TrioMDR: Detecting SNP interactions in trio families with model-based multifactor dimensionality reduction

Single nucleotide polymorphism (SNP) interactions can explain the missing heritability of common complex diseases. Many interaction detection methods have been proposed in genome-wide association studies, and they can be divided into two types: population-based and family-based. Compared with population-based methods, family-based methods are robust vs. population stratification. Several family-based methods have been proposed, among which Multifactor Dimensionality Reduction (MDR)-based methods are popular and powerful. However, current MDR-based methods suffer from heavy computational burden. Furthermore, they do not allow for main effect adjustment. In this work we develop a two-stage model-based MDR approach (TrioMDR) to detect multi-locus interaction in trio families (i.e., two parents and one affected child). TrioMDR combines the MDR framework with logistic regression models to check interactions, so TrioMDR can adjust main effects. In addition, unlike consuming permutation procedures used in traditional MDR-based methods, TrioMDR utilizes a simple semi-parameter P-values correction procedure to control type I error rate, this procedure only uses a few permutations to achieve the significance of a multi-locus model and significantly speeds up TrioMDR. We performed extensive experiments on simulated data to compare the type I error and power of TrioMDR under different scenarios. The results demonstrate that TrioMDR is fast and more powerful in general than some recently proposed methods for interaction detection in trios. The R codes of TrioMDR are available at: https://github.com/TrioMDR/TrioMDR.     

Production of fuels and chemicals from renewable resources using engineered Escherichia coli

Biotechnological production of fuels and chemicals from renewable resources is an appealing way to move from the current petroleum-based economy to a biomass-based green economy. Recently, the feedstocks that can be used for bioconversion or fermentation have been expanded to plant biomass, microbial biomass, and industrial waste. Several microbes have been engineered to produce chemicals from renewable resources, among which Escherichia coli is one of the best studied. Much effort has been made to engineer E. coli to produce fuels and chemicals from different renewable resources. In this paper, we focused on E. coli and systematically reviewed a range of fuels and chemicals that can be produced from renewable resources by engineered E. coli. Moreover, we proposed how can we further improve the efficiency for utilizing renewable resources by engineered E. coli, and how can we engineer E. coli for utilizing alternative renewable feedstocks. e.g. C1 gases and methanol. This review will help the readers better understand the current progress in this field and provide insights for further metabolic engineering efforts in E. coli.     

北京市怀沙-怀九河市级水生野生动物保护区鱼类物种多样性及其资源保护

怀沙河和怀九河是两条自然汇入北京怀柔水库的河流,被规划为北京市第一个市级水生野生动物保护区。2004年3月~2005年2月,作者对该保护区内野生鱼类资源进行了本底调查。调查区域内野生淡水鱼类共计24种(不计引入种),隶属于6目11科24属,以鲤形目鲤科鱼类为主,多为山区溪流小型鱼类。鱼类物种多样性在空间分布上有所不同,两河下游近水库河段物种多样性最高,这可能与两个不同生态环境交界处的边缘效应有关;其多样性在时间上春夏季高于秋冬季。结合区域内的生境特点,建议加强对核心区的保护力度,重新规划缓冲区和过渡区;在保护自然环境的同时,兼顾当地居民的经济利益,达到人与资源的和谐发展。     

Differential channelling of liver lipids in relation to susceptibility to hepatic steatosis in two species of ducks

In the human, hepatic steatosis can be associated with an imbalance between synthesis, secretion and storage of hepatic lipids, and exhibits a genetic susceptibility. The effect of overfeeding on hepatic lipid channelling was investigated in two genotypes of ducks that differ in their susceptibility to fatty liver, i.e. the common duck, Anas platyrhynchos, and the Muscovy duck, Cairina moschata. Before overfeeeding, the Muscovy duck exhibited a lower subcutaneous adiposity and a higher muscular development, whereas hepatic composition was similar in both genotypes (>5% lipids and triglycerides accounting for 6–10% lipids). In the plasma lipoprotein profile, HDL predominated (5.5–7.8 g/l) over VLDL (0.09–0.25 g/l) and LDL (0.65–1.06 g/l). All lipid and lipoprotein concentrations were lower in the Muscovy duck. In response to overfeeding, the Muscovy duck exhibited a higher degree of hepatic steatosis (62 vs. 50% lipids), and a lower increase in adiposity and in the concentration of plasma triglycerides (6-fold vs. 10-fold) and VLDL (23-fold vs. 34-fold). Thus, certain genotypes may be more responsive to the dietary induction of fatty liver because of a less efficient channelling of hepatic lipids towards secretion into plasma and adipose storage, and the duck may represent a suitable model in which to study the development of hepatic steatosis and its pathogenesis.     

北京西山侏罗纪大同锥叶蕨的研究

大同锥叶蕨Coniopteris tatungensis 是侏罗纪植物群常见的分子。由于对该植物特征认识的不同, 对其在分类上的归属有不同意见,或归入膜蕨型锥叶蕨C．hymenophylloides,或归入简单锥叶蕨C. simplex。通过对产自北京西山斋堂地区窑坡组下段的标本的深入研究,特别是用扫描电子显微镜对该 标本的孢子囊群和孢子囊的观察,确认大同锥叶蕨在锥叶蕨属的种级分类上的独立性。文中还初步讨论了其分类和地理分布。     

Treatment and utilization of wastewater in the Beijing Zoo by an aquatic macrophyte system

This paper deals with a nutrient cycling experiment in the Beijing Zoo that uses macrophytes as the added link to make a purification system. The whole system consisted of macrophyte cultivating area and no macrophyte area. By making up the different functional groups of aquatic plants, a multilevel cycling network is formed, which has a rather high purification capability. During the experimental period, the water quality of the Waterfowl Lake and the Peony Pavilion Lake improved significantly, with total nitrogen and total phosphorus reductions of up to 58 and 38%, respectively. Other parameters also confirmed the good purification effect of this system. The economic and social benefits met the requirement of the original design.     

上海口岸输入性传染性肺结核病患者中结核分枝杆菌北京型特征及耐药性分析

本研究旨在了解上海口岸输入性传染性肺结核病患者中结核分枝杆菌北京型特征及其对一线抗结核药物的耐药情况,从而正确评估输入性结核病给上海地区带来的公共卫生危害,同时为地区传染性结核病防治策略的制定提供依据。针对2009年1月～2013年5月上海口岸入境体检人员中胸部影像学诊断疑似活动性肺结核病的人群,采集其连续3 d的晨痰分离培养结核分枝杆菌,用MGIT960培养法分析其对抗结核药物（链霉素、异烟肼、利福平、乙胺丁醇、吡嗪酰胺）的耐药情况,用目标缺失多重聚合酶链反应（DTM-PCR ）进行结核分枝杆菌北京型分子分型,同时采集其人口学资料。期间共监测到入境外籍疑似活动性肺结核病者193例,其中50例痰液中分离培养到结核分枝杆菌,菌培阳率为25．9％,与我国结核病普查工作中活动性肺结核病菌培阳率（25．9％）相同。分离培养并成功传代、分型的40株结核分枝杆菌中,北京型占57．5％（23／40）,显著低于同期上海口岸出境人群中的90．2％（37／41）。输入性结核分枝杆菌北京型主要来自东南亚地区（71．4％,5／7）和西太平洋地区（57．1％,16／28）。一线5种抗结核药物的耐药性检测结果显示,输入性结核分枝杆菌北京型的总耐药率为30．4％（7／23）,接近上海口岸出境人群的34．1％。输入性耐多药菌株占2．4％（1／42）,分子分型结果显示为非北京型。输入性传染性肺结核病对吡嗪酰胺的耐药率为16．7％,显著高于上海口岸出境人群的2．4％。结果提示,上海口岸输入性肺结核病患者中结核分枝杆菌北京型所占比例显著低于同期出境人群,未发现与性别和年龄相关,未发现输入性结核分枝杆菌北京型对抗结核药物耐药性的显著变化。输入性耐药性结核病带来的公共卫生危害不容忽视,在直接督导下的短程化疗（DOTS）方案中需考虑其高吡嗪酰胺耐药特征。在口岸公共卫生安全风险评估中,需重视输入性结核分枝杆菌北京型与本地流行株的差异。     

北京市大气细颗粒污染物与老年呼吸系统疾病急诊就医关系的病例交叉研究

目的:探讨北京市大气细颗粒污染物对呼吸系统疾病急诊的影响。方法:收集2013年3月-2014年3月解放军305医院以及西三环的总参军训部北京第八干休所门诊部的临床病例急诊数据、北京市环境监测中心的大气细颗粒污染物和气象条件数据资料,应用病例交叉设计研究方法进行数据分析。结果:在控制气温、相对湿度的影响后,单向回顾性1:1配对病例交叉分析结果显示,滞后0天细颗粒物污染对慢性支气管炎、哮喘、慢性阻塞性肺病急诊影响的OR值最大,细颗粒物日平均浓度每升高10μg/m3,对应的OR值分别为1.032、1.033、1.035。结论:该研究区域内大气细颗粒物污染物浓度升高可以导致呼吸系统疾病相关的慢性支气管炎、哮喘、慢性阻塞性肺病疾病的急诊增加。