Genome-wide RNAi screen in IFN-γ-treated human macrophages identifies genes mediating resistance to the intracellular pathogen Francisella tularensis

Interferon-gamma (IFN-γ) inhibits intracellular replication of Francisella tularensis in human monocyte-derived macrophages (HMDM) and in mice, but the mechanisms of this protective effect are poorly characterized. We used genome-wide RNA interference (RNAi) screening in the human macrophage cell line THP-1 to identify genes that mediate the beneficial effects of IFN-γ on F. tularensis infection. A primary screen identified ～200 replicated candidate genes. These were prioritized according to mRNA expression in IFN-γ-primed and F. tularensis-challenged macrophages. A panel of 20 top hits was further assessed by re-testing using individual shRNAs or siRNAs in THP-1 cells, HMDMs and primary human lung macrophages. Six of eight validated genes tested were also found to confer resistance to Listeria monocytogenes infection, suggesting a broadly shared host gene program for intracellular pathogens. The F. tularensis-validated hits included 'druggable' targets such as TNFRSF9, which encodes CD137. Treating HMDM with a blocking antibody to CD137 confirmed a beneficial role of CD137 in macrophage clearance of F. tularensis. These studies reveal a number of important mediators of IFN-γ activated host defense against intracellular pathogens, and implicate CD137 as a potential therapeutic target and regulator of macrophage interactions with Francisella tularensis.     

Alleviation of gut inflammation by Cdx2/Pxr pathway in a mouse model of chemical colitis

Pregnane X Receptor (PXR), a master regulator of drug metabolism and inflammation, is abundantly expressed in the gastrointestinal tract. Baicalein and its O-glucuronide baicalin are potent anti-inflammatory and anti-cancer herbal flavonoids that undergo a complex cycle of interconversion in the liver and gut. We sought to investigate the role these flavonoids play in inhibiting gut inflammation by an axis involving PXR and other potential factors. The consequences of PXR regulation and activation by the herbal flavonoids, baicalein and baicalin were evaluated in vitro in human colon carcinoma cells and in vivo using wild-type, Pxr-null, and humanized (hPXR) PXR mice. Baicalein, but not its glucuronidated metabolite baicalin, activates PXR in a Cdx2-dependent manner in vitro, in human colon carcinoma LS174T cells, and in the murine colon in vivo. While both flavonoids abrogate dextran sodium sulfate (DSS)-mediated colon inflammation in vivo, oral delivery of a potent bacterial β-glucuronidase inhibitor eliminates baicalin's effect on gastrointestinal inflammation by preventing the microbial conversion of baicalin to baicalien. Finally, reduction of gastrointestinal inflammation requires the binding of Cdx2 to a specific proximal site on the PXR promoter. Pharmacological targeting of intestinal PXR using natural metabolically labile ligands could serve as effective and potent therapeutics for gut inflammation that avert systemic drug interactions.     

Effects of Grazing Intensity and Environmental Factors on Species Composition and Diversity in Typical Steppe of Inner Mongolia,China

In the present study, we aim to analyze the effect of grazing, precipitation and temperature on plant species dynamics in the typical steppe of Inner Mongolia, P.R. China. By uncoupling biotic and abiotic factors, we provide essential information on the main drivers determining species composition and species diversity. Effects of grazing by sheep were studied in a controlled experiment along a gradient of seven grazing intensities (from ungrazed to very heavily grazed) during six consecutive years (2005–2010). The results show that plant species composition and diversity varied among years but were little affected by grazing intensity, since the experimental years were much dryer than the long term average, the abiotic constraints may have overridden any grazing effect. Among-year differences were predominantly determined by the abiotic factors of precipitation and temperature. Most of the variation in species dynamics and coexistence between C3 and C4 species was explained by seasonal weather conditions, i.e. precipitation and temperature regime during the early-season (March-June) were most important in determining vegetation dynamics. The dominant C3 species Stipa grandis was highly competitive in March-June, when the temperature levels were low and rainfall level was high. In contrast, the most common C4 species Cleistogenes squarrosa benefited from high early-season temperature levels and low early-season rainfall. However, biomass of Stipa grandis was positively correlated with temperature in March, when effective mean temperature ranges from 0 to 5°C and thus promotes vernalization and vegetative sprouting. Our results suggest that, over a six-year term, it is temporal variability in precipitation and temperature rather than grazing that determines vegetation dynamics and species co-existence of grazed steppe ecosystems. Furthermore, our data support that the variability in the biomass of dominant species, rather than diversity, determine ecosystem functioning. The present study provides fundamental knowledge on the complex interaction of grazing – vegetation – climate.     

Immune-related GTPase M (IRGM1) regulates neuronal autophagy in a mouse model of stroke

Autophagy is an important cellular recycling mechanism through self-digestion in responses to cellular stress such as starvation. Studies have shown that autophagy is involved in maintaining the homeostasis of the neural system during stroke. However, molecular mechanisms underlying neuronal autophagy in ischemic stroke remain poorly understood. Previously, we and others have shown that immune-related GTPase M (IRGM; termed IRGM1 in the mouse nomenclature) can regulate the survival of immune cells through autophagy in response to infections and autoimmune conditions. Here, using a permanent middle cerebral artery occlusion (pMCAO) mouse model, we found that IRGM1 was upregulated in the ischemic side of the brain, which was accompanied by a significant autophagic response. In contrast, neuronal autophagy was almost complete lost in Irgm1 knockout (KO) mice after pMCAO induction. In addition, the infarct volume in the Irgm1-KO pMCAO mice was significantly increased as compared to wild-type mice. Histological studies suggested that, at the early stage (within 24 h) of ischemia, the IRGM1-dependent autophagic response is associated with a protection of neurons from necrosis in the ischemic core but a promotion of neuronal apoptosis in the penumbra area. These data demonstrate a novel role of IRGM1 in regulating neuronal autophagy and survival during ischemic stroke.     

Quantitative trait loci mapping of dark-induced senescence in winter wheat (Triticum aestivum)

In order to explore the genetics of dark-induced senescence in winter wheat(Triticum aestivum L.),a quantitative trait loci(QTL)analysis was carried out in a doubled haploid population developed from a cross between the varieties Hanxuan 10(HX)and Lumai 14(LM).The senescence parameters chlorophyll content(Chl a+b,Chl a,and Chl b),original fluorescence(Fo),maximum fluorescence level(Fm),maximum photochemical efficiency(Fv/Fm),and ratio of variable fluorescence to original fluorescence(Fv/Fo)were evaluated in the second leaf of whole three-leaf seedlings subjected to 7 d of darkness.A total of 43 QTLs were identified that were associated with dark-induced senescence using composite interval mapping.These QTLs were mapped to 20 loci distributed on 11 chromosomes:1B,1D,2A,2B,3B,3D,5D,6A,6B,7A,and 7B.The phenotypic variation explained by each QTL ranged from 7.5% to 19.4%.Eleven loci coincided with two or more of the analyzed parameters.In addition,14 loci co-located or were linked with previously reported QTLs regulating flag leaf senescence,tolerance to high light stress,and grain protein content(Gpc),separately.     

食管鳞癌组织中CDC2、CLDN5蛋白表达及其临床病理意义的研究

目的探讨CDC2及CLDN5在食管鳞癌中表达及其临床病理特征的关系。方法应用免疫组化Elivision法检测90例食管鳞癌组织、28例正常食管黏膜组织及16例重度不典型增生组织中CDC2和CLDN5的蛋白表达情况。结果在食管鳞癌和正常食管黏膜组织中CDC2和CI。DN5的阳性表达率分别为88．89％（80／90）、85．56％（77／90）和48．86％（12／28）、25．00％（7／28）,两者差异有统计学意义（P〈O．05）。CDC2蛋白表达在低分化食管鳞癌中明显高于高分化食管鳞癌;临床分期Ⅲ＋Ⅳ期组的CDC2蛋白的表达显著高于I期、Ⅱ期组（P〈O．05）。CDC2和CLDN5在食管鳞癌中表达呈正相关（r=0．537,P〈o．05）。结论CDC2和CLDN5在食管鳞癌的发生、发展过程中可能发挥重要作用,可能作为食管癌临床早期诊断的重要指标。     

Insights into Pancreatic Cancer Etiology from Pathway Analysis of Genome-Wide Association Study Data

Background

Pancreatic cancer is the fourth leading cause of cancer death in the U.S. and the etiology of this highly lethal disease has not been well defined. To identify genetic susceptibility factors for pancreatic cancer, we conducted pathway analysis of genome-wide association study (GWAS) data in 3,141 pancreatic cancer patients and 3,367 controls with European ancestry.

Methods

Using the gene set ridge regression in association studies (GRASS) method, we analyzed 197 pathways identified from the Kyoto Encyclopedia of Genes and Genomes database. We used the logistic kernel machine (LKM) test to identify major contributing genes to each pathway. We conducted functional enrichment analysis of the most significant genes (P<0.01) using the Database for Annotation, Visualization, and Integrated Discovery (DAVID).

Results

Two pathways were significantly associated with risk of pancreatic cancer after adjusting for multiple comparisons (P<0.00025) and in replication testing: neuroactive ligand-receptor interaction, (Ps<0.00002), and the olfactory transduction pathway (P = 0.0001). LKM test identified four genes that were significantly associated with risk of pancreatic cancer after Bonferroni correction (P<1×10⁻⁵): ABO, HNF1A, OR13C4, and SHH. Functional enrichment analysis using DAVID consistently found the G protein-coupled receptor signaling pathway (including both neuroactive ligand-receptor interaction and olfactory transduction pathways) to be the most significant pathway for pancreatic cancer risk in this study population.

Conclusion

These novel findings provide new perspectives on genetic susceptibility to and molecular mechanisms of pancreatic cancer.     

作物QTL定位常用作图群体

作物大多重要农艺性状是数量性状,受多基因控制,基因之间及基因与环境之间都会发生互作,这为研究带来了很大的不便。因此,好的QTL作图群体,是研究QTL间的互作、QTL与环境的互作、QTL定位以及基因克隆的最根本保障。随着分子标记技术的发展,QTL定位的作图群体也在不断的发展并逐渐满足研究者对于QTL的精细定位及基因克隆等研究的进一步要求。文章主要综述了作物QTL定位常用作图群体的构建及优缺点。