A Model for Transgenerational Imprinting Variation in Complex Traits

Despite the fact that genetic imprinting, i.e., differential expression of the same allele due to its different parental origins, plays a pivotal role in controlling complex traits or diseases, the origin, action and transmission mode of imprinted genes have still remained largely unexplored. We present a new strategy for studying these properties of genetic imprinting with a two-stage reciprocal F mating design, initiated with two contrasting inbred lines. This strategy maps quantitative trait loci that are imprinted (i.e., iQTLs) based on their segregation and transmission across different generations. By incorporating the allelic configuration of an iQTL genotype into a mixture model framework, this strategy provides a path to trace the parental origin of alleles from previous generations. The imprinting effects of iQTLs and their interactions with other traditionally defined genetic effects, expressed in different generations, are estimated and tested by implementing the EM algorithm. The strategy was used to map iQTLs responsible for survival time with four reciprocal F populations and test whether and how the detected iQTLs inherit their imprinting effects into the next generation. The new strategy will provide a tool for quantifying the role of imprinting effects in the creation and maintenance of phenotypic diversity and elucidating a comprehensive picture of the genetic architecture of complex traits and diseases.     

Structural basis of ALMT1-mediated aluminum resistance in Arabidopsis

The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance...     

The NLRP3 inflammasome is differentially activated by pneumolysin variants and contributes to host defense in pneumococcal pneumonia

Streptococcus pneumoniae is a leading cause of pneumonia, meningitis, and sepsis. Pneumococci can be divided into >90 serotypes that show differences in the pathogenicity and invasiveness. We tested the hypotheses that the innate immune inflammasome pathway is involved in fighting pneumococcal pneumonia and that some invasive pneumococcal types are not recognized by this pathway. We show that human and murine mononuclear cells responded to S. pneumoniae expressing hemolytic pneumolysin by producing IL-1β. This IL-1β production depended on the NOD-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome. Some serotype 1, serotype 8, and serotype 7F bacteria, which have previously been associated with increased invasiveness and with production of toxins with reduced hemolytic activity, or bacterial mutants lacking pneumolysin did not stimulate notable IL-1β production. We further found that NLRP3 was beneficial for mice during pneumonia caused by pneumococci expressing hemolytic pneumolysin and was involved in cytokine production and maintenance of the pulmonary microvascular barrier. Overall, the inflammasome pathway is protective in pneumonia caused by pneumococci expressing hemolytic toxin but is not activated by clinically important pneumococcal sequence types causing invasive disease. The study indicates that a virulence factor polymorphism may substantially affect the recognition of bacteria by the innate immune system.     

Serum LDL- and HDL-cholesterol determined by ultracentrifugation and HPLC

Simple and precise methods for LDL-cholesterol (LDL-C) and HDL-cholesterol (HDL-C) measurements are essential for assessment of cardiovascular disease (CVD) risks and for lipid and lipoprotein studies. We report here an ultracentrifugation (UC) and HPLC method that requires substantially less specimen volume and provides the necessary reliability and throughput required by large-volume, high-quality research and clinical studies. 2-Mercaptoethanol (ME) was used to dissociate serum lipoprotein [a] (Lp[a]) into apolipoprotein [a] and Lp[a] remnant (Lp[a-]) and eliminated the contamination of Lp[a] in HDL separated by UC. Serum aliquots were centrifuged at a density of 1.006 kg/l for the separation of HDL plus LDL, and in the presence of ME at a density of 1.063 kg/l for the separation of HDL. Cholesterol concentrations of the bottom fractions were analyzed by HPLC. LDL-C and HDL-C determined using this method were equivalent to those with β-quantification and the designated comparison method of the Centers for Disease Control. The total coefficient of variations for LDL-C and HDL-C were 0.65-1.12% and 0.96-2.07%, respectively. This method requires a small amount of specimen and is easy to operate. This method may be used in research or in clinical laboratories where precise and specific lipoprotein cholesterol analysis is needed.     

冬季郑州市12个常绿树种的光合特性及滞尘能力

为筛选出北方城市冬季生态效益突出的常绿树种,以缓解大气CO_2和粉尘颗粒物污染,并为这些树种的园林应用提供科学支持,该文选取郑州市园林绿化应用广泛的12个常绿树种,利用LI-6400便携式光合测定仪和洗脱-质量差值法,并对其光合特性及滞尘能力进行测定,计算出其光合参数[叶片的净光合速率(Pn)、蒸腾速率(Tr)、气孔导度(Gs)、胞间CO_2浓度(Ci)]和滞尘参数(单位叶面积滞尘量、单叶滞尘量、单位面积树冠滞尘量),并分别进行聚类分析。结果表明:(1)大叶女贞、黄杨、海桐、枇杷叶片Pn、Tr、Gs值均极显著高于其他树种(P0.01);香樟、银木、黄杨、枇杷叶片Ci值极显著高于其他树种(P0.01)。大叶女贞、海桐、石楠叶肉细胞保持着较高的光合活性,而香樟、银木叶片光合活性较弱,低温抑制明显。(2)洗淋后7 d和14 d,枇杷、广玉兰、桂花各滞尘参数均极显著高于其他树种(P0.01)。洗淋后14 d,枇杷、广玉兰、桂花单位面积树冠的滞尘量累积在6.65 g·m~(-2)·crown~(-1)以上,滞尘能力强;石楠、银木、大叶女贞、法国冬青、黄杨单位面积树冠的滞尘量在3.99 g·m~(-2)·crown~(-1)以上。(3)聚类分析结果表明,黄杨、大叶女贞和海桐光合特性优势明显,其次为法国冬青、广玉兰、枇杷、石楠和乐东拟单性木兰;广玉兰、桂花、枇杷滞尘能力最强,其次为大叶女贞、法国冬青、石楠和银木。综上所述,大叶女贞、广玉兰、枇杷、法国冬青、黄杨、石楠对改善北方城市冬季空气质量及滞尘均有重要贡献,生态调节能力强,可作为园林绿化优先选用树种。     

On generalized Simes critical constants

We consider the problem treated by Simes of testing the overall null hypothesis formed by the intersection of a set of elementary null hypotheses based on ordered p‐values of the associated test statistics. The Simes test uses critical constants that do not need tabulation. Cai and Sarkar gave a method to compute generalized Simes critical constants which improve upon the power of the Simes test when more than a few hypotheses are false. The Simes constants can be viewed as the first order (requiring solution of a linear equation) and the Cai‐Sarkar constants as the second order (requiring solution of a quadratic equation) constants. We extend the method to third order (requiring solution of a cubic equation) constants, and also offer an extension to an arbitrary kth order. We show by simulation that the third order constants are more powerful than the second order constants for testing the overall null hypothesis in most cases. However, there are some drawbacks associated with these higher order constants especially for , which limits their practical usefulness.     

Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis

Alexander disease (AxD) is a rare and fatal neurodegenerative disorder caused by mutations in the gene encoding glial fibrillary acidic protein (GFAP). In this report, a mouse model of AxD (GFAP^Tg;Gfap^+/R236H) was analyzed that contains a heterozygous R236H point mutation in murine Gfap as well as a transgene with a GFAP promoter to overexpress human GFAP. Using label-free quantitative proteomic comparisons of brain tissue from GFAP^Tg;Gfap^+/R236H versus wild-type mice confirmed upregulation of the glutathione metabolism pathway and indicated proteins were elevated in the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which had not been reported previously in AxD. Relative protein-level differences were confirmed by a targeted proteomics assay, including proteins related to astrocytes and oligodendrocytes. Of particular interest was the decreased level of the oligodendrocyte protein, 2-hydroxyacylsphingosine 1-beta-galactosyltransferase (Ugt8), since Ugt8-deficient mice exhibit a phenotype similar to GFAP^Tg;Gfap^+/R236H mice (e.g., tremors, ataxia, hind-limb paralysis). In addition, decreased levels of myelin-associated proteins were found in the GFAP^Tg;Gfap^+/R236H mice, consistent with the role of Ugt8 in myelin synthesis. Fabp7 upregulation in GFAP^Tg;Gfap^+/R236H mice was also selected for further investigation due to its uncharacterized association to AxD, critical function in astrocyte proliferation, and functional ability to inhibit the anti-inflammatory PPAR signaling pathway in models of amyotrophic lateral sclerosis (ALS). Within Gfap⁺ astrocytes, Fabp7 was markedly increased in the hippocampus, a brain region subjected to extensive pathology and chronic reactive gliosis in GFAP^Tg;Gfap^+/R236H mice. Last, to determine whether the findings in GFAP^Tg;Gfap^+/R236H mice are present in the human condition, AxD patient and control samples were analyzed by Western blot, which indicated that Type I AxD patients have a significant fourfold upregulation of FABP7. However, immunohistochemistry analysis showed that UGT8 accumulates in AxD patient subpial brain regions where abundant amounts of Rosenthal fibers are located, which was not observed in the GFAP^Tg;Gfap^+/R236H mice.     

东海北部滨海湿地铁氧化细菌的分布及其对不同氧气穿透深度的响应

【目的】滨海湿地生态系统位于淡水与海水交互地带,含有高浓度Fe²⁺的地下水渗透到沉积物表层形成的湿地径流和周期性潮汐淹水形成的含氧-缺氧界面有利于铁氧化细菌介导的Fe²⁺的生物氧化过程发生。然而,目前缺乏对滨海湿地生态系统中铁氧化细菌类群的全面评估。【方法】以上海崇明西沙湿地公园及浙江舟山市朱家尖岛东沙沙滩两地共5处滨海湿地沉积物为研究对象,分析沉积物的氧气穿透深度等环境参数,并基于16S rRNA基因扩增子测序技术,全面解析不同滨海湿地生态系统中细菌与铁氧化细菌的群落组成与分布特征。【结果】与崇明西沙湿地相比,朱家尖岛东沙沙滩有更深的氧气穿透深度,达到10 mm以上。非度量多尺度分析(non-metric multidimensional scaling, NMDS)统计结果表明,细菌群落结构主要受到区域位置不同导致的环境条件差异的影响,而铁氧化细菌的群落结构则受到采样的区域位置和沉积物氧气穿透深度的共同影响。崇明西沙湿地和朱家尖岛东沙沙滩的优势细菌为蓝细菌门(Cyanobacteria)、γ-变形菌纲(Gammaproteobacteria)、拟杆菌门(Bacteroidetes)、α-变形菌纲(Alphaproteobacteria)和放线菌门(Actinobacteria);优势铁氧化细菌为嘉利翁氏菌属(Gallionella)、红细菌属(Rhodobacter)、Lepthothrix和Sideroxydans。【结论】通过对崇明西沙湿地和朱家尖岛东沙沙滩沉积物中栖息的铁氧化菌的调查发现,铁氧化细菌的群落组成与湿地沉积物类型导致的氧气穿透深度差异具有密切联系。     

A Preliminary Genetic Analysis of Complement 3 Gene and Schizophrenia

Complement pathway activation was found to occur frequently in schizophrenia, and complement 3 (C3) plays a major role in this process. Previous studies have provided evidence for the possible role of C3 in the development of schizophrenia. In this study, we hypothesized that the gene encoding C3 (C3) may confer susceptibility to schizophrenia in Han Chinese. We analyzed 7 common single nucleotide polymorphisms (SNPs) of C3 in 647 schizophrenia patients and 687 healthy controls. Peripheral C3 mRNA expression level was measured in 23 drug-naïve patients with schizophrenia and 24 controls. Two SNPs (rs1047286 and rs2250656) that deviated from Hardy-Weinberg equilibrium were excluded for further analysis. Among the remaining 5 SNPs, there was no significant difference in allele and genotype frequencies between the patient and control groups. Logistic regression analysis showed no significant SNP-gender interaction in either dominant model or recessive model. There was no significant difference in the level of peripheral C3 expression between the drug-naïve schizophrenia patients and healthy controls. In conclusion, the results of this study do not support C3 as a major genetic susceptibility factor in schizophrenia. Other factors in AP may have critical roles in schizophrenia and be worthy of further investigation.