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Results for “Functional Genomics”

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At least 523 records · Page 29Linked to original sources
PubMed2002

High-density synthetic peptide microarrays: emerging tools for functional genomics and proteomics.

New approaches for manufacturing and application of peptide arrays on planar surfaces are emerging, thereby opening advanced opportunities to probe the expression and function of the proteome. In complementing DNA and protein array analyses, peptide fragment screening directly addresses functional protein interaction sites, leading to a detailed insight into the discovered molecular recognition events, placing them in the context of the whole genome, and even allowing rapid determination of the chemical nature of these interactions. This information can then be transferred into powerful small peptide tools that interfere with these interactions in vivo and help to link targets with phenotypes. With the spreading of new peptide array tools, peptide screening will extend its impact on modern genome-driven molecular biology. This will advance the systematic discovery and validation of new pharmaceutical targets as well as the development of potent molecular diagnostics for medical and ecological monitoring.

Animals↗
PubMed2006

Functional genomics in hypertension.

PURPOSE OF REVIEW: Essential hypertension is a complex polygenetic disease with a major impact on health worldwide. Despite earlier detection of promising candidate genes, only recent advances in genotyping technology and new approaches to examining gene and protein function have provided the tools to unravel the genetic basis of hypertension. RECENT FINDINGS: In humans, genome-wide scans resulted in the identification of several chromosomal loci that are linked to hypertension. These regions still contain a large number of potential candidate genes, but high-throughput genotyping methods will facilitate the detection and analysis of single-nucleotide polymorphisms within these genes. The focus will be on animal models of hypertension, specifically rats. Congenic strains facilitate the identification of genetic determinants of hypertension, and new technologies such as RNA interference (which silences the expression of target genes) and transgenic rescue models will help us to analyse the relationship between genes and function. Analysis of conserved synteny (preserved order of genes) between species allows translation of findings from rodent models to essential hypertension in humans. Recent discoveries and approaches beyond genomics will also be discussed, including the regulatory role of microRNA and the concept of proteomics. SUMMARY: The genetic basis of hypertension is complex, and the examination of the functional consequences of genetic variants in particular is still challenging. A number of tools are now available with which to examine gene-function relationships, and these will provide an improved understanding of cardiovascular genomics. This will eventually lead to targeted prevention and treatment strategies in patients with hypertension and other cardiovascular diseases.

Animals↗
PubMed2004

Development through the eyes of functional genomics.

In many of the model organisms used to study development, it is becoming relatively routine to carry out global analyses of gene function. These analyses take many forms, from microarray analyses to the construction of physical interaction maps to the systematic analyses of loss-of-function phenotypes. Such large-scale datasets can be integrated to generate complex gene networks, and we explore how these gene networks can contribute to an understanding of developmental pathways. In particular, we examine how combining large-scale expression experiments and gene networks may move us towards a molecular description of the events of development, embodied in a succession of stage-specific subnetworks sampled from an organism's overall gene network.

Animals↗
PubMed2006

Mouse coat color mutations: from fancy mice to functional genomics.

Mouse coat color mutations have a long history in biomedical research. The viable and visible phenotype of most coat color mutations has made the pigment cell, the melanocyte, an ideal system for genetic, molecular, and cellular analysis. Molecular cloning and analysis of many of the different coat color mutations have revealed the roles of a diverse range of genes, and today we know more about the pathways and proteins that regulate the development and function of pigment cells than we know about most other cell types in mammalian organisms. Coat color mutations have also provided novel insights into stem cell biology and human diseases, including melanoma. In the future, it will be important to build on this history and knowledge by taking advantage of the extensive repertoire of recently developed genome-wide methodologies, available genomic information, and the powerful methods that have been developed for modifying the mouse genome to systematically dissect the development and function of this important cell type. The usefulness of coat color mutations has just begun to emerge.

Animals↗
PubMed2001

The use of functional genomics in C. elegans for studying human development and disease.

The 100 Mb Caenorhabditis elegans genome sequence is the first animal genome to be sequenced in its entirety. Many reverse-genetics tools have been developed to mine the genome sequence and to facilitate the jump between the identification of a gene sequence and the understanding of its function. Here we discuss how C. elegans can contribute to understanding of the function of genes involved in human development and disease.

Animals↗
PubMed2000

Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics.

If bioinformatics tools are constructed to reproduce the natural, evolutionary history of the biosphere, they offer powerful approaches to some of the most difficult tasks in genomics, including the organization and retrieval of sequence data, the updating of massive genomic databases, the detection of database error, the assignment of introns, the prediction of protein conformation from protein sequences, the detection of distant homologs, the assignment of function to open reading frames, the identification of biochemical pathways from genomic data, and the construction of a comprehensive model correlating the history of biomolecules with the history of planet Earth.

Amino Acid Sequence↗
PubMed2006

[Noncoding RNA, a new focus of functional genomic study].

Approximately 97% of all transcriptional output of the human being is noncoding RNA (ncRNA), which has been found to play roles in a great variety of processes, and is becoming more and more attractive. This review is a general introduction to the concept, classification and functions of ncRNA.

Genomics↗
PubMed2004

A functional genomics strategy reveals Rora as a component of the mammalian circadian clock.

The mammalian circadian clock plays an integral role in timing rhythmic physiology and behavior, such as locomotor activity, with anticipated daily environmental changes. The master oscillator resides within the suprachiasmatic nucleus (SCN), which can maintain circadian rhythms in the absence of synchronizing light input. Here, we describe a genomics-based approach to identify circadian activators of Bmal1, itself a key transcriptional activator that is necessary for core oscillator function. Using cell-based functional assays, as well as behavioral and molecular analyses, we identified Rora as an activator of Bmal1 transcription within the SCN. Rora is required for normal Bmal1 expression and consolidation of daily locomotor activity and is regulated by the core clock in the SCN. These results suggest that opposing activities of the orphan nuclear receptors Rora and Rev-erb alpha, which represses Bmal1 expression, are important in the maintenance of circadian clock function.

ARNTL Transcription Factors↗
PubMed2005

Databases, models, and algorithms for functional genomics: a bioinformatics perspective.

A variety of patterns have been observed on the DNA and protein sequences that serve as control points for gene expression and cellular functions. Owing to the vital role of such patterns discovered on biological sequences, they are generally cataloged and maintained within internationally shared databases. Furthermore,the variability in a family of observed patterns is often represented using computational models in order to facilitate their search within an uncharacterized biological sequence. As the biological data is comprised of a mosaic of sequence-levels motifs, it is significant to unravel the synergies of macromolecular coordination utilized in cell-specific differential synthesis of proteins. This article provides an overview of the various pattern representation methodologies and the surveys the pattern databases available for use to the molecular biologists. Our aim is to describe the principles behind the computational modeling and analysis techniques utilized in bioinformatics research, with the objective of providing insight necessary to better understand and effectively utilize the available databases and analysis tools. We also provide a detailed review of DNA sequence level patterns responsible for structural conformations within the Scaffold or Matrix Attachment Regions (S/MARs).

Animals↗
PubMed2004

A transcriptomics resource for wheat functional genomics.

Grain development, germination and plant development under abiotic stresses are areas of biology that are of considerable interest to the cereal community. Within the Investigating Gene Function programme we have produced the resources required to investigate alterations in the transcriptome of hexaploid wheat during these developmental processes. We have single pass sequenced the cDNAs of between 700 and 1300 randomly picked clones from each of 35 cDNA libraries representing highly specific stages of grain and plant development. Annotated sequencing results have been stored in a publicly accessible, online database at http://www.cerealsdb.uk.net. Each of the tissue stages used has also been photographed in detail, resulting in a collection of high-quality micrograph images detailing wheat grain development. These images have been collated and annotated in order to produce a web site focused on wheat development (http://www.wheatbp.net/). We have also produced high-density microarrays of a publicly available wheat unigene set based on the 35 cDNA libraries and have completed a number of microarray experiments which validate their quality.

Journal Article↗
PubMedDate not supplied

Integration of steroid hormone initiated membrane action to genomic function in the brain.

Estrogen is a ligand for the estrogen receptor (ER), which on binding 17beta-estradiol, functions as a ligand-activated transcription factor and regulates the transcription of target genes. This is the slow genomic mode of action. However, rapid non-genomic actions of estrogen also exist at the cell membrane. Using a novel two-pulse paradigm in which the first pulse rapidly initiates non-genomic actions using a membrane-limited estrogen conjugate (E-BSA), while the second pulse promotes genomic transcription from a consensus estrogen response element (ERE), we have demonstrated that rapid actions of estrogen potentiate the slower transcriptional response from an ERE-reporter in neuroblastoma cells. Since rapid actions of estrogen activate kinases, we used selective inhibitors in the two-pulse paradigm to determine the intracellular signaling cascades important in such potentiation. Inhibition of protein kinase A (PKA), PKC, mitogen activated protein kinase (MAPK) or phosphatidylinositol 3-OH kinase (PI-3K) in the first pulse decreases potentiation of transcription. Also, our data with both dominant negative and constitutive mutants of Galpha subunits show that Galpha(q) initiates the rapid signaling cascade at the membrane in SK-N-BE(2)C neuroblastoma cells. We discuss two models of multiple kinase activation at the membrane Pulses of estrogen induce lordosis behavior in female rats. Infusion of E-BSA into the ventromedial hypothalamus followed by 17beta-estradiol in the second pulse could induce lordosis behavior, demonstrating the applicability of this paradigm in vivo. A model where non-genomic actions of estrogen couple to genomic actions unites both aspects of hormone action.

Animals↗
PubMed2006

Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters.

The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokaryotes. For functional annotation of genes, we used two comparative genomic approaches: identification of regulatory signals and analysis of the genomic positions of genes encoding candidate nickel/cobalt transporters. The nickel-responsive repressor NikR regulates many nickel uptake systems, though the NikR-binding signal is divergent in various taxonomic groups of bacteria and archaea. B(12) riboswitches regulate most of the candidate cobalt transporters in bacteria. The nickel/cobalt transporter genes are often colocalized with genes for nickel-dependent or coenzyme B(12) biosynthesis enzymes. Nickel/cobalt transporters of different families, including the previously known NiCoT, UreH, and HupE/UreJ families of secondary systems and the NikABCDE ABC-type transporters, showed a mosaic distribution in prokaryotic genomes. In silico analyses identified CbiMNQO and NikMNQO as the most widespread groups of microbial transporters for cobalt and nickel ions. These unusual uptake systems contain an ABC protein (CbiO or NikO) but lack an extracytoplasmic solute-binding protein. Experimental analysis confirmed metal transport activity for three members of this family and demonstrated significant activity for a basic module (CbiMN) of the Salmonella enterica serovar Typhimurium transporter.

ATP-Binding Cassette Transporters↗
PubMed2003

Utilizing functional genomics to identify new pain treatments : the example of nociceptin.

Nociceptin/orphanin FQ (noc/oFQ) is the first novel bioactive substance to have been discovered by the implementation of a functional genomics/reverse pharmacology approach. The neuropeptide was indeed identified in brain extracts as the natural ligand of a previously cloned orphan G protein-coupled receptor, the opioid receptor-like 1 (ORL1) receptor. Since its discovery in 1995, noc/oFQ has been the subject of intensive study to establish its role in normal brain function and its possible involvement in neurophysiopathology. Although the neuropeptide, an inhibitor of neuronal activity, has been found to have a wide spectrum of pharmacological effects in vivo, none has been as intensively investigated as its action on nociception and nociceptive processing. There is now substantial evidence that noc/oFQ has a modulatory role in nociception. However, dependent on the dose and site of injection, and possibly the animal's genetic background and even psychological status, the peptide has been variously reported to cause allodynia, hyperalgesia, analgesia, and even pain, in rodents. Overall, noc/oFQ tends to facilitate pain when administered supraspinally, and to inhibit it when administered spinally. These opposing effects beg the obvious, yet still unanswered, question as to what would be the net effect on nociception of an ORL1 receptor ligand, agonist or antagonist, able to target supraspinal and spinal sites simultaneously. Owing to the research effort of several drug companies, such ligands, i.e. nonpeptidic, brain-penetrating agonists and antagonists, have recently been produced whose systematic screening in animal models of acute and inflammatory pain may help validate the ORL1 receptor as the target for novel, non-opioid analgesics.

Animals↗
PubMed2001

Protein structural alignments and functional genomics.

Structural genomics-the systematic solution of structures of the proteins of an organism-will increasingly often produce molecules of unknown function with no close relative of known function. Prediction of protein function from structure has thereby become a challenging problem of computational molecular biology. The strong conservation of active site conformations in homologous proteins suggests a method for identifying them. This depends on the relationship between size and goodness-of-fit of aligned substructures in homologous proteins. For all pairs of proteins studied, the root-mean-square deviation (RMSD) as a function of the number of residues aligned varies exponentially for large common substructures and linearly for small common substructures. The exponent of the dependence at large common substructures is well correlated with the RMSD of the core as originally calculated by Chothia and Lesk (EMBO J 1986;5:823-826), affording the possibility of reconciling different structural alignment procedures. In the region of small common substructures, reduced aligned subsets define active sites and can be used to suggest the locations of active sites in homologous proteins.

Bacillus subtilis↗
PubMed2000

Functional genomics of Escherichia coli in Japan.

Completion of the genome sequence of the model bacterium Escherichia coli has produced nearly 2000 open reading frames (ORFs) that remain to be functionally characterized. To accomplish this goal, we have organized a working project team in Japan and have begun construction of clones containing each of the putative ORFs. The procedure has been conceived such that we shall be able to perform systematic analysis of the shut-off as well as forced expression in vivo of each ORF and purification of its protein product for further biochemical studies. In addition, we have started a collection of various genetic and biochemical data of E. coli published in the past, and analyses of the data from a bio-informatics point of view. Thus, we aim at reaching complete understanding of this model organism in the near future.

Bacterial Proteins↗
PubMed2003

In vivo functional genomics of Pseudomonas aeruginosa for high-throughput screening of new virulence factors and antibacterial targets.

Pseudomonas aeruginosa is a model for studying opportunistic pathogens that are highly resistant to most classes of antibiotics and cause chronic pulmonary infections. We have developed and adapted a multiplex polymerase chain reaction-based signature-tagged mutagenesis (STM) for high-throughput screening of a collection of 7968 P. aeruginosa mutants in a rat model of chronic respiratory infection. After three rounds of screening, a total of 214 mutants, representing transposition events into 148 open reading frames, were shown to be attenuated in lung infection and were retained for further analysis. As proof of concept supporting this technology, we identified 11 insertions in typical virulence genes such as those coding for pili implicated in motility, attachment and swarming, alginate synthesis and its expression, a mucus transcription regulator, extracellular enzymes such as alkaline protease, esterase and amino peptidase, a rhamnosyl surfactant transferase and a lipopolysaccharide glycosyl transferase. Detailed analysis of the 148 STM mutants, including seven auxotrophs, revealed insertions in 21 of the 26 known gene classes used to characterize sequenced bacterial genomes. We noted that at least 46% of STM mutants identified had insertions in hypothetical proteins or proteins of unknown function and that approximately 40% of all STM mutants had insertions in surface proteins including the outer membrane, the periplasm and the inner membrane. Interestingly, 11 STM mutants attenuated for lung infection were also identified in microarray and transcriptome for quorum sensing and mucoidy production. The remaining 130 mutants were systematically analysed for their capability to express fully known virulence factors. In addition, testing the ability of these mutants to infect alternative model host Drosophila melanogaster revealed 36 STM mutants defective in protease, twitching motility, swimming and swarming. Finally, we identified many genes, the activity of which in respiratory infection was not fully appreciated.

Alkaline Phosphatase↗