuming insects from Orthoptera, Coleoptera, and Lepidoptera orders, respectively. Generally speaking, the enzyme activity assays have shown that the cellulase and xylanase activities for grasshopper and woodborer guts are significantly higher than those of silkworm under various conditions. In addition, both pH and temperature have a significant impact on the enzyme activities in the gut contents. For the grasshopper gut, the means of xylanase and cellulase activities at pH 7 were 3,397 and 404 μM mg^?1 min^?1, which are significantly higher than the activities at pH 4 and 10 (P?<?0.05). However, woodborer guts have shown the highest cellulase activity at pH 10. The results suggested that systems similar to woodborer guts could be good resources for discovering alkaline-tolerant enzymes. Moreover, the enzyme activities in response to different substrate concentrations were also analyzed, which indicated that grasshopper gut had particularly high cellulase activity. The enzyme activities in response to the reaction time were also examined, and we found that the enzyme activities (micromolar per milligram per minute) of different insect gut juices in response to the increase of incubation time fit well to the power function equation (E _c = K ? t ^b ) with high coefficients (r ²?>?0.99). The newly developed model serves well to compare the characteristics of the enzyme mixtures among different insect species, which can be applied to other studies of natural biocatalyst systems for the future. Overall, the data indicated that grasshopper and woodborer guts are valuable resources for discovering the novel biocatalysts for various biorefinery applications.     

Stability analysis of liver cancer-related microRNAs

MicroRNAs (miRNAs) are non-coding, single-stranded RNAs of approximately 22 nt and constitute a novel class of gene regulators that are found in both plants and animals. Several studies have demonstrated that serum miRNAs could serve as potential biomarkers for the detection of various cancers and other diseases. A few documents regarding the stability of liver cancer-related miRNAs in serum are available. A systemic analysis of the stability of miRNA in serum is quite necessary. The purpose of this study was to evaluate the stability of miRNAs from three different sources, cultured liver cancer Huh-7 cell line, clinical liver cancer, and serum under different experimental conditions, including different temperature, time duration, pH values, RNase A digestion, DNase I digestion, and various freeze-thaw cycles. The qRT-PCR analysis demonstrated that liver cancer-related miRNAs were detectable under each of test conditions, indicating that miRNAs were extremely stable and resistant to destruction and degradation under harsh environmental conditions. However, ribosomal RNA was fragile and easily degraded by demonstrating sharp decrease of relative expression under the non-physiological test conditions. We also established a robust procedure for serum RNA extraction, which is greatly important not only for the miRNA profiling studies but also for the disease prognosis based on abnormal miRNA expression.     

Evolution of vertebrate central nervous system is accompanied by novel expression changes of duplicate genes

The evolution of the central nervous system (CNS) is one of the most striking changes during the transition from invertebrates to vertebrates. As a major source of genetic novelties, gene duplication might play an important role in the functional innovation of vertebrate CNS. In this study, we focused on a group of CNS-biased genes that duplicated during early vertebrate evolution. We investigated the tempo-spatial expression patterns of 33 duplicate gene families and their orthologs during the embryonic development of the vertebrate Xenopus laevis and the cephalochordate Brachiostoma belcheri. Almost all the identified duplicate genes are differentially expressed in the CNS in Xenopus embryos, and more than 50% and 30% duplicate genes are expressed in the telencephalon and mid-hindbrain boundary, respectively, which are mostly considered as two innovations in the vertebrate CNS. Interestingly, more than 50% of the amphioxus orthologs do not show apparent expression in the CNS in amphioxus embryos as detected by in situ hybridization, indicating that some of the vertebrate CNS-biased duplicate genes might arise from non-CNS genes in invertebrates. Our data accentuate the functional contribution of gene duplication in the CNS evolution of vertebrate and uncover an invertebrate non-CNS history for some vertebrate CNS-biased duplicate genes.     

湖南湖北两省H6亚型禽流感病毒表面基因的序列分析

2008年至2009年间,在湖南和湖北两省的活禽市场中分离到了14株H6亚型禽流感病毒,为了解这14株病毒之间的分子特征和差异,我们运用PCR和测序鉴定对这14株病毒的NA基因进行了分型,并对其表面基因HA和NA进行序列测定及序列分析.14株H6亚型病毒中,H6N2亚型12株,H6N6亚型2株.序列测定和进化分析结果显示:DK/HN/284的HA基因与其它13株的HA差异性较大,差异性达到19.4%～20.2%,其余13株毒同源性在94.2%～99.9%;N2亚型NA基因的同源性在91.1%～99.9%,差异性比较大;两株N6亚型NA基因同源性为89.5%,差异明显.这些数据表明:不同毒株呈现一定的地域性差异.与我国周边其它地区的H6亚型禽流感毒株序列进行比较发现,只有DK/HN/284的HA基因与香港早期的毒株可能有着共同的来源,其余都与香港和韩国等的毒株有着较大的差异性,并且各个毒株的HA基因上潜在的糖基化位点和受体结合位点也有所不同,这些数据表明,这些毒株表现出明显的异源性.