水解酸化-SBR法处理生物制药废水

对采用水解酸化-SBR法处理生物制药废水的调试运行作了详细说明。工程实践表明，该工艺对处理有机物浓度高、水质水量波动大的生物制药废水是切实可行的，出水水质可达到国家污水综合排放标准一级标准．剩余污泥也得到有效处理处置。该工艺结构简单，操作简便，占地面积小，运行效果稳定，具有推广应用价值。     

不同时期排泥对培养SBBR生物膜的影响

序批式生物膜反应器（sequencing biofilm batch reactor, SBBR）是应用广泛的污水处理方法。为探究不同时期排泥对SBBR污染物去除效果与微生物群落结构的影响，本研究设置了挂膜初期、中期和后期进行排泥的反应器处理生活污水，同时结合16S rDNA高通量测序技术对微生物群落结构进行分析，并采用机器学习（machine learning, ML）的方法，在传统的微生物优势种分析基础上，对测序数据进行深度挖掘，寻找造成组间差异的关键物种。水质测定结果显示，COD去除效果在不同时期排泥的SBBR间没有明显差异，出水COD均低于30mg/L。挂膜中期排泥的SBBR的NH₃-N去除率先达到稳定且高于前期和后期排泥的系统。高通量测序结果显示，各SBBR中微生物优势种均以降解有机物的物种为主。挂膜中期排泥的SBBR中，ML筛选得到的NH₃-N去除相关物种（Hydrogenophaga、Gemmata和Nitrospira）与差异关键物种丰度更高，微生物群落结构稳定性更强，可从微生物层面解释分析SBBR污染物去除效果的差异。     

短程硝化-强化生物除磷序批式反应器处理畜禽养殖废水

畜禽养殖废水有机物水质水量变化大,有机物、氨氮与磷的浓度较高,直接排放会严重危害环境。通过构建厌氧-好氧序批式反应器（SBR）处理预酸化畜禽养殖废水,分析了不同进水负荷条件下反应器对污染物的去除性能和微生物群落结构的变化规律。结果表明：SBR反应器对高负荷进水中TN、PO^3-₄—P和COD的平均去除率可分别达到64.5%、97.5%和94.5%。反应器出现NH⁺₄—N和NO₂—N亚硝酸同时积累的短程硝化现象,这可能与高进水负荷对氨氧化菌和亚硝酸盐氧化菌的活性和种群的影响有关。与乙酸盐相比,以丙酸盐作碳源时污泥的强化生物除磷活性更高。随着进水负荷的增大,聚糖菌（GAOs）的相对丰度明显升高。四联球状菌（Tetrasphaera）为反应器中始终占优势的聚磷菌（PAOs）,对反应器除磷性能有重要贡献。在高有机负荷条件下,SBR内PAOs与GAOs之间不存在明显的底物竞争关系,系统脱氮除磷性能未受影响。     

Genome-wide genetic diversity may help identify fine-scale genetic structure among lake whitefish spawning groups in Lake Erie

In Lake Erie, lake whitefish Coregonus clupeaformis supported lucrative fisheries before populations were decimated by overfishing and water quality degradation. In recent years, there has been a renewed interest in lake whitefish and management of the fishery they support. Lake whitefish spawn on several reefs throughout Lake Erie, but the relative recruitment dynamics and contributions of spawning groups to the fishery are not well understood. Modern high-throughput sequencing approaches offer new opportunities to census population diversity and to identify subtle differences among closely related populations. We used high-throughput sequencing data to evaluate the genetic structure and diversity of lake whitefish collected opportunistically across broad spatial scales in Lake Erie. Using RAD-capture (Rapture), we sequenced and genotyped individuals (N = 88) from the west, central, and east basin of Lake Erie at 120,268 single nucleotide polymorphisms (SNPs). Lake whitefish from Niagara and Crib Reefs (west basin) diverged from the three collections. Interestingly, these were the only lake whitefish collected during the act of spawning (late November), and all other fish were collected pre-spawn (August-early November). These results suggest that some lake whitefish spawning reefs may be reproductively isolated, though definition of these groups into stocks will require more intentional sampling during the act of spawning.     

下一代测序纠错方法综述

在面向下一代的测序技术中,前期纠错方法决定着测序的最终序列质量,因此成为当前研究热点,很多不同的纠错方法被提出,对于这些方法的优缺点以及它们适合的应用,应该有清晰的认识和公正的评估. 介绍了现存的各种下一代测序的纠错技术. 首先,从各种不同工具所基于的底层算法进行分析;接着,从测序不同平台来看读段错误形成的特点;然后,从各种不同的测序应用角度来观察读段序列错误特征;最后,总结并阐述读段序列纠错工具存在的问题和发展趋势.     

低温SBR系统活性污泥硝化效能的pH调控

为进一步提高低温(15 ℃)SBR系统的硝化效能,通过间歇培养实验探讨pH对系统活性污泥硝化效能的调控与影响．结果表明,将初始pH控制为8.0～9.0,低温SBR系统的活性污泥(以MLSS计)具有最佳的氨氮氧化能力,在NO₂--N积累阶段对NH₄+-N的比去除速率可达25.49 g·kg-1·d-1,NO₂--N的比生成速率达22 g·kg-1·d-1;初始pH为7.5～8.0时,NO₂--N氧化效果最佳,NO₃--N的比生成速率可达35.6 g·kg-1·d-1;将反应系统的pH维持在8.0,可使亚硝酸菌和硝酸菌代谢活性均保持在较高水平,达到良好的硝化效果．     

基于De Bruijn图的De Novo序列组装软件性能分析

随着新一代测序技术的发展,一些新的全基因组组装算法应运而生,特别是针对第三代高通量测序仪产生的海量短序列的组装软件被不断开发出来,这些组装软件渐渐走向市场。但是,由于这些组装软件的适用性和其性能的差别,选择一款性能优良的组装工具或者开发并行高吞吐的组装工具成为了当前面临的一大难题。本文选取基于 De Bruijn 图算法开发的 4 款 De Novo 组装的软件（Velvet、SOAPdenovo、IDBA、ABySS）对 4 种物种的基因组的模拟数据进行测试,并从软件的算法、组装性能和组装质量 3 个方面分析这 4 个软件的性能,同时根据其算法特点推断影响这些软件性能的关键因素,并给出软件的使用建议以及开发并行序列组装工具来组装超大规模的基因数据应该注意的问题。     

An ant colony optimization algorithm for DNA sequencing by hybridization

The reconstruction of DNA sequences from DNA fragments is one of the most challenging problems in computational biology. In recent years the specific problem of DNA sequencing by hybridization has attracted quite a lot of interest in the optimization community. Several metaheuristics such as tabu search and evolutionary algorithms have been applied to this problem. However, the performance of existing metaheuristics is often inferior to the performance of recently proposed constructive heuristics. On the basis of these new heuristics we develop an ant colony optimization algorithm for DNA sequencing by hybridization. An important feature of this algorithm is the implementation in a so-called multi-level framework. The computational results show that our algorithm is currently a state-of-the-art method for the tackled problem.     

脱水过程中无核白葡萄转录组测序及膜脂降解代谢中关键基因的筛选

该研究以吐鲁番地区无核白葡萄为试验材料,在25 ℃常温和30 ℃热风干燥后,取失水25%、50%时褐变和未褐变的样品。利用转录组测序技术筛选出膜脂降解代谢相关的关键基因,并利用实时荧光定量PCR技术对其进行验证,研究结果显示,转录组测序共获得了11.63亿的clean data,当无核白失水50%时未褐变与褐变的相比,在快速脱水组筛选出718个差异表达基因,慢速脱水组2 259个。将上述基因进行GO功能富集和KEGG富集分析后,筛选出43个膜脂代谢相关的差异基因,归类于5种代谢途径。从已获得的差异基因中最终筛选出乙醛脱氢酶7B4（Aldehyde Dehydrogenase7B4,ALDH7B4）、双半乳糖甘油二酯合成酶1（Digalactose Diglycerol Synthetase1,DGD1）、脂氧合酶（Lipoxygenase,LOX）、磷脂磷酸水解酶2（Lipid Phosphate Phosphatase2,LPP2）、二酰基甘油激酶5（Diacylglycerol Kinase5,DGK5）、非特异性磷脂酶C4（Non-specific Phospholipase C4,NPC4）、磷脂酶Dα1（Phospholipase Dα1,PLDα1）7个膜脂代谢相关的关键基因,经qRT-PCR验证,基因表达趋势与转录组测序结果基本一致。结果表明,膜脂降解代谢相关基因表达量变化对无核白脱水褐变有一定影响。     

Feature sequencing in the rapid design system using a genetic algorithm

This paper addresses the feature sequencing problem in the Rapid Design System (RDS). The RDS is a feature-based design system that integrates product design and process planning. An important issue in feature-based process planning for machined parts is the order in which material is removed to form the resultant part. The order, or sequence, is partially dependent on the geometric relationships between features. The sequence affects the safety, the time it takes to machine the part, and the quality of the finished part. The sequence of material removal depends on two types of relations between features: (1) intersections and (2) interfeature associations. Both types of relations compound the search for an optimal sequence of material removal. Therefore, the research problem has been the discovery and development of a genetic algorithm (GA) that efficiently searches the solution space for all possible sequences and identifies the best sequences in terms of safety, time and quality.