The efficiency of pooling mRNA in microarray experiments

In a microarray experiment, messenger RNA samples are oftentimes pooled across subjects out of necessity, or in an effort to reduce the effect of biological variation. A basic problem in such experiments is to estimate the nominal expression levels of a large number of genes. Pooling samples will affect expression estimation, but the exact effects are not yet known as the approach has not been systematically studied in this context. We consider how mRNA pooling affects expression estimates by assessing the finite-sample performance of different estimators for designs with and without pooling. Conditions under which it is advantageous to pool mRNA are defined; and general properties of estimates from both pooled and non-pooled designs are derived under these conditions. A formula is given for the total number of subjects and arrays required in a pooled experiment to obtain gene expression estimates and confidence intervals comparable to those obtained from the no-pooling case. The formula demonstrates that by pooling a perhaps increased number of subjects, one can decrease the number of arrays required in an experiment without a loss of precision. The assumptions that facilitate derivation of this formula are considered using data from a quantitative real-time PCR experiment. The calculations are not specific to one particular method of quantifying gene expression as they assume only that a single, normalized, estimate of expression is obtained for each gene. As such, the results should be generally applicable to a number of technologies provided sufficient pre-processing and normalization methods are available and applied.     

Toxicology and genetic toxicology in the new era of "toxicogenomics": impact of "-omics" technologies.

The unprecedented advances in molecular biology during the last two decades have resulted in a dramatic increase in knowledge about gene structure and function, an immense database of genetic sequence information, and an impressive set of efficient new technologies for monitoring genetic sequences, genetic variation, and global functional gene expression. These advances have led to a new sub-discipline of toxicology: "toxicogenomics". We define toxicogenomics as "the study of the relationship between the structure and activity of the genome (the cellular complement of genes) and the adverse biological effects of exogenous agents". This broad definition encompasses most of the variations in the current usage of this term, and in its broadest sense includes studies of the cellular products controlled by the genome (messenger RNAs, proteins, metabolites, etc.). The new "global" methods of measuring families of cellular molecules, such as RNA, proteins, and intermediary metabolites have been termed "-omic" technologies, based on their ability to characterize all, or most, members of a family of molecules in a single analysis. With these new tools, we can now obtain complete assessments of the functional activity of biochemical pathways, and of the structural genetic (sequence) differences among individuals and species, that were previously unattainable. These powerful new methods of high-throughput and multi-endpoint analysis include gene expression arrays that will soon permit the simultaneous measurement of the expression of all human genes on a single "chip". Likewise, there are powerful new methods for protein analysis (proteomics: the study of the complement of proteins in the cell) and for analysis of cellular small molecules (metabonomics: the study of the cellular metabolites formed and degraded under genetic control). This will likely be extended in the near future to other important classes of biomolecules such as lipids, carbohydrates, etc. These assays provide a general capability for global assessment of many classes of cellular molecules, providing new approaches to assessing functional cellular alterations. These new methods have already facilitated significant advances in our understanding of the molecular responses to cell and tissue damage, and of perturbations in functional cellular systems.As a result of this rapidly changing scientific environment, regulatory and industrial toxicology practice is poised to undergo dramatic change during the next decade. These advances present exciting opportunities for improved methods of identifying and evaluating potential human and environmental toxicants, and of monitoring the effects of exposures to these toxicants. These advances also present distinct challenges. For example, the significance of specific changes and the performance characteristics of new methods must be fully understood to avoid misinterpretation of data that could lead to inappropriate conclusions about the toxicity of a chemical or a mechanism of action. We discuss the likely impact of these advances on the fields of general and genetic toxicology, and risk assessment. We anticipate that these new technologies will (1) lead to new families of biomarkers that permit characterization and efficient monitoring of cellular perturbations, (2) provide an increased understanding of the influence of genetic variation on toxicological outcomes, and (3) allow definition of environmental causes of genetic alterations and their relationship to human disease. The broad application of these new approaches will likely erase the current distinctions among the fields of toxicology, pathology, genetic toxicology, and molecular genetics. Instead, a new integrated approach will likely emerge that involves a comprehensive understanding of genetic control of cellular functions, and of cellular responses to alterations in normal molecular structure and function.     

Insights into the molecular basis of social behaviour from studies on the honeybee, <Emphasis Type="Italic">Apis mellifera</Emphasis>

The honeybee, Apis mellifera, has been the most important insect species for the study of social behaviour. With the recent release of its genome sequence, the honeybee has emerged as an excellent model for molecular studies of social behaviour. A key feature of eusocial species is a complex division of labour. Adult honeybees perform a series of tasks in the hive when they are young and then shift to foraging for nectar or pollen outside the hive when they are 2–3 weeks of age. This transition from working in the hive to foraging involves changes in the expression of thousands of genes. In this review, we focus first on recent advances in understanding of the widespread changes in gene activity that accompany the transition to foraging. Thereafter, we examine three genes in particular, foraging, malvolio and vitellogenin, all implicated in this striking behavioural change in the life of the honeybee.     

Microarrays and the relationship of mRNA variation to protein variation during the cell cycle

Microarray analyses have led to the postulated existence and identification of numerous genes that are believed to be expressed and presumably to act in a cell-cycle-specific manner because their expression varies during the cell cycle. It is important to see how protein variation can be produced from mRNA variation. We have calculated the protein content throughout the cell cycle resulting from cell-cycle-specific mRNA expression, and compared the result to protein content resulting from constant, cell-cycle independent, mRNA expression. For stable proteins, cell-cycle-specific mRNA expression leads to a maximum 2-fold change in protein content compared to proteins synthesized from constantly expressed mRNA. More realistic sinusoidal patterns of mRNA expression exhibit much smaller ratios of 1.25 or lower, even for extremely large amplitudes in mRNA expression. For unstable proteins that have a cycle-independent half-life, only at extremely short protein half-lives does mRNA variation have a significant impact on variation of protein content during the division cycle. We also apply these findings to proteins with a cycle-specific decay pattern. mRNA variations during the eukaryotic division cycle variation of mRNA during the cell cycle can have only a minimal affect on the variation of protein content during the cell cycle. We conclude that mRNA variations during the division cycle, as measured by microarrays, cannot by themselves, identify cycle-specific functions related to protein variations.     

Chronomics of Pressure Overload–Induced Cardiac Hypertrophy in Mice Reveals Altered Day/Night Gene Expression and Biomarkers of Heart Disease

There is critical demand in contemporary medicine for gene expression markers in all areas of human disease, for early detection of disease, classification, prognosis, and response to therapy. The integrity of circadian gene expression underlies cardiovascular health and disease; however time-of-day profiling in heart disease has never been examined. We hypothesized that a time-of-day chronomic approach using samples collected across 24-h cycles and analyzed by microarrays and bioinformatics advances contemporary approaches, because it includes sleep-time and/or wake-time molecular responses. As proof of concept, we demonstrate the value of this approach in cardiovascular disease using a murine Transverse Aortic Constriction (TAC) model of pressure overload–induced cardiac hypertrophy in mice. First, microarrays and a novel algorithm termed DeltaGene were used to identify time-of-day differences in gene expression in cardiac hypertrophy 8 wks post-TAC. The top 300 candidates were further analyzed using knowledge-based platforms, paring the list to 20 candidates, which were then validated by real-time polymerase chain reaction (RTPCR). Next, we tested whether the time-of-day gene expression profiles could be indicative of disease progression by comparing the 1- vs. 8-wk TAC. Lastly, since protein expression is functionally relevant, we monitored time-of-day cycling for the analogous cardiac proteins. This approach is generally applicable and can lead to new understanding of disease. (Author correspondence: tmartino@uoguelph.ca)     

人类癌组织中端粒酶活性与p16基因表达的相关性

端粒酶是一种由RNA和蛋白质组成的RNA酶,依其自身序列逆转录合成端粒序列并添加到染色体末端,以保证细胞分裂的稳定性。近年来的研究已证实端粒酶的激活是许多恶性肿瘤发生的先决条件。p16基因作为一种重要的抑癌基因,其编码产物P16蛋白可通过p16-cyclinD/CDK-pRB途径调控细胞周期。在多种肿瘤中均出现p16基因表达异常,其表达缺失与人类肿瘤的发生发展关系密切。就端粒酶活性与p16基因表达在人类癌组织中的相关性及其可能作用机制进行总结分析。     

Global gene expression during the human organogenesis: from transcription profiles to function predictions

Human embryogenesis includes an integrated set of complex yet coordinated development of different organs and tissues, which is regulated by the spatiotemporal expression of many genes. Deciphering the gene regulation profile is essential for understanding the molecular basis of human embryo development. While molecular and genetic studies in mouse have served as a valuable tool to understand mammalian development, significant differences exists in human and mouse development at morphological and genomic levels. Thus it is important to carry out research directly on human embryonic development. Here we will review some recent studies on gene regulation during human embryogenesis with particular focus on the period of organogenesis, which had not been well studied previously. We will highlight a gene expression database of human embryos from the 4(th) to the 9(th) week. The analysis of gene regulation during this period reveals that genes functioning in a given developmental process tend to be coordinately regulated during human embryogenesis. This feature allows us to use this database to identify new genes important for a particular developmental process/pathway and deduce the potential function of a novel gene during organogenesis. Such a gene expression atlas should serve as an important resource for molecular study of human development and pathogenesis.     

p53蛋白多肽片段在大肠杆菌中的表达

在所有研究过的人体肿瘤组织或细胞中,ｐ５３似乎是突变频率最高的一个基因,研究和检测ｐ５３基因及其编码产物的变化将具有重要的意义。我们将野生型ｐ５３基因编码区３’端７０３ｂｐ的ｃＤ－ＮＡ片段插入到大肠杆菌表达载体ｐＢＶ２２０中,得到了一个重组体表达质粒ｐＲＲ３３,经热诱导表达,用ＳＤＳ－ＰＡＧＥ和Ｗｅｓｔｅｒｎ印迹法证实ｐ５３蛋白多肽在大肠杆菌中得到了表达,它不仅可用于抗ｐ５３蛋白抗体的制备,而且也可用于对ｐ５３蛋白羧基端多肽功能的研究。     

Genes associated with the end of dormancy in grapes

A grape bud EST library was constructed and 4,270 ESTs sequenced. The library clones were arrayed for the purpose of investigating the level of gene expression over time, particularly leading up to the buds release from dormancy. The arrays were hybridized with P³³-labeled probes produced from samples of buds collected at weekly intervals. These probes covered the time from 9 weeks prior to bud burst until just after the emergence of the shoots. Expression patterns from these genes have been examined. It was found that 74% of the genes in the data set were homologous to known proteins. Genes were then assigned to functional categories according to their primary BLAST match. Of these 13% were involved with photosynthesis, 13% with disease resistance and defense, 5% energy, 12% metabolism, 20% protein production and processing, 25% cell structure and plant growth and the remaining 12% were unclassified The expression pattern of a selection of candidate genes retrieved from literature previously reporting an association with dormancy changes was assessed. On closer examination most of these genes relate to the oxidative processes and stress responses within the cell. The results of this study show that even in the dormant state, gene expression in the buds is high.     

癌基因iASPP的克隆、表达与纯化

iASPP是新近发现的高度保守的p53相关基因,其蛋白产物定位于细胞核内,具有结合NFκBp65亚基和p53功能,进而抑制NFκB的转录调节和p53对凋亡的调节功能。利用RTPCR方法从人白血病细胞系U937中克隆出癌基因iASPP,将其克隆至原核表达载体pET28a(+)中,成功构建iASPP表达载体PIAF,重组质粒读码框和序列与预期一致。在IPTG诱导下,重组载体大肠杆菌Rosetta(DE3)菌株,表达产物经SDSPAGE和Westernblot方法分析证实系iASPP融合蛋白。利用Ni离子鳌合层析的方法纯化iASPP融合蛋白,经SDSPAGE鉴定其纯度超过80%。     

The transport of ions across plant cell members

Procedures developes to transform the genome of animasl have improves our fundamental understanding of the mechanisms of gene expression. Techniques in molecular biology are now allowing transformation with foreign genes that code for proteins of high value in this exciting area, and some prospects for this technology in the future.