对于核小体定位检测方法的比较研究

在真核细胞中,核小体是组成染色质的基本结构单位,是由DNA紧密缠绕在组蛋白八聚体上所形成的一个复合体结构。而DNA与组蛋白的结合并不是固定不变的,没有核小体结合的DNA区域易于各种调节蛋白的接近与结合。因此人们怀疑核小体的定位与基因的转录调节之间存在某种内在联系。对现行的核小体定位的检测方法进行了归类,并对其优缺点进行了分析整理。对更深入的探索核小体定位检测方法的应用有一定意义。     

Graph algorithms for DNA sequencing – origins,current models and the future

With the ubiquitous presence of next-generation sequencing in modern biological, genetic, pharmaceutical and medical research, not everyone pays attention to the underlying computational methods. Even fewer researchers know what were the origins of the current models for DNA assembly. We present original graph models used in DNA sequencing by hybridization, discuss their properties and connections between them. We also explain how these graph models evolved to adapt to the characteristics of next-generation sequencing. Moreover, we present a practical comparison of state-of-the-art DNA de novo assembly tools representing these transformed models, i.e. overlap and decomposition-based graphs. Even though the competition is tough, some assemblers perform better and certainly large differences may be observed in hardware resources utilization. Finally, we outline the most important trends in the sequencing field, and try to predict their impact on the computational models in the future.     

Convex games with an infinite number of players and sequencing situations

In this paper we study convex games with an infinite countable set of agents and provide characterizations of this class of games. To do so, and in order to overcome some shortcomings related to the difficulty of dealing with infinite orderings, we need to use a continuity property. Infinite sequencing situations where the number of jobs is infinite countable can be related to convex cooperative TU games. It is shown that some allocations turn out to be extreme points of the core of an infinite sequencing game.     

Using Unfold‐PCA for batch‐to‐batch start‐up process understanding and steady‐state identification in a sequencing batch reactor

In chemical and biochemical processes, steady‐state models are widely used for process assessment, control and optimisation. In these models, parameter adjustment requires data collected under nearly steady‐state conditions. Several approaches have been developed for steady‐state identification (SSID) in continuous processes, but no attempt has been made to adapt them to the singularities of batch processes. The main aim of this paper is to propose an automated method based on batch‐wise unfolding of the three‐way batch process data followed by a principal component analysis (Unfold‐PCA) in combination with the methodology of Brown and Rhinehart 2 for SSID. A second goal of this paper is to illustrate how by using Unfold‐PCA, process understanding can be gained from the batch‐to‐batch start‐ups and transitions data analysis. The potential of the proposed methodology is illustrated using historical data from a laboratory‐scale sequencing batch reactor (SBR) operated for enhanced biological phosphorus removal (EBPR). The results demonstrate that the proposed approach can be efficiently used to detect when the batches reach the steady‐state condition, to interpret the overall batch‐to‐batch process evolution and also to isolate the causes of changes between batches using contribution plots. Copyright © 2007 John Wiley & Sons, Ltd.     

生物电化学系统降解多环芳烃萘及微生物群落研究

采用单室空气阴极微生物燃料电池(MFC)反应器构型, 以不同浓度萘为基底物质, 考察MFC的产电性能、 萘降解率、 化学需氧量(COD)和总有机碳含量(TOC)降解率及MFC阴阳极微生物活性和多样性. 结果表明, 循环伏安曲线受不同浓度萘的影响变化较为明显, 随着萘浓度的增大, 最大功率密度呈下降趋势, 且萘对MFC的阴极电极电势影响较大; 当萘的浓度为15 mg/L时, MFC最大功率密度可达(645.841±28.08) mW/m ²; 对萘的降解率高达100%, 且MFC对COD和TOC的降解率随着萘浓度的提高而增大, 但是增大的速率逐渐减小. 对MFC阳极微生物膜进行高通量测序发现, Geobacter是优势菌属, 相对丰度达81%, 阴极主要以Aquamicrobium为主.     

Simulating the Monty Hall problem in a DNA sequencing machine

The Monty Hall problem is a decision problem with an answer that is surprisingly counter-intuitive yet provably correct. Here we simulate and prove this decision in a high-throughput DNA sequencing machine, using a simple encoding. All possible scenarios are represented by DNA oligonucleotides, and gameplay decisions are implemented by sequencing these oligonucleotides from specific positions, with a single run simulating more than 12,000,000 independent games. This work highlights high-throughput DNA sequencing as a new tool that could extend existing capabilities and enable new encoding schemes for problems in DNA computing.     

Laser‐Induced Fluorometry for Capillary Electrophoresis

Laser‐induced fluorometry (LIF) has achieved the detection of single molecules, which ranks it among the most sensitive of detection techniques, whereas capillary electrophoresis (CE) is known as a powerful separation method with resolution that is beyond the reach of many other types of chromatography. Therefore, a coupling of LIF with CE has established an unrivaled analytical technique in terms of sensitivity and resolution. CE‐LIF has demonstrated excellent performance in bioanalytical chemistry for the high‐resolution separation and highly sensitive detection of DNAs, proteins, and small bioactive molecules. This review describes the CE‐LIF methods developed by the author's group that include indirect and direct detection using diode lasers, post‐column derivatization, and Hadamard transformation, as well as applications to the binding assays of specific DNA immunoassays of proteins and to the determination of anticancer drugs.     

一款基于转录组差异基因表达分析的软件包——findDEG

【目的】随着二代测序技术的不断发展,转录组测序技术在许多物种里已被广泛地应用于基因差异表达分析和基因注释研究。现有的多种基因差异表达分析软件,分析步骤多而且复杂,不同分析方法其结果差别也较大,这给研究者分析实际数据带来了不少困难。为了简化基因差异表达分析的过程,利用现有的软件开发一个集成的软件包。【方法】针对Trinity、TopHat+Cufflinks和HISAT2+StringTie 3种比较成熟的基因差异表达分析流程,考虑研究对象有无参考基因组序列、样本数据是否有重复、单端还是双端测序、不同基因表达量的计算方法以及不同的基因差异表达显著性检验方法等因素,将多种转录组测序数据分析软件整合起来形成一个集成的软件包。【结果】 使用Perl语言开发了一个名为findDEG软件包用于转录组测序数据的基因差异表达分析。软件包共分为3个模块,即Trinity、TopHat+Cufflinks和HISAT2+StringTie模块。Trinity模块提供3种计算转录本表达量方法和4种差异表达基因显著性检验方法,TopHat+Cufflinks模块可供用户选择新版或旧版的Cufflinks分析方案,HISAT2+StringTie模块则只有一种分析方案。该软件包可以自由下载使用,其网址为http://www.bioseqdata.com/findDEG/findDEG.htm。采用新版和旧版的Cufflinks分析方案以及一种Trinity组合方法,分别对小叶杨在正常和干旱胁迫条件下的转录组数据进行了分析。结果两种Cufflinks方法分别识别出了53和33个差异表达基因,其中25个是相同的; Trinity方法识别了高达1 641个差异表达基因,其中与Cufflinks两种方法相同的分别有14和3个。【结论】 新开发的软件包findDEG有十多种基因差异表达分析方案可供选择,采用一键的方式进行数据计算分析,避免了中间环节参数输入和结果利用等操作步骤,使用方便。     

Venomics: unravelling the complexity of animal venoms with mass spectrometry

Animal venoms and toxins are now recognized as major sources of bioactive molecules that may be tomorrow's new drug leads. Their complexity and their potential as drug sources have been demonstrated by application of modern analytical technologies, which have revealed venoms to be vast peptide combinatorial libraries. Structural as well as pharmacological diversity is immense, and mass spectrometry is now one of the major investigative tools for the structural investigation of venom components. Recent advances in its use in the study of venom and toxins are reviewed. The application of mass spectrometry techniques to peptide toxin sequence determination by de novo sequencing is discussed in detail, in the light of the search for novel analgesic drugs. We also present the combined application of LC-MALDI separation with mass fingerprinting and ISD fragmentation for the determination of structural and pharmacological classes of peptides in complex spider venoms. This approach now serves as the basis for the full investigation of complex spider venom proteomes, in combination with cDNA analysis.