BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data

Cytosine methylation is one of the most important RNA epigenetic modifications. With the development of experimental technology, scientists attach more importance to RNA cytosine methylation and find bisulfite sequencing is an effective experimental method for RNA cytosine methylation study. However, there are only a few tools can directly deal with RNA bisulfite sequencing data efficiently. Herein, we developed a specialized tool BS-RNA, which can analyze cytosine methylation of RNA based on bisulfite sequencing data and support both paired-end and single-end sequencing reads from directional bisulfite libraries. For paired-end reads, simply removing the biased positions from the 5′ end may result in “dovetailing” reads, where one or both reads seem to extend past the start of the mate read. BS-RNA could map “dovetailing” reads successfully. The annotation result of BS-RNA is exported in BED (.bed) format, including locations, sequence context types (CG/CHG/CHH, H = A, T, or C), reference sequencing depths, cytosine sequencing depths, and methylation levels of covered cytosine sites on both Watson and Crick strands. BS-RNA is an efficient, specialized and highly automated mapping and annotation tool for RNA bisulfite sequencing data. It performs better than the existing program in terms of accuracy and efficiency. BS-RNA is developed by Perl language and the source code of this tool is freely available from the website: http://bs-rna.big.ac.cn.     

Novel quasi-interpenetrating network/gold nanoparticles composite matrices for DNA sequencing by CE

In order to further improve ssDNA sequencing performances using quasi-interpenetrating network (quasi-IPN) as a matrix composed of linear polyacrylamide (LPA) with lower viscosity-average molecular mass (3.3 MDa) and poly(N,N-dimethylacrylamide) (PDMA), gold nanoparticles (GNPs) were prepared and added into this quasi-IPN to form polymer/metal composite sieving matrices. The studies of intrinsic viscosity and differential scanning calorimetry (DSC) on quasi-IPN and quasi-IPN/GNPs indicate that there were interactions between GNPs and polymer chains. The sequencing performances on ssDNA using quasi-IPN and quasi-IPN/GNPs (with different GNPs concentrations) as sieving matrices were studied and compared by CE at different temperatures. The results show that resolutions of quasi-IPN/GNPs were higher than those of quasi-IPN without GNPs and approximated those of quasi-IPN composed of LPA with higher MW (6.5 MDa) and PDMA without GNPs in the bare fused-silica capillaries. Furthermore, the sequencing time of quasi-IPN/GNPs was shorter than that of quasi-IPN under the same sequencing conditions. The influences of GNPs and sequencing temperature on the sequencing performances of ssDNA were also discussed. The separation reproducibility of quasi-IPN/GNPs solution was excellent and its shelf life was more than 8 months.     

Influence of temperature on performance of an anaerobic sequencing biofilm batch reactor with circulation applied to treatment of low-strength wastewater

The effect of temperature on the performance of an anaerobic sequencing biofilm batch reactor (ASBBR) with liquid-phase recirculation was assessed. Assays were performed using a recirculation velocity of 0.20 cm/s, 8-h cycles, and an average treated synthetic wastewater volume of 2 L/cycle with a concentration of 500 mg of Chemical Oxygen Demand (COD)/L. Operation temperatures were 15, 20, 25, 30, and 35°C. At 25, 30, and 35°C, organic matter removal efficiencies for filtered samples ranged from 81 to 83%. At lower temperatures, namely 15 and 20°C, removal efficiency decreased significantly to 61 and 65%, respectively. A first-order model could be fitted to the experimental concentration profile values. The first-order kinetic parameter value of this model varied from 0.46 to 0.81 h¹ considering the lowest and highest temperature studied. Moreover, analysis of the removal profile values allowed fitting of an Arrhenius-type equation with an activation energy of 5715 cal/mol.     

Cloning, sequencing and expression of a swine IgG H chain gene inE. coli

A DNA fragment about 1.5 kb has been isolated from spleen of adult Chinese swine by RT-PCR. The DNA fragment encodes immunoglobulin IgG H chain gene. Sequencing analysis showed that the DNA fragment is 1 425 bp long, complete CDS. The C region of the gene has been classified as Subclass Ig γ3, and is the same as reported by Sun et al., but V region of the present gene is 42 bp less by comparison. The gene has been ligated into expression vector pET-3b (NSEB)( - ). A protein about 52 ku has been expressed in E. coli with an expression level of about 21 % .     

嘉陵江流域南充金城山森林群落的模糊数学分析

将模糊数学中的聚类法和综合评判法与常规聚类法相结合,直接从群落整体和其外部环境两个方面对嘉陵江流域南充金城山植被进行分类和排序,得到比常规方法更为精确的结果。     

基于分级规划的加工方法排序规则研究

结合工艺决策的分级规划策略,构造了一种新的实用化的加工方法排序规则,该排序规则将传统排序规则分解成两个相关的部分：工序排序规则与工步排序规则．工序排序规则代表了排序规则的普遍性,描述了一类零件的总体加工过程,只与加工方法有关,与组成零件的形状特征等其他因素无关;工步排序规则代表了排序规则的特殊性,描述了工序中各特征的加工顺序,与特征有关而与加工方法无关．     

终端区飞机排序的人工蜂群算法

摘 要：为缓解终端区空中交通压力,研究了人工蜂群算法在终端区飞机降落排序中的应用。建立以航班总延误时间最小为目标函数的规划模型,运用人工蜂群算法,对着陆飞机排序问题进行了仿真计算,并与先到先服务算法、模拟退火算法、蚁群算法进行了对比研究。仿真结果表明：在双跑道模型下,人工蜂群算法比先到先服务算法,延误减少了48%。与模拟退火算法和蚁群算法相比,人工蜂群算法求解的结果最优且用时最少。说明应用人工蜂群算法求解终端区飞机排序问题是可行的。     

耐热菌剂对堆肥有机质降解及细菌演替的影响

针对传统堆肥周期长、有机质降解效率低的问题,将耐热复合菌剂接种于餐厨废弃物高温堆肥中,研究其对有机质降解及微生物群落动态变化的影响。结果表明,接种耐热复合菌剂有利于：有机质降解,堆肥细菌群落丰富度和多样性的提高,厚壁菌门(Firmicutes)和尿素芽胞杆菌属(Ureibacillus)相对丰度的提高,冗余分析的结果表明,厚壁菌门(Firmicutes)对有机质降解的影响最强;网络分析结果表明,堆肥过程中尿素芽孢杆菌属(Ureibacillus)相对丰度的增加以及乳杆菌属(Lactobacillus)相对丰度的降低促进了有机质的降解。因此,接种耐热复合菌剂可以提高高温堆肥的质量和效率。     

煤矿复垦区不同恢复年限沙棘人工林土壤细菌群落结构与功能预测

为揭示煤矿复垦区恢复年限对沙棘人工林土壤细菌群落结构及功能特征的影响,以鄂尔多斯聚鑫龙煤矿复垦区不同恢复年限（3a、4a、5a、6a、7a）沙棘人工林为研究对象,撂荒草地为对照,对研究区土样进行采集,通过Illumina Miseq高通量测序技术对土样细菌群落测序,使用PICRUSt进行功能预测。结果表明：（1）研究区共检测到细菌29门、91纲、193目、305科和438属,门分类水平上优势类群为放线菌门、变形菌门;属分类水平上无优势类群,常见类群为不动杆菌属、类诺卡氏菌属。（2）与草地相比,沙棘人工林的建植使土壤有机质、碱解氮、速效钾、含水量呈增加趋势,土壤pH和全磷变化不明显。（3）沙棘林土壤中的不动杆菌属、类诺卡氏菌属相对丰度整体高于草地;随着恢复年限的延长,栖热菌属和奇球菌属相对丰度随恢复年限延长逐渐降低,CL500-29 marine group、链霉菌属相对丰度则逐渐增加。土壤pH和速效钾是影响研究区沙棘人工林土壤细菌群落结构的主要影响因子。（4）研究区沙棘林和草地土壤细菌主要包含5个一级功能和35个子功能。细菌代谢功能是最主要的功能,其在沙棘林中的代谢潜力高于草地。沙棘林的建植有利于细菌代谢水平和土壤养分的提高。     

基于高通量测序的液态奶中微生物多样性研究

目的 为探究不同液态奶样品中微生物的菌群组成和其多样性。方法 采用高通量测序技术对液态奶中细菌16S rRNA的V₃-V₄区进行测序,研究了四组液态奶样品在门水平和属水平的菌群结构。结果 四组样品中共有分类操作单元(Operational Taxonomic Unit, OTU)数目为119个,独有的OTU数分别占15.0%、6.85%、8.86%和12.35%。在门水平,厚壁菌门和变形菌门是四组液态奶的共有菌门,其中4组样品中厚壁菌门的相对丰度分别为38.9%、73.8%、20.9%、29.6%,变形菌门的相对丰度分别为46.9%、10.0%、28.0%、17.2%;在属水平,4组液态奶中的优势菌属分别是芽孢杆菌属、短波单胞菌属;芽孢杆菌属;Cloacibacterium和寡养单胞菌属;芽孢杆菌属、微杆菌属和异常球菌属。结论 四组样品在门水平的菌群组成基本相似。属水平上,液态奶中含有的不动杆菌属、芽孢杆菌属和克雷伯氏菌属属于嗜冷菌,这些菌属可以导致液态奶发生腐败变质等现象。这为今后探索液态奶中腐败菌防治措施提供重要依据。