Home About us Contact
|
Home About us Contact | ||
|
|
||
Genomic Information (genomic + information)
Selected AbstractsComparative and developmental study of the immune system in XenopusDEVELOPMENTAL DYNAMICS, Issue 6 2009Jacques Robert Abstract Xenopus laevis is the model of choice for evolutionary, comparative, and developmental studies of immunity, and invaluable research tools including MHC-defined clones, inbred strains, cell lines, and monoclonal antibodies are available for these studies. Recent efforts to use Silurana (Xenopus) tropicalis for genetic analyses have led to the sequencing of the whole genome. Ongoing genome mapping and mutagenesis studies will provide a new dimension to the study of immunity. Here we review what is known about the immune system of X. laevis integrated with available genomic information from S. tropicalis. This review provides compelling evidence for the high degree of similarity and evolutionary conservation between Xenopus and mammalian immune systems. We propose to build a powerful and innovative comparative biomedical model based on modern genetic technologies that takes take advantage of X. laevis and S. tropicalis, as well as the whole Xenopus genus. Developmental Dynamics 238:1249,1270, 2009. © 2009 Wiley-Liss, Inc. [source] Ecological perspectives on the sequenced genome collectionECOLOGY LETTERS, Issue 12 2005Jennifer B. Hughes Martiny Abstract Our complete genome collection is one of our most valuable biological resources. A key challenge for the future is the interpretation of these genomes from an ecological perspective. In this review, we discuss current work at this increasingly important interface. In particular, we review ongoing work aimed at developing high quality data sets that combine ecological, environmental, evolutionary and genomic information. Such data will help to identify biases in the sequence collection and facilitate future discoveries about the nature of ecological adaptation at the genome level. These efforts will be greatly enhanced by the contributions of ecologists. [source] Phylogenetic diversity and metagenomics of candidate division OP3ENVIRONMENTAL MICROBIOLOGY, Issue 5 2010Jana Glöckner Summary Except for environmental 16S rRNA gene sequences, no information is available for members of the candidate division OP3. These bacteria appear to thrive in anoxic environments, such as marine sediments, hypersaline deep sea, freshwater lakes, aquifers, flooded paddy soils and methanogenic bioreactors. The 16S rRNA phylogeny suggests that OP3 belongs to the Planctomycetes/Verrucomicrobia/Chlamydiae (PVC) superphylum. Metagenomic fosmid libraries were constructed from flooded paddy soil and screened for 16S rRNA gene-containing fragments affiliated with the PVC superphylum. The screening of 63 000 clones resulted in 23 assay-positive fosmids, of which three clones were affiliated with OP3. The 16S rRNA gene sequence divergence between the fragments OP3/1, OP3/2 and OP3/3 ranges from 18% to 25%, indicating that they belong to different OP3 subdivisions. The 23S rRNA phylogeny confirmed the membership of OP3 in the PVC superphylum. Sequencing the OP3 fragments resulted in a total of 105 kb of genomic information and 90 ORFs, of which 47 could be assigned a putative function and 11 were conserved hypothetical. Using BLASTP searches, a high proportion of ORFs had best matches to homologues from Deltaproteobacteria, rather than to those of members of the PVC superphylum. On the fragment OP3/3, a cluster of nine ORFs was predicted to encode the bacterial NADH dehydrogenase I. Given the high proportion of homologues present in deltaproteobacteria and anoxic conditions in the natural environment of OP3 bacteria, the detection of NADH dehydrogenase I may suggest an anaerobic respiration mode. Oligonucleotide frequencies calculated for OP3/1, OP3/2 and OP/3 show high intraphylum correlations. This novel sequence information could therefore be used to identify OP3-related fragments in large metagenomic data sets using marker gene-independent procedures in the future. In addition to the OP3 fragments, a single metagenomic fragment affiliated with the candidate division BRC1 was obtained and analysed. [source] Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeoteFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Hélène Moussard Abstract The polychaete Alvinella pompejana lives in organic tubes on the walls of active hydrothermal chimneys along the East Pacific Rise. To examine the diversity of the archaeal community associated with the polychaete tubes, we constructed libraries by direct PCR amplification and cloning of 16S rRNA genes. Almost half of the sequences of the 16S rRNA gene libraries clustered with uncultured archaeal groups. In an effort to access genomic information from uncultured archaeal members we further constructed a fosmid library from the same DNA source. One of the clones, Alv-FOS5, was sequenced completely. Its sequence analysis revealed an incomplete rRNA operon and 32 predicted ORFs. Seventeen of these ORFs have been assigned putative functions, including transcription and translation, cellular processes and signalling, transport systems and metabolic pathways. Phylogenetic analyses of the 16S rRNA gene suggested that Alv-FOS5 formed a new lineage related to members of Deep-Sea Hydrothermal Vent Euryarchaeota group II. Phylogenetic analyses of predicted proteins revealed the existence of likely cases of horizontal gene transfer, both between Crenarchaeota and Euryarchaeota and between Archaea and Bacteria. This study is the first step in using genomics to reveal the physiology of an as yet uncultured group of archaea from deep-sea hydrothermal vents. [source] Myocilin allele-specific glaucoma phenotype database,HUMAN MUTATION, Issue 2 2008Alex W. Hewitt Abstract Glaucoma, a complex heterogenous disease, is the leading cause for optic nerve,related blindness worldwide. Since 1997, when mutations in the myocilin (MYOC) gene were identified as causing juvenile onset as well as a proportion of primary open-angle glaucoma (POAG), more than 180 variants have been documented. Approximately one in 30 unselected patients with POAG have a disease-causing myocilin mutation and it has been shown that firm genotype,phenotype correlations exist. We have compiled an online catalog of myocilin variants and their associated phenotypes. This locus-specific resource, to which future submissions can be made, is available online (www.myocilin.com; last accessed 28 August 2007). The database, constructed using MySQL, contains three related sheets that contain data pertaining to the information source, variant identified, and relevant study data, respectively. The website contains a list of all identified variants and summary statistics as well as background genomic information, such as the annotated sequence and cross-protein/species homology. Phenotypic data such as the mean±standard deviation (SD) age at POAG diagnosis, mean±SD maximum recorded intraocular pressure, proportion of patients requiring surgical intervention, and age-related penetrance can be viewed by selecting a particular mutation. Approximately 40% of the identified sequence variants have been characterized as disease causing, with the majority (,85%) of these being missense mutations. Preliminary data generated from this online resource highlight the strong genotype,phenotype correlations associated with specific myocilin mutations. The large-scale assimilation of relevant data allows for accurate comprehensive genetic counseling and the translation of genomic information into the clinic. Hum Mutat 29(2), 207,211, 2008. © 2007 Wiley-Liss, Inc. [source] Molecular characterization of two novel esterase genes from carmine spider mite, Tetranychus cinnabarinus (Acarina: Tetranychidae)INSECT SCIENCE, Issue 2 2010Wei Sun Abstract, Two novel esterase complementary DNAs were identified and cloned from the insecticide-susceptible strain of Tetranychus cinnabarinus (Boisduval) (Acarina: Tetranychidae), which were designated as TCE1 and TCE2, respectively. The cDNA of TCE1 gene contained an open reading frame (ORF) of 1701 bp encoding 567 amino acids, and a predicted molecular weight of 62.75 kDa, the cDNA of TCE2 contained an ORF of 1680 bp encoding 560 amino acids, and a predicted molecular weight of 63.14 kDa. TCE1 and TCE2 were submitted to GenBank, accession number EU130461 and EU130462. The well-conserved sequence motif, GXSXG, used as a signature pattern in the esterase family are present in both TCE1 and TCE2 (GQSAG in TCE1, whereas GESAG in TCE2), indicating that these two genes are predicted to be esterases. Comparison of the deduced amino acid sequence with the published mite esterase sequence coming from Boophilus microplus showed that TCE1 shares 33.98% identity and TCE2 shares 33.46% identity. TCE1 and TCE2 share 46.4% identity. Quantitative real-time polymerase chain reaction revealed that expression level of the TCE2 gene was relatively higher than that of the TCE1 in all instars examined except the protonymph, and the expression level of these two esterase genes in adults of T. cinnabarinus was significantly higher than that in any other instars, respectively. T. cinnabarinus is an important agricultural mite pest and esterases are important in the metabolisms of insects and mites; the genomic information obtained in this study will contribute to esterase molecular biological study on mite pest species. [source] Role of xenobiotic transporters in bacterial drug resistance and virulenceIUBMB LIFE, Issue 9 2008Kunihiko Nishino Abstract Since the discovery of antibiotic therapeutics, the battles between humans and infectious diseases have never been stopped. Humans always face the appearance of a new bacterial drug-resistant strain followed by new antibiotic development. However, as the genome sequences of infectious bacteria have been gradually determined, a completely new approach has opened. This approach can analyze the entire gene resources of bacterial drug resistance. Through analysis, it may be possible to discover the underlying mechanism of drug resistance that will appear in the future. In this review article, we will first introduce the method to analyze all the xenobiotic transporter genes by using the genomic information. Next, we will discuss the regulation of xenobiotic transporter gene expression through the two-component signal transduction system, the principal environmental sensing and response system in bacteria. Furthermore, we will also introduce the virulence roles of xenobiotic transporters, which is an ongoing research area. © 2008 IUBMB IUBMB Life, 60(9): 569,574, 2008 [source] Genome-scale modeling of Synechocystis sp.JOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 4 2009PCC 680, prediction of pathway insertion Abstract BACKGROUND: Cyanobacterium Synechocystis sp. PCC 6803 has been used widely as a model system for the study of photosynthetic organisms and higher plants. The aim of this work was to integrate the genomic information, biochemistry and physiological information available for Synechocystis sp. PCC 6803 to reconstruct a metabolic network for system biology investigations. RESULTS: A genome-scale Synechocystis sp. PCC 6803 metabolic network, including 633 genes, 704 metabolites and 831 metabolic reactions, was reconstructed for the study of optimal Synechocystis growth, network capacity and functions. Heterotrophic, photoautotrophic and mixotrophic growth conditions were simulated. The Synechocystis model was used for in silico predictions for the insertion of ethanol fermentation pathway, which is a novel approach for bioenergy and biofuels production developed in the authors' laboratory. Simulations of Synechocystis cell growth and ethanol production were compared with actual metabolic measurements which showed a satisfactory agreement. CONCLUSION: The Synechocystis metabolic network developed in this study is the first genome-scale mathematical model for photosynthetic organisms. The model may be used not only in global understanding of cellular metabolism and photosynthesis, but also in designing metabolic engineering strategies for desirable bio-products. Copyright © 2008 Society of Chemical Industry [source] Bayesian approaches in evolutionary quantitative geneticsJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2008R. B. O'HARA Abstract The study of evolutionary quantitative genetics has been advanced by the use of methods developed in animal and plant breeding. These methods have proved to be very useful, but they have some shortcomings when used in the study of wild populations and evolutionary questions. Problems arise from the small size of data sets typical of evolutionary studies, and the additional complexity of the questions asked by evolutionary biologists. Here, we advocate the use of Bayesian methods to overcome these and related problems. Bayesian methods naturally allow errors in parameter estimates to propagate through a model and can also be written as a graphical model, giving them an inherent flexibility. As packages for fitting Bayesian animal models are developed, we expect the application of Bayesian methods to evolutionary quantitative genetics to grow, particularly as genomic information becomes more and more associated with environmental data. [source] Proteome analysis of non-model plants: A challenging but powerful approachMASS SPECTROMETRY REVIEWS, Issue 4 2008Sebastien Christian Carpentier Abstract Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. Some features and processes are unique to these plant species or families and cannot be approached via a model plant. The power of all proteomic and transcriptomic methods, that is, high-throughput identification of candidate gene products, tends to be lost in non-model species due to the lack of genomic information or due to the sequence divergence to a related model organism. Nevertheless, a proteomics approach has a great potential to study non-model species. This work reviews non-model plants from a proteomic angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-model organism. The review tackles problems associated with (i) sample preparation, (ii) the analysis and interpretation of a complex data set, (iii) the protein identification via MS, and (iv) data management and integration. We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 354,377, 2008 [source] Application of Physiological Genomics to the MicrocirculationMICROCIRCULATION, Issue 1 2002Dr. Andrew S. Greene Physiological genomics represents a new challenge in the biological sciences,the quest to define the functions of thousands of genes that will emerge from the sequencing of the human genome and the genomes of other model organisms. Because the attention of the scientific community has focused on this task, new tools that will allow high-efficiency identification of gene function are being developed at remarkable speed. Physiological genomic approaches to understanding integrated systems function are now becoming widely used in many areas of biological research. The availability of genomic information across species has now revealed a striking degree of conservation of both gene order and function, allowing researchers to easily move from model organisms to man in the hunt for gene function. Physiological genomics approaches in the cardiovascular system have focused on disease-based models and the behavior of large vessels. In the microcirculation, genomic studies have largely been confined to the use of single gene knockouts or to the study of angiogenesis. This review summarizes the strategies for physiological genomics that are appropriate to the study of the microcirculation and discusses several key discoveries that have been made by using these approaches. [source] Compatible and Incompetent Paxillus involutus Isolates for Ectomycorrhiza Formation in vitro with Poplar (Populus×canescens) Differ in H2O2 ProductionPLANT BIOLOGY, Issue 1 2004A. Gafur Abstract: Isolates of Paxillus involutus (Batsch) Fr. collected from different hosts and environmental conditions were screened for their ability to form ectomycorrhizal symbiosis with hybrid poplar P.×canescens (= Populus tremula L. ×P. alba) in vitro. The ability to form ectomycorrhiza varied between the fungal isolates and was not correlated with the growth rate of the fungi on agar-based medium. The isolate MAJ, which was capable of mycorrhiza synthesis under axenic conditions, and the incompetent isolate NAU were characterized morphologically and anatomically. MAJ formed a typical hyphal mantle and a Hartig net, whereas NAU was not able to penetrate the host cell walls and caused thickenings of the outer cell walls of the host. MAJ, but not NAU, displayed strong H2O2 accumulation in the outer hyphal mantle. Increases in H2O2 in the outer epidermal walls and adjacent hyphae of the incompetent isolate were moderate. No increases of H2O2 in response to the mycobionts were found inside roots. Suggested functions of H2O2 production in the outer hyphal mantle of the compatible interaction are: growth regulation of the host's roots, defence against other invading microbes, or increasing plant-innate immunity. The system established here for P.×canescens compatible and incompetent fungal associations will be useful to take advantage of genomic information now available for poplar to study tree-fungal interactions at the molecular and physiological level. [source] Copyright versus Database Right of Protection in the UK: The Bioinformatics Bone of ContentionTHE JOURNAL OF WORLD INTELLECTUAL PROPERTY, Issue 1 2006Mahesh Madhavan Bioinformatics is the development and use of databases for storing and interpreting genomic information. The information explosion in these databases has raised a plethora of intellectual property issues for the scientists who depend on them. Copyright and database protection are two notable and significant methods of exploiting innovations in bioinformatics. This article makes an in-depth analysis of the scope and utility of copyright and database protection laws in bioinformatics. This article focuses initially on the working of bioinformatics databases, and then delves into the issues and implications of copyright and database protection in bioinformatics. The article concludes that copyright in comparison to database laws serves as a better platform in keeping the balance between the interests of bioinformatics database makers and its users. [source] Comparative genomics enabled the isolation of the R3a late blight resistance gene in potatoTHE PLANT JOURNAL, Issue 2 2005Sanwen Huang Summary Comparative genomics provides a tool to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. In this report, we adopted a local RGA approach using genomic information from the model Solanaceous plant tomato to isolate R3a, a potato gene that confers race-specific resistance to the late blight pathogen Phytophthora infestans. R3a is a member of the R3 complex locus on chromosome 11. Comparative analyses of the R3 complex locus with the corresponding I2 complex locus in tomato suggest that this is an ancient locus involved in plant innate immunity against oomycete and fungal pathogens. However, the R3 complex locus has evolved after divergence from tomato and the locus has experienced a significant expansion in potato without disruption of the flanking colinearity. This expansion has resulted in an increase in the number of R genes and in functional diversification, which has probably been driven by the co-evolutionary history between P. infestans and its host potato. Constitutive expression was observed for the R3a gene, as well as some of its paralogues whose functions remain unknown. [source] A radiation hybrid comparative map of ovine chromosome 1 aligned to the virtual sheep genomeANIMAL GENETICS, Issue 4 2009C. H. Wu Summary Ovis aries chromosome one (OAR1) is the largest submetacentric chromosome in the sheep genome and is homologous to regions on human chromosomes 1, 2, 3 and 21. Using the USUoRH5000 ovine whole-genome radiation hybrid (RH) panel, we have constructed a RH map of OAR1 comprising 102 framework and 75 placed/binned markers across five linkage groups spanning 3759.43 cR5000, with an average marker density of 21.2 cR5000/marker. The alignment of our OAR1 RH map shows good concordance with the recently developed virtual sheep genome, with fewer than 1.86% discrepancies. A comparative map of OAR1 was constructed by examining the location of RH-mapped orthologues in sheep within the genomes of cow, human, horse and dog. Analysis of the comparative map indicates that conserved syntenies within the five ovine RH linkage groups underwent internal chromosomal rearrangements which, in general, reflect the evolutionary distances between sheep and each of these four species. The ovine RH map presented here integrates all available mapping data and includes new genomic information for ovine chromosome 1. [source] Stoichiometric model and metabolic flux analysis for Leptospirillum ferrooxidansBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010M.P. Merino Abstract A metabolic model for Leptospirillum ferrooxidans was developed based on the genomic information of an analogous iron oxidizing bacteria and on the pathways of ferrous iron oxidation, nitrogen and CO2 assimilation based on experimental evidence for L. ferrooxidans found in the literature. From this metabolic reconstruction, a stoichiometric model was built, which includes 86 reactions describing the main catabolic and anabolic aspects of its metabolism. The model obtained has 2 degrees of freedom, so two external fluxes were estimated to achieve a determined and observable system. By using the external oxygen consumption rate and the generation flux biomass as input data, a metabolic flux map with a distribution of internal fluxes was obtained. The results obtained were verified with experimental data from the literature, achieving a very good prediction of the metabolic behavior of this bacterium at steady state. Biotechnol. Bioeng. 2010;107:696,706. © 2010 Wiley Periodicals, Inc. [source] Come in and take your coat off , how host cells provide endocytosis for virus entryCELLULAR MICROBIOLOGY, Issue 10 2010Mario Schelhaas Summary Viruses are intracellular parasites that rely upon the host cell machinery for their life cycle. Newly generated virus particles have to transmit their genomic information to uninfected cells/organisms. Viral entry is the process to gain access to viral replication sites within uninfected cells, a multistep course of events that starts with binding to target cells. Since viruses are simple in structure and composition and lack any locomotive capacity, viruses depend on hundreds of host cell proteins during entry. Most animal viruses take advantage of endocytosis to enter cells. Cell biological, morphological and biochemical studies, live cell imaging and systematic approaches have identified various new endocytic mechanisms besides clathrin-mediated endocytosis, macropinocytosis and caveolar/lipid raft-mediated endocytosis. Hence, studying virus entry has become ever more complex. This review provides a cell biological overview of the existing endocytic mechanisms and strategies used or potentially used by viruses to enter cells. [source] | ||||||||||||||||||||||