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At least 1,495 records · Page 83Linked to original sources
PubMed2003

Genome-wide patterns of expression in Drosophila pure species and hybrid males.

One of the most fundamental questions for understanding the origin of species is why genes that function to cause fertility in a pure-species genetic background fail to produce fertility in a hybrid genetic background. A related question is why the sex that is most often sterile or inviable in hybrids is the heterogametic (usually male) sex. In this survey, we have examined the extent and nature of differences in gene expression between fertile adult males of two Drosophila species and sterile hybrid males produced from crosses between these species. Using oligonucleotide microarrays and real-time quantitative polymerase chain reaction, we have identified and confirmed that differences in gene expression exist between pure species and hybrid males, and many of these differences are quantitative rather than qualitative. Furthermore, genes that are expressed primarily or exclusively in males, including several involved in spermatogenesis, are disproportionately misexpressed in hybrids, suggesting a possible genetic cause for their sterility.

Animals↗
PubMed2005

Methods for genome-wide analysis of gene expression changes in polyploids.

Polyploidy is an evolutionary innovation, providing extra sets of genetic material for phenotypic variation and adaptation. It is predicted that changes of gene expression by genetic and epigenetic mechanisms are responsible for novel variation in nascent and established polyploids (Liu and Wendel, 2002; Osborn et al., 2003; Pikaard, 2001). Studying gene expression changes in allopolyploids is more complicated than in autopolyploids, because allopolyploids contain more than two sets of genomes originating from divergent, but related, species. Here we describe two methods that are applicable to the genome-wide analysis of gene expression differences resulting from genome duplication in autopolyploids or interactions between homoeologous genomes in allopolyploids. First, we describe an amplified fragment length polymorphism (AFLP)--complementary DNA (cDNA) display method that allows the discrimination of homoeologous loci based on restriction polymorphisms between the progenitors. Second, we describe microarray analyses that can be used to compare gene expression differences between the allopolyploids and respective progenitors using appropriate experimental design and statistical analysis. We demonstrate the utility of these two complementary methods and discuss the pros and cons of using the methods to analyze gene expression changes in autopolyploids and allopolyploids. Furthermore, we describe these methods in general terms to be of wider applicability for comparative gene expression in a variety of evolutionary, genetic, biological, and physiological contexts.

Arabidopsis↗
PubMed2006

Functional genomic responses to cystic fibrosis transmembrane conductance regulator (CFTR) and CFTR(delta508) in the lung.

Cystic fibrosis (CF), a common lethal pulmonary disorder in Caucasians, is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) that disturbs fluid homeostasis and host defense in target organs. The effects of CFTR and delta508-CFTR were assessed in transgenic mice that 1) lack CFTR expression (Cftr-/-); 2) express the human delta508 CFTR (CFTR(delta508)); 3) overexpress the normal human CFTR (CFTR(tg)) in respiratory epithelial cells. Genes were selected from Affymetrix Murine Gene-Chips analysis and subjected to functional classification, k-means clustering, promoter cis-elements/modules searching, literature mining, and pathway exploring. Genomic responses to Cftr-/- were not corrected by expression of CFTR(delta508). Genes regulating host defense, inflammation, fluid and electrolyte transport were similarly altered in Cftr-/- and CFTR(delta508) mice. CFTR(delta508) induced a primary disturbance in expression of genes regulating redox and antioxidant systems. Genomic responses to CFTR(tg) were modest and were not associated with lung pathology. CFTR(tg) and CFTR(delta508) induced genes encoding heat shock proteins and other chaperones but did not activate the endoplasmic reticulum-associated degradation pathway. RNAs encoding proteins that directly interact with CFTR were identified in each of the CFTR mouse models, supporting the hypothesis that CFTR functions within a multiprotein complex whose members interact at the level of protein-protein interactions and gene expression. Promoters of genes influenced by CFTR shared common regulatory elements, suggesting that their co-expression may be mediated by shared regulatory mechanisms. Genes and pathways involved in the response to CFTR may be of interest as modifiers of CF.

Animals↗
PubMed2003

Searching for virulence Burkholderia pseudomallei genes by immunoscreening the lambda ZAPII expressed genomic library.

The lambdaZAP II expressed genomic library of B. pseudomallei was screened with pooled melioidosis serum preabsorbed with E. coli host cell. The positive clones were detected by using protein A-CDP-star chemiluminescence. All of 14 positive clones reacted with only the pooled absorbed melioidosis serum and not the pooled absorbed normal serum when tested with the plaque dot blot analysis. The expressed genes were detected by using a combination of immunoscreening, bioinformatics and molecular biology. At least six in vivo expressed genes were identified by this approach. Two were well known virulent genes, gmhA (a capsule biosynthetic gene) and bipD (type III secretion protein gene). Another two were genes coded for conserved hypothetical protein. The last two isolated genes were groEL (a chaperonine protein gene), and a gene encoding transmembrane protein.

Bacterial Proteins↗
PubMed2004

Genome-wide analysis of gene expression in neuroblastomas detected by mass screening.

Neuroblastoma (NB) is the most common extracranial solid tumor of childhood and the third most common pediatric cancer. Although numerous factors including patient age, disease stage and genetic abnormalities have been shown to be predictive of outcome, the mechanisms responsible for the highly variable clinical behavior of this tumor remain largely unknown. In order to gain new insights into the biology of this tumor, we performed microarray analysis and compared the gene expression patterns of NB detected by mass screening, characterized by highly probable spontaneous regression, versus stage 4 NB with poor prognosis. The bioinformatics analysis revealed a set of 19 discriminatory genes that may play a significant role in the natural progression of the disease. Validation of these results and further mechanistic studies would shed new light on the biology of tumor progression, and provide new tools to predict clinical outcome in children with NB.

Child, Preschool↗
PubMed2005

A novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes.

We have designed a novel transcriptome subtraction method for the genome-scale analysis of differential gene expression in highly complex eukaryotes, in which suppression subtractive hybridization (SSH) is performed first to enrich the target and, after exchange of adapters, negative subtraction chain (NSC) is then used to eliminate the remaining background. NSC evolved from differential subtraction chain (DSC). We designed novel adapters which make the subtraction system more robust. SSH and NSC were then combined to successfully detect differentially expressed genes in Solanum. The combined technique improves qualitatively upon SSH, the only commercially available transcriptome subtraction system, by detecting target genes in the middle abundance class, to which most differentially expressed genes in highly complex eukaryotes are expected to belong. The main advantage of the combined technique with SSH/NSC is its ability to isolate differentially expressed genes quickly and cost-efficiently from non-standard models, for those microarrays are unavailable.

Gene Expression Profiling↗
PubMed2006

DNA microarray wet lab simulation brings genomics into the high school curriculum.

We have developed a wet lab DNA microarray simulation as part of a complete DNA microarray module for high school students. The wet lab simulation has been field tested with high school students in Illinois and Maryland as well as in workshops with high school teachers from across the nation. Instead of using DNA, our simulation is based on pH indicators, which offer many ideal teaching characteristics. The simulation requires no specialized equipment, is very inexpensive, is very reliable, and takes very little preparation time. Student and teacher assessment data indicate the simulation is popular with both groups, and students show significant learning gains. We include many resources with this publication, including all prelab introductory materials (e.g., a paper microarray activity), the student handouts, teachers notes, and pre- and postassessment tools. We did not test the simulation on other student populations, but based on teacher feedback, the simulation also may fit well in community college and in introductory and nonmajors' college biology curricula.

Curriculum↗
PubMedDate not supplied

Elucidating endometrial function in the post-genomic era.

The post-genomic era has now arrived, and science and biology are on the threshold of a transition from understanding functions of single molecules and pathways in cells, tissues and whole organisms to understanding integrative systems. The endometrium is a dynamic tissue that responds to multiple stimuli, depending on physiological and environmental conditions, including steroid hormones, an implanting conceptus, withdrawal of steroid hormones, contraceptive steroids, selective steroid hormone receptor modulators, infection, transient cell populations, and metaplastic and neoplastic agents. High throughput technologies with regard to DNA, RNA and proteins are well positioned to enable a thorough understanding of the dynamic changes and integrative systems involved in endometrial maturation, desquamation, receptivity to implantation, infertility, pregnancy maintenance and failure, inflammation and infection, and malignant transformation. This monograph reviews some of the salient features of the new technologies and summarizes current information on endometrial biology derived from these approaches.

Embryo Implantation↗
PubMed2004

From ORFeome to biology: a functional genomics pipeline.

As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a human ORFeome resource and established a functional genomics and proteomics analysis pipeline to address the major topics in the post-genome-sequencing era: the identification of human genes and splice forms, and the determination of protein localization, activity, and interaction. Combined with the understanding of when and where gene products are expressed in normal and diseased conditions, we create information that is essential for understanding the interplay of genes and proteins in the complex biological network. We have implemented bioinformatics tools and databases that are suitable to store, analyze, and integrate the different types of data from high-throughput experiments and to include further annotation that is based on external information. All information is presented in a Web database (http://www.dkfz.de/LIFEdb). It is exploited for the identification of disease-relevant genes and proteins for diagnosis and therapy.

Animals↗
PubMed2005

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.

BACKGROUND: Alignments of homologous DNA sequences are crucial for comparative genomics and phylogenetic analysis. However, multiple alignment represents a computationally difficult problem. For protein-coding DNA sequences, it is more advantageous in terms of both speed and accuracy to align the amino-acid sequences specified by the DNA sequences rather than the DNA sequences themselves. Many implementations making use of this concept of "translated alignments" are incomplete in the sense that they require the user to manually translate the DNA sequences and to perform the amino-acid alignment. As such, they are not well suited to large-scale automated alignments of large and/or numerous DNA data sets. RESULTS: transAlign is an open-source Perl script that aligns protein-coding DNA sequences via their amino-acid translations to take advantage of the superior multiple-alignment capabilities and speed of an amino-acid alignment. It operates by translating each DNA sequence into its corresponding amino-acid sequence, passing the entire matrix to ClustalW for alignment, and then back-translating the resulting amino-acid alignment to derive the aligned DNA sequences. In the translation step, transAlign determines the optimal orientation and reading frame for each DNA sequence according to the desired genetic code. It also checks for apparent frame shifts in the DNA sequences and can handle frame-shifted sequences in one of three ways (delete, align as amino acids regardless, or profile align as DNA). As a set of comparative benchmarks derived from six protein-coding genes for mammals shows, the strategy implemented in transAlign always improves the speed and usually the apparent accuracy of the alignment of protein-coding DNA sequences. CONCLUSION: transAlign represents one of few full and cross-platform implementations of the concept of translated alignments. Both the advantages accruing from performing a translated alignment and the suite of user-definable options available in the program mean that transAlign is ideally suited for large-scale automated alignments of very large and/or very numerous protein-coding DNA data sets. However, the good performance offered by the program also translates to the alignment of any set of protein-coding sequences. transAlign, including the source code, is freely available at http://www.tierzucht.tum.de/Bininda-Emonds/ (under "Programs").

Algorithms↗
PubMed2007

Ontology annotation: mapping genomic regions to biological function.

With numerous whole genomes now in hand, and experimental data about genes and biological pathways on the increase, a systems approach to biological research is becoming essential. Ontologies provide a formal representation of knowledge that is amenable to computational as well as human analysis, an obvious underpinning of systems biology. Mapping function to gene products in the genome consists of two, somewhat intertwined enterprises: ontology building and ontology annotation. Ontology building is the formal representation of a domain of knowledge; ontology annotation is association of specific genomic regions (which we refer to simply as 'genes', including genes and their regulatory elements and products such as proteins and functional RNAs) to parts of the ontology. We consider two complementary representations of gene function: the Gene Ontology (GO) and pathway ontologies. GO represents function from the gene's eye view, in relation to a large and growing context of biological knowledge at all levels. Pathway ontologies represent function from the point of view of biochemical reactions and interactions, which are ordered into networks and causal cascades. The more mature GO provides an example of ontology annotation: how conclusions from the scientific literature and from evolutionary relationships are converted into formal statements about gene function. Annotations are made using a variety of different types of evidence, which can be used to estimate the relative reliability of different annotations.

Animals↗
PubMed2006

Genomic organization and expression analyses of putrescine pathway genes in soybean.

Putrescine is synthesized using one of two alternative pathways in plants, from arginine by arginine decarboxylase (ADC) or from ornithine by ornithine decarboxylase (ODC) and is catabolized by diamine oxidase (DAO). A survey of approximately 310,000 expressed sequenced tags (ESTs) in soybean EST libraries identified diverse representation of ADC, ODC, and DAO ESTs, with ODC being least frequent and DAO ESTs most abundant. Southern analysis suggested that ADC and ODC belong to small gene families, and DAO is the most divergent. Using three bacterial artificial chromosome (BAC) libraries, 26X genome equivalents, two common loci for ADC and DAO and one independent DAO locus were identified. ADC and DAO are physically linked in the soybean genome within approximately 150 kb. Identification of genomic regions encoding ODC proved difficult and required using additional BAC libraries, increasing genome coverage to approximately 40X. Using Real Time reverse transcriptase-polymerase chain reaction (RT-PCR), higher steady-state levels of ADC than ODC in roots, leaves, shoot apices, and dry seeds suggested that ADC is the predominant pathway for putrescine biosynthesis in soybean. However, organ-specific expression showed that root is the major site of ODC transcription. Significantly elevated accumulation of ADC mRNA and elevated putrescine content in seeds of the fasciation mutant compared with the wild type may stimulate cell divisions and establishment of enlarged apical meristem during early mutant ontogeny. The DAO frequent representation in EST libraries constructed from root tissue and elevated steady-state levels in roots compared to above ground tissues show DAO is critical for regulation of putrescine content in soybean roots.

Amine Oxidase (Copper-Containing)↗
PubMed2006

ECgene: an alternative splicing database update.

ECgene (http://genome.ewha.ac.kr/ECgene) was developed to provide functional annotation for alternatively spliced genes. The applications encompass the genome-based transcript modeling for alternative splicing (AS), domain analysis with Gene Ontology (GO) annotation and expression analysis based on the EST and SAGE data. We have expanded the ECgene's AS modeling and EST clustering to nine organisms for which sufficient EST data are available in the GenBank. As for the human genome, we have also introduced several new applications to analyze differential expression. ECprofiler is an ontology-based candidate gene search system that allows users to select an arbitrary combination of gene expression pattern and GO functional categories. DEGEST is a database of differentially expressed genes and isoforms based on the EST information. Importantly, gene expression is analyzed at three distinctive levels-gene, isoform and exon levels. The user interfaces for functional and expression analyses have been substantially improved. ASviewer is a dedicated java application that visualizes the transcript structure and functional features of alternatively spliced variants. The SAGE part of the expression module provides many additional features including SNP, differential expression and alternative tag positions.

Alternative Splicing↗
PubMed2005

Visualization-based discovery and analysis of genomic aberrations in microarray data.

BACKGROUND: Chromosomal copy number changes (aneuploidies) play a key role in cancer progression and molecular evolution. These copy number changes can be studied using microarray-based comparative genomic hybridization (array CGH) or gene expression microarrays. However, accurate identification of amplified or deleted regions requires a combination of visual and computational analysis of these microarray data. RESULTS: We have developed ChARMView, a visualization and analysis system for guided discovery of chromosomal abnormalities from microarray data. Our system facilitates manual or automated discovery of aneuploidies through dynamic visualization and integrated statistical analysis. ChARMView can be used with array CGH and gene expression microarray data, and multiple experiments can be viewed and analyzed simultaneously. CONCLUSION: ChARMView is an effective and accurate visualization and analysis system for recognizing even small aneuploidies or subtle expression biases, identifying recurring aberrations in sets of experiments, and pinpointing functionally relevant copy number changes. ChARMView is freely available under the GNU GPL at http://function.princeton.edu/ChARMView.

Algorithms↗
PubMed2005

Illumina, Inc.

Illumina, Inc., based in San Diego (CA, USA), is a genomics tool company that develops and markets integrated array-based systems and assays for a broad range of applications including genotyping, gene expression and epigenetics. Product offerings range from focused assay sets (up to 1,536 multiplexed assays) to whole-genome analysis (>100,000 assays/sample). Illumina's two microarray platforms, the Sentrix Array Matrix and the Sentrix BeadChip, are characterized by small (3 microm) feature size, dense feature packing (over 10 million features can be deployed on a single microarray) and the ability to analyze, in parallel, multiple samples on the same device. Illumina has developed a spectrum of proprietary assays (GoldenGate, Infinium, and DASL) for application on our microarray platform. These assays have been successfully employed for a number of applications, including collection of the majority of the Phase I genotyping data for the International HapMap Project. Illumina are focusing our activities on extending the applications of the above assays and developing new assays for future products. Illumina's goal is to deliver high-performance, high-throughput solutions that enable researchers to expand experimental scale while reducing the cost of large-scale research.

Gene Expression↗
PubMed2005

The use of toxicogenomic data in risk assessment: a regulatory perspective.

Recent advances in genomic research have provided new insights into mechanisms of toxicity evoked by drugs or xenobiotics. Several governmental and commercial organizations are at present actively building up databases containing large amounts of toxicogenomics information. With promises to improve our ability to characterize hazard, scientists are facing the challenge as to how to link patterns of gene expression and gene clustering to specific adverse effects of toxicants or classes of toxicants. The future of toxicogenomics lies in the robustness of the databases generated. Regulators are working together with institutes and industry in exploring the potential use of these databases in regulatory purposes. It is, however, anticipated that regulatory use of the toxicogenomic databases as supportive information in the assessment procedure of new drug applications will be on a case-by-case basis until the predictive value of the databases is firmly established.

Biomarkers↗
PubMed2006

Comparison of different approaches for comparative genetic analysis using microarray hybridization.

A robust analysis of comparative genomic microarray data is critical for meaningful genomic comparison studies. In this paper, we compare our method (implemented in a new software tool, GENCOM, freely available at http://www.ifr.ac.uk/safety/gencom ) with three commonly used analysis methods: GACK (freely available at http://falkow.stanford.edu ), an empirical cut-off value of twofold difference between the fluorescence intensities after LOWESS normalization or after AVERAGE normalization in which the fluorescence intensity is divided by the average fluorescence intensity of the entire data set. Each method was tested using data sets from real experiments with prior knowledge of conserved and divergent genes. GENCOM and GACK were superior when a high proportion of genes were divergent. GENCOM was the most suitable method for the data set in which the relationship between the fluorescence intensities was not linear. GENCOM has proved robust in an analysis of all the data sets tested.

Algorithms↗
PubMed2006

Spotting and validation of a genome wide oligonucleotide chip with duplicate measurement of each gene.

The quality of DNA microarray based gene expression data relies on the reproducibility of several steps in a microarray experiment. We have developed a spotted genome wide microarray chip with oligonucleotides printed in duplicate in order to minimise undesirable biases, thereby optimising detection of true differential expression. The validation study design consisted of an assessment of the microarray chip performance using the MessageAmp and FairPlay labelling kits. Intraclass correlation coefficient (ICC) was used to demonstrate that MessageAmp was significantly more reproducible than FairPlay. Further examinations with MessageAmp revealed the applicability of the system. The linear range of the chips was three orders of magnitude, the precision was high, as 95% of measurements deviated less than 1.24-fold from the expected value, and the coefficient of variation for relative expression was 13.6%. Relative quantitation was more reproducible than absolute quantitation and substantial reduction of variance was attained with duplicate spotting. An analysis of variance (ANOVA) demonstrated no significant day-to-day variation.

Gene Expression Profiling↗