Multiple trait multiple interval mapping of quantitative trait loci from inbred line crosses

ABSTRACT: BACKGROUND: Although many experiments have measurements on multiple traits, most studies performed the analysis of mapping of quantitative trait loci (QTL) for each trait separately using single trait analysis. Single trait analysis does not take advantage of possible genetic and environmental correlations between traits. In this paper, we propose a novel statistical method for multiple trait multiple interval mapping (MTMIM) of QTL for inbred line crosses. We also develop a novel score-based method for estimating genome-wide significance level of putative QTL effects suitable for the MTMIM model. The MTMIM method is implemented in the freely available and widely used Windows QTL Cartographer software. RESULTS: Throughout the paper, we provide compelling empirical evidences that: (1) the score-based threshold maintains proper type I error rate and tends to keep false discovery rate within an acceptable level; (2) the MTMIM method can deliver better parameter estimates and power than single trait multiple interval mapping method; (3) an analysis of Drosophila dataset illustrates how the MTMIM method can better extract information from datasets with measurements in multiple traits. CONCLUSIONS: The MTMIM method represents a convenient statistical framework to test hypotheses of pleiotropic QTL versus closely linked nonpleiotropic QTL, QTL by environment interaction, and to estimate the total genotypic variance-covariance matrix between traits and to decompose it in terms of QTL-specific variance-covariance matrices, therefore, providing more details on the genetic architecture of complex traits.     

TLR4在气道上皮细胞诱导的哮喘气道平滑肌细胞迁移中的作用

目的:探讨Toll样受体4(TLR4)的激活在气道上皮细胞诱导的哮喘气道平滑肌细胞(ASMCs)迁移中的作用。方法:细胞消化法培养原代哮喘ASMCs,TNF-α刺激上皮细胞系RTE细胞收集细胞培养上清液,检测上清液中IL-8和RANTES的含量,改良Boyden趋化小室检测哮喘ASMCs的跨膜迁移,以TLR4抗体作为工具药,观察其在上皮细胞诱导的哮喘ASMCs跨膜迁移中的作用。结果:各TNF-α组培养上清液中IL-8和RANTES水平均显著增高,20 ng/ml组较其他组显著增高(P<0.01)。各组哮喘ASMCs跨膜迁移较正常组均增加(P<0.01);哮喘组和TNF-α+TLR4抗体组哮喘ASMCs跨膜迁移数较TNF-α组显著减少(P<0.01)。TLR4抗体组哮喘ASMCs跨膜迁移数较哮喘组增加(P<0.05)。结论:气道上皮细胞可能通过分泌细胞因子激活哮喘ASMCs表面的TLR4,诱导增强ASMCs的跨膜迁移,在哮喘的气道重构中发挥一定的作用。     

Identification and expansion of cancer stem cells in tumor tissues and peripheral blood derived from gastric adenocarcinoma patients

Gastric cancer is the fourth most common cancer worldwide, with a high rate of death and low 5-year survival rate. To date, there is a lack of efficient therapeutic protocols for gastric cancer. Recent studies suggest that cancer stem cells (CSCs) are responsible for tumor initiation, invasion, metastasis, and resistance to anticancer therapies. Thus, therapies that target gastric CSCs are attractive. However, CSCs in human gastric adenocarcinoma (GAC) have not been described. Here, we identify CSCs in tumor tissues and peripheral blood from GAC patients. CSCs of human GAC (GCSCs) that are isolated from tumor tissues and peripheral blood of patients carried CD44 and CD54 surface markers, generated tumors that highly resemble the original human tumors when injected into immunodeficient mice, differentiated into gastric epithelial cells in vitro, and self-renewed in vivo and in vitro. Our findings suggest that effective therapeutic protocols must target GCSCs. The capture of GCSCs from the circulation of GAC patients also shows great potential for identification of a critical cell population potentially responsible for tumor metastasis, and provides an effective protocol for early diagnosis and longitudinal monitoring of gastric cancer.     

Nudel is crucial for the WAVE complex assembly in vivo by selectively promoting subcomplex stability and formation through direct interactions

The WAVE regulatory complex (WRC), consisting of WAVE, Sra, Nap, Abi, and HSPC300, activates the Arp2/3 complex to control branched actin polymerization in response to Rac activation. How the WRC is assembled in vivo is not clear. Here we show that Nudel, a protein critical for lamellipodia formation, dramatically stabilized the Sra1-Nap1-Abi1 complex against degradation in cells through a dynamic binding to Sra1, whereas its physical interaction with HSPC300 protected free HSPC300 from the proteasome-mediated degradation and stimulated the HSPC300-WAVE2 complex formation. By contrast, Nudel showed little or no interactions with the Sra1-Nap1-Abi1-WAVE2 and the Sra1-Nap1-Abi1-HSPC300 complexes as well as the mature WRC. Depletion of Nudel by RNAi led to general subunit degradation and markedly attenuated the levels of mature WRC. It also abolished the WRC-dependent actin polymerization in vitro and the Rac1-induced lamellipodial actin network formation during cell spreading. Therefore, Nudel is important for the early steps of the WRC assembly in vivo by antagonizing the instability of certain WRC subunits and subcomplexes.     

林下植被去除与氮添加对樟子松人工林土壤化学和生物学性质的影响

通过析因试验设计,研究了科尔沁沙地樟子松人工林生态系统内土壤无机氮(NO3--N+NH4+-N)含量,潜在净氮矿化(PNM)、硝化速率(PNN),微生物生物量碳(MBC)、氮(MBN)及MBC/MBN,土壤脲酶、酸性磷酸单酯酶活性和土壤有效磷(Olsen-P)含量对林下植被管理(对照和去除)和氮添加(对照和添加8g·m-2)的短期响应.结果表明:林下植被去除显著降低了土壤NH4+-N含量、PNM、MBC和MBC/MBN比值,提高了土壤Olsen-P含量,而对土壤NO3--N含量、PNN和土壤酶活性的影响不显著.氮添加提高了土壤NO3--N含量、PNM和PNN,但对其他指标的影响不明显,可能与试验处理时间较短有关.土壤NH4+-N含量对林下植被去除与氮添加的交互作用的响应显著;而NO3--N含量虽对林下植被去除与氮添加处理的交互作用响应不显著,但在氮添加同时进行林下植被去除的样地中的土壤NO3--N含量比只进行氮添加处理的样地提高了27％,有可能导致土壤中NO3-的淋失.林下植被是影响樟子松人工林土壤化学和微生物学性质的重要因素,因此在森林管理和恢复过程中,不能忽视林下植被的作用.     

Tissue biomarkers for prostate cancer radiation therapy

Prostate cancer is the most common cancer and second leading cause of cancer deaths among men in the United States. Most men have localized disease diagnosed following an elevated serum prostate specific antigen test for cancer screening purposes. Standard treatment options consist of surgery or definitive radiation therapy directed by clinical factors that are organized into risk stratification groups. Current clinical risk stratification systems are still insufficient to differentiate lethal from indolent disease. Similarly, a subset of men in poor risk groups need to be identified for more aggressive treatment and enrollment into clinical trials. Furthermore, these clinical tools are very limited in revealing information about the biologic pathways driving these different disease phenotypes and do not offer insights for novel treatments which are needed in men with poor-risk disease. We believe molecular biomarkers may serve to bridge these inadequacies of traditional clinical factors opening the door for personalized treatment approaches that would allow tailoring of treatment options to maximize therapeutic outcome. We review the current state of prognostic and predictive tissue-based molecular biomarkers which can be used to direct localized prostate cancer treatment decisions, specifically those implicated with definitive and salvage radiation therapy.     

Development of quantitative metabolomics for <Emphasis Type="Italic">Pichia pastoris</Emphasis>

Accurate, reliable and reproducible measurement of intracellular metabolite levels has become important for metabolic studies of microbial cell factories. A first critical step for metabolomic studies is the establishment of an adequate quenching and washing protocol, which ensures effective arrest of all metabolic activity and removal of extracellular metabolites, without causing leakage of metabolites from the cells. Five different procedures based on cold methanol quenching and cell separation by filtration were tested for metabolomics of Pichia pastoris regarding methanol content and temperature of the quenching solution as key parameters. Quantitative evaluation of these protocols was carried out through mass balance analysis, based on metabolite measurements in all sample fractions, those are whole broth, quenched and washed cells, culture filtrate and quenching and washing solution. Finally, the optimal method was used to study the time profiles of free amino acid and central carbon metabolism intermediates in glucose-limited chemostat cultures. Acceptable recoveries (>90%) were obtained for all quenching procedures tested. However, quenching at −27°C in 60% v/v methanol performed slightly better in terms of leakage minimization. We could demonstrate that five residence times under glucose limitation are enough to reach stable intracellular metabolite pools. Moreover, when comparing P. pastoris and S. cerevisiae metabolomes, under the same cultivation conditions, similar metabolite fingerprints were found in both yeasts, except for the lower glycolysis, where the levels of these metabolites in P. pastoris suggested an enzymatic capacity limitation in that part of the metabolism.     

An APC/C inhibitor stabilizes cyclin B1 by prematurely terminating ubiquitination

The anaphase-promoting complex/cyclosome (APC) is a ubiquitin ligase that is required for exit from mitosis. We previously showed that tosyl arginine methyl ester (TAME) inhibits APC-dependent proteolysis by competing with the C-terminal isoleucine-arginine tail of the APC activator cell division cycle 20 (Cdc20) for APC binding. Here we show that in the absence of APC substrates, TAME ejects Cdc20 from the APC by promoting Cdc20 autoubiquitination in its N-terminal region. Cyclin B1 antagonizes TAME's effect by promoting binding of free Cdc20 to the APC and by suppressing Cdc20 autoubiquitination. Nevertheless, TAME stabilizes cyclin B1 in Xenopus extracts by two mechanisms. First, it reduces the k(cat) of the APC-Cdc20-cyclin B1 complex without affecting the K(m), slowing the initial ubiquitination of unmodified cyclin B1. Second, as cyclin B1 becomes ubiquitinated, it loses its ability to promote Cdc20 binding to the APC in the presence of TAME. As a result, cyclin B1 ubiquitination terminates before reaching the threshold necessary for proteolysis.