A preprocessing method for inferring genetic interaction from gene expression data using Boolean algorithm

Unknown genetic regulation mechanisms are expected to be discovered by information technology using large amount of biological data especially for gene expression data. In this study, we propose a novel inferring method for genetic interactions that combines our original preprocessing method and the Boolean algorithm. First, the performance of our method was evaluated using artificial data. The results showed that our method was able to infer genetic interactions with high specificity (specificity=0.629). Then, using our method, the genetic interaction was inferred from the experimental time course data collected using microarray on 69 genes of cell cycle for Saccharomyces cerevisiae. Our method estimated about 80% of all genetic interactions in Kyoto Encyclopedia Genes and Genomes (KEGG) for these genes. Furthermore, our method was able to infer several other genetic interactions that are not included in KEGG but whose existence is supported by other biological reports.     

Immunoglobulin E epitope mapping by microarray immunoassay reveals differences in immune response to genetic variants of caseins from different ruminant species

The allergenicity of the caseins (CN), one of the major allergens in cow milk, is well characterized and their immunoglobulin E (IgE)-binding epitopes have been identified. However, investigations about the allergenic potential of the genetic variants occurring in the caseins are lacking. Therefore, this study determined the influence of the genetic polymorphism on IgE binding to epitopes of bovine casein variants. Furthermore, differences in IgE binding between epitopes of goats and water buffaloes were analyzed. A set of 187 peptides, covering the previously identified sequential IgE-binding epitopes of α_S1-, α_S2-, β-, and κ-CN variants from cows and the corresponding homologous peptides of water buffaloes and goats, were synthesized and tested by means of peptide microarray for IgE binding, using sera from 16 cow milk-sensitized individuals. Seven of the 16 sera samples showed positive signals on microarrays and were included in this study. In 5 α_S1-CN variants (A, B, C, E, and I), the AA substitution or deletion affected the immunoreactivity of epitopes AA 4 to 23, AA 17 to 36, AA 83 to 102, AA 173 to 192, and AA 175 to 194, as well as of the variant-specific peptides AA 184 to 196, AA 187 to 199, AA 174 to 193, and AA 179 to 198, which were found to resist gastrointestinal digestion. Variation in IgE binding was further detected for peptides AA 103 to 123 and AA 108 to 129 of 3 β-CN variants (A¹, A², and B). The majority of sera showed IgE binding to α_S1-CN peptides of cows and the homologous counterpart of goats and water buffaloes. However, α_S1- and β-CN epitopes from goats and water buffaloes had lower immunoreactivity than those of cows, but, in some cases, higher or exclusive IgE binding was observed. The results of this study indicate that genetic variants of the caseins differ in their allergenicity. This might be useful in the search for a suitable protein source for cow milk-allergic patients. In addition, milk from water buffaloes and goats harbor an allergenic potential due to cross-reactivity of IgE antibodies with cow milk caseins and are, therefore, not an acceptable alternative in the nutrition of cow milk-allergic patients.     

Unveiling the molecular basis of intrinsic skin aging(1)

The process of skin aging is a combination of an extrinsic and intrinsic aspect, and knowing the molecular changes underlying both is a prerequisite to being able to effectively counter it. However, despite its importance for a deeper understanding of skin aging as a whole, the process of intrinsic skin aging in particular has barely been investigated. In this study, the molecular changes of intrinsic skin aging were analyzed by applying 'Serial Analysis of Gene Expression' (SAGE(TM)) to skin biopsies of young and aged donors. The analysis resulted in several hundred differentially expressed genes with varying statistical significance. Of these, several genes were identified that either have never been described in skin aging before (e.g. APP) or have no identified function, e.g. EST sequences. This is the first time that intrinsic skin aging has been analyzed in such a comprehensive manner, offering a new and partially unexpected set of target genes that have to be analyzed in more detail in terms of their contribution to the skin aging process.     

Functional genomics of commercial baker's yeasts that have different abilities for sugar utilization and high-sucrose tolerance under different sugar conditions

In the modern baking industry, high-sucrose-tolerant (HS) and maltose-utilizing (LS) yeast were developed using breeding techniques and are now used commercially. Sugar utilization and high-sucrose tolerance differ significantly between HS and LS yeasts. We analysed the gene expression profiles of HS and LS yeasts under different sucrose conditions in order to determine their basic physiology. Two-way hierarchical clustering was performed to obtain the overall patterns of gene expression. The clustering clearly showed that the gene expression patterns of LS yeast differed from those of HS yeast. Quality threshold clustering was used to identify the gene clusters containing upregulated genes (cluster 1) and downregulated genes (cluster 2) under high-sucrose conditions. Clusters 1 and 2 contained numerous genes involved in carbon and nitrogen metabolism, respectively. The expression level of the genes involved in the metabolism of glycerol and trehalose, which are known to be osmoprotectants, in LS yeast was higher than that in HS yeast under sucrose concentrations of 5-40%. No clear correlation was found between the expression level of the genes involved in the biosynthesis of the osmoprotectants and the intracellular contents of the osmoprotectants. The present gene expression data were compared with data previously reported in a comprehensive analysis of a gene deletion strain collection. Welch's t-test for this comparison showed that the relative growth rates of the deletion strains whose deletion occurred in genes belonging to cluster 1 were significantly higher than the average growth rates of all deletion strains.     

Presence of low concentrations of acetic acid improves yeast tolerance to hydroxymethylfurfural (HMF) and furfural

BackgroundHydrolysates derived from lignocellulosic material contain a complex mix of inhibitory compounds dependant on the type of biomass and the pre-treatment process employed. These inhibitors prevent the subsequent fermentation of available sugars by yeast into ethanol.ResultsInhibitory compounds normally work synergistically to reduce metabolic output, rates of budding and viability; however, it was observed in this study that the presence of weak acids actually improved tolerance to hydroxymethyl furfural (HMF) and furfural in Saccharomyces cerevisiae. The protective role of weak acids in HMF or furfural stressed cells was only apparent with relatively low concentrations of acetic acid (20 mM), however, there was an improvement in glucose utilisation and ethanol production when compared with HMF or furfural stressed cells. Focusing on HMF stressed cells quantitative trait loci (QTL) analysis identified a region on chromosome VI related to the enhanced tolerance to HMF in the presence of acetic acid. Two genes FET5 and HAC1 located in this region were up-regulated under the combined stress of acetic acid with HMF stress and null mutants exhibited a return to HMF sensitivity.ConclusionsPresence of acetic acid helps yeast cells overcome HMF stress, QTL analysis identified two genes on a loci on chromosome VI, knocking out these genes returns the cell to HMF sensitivity.     

总黄曲霉毒素ELISA定量检测方法的研制

为敏感、特异和快速地检测食品中总黄曲霉毒素的污染水平,在抗总黄曲霉毒素单克隆抗体的基础上,研制了间接竞争ELISA检测方法,包被抗原为AFB1-BSA,包被量为0.0625μgml,抗体工作浓度为1:1.6×106。该方法对黄曲霉毒素B+G标准品的最低检出浓度为0.13ngml,对样品的最低检出量为1.50μgkg。校正曲线的线性范围为0.26～20.00ngml,线性方程y=-0.4463x+0.3532(R2=0.9915);对黄曲霉毒素B+G50%的抑制浓度为2.08ngml;对玉米2个加标水平的平均回收率分别为94.56%和112.05%,对花生2个加标水平的平均回收率分别为87.50%和85.60%。该方法所用抗总黄曲霉毒素单克隆抗体对黄曲霉毒素B1、B2、G1、G2的交叉反应率分别为100%、57.5%、104%和19%,与其它真菌毒素无交叉反应。     

双波长生物芯片荧光检测数据归一化方法研究

基于总值归一化法,通过顺序形态变换实现双色荧光图像数据的校正,对双通道检测的2种不同波长的Cy3、Cy5荧光图像进行了背景分析和归一化系数计算,数据分析显示双色荧光图像背景分割准确,依据其计算双色荧光校正信号,能消除检测通道(PMT)等因素造成的差异.该方法也适用于多波长荧光数据归一化.     

Book Reviews

Book reviewed in this article: Against the Mainstream: The Selected Works of George Gerbner Edited by Michael Morgan. Global Complexity By John Urry. Framing the South: Hollywood, Television, and Race During the Civil Rights Struggle By Allison Graham. Crime and Local Television News: Dramatic, Breaking, and Live From the Scene By Jeremy H. Lipschultz and Michael L. Hilt. The 11 Myths of Media Violence By W. James Potter. Censorship Inc.: The Corporate Threat to Freedom of Speech By Lawrence Soley. Canonic Texts in Media Research: Are There Any? Should There Be? How About These? Edited by Elihu Katz, John Durham Peters, Tamar Liebes, & Avril Orloff.     

硅微喷阵列芯片的设计、制作与应用研究

介绍了一种用于制作生物微阵列的新型微喷阵列芯片。基于半导体光刻技术和干法刻蚀技术,成功制作了喷孔外侧含有间隙环的硅微喷阵列芯片,解决了溶液进样难、微阵列样品点缺失、样品点漂移以及液体回流等问题。在5 kPa气压驱动下,该芯片中的样品能在3.4 mm×3.4 mm的玻璃片上制成5×5样品微阵列,25个点的直径平均值为356μm,直径的变异系数(25个点直径的标准偏差与算术平均值的比值)为2.8%。计算流体力学模拟结果和实验结果均表明,该微喷阵列芯片能快速、稳定地制作出样品点大小均一的微阵列,进一步推动了微阵列芯片的应用和发展。     

Politics As Usual,or Politics Unusual? Position Taking and Dialogue on Campaign Websites in the 2002 U.S. Elections

Many consider the World Wide Web to be nothing more than an additional medium alongside others in which established patterns of political behavior and information flows are played out anew; others contend that the special characteristics of the Web hold the potential to produce fundamentally different patterns of political behavior than those found offline. This article analyzes the occurrence of position taking and issue dialogue on campaign websites associated with a random sample of 200 races from the U.S. 2002 election cycle. Though this study found some similarities between online and offline campaigning, it also identified ways in which the individual messages and overall political information environment created by candidates and available to voters through the Web in 2002 did not conform to the usual patterns found in the offline world of print and broadcast communication.