New developments in the analysis of gene expression

An understanding of the relationship between gene expression, protein expression and the influences of genetic responses upon gene function is vital before we can understand the complexity of genomes. Traditional methods for the study of gene expression are limited to studying small groups of genes at a time and a source of pure starting material has been difficult to obtain. Recent technological advances have enabled large numbers of genes, from specific cell populations, to be studied in a single experiment. Laser capture microdissection (LCM) and microarray technology are providing the next revolution in the study of gene expression. LCM-based molecular analysis of histopathological lesions can be applied to any disease process that is accessible through tissue sampling. Examples include: (i) mapping the field of genetic changes associated with oxidative stress; (ii) analysis of gene expression patterns in atherosclerotic tissues, sites of inflammation and Alzheimer's disease plaques; (iii) infectious micro-organism diagnosis; and (iv) typing of cells within disease foci. Microarray hybridisation glass chips spotted with sets of genes can then be used to obtain a molecular fingerprint of gene expression in the microdissected cells. The variation of expressed genes or alterations in the cellular DNA that correlate with a particular disease state can be compared within or between individual samples. The identification of gene expression patterns may provide vital information for the understanding of the disease process and may contribute to diagnostic decisions and therapies tailored to the individual patient. Molecules found to be associated with defined pathological lesions may provide clues about new therapeutic targets in the future.     

New developments in the trace analysis of organic water pollutants

Challenging tasks, increasing demands, and new generations of powerful analytical instruments initiated considerable progress in aquatic environmental analysis and led to a considerable improvement of analytical performance during the last few years. The ever growing number of emerging pollutants is tackled by specific and highly sensitive analytical methods with detection limits of a few nanogram per liter and even lower. Wide-scope monitoring techniques and multiclass and multiresidue analysis allow for the simultaneous determination of hundreds of compounds. The high mass resolution capability and mass accuracy of advanced mass spectrometric instruments, i.e., time-of-flight (TOF) MS or Fourier transform (FT)–Orbitrap MS, enable combined target and non-target analysis, including the identification of metabolites and abiotic degradation products. This minireview highlights some of the most recent developments in the trace analysis of important organic water pollutants and focuses on some specific groups of emerging contaminants, i.e., pharmaceuticals, flame retardants, disinfection by-products, surfactants, per- and polyfluorinated compounds, benzotriazoles, and benzothiazoles, as well as on the identification of transformation products and on non-target analysis. References were selected according to their exemplary and innovative character and to their practical relevance.     

New experimental and computational approaches to the analysis of gene expression.

Public and private EST (Expressed Sequence Tag) programs provide access to a large number of ESTs from a number of plant species, including Arabidopsis, corn, soybean, rice, wheat. In addition to the homology of each EST to genes in GenBank, information about homology to all other ESTs in the data base can be obtained. To estimate expression levels of genes represented in the DuPont EST data base we count the number of times each gene has been seen in different cDNA libraries, from different tissues, developmental stages or induction conditions. This quantitation of message levels is quite accurate for highly expressed messages and, unlike conventional Northern blots, allows comparison of expression levels between different genes. Lists of most highly expresses genes in different libraries can be compiled. Also, if EST data is available for cDNA libraries derived from different developmental stages, gene expression profiles across development can be assembled. We present an example of such a profile for soybean seed development. Gene expression data obtained from Electronic Northern analysis can be confirmed and extended beyond the realm of highly expressed genes by using high density DNA arrays. The ESTs identified as interesting can be arrayed on nylon or glass and probed with total labeled cDNA first strand from the tissue of interest. Two-color fluorescent labeling allows accurate mRNA ratio measurements. We are currently using the DNA array technology to study chemical induction of gene expression and the biosynthesis of oil, carbohydrate and protein in developing seeds.     

'Shocking' developments in chick embryology: electroporation and in ovo gene expression

Efficient gene transfer by electroporation of chick embryos in ovo has allowed the development of new approaches to the analysis of gene regulation, function and expression, creating an exciting opportunity to build upon the classical manipulative advantages of the chick embryonic system. This method is applicable to other vertebrate embryos and is an important tool with which to address cell and developmental biology questions. Here we describe the technical aspects of in ovo electroporation, its different applications and future perspectives.     

New developments in museum-based informatics and applications in biodiversity analysis

Information from natural history collections (NHCs) about the diversity, taxonomy and historical distributions of species worldwide is becoming increasingly available over the Internet. In light of this relatively new and rapidly increasing resource, we critically review its utility and limitations for addressing a diverse array of applications. When integrated with spatial environmental data, NHC data can be used to study a broad range of topics, from aspects of ecological and evolutionary theory, to applications in conservation, agriculture and human health. There are challenges inherent to using NHC data, such as taxonomic inaccuracies and biases in the spatial coverage of data, which require consideration. Promising research frontiers include the integration of NHC data with information from comparative genomics and phylogenetics, and stronger connections between the environmental analysis of NHC data and experimental and field-based tests of hypotheses.     

New developments in silvichemicals

A discussion of the activities of Crown Zellerbach Corporation in the field of developing, producing and worldwide marketing of pure chemicals of commerce from the forest, including comments on some new chemicals being developed.     

New developments in cytogenetics

Novel methods allowing to analyze the human genome make it possible to assess old questions such as the molecular basis of structural chromosome anomalies and the diathesis to aneuploidy. The architecture of the human genome as unravelled by the human genome sequencing project allows to explain the recurrence of microdeletions and microduplications caused by a non allelic homologous recombination involving segmental duplications created during the evolution of primates. This structural feature of the human genome is associated with a novel class of genetic diseases called genomic disorders as opposed to genetic diseases due to gene mutations. The study of the parental and cellular origin of aneuploidy shed new light on the different mechanisms controlling meiosis in man and woman. In addition it contributes to define the role of maternal age and genetic recombination on the behavior of chromosomes during meiosis. These new data greatly contribute to our understanding of human chromosomal diseases.     

New developments in the treatment of zygomycosis

Zygomycosis is the third most common cause of systemic fungal infection after candidiasis and aspergillosis. Treatment with all available modalities is often the best approach. Amphotericin B (AmB) and its lipid formulations are the mainstay of therapy. Liposomal AmB (L-AmB) penetrates best in the brain. The new azole, posaconazole, has been shown to be effective as salvage treatment, but existing studies do not support its use as first-line monotherapy. Some in vitro and animal model studies have shown synergy between the polyenes and the echinocandins. An ongoing clinical study is comparing the iron chelator deferasirox in combination with L-AmB versus L-AmB monotherapy. Other adjunctive treatments, such as granulocyte colony-stimulating factor and granulocyte-macrophage colony-stimulating factor, are under investigation.     

Principal-oscillation-pattern analysis of gene expression

Principal-oscillation-pattern (POP) analysis is a multivariate and systematic technique for identifying the dynamic characteristics of a system from time-series data. In this study, we demonstrate the first application of POP analysis to genome-wide time-series gene-expression data. We use POP analysis to infer oscillation patterns in gene expression. Typically, a genomic system matrix cannot be directly estimated because the number of genes is usually much larger than the number of time points in a genomic study. Thus, we first identify the POPs of the eigen-genomic system that consists of the first few significant eigengenes obtained by singular value decomposition. By using the linear relationship between eigengenes and genes, we then infer the POPs of the genes. Both simulation data and real-world data are used in this study to demonstrate the applicability of POP analysis to genomic data. We show that POP analysis not only compares favorably with experiments and existing computational methods, but that it also provides complementary information relative to other approaches.     

小片段基因表达分析（MAGE）

人类基因组计划即将完成 ,应运而生的就是研究基因的转录和功能。为了解决如此复杂的问题 ,在技术上就必须有所创新。1 998年Ｒｙｏ等[1] 提出了小片断基因表达分析(Ｍｉｎｉ -ｆｒａｇｍｅｎｔＡｎａｌｙｓｉｓｏｆＧｅｎｅＥｘｐｒｅｓｓｉｏｎ ,ＭＡＧＥ)技术 ,像基因系列表达分析 (ＳｅｒｉａｌＡｎａｌｙｓｉｓｏｆＧｅｎｅＥｘｐｒｅｓｓｉｏｎ ,ＳＡＧＥ)一样 ,能同时对成千上万个转录产物进行研究。1　ＭＡＧＥ的原理和实验路线1 1　ＭＡＧＥ的原理ＭＡＧＥ与ＳＡＧＥ的主要依据是相同的。第一 ,一个 1 2ｂｐ寡核苷酸的序列标签 (…     

EST-based analysis of gene expression in the porcine brain

Since pig is an important livestock species worldwide, its gene expression has been investigated intensively, but rarely in brain. In order to study gene expression profiles in the pig central nervous system, we sequenced and analyzed 43,122 highquality 5’ end expressed sequence tags (ESTs) from porcine cerebellum, cortex cerebrum, and brain stem cDNA libraries, involving several different prenatal and postnatal developmental stages. The initial ESTs were assembled into 16,101 clusters and compared to protein and nucleic acid databases in GenBank. Of these sequences, 30.6% clusters matched protein databases and represented function known sequences; 75.1% had significant hits to nucleic acid databases and partial represented known function; 73.3% matched known porcine ESTs; and 21.5% had no matches to any known sequences in GenBank. We used the categories defined by the Gene Ontology to survey gene expression in the porcine brain.     

Single-cell analysis of gene expression in the nervous system

The characteristic functions of tissues and organs results from the integrated activity of individual cells. Nowhere is this more evident than in the nervous system, where the activities of single neurons communicating via electrical and chemical signals mediate complex functions, such as learning and memory. The past decade has seen an explosion in the identification of genes encoding proteins, such as voltage-gated channels and neurotransmitter receptors, responsible for neuronal excitability. These studies have highlighted the fact that even within a neuroanatomically defined region, the coexistence of multiple cell types makes it difficult, if not impossible, to correlate patterns of gene expression with function The recent development of techniques sensitive enough to, study gene expression at the single-cell level promises to break this bottleneck to our further understanding. Using examples taken from our own laboratories and the work of others, we review these techniques, their application, and discuss some of the difficulties associated with the interpretation of the data.     

Microarray analysis of gene expression in lupus

Recent advances in the study of global patterns of gene expression with the use of microarray technology, coupled with data analysis using sophisticated statistical algorithms, have provided new insights into pathogenic mechanisms of disease. Complementary and reproducible data from multiple laboratories have documented the feasibility of analysis of heterogeneous populations of peripheral blood mononuclear cells from patients with rheumatic diseases through use of this powerful technology. Although some patterns of gene expression, including increased expression of immune system cell surface activation molecules, confirm previous data obtained with other techniques, some novel genes that are differentially expressed have been identified. Most interesting is the dominant pattern of interferon-induced gene expression detected among blood mononuclear cells from patients with systemic lupus erythematosus and juvenile dermatomyositis. These data are consistent with longstanding observations indicating increased circulating interferon-alpha in the blood of patients with active lupus, but draw attention to the dominance of the interferon pathway in the hierarchy of gene expression pathways implicated in systemic autoimmunity.