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The driving force behind genomic diversity  [PDF]
Salla Jaakkola,Sedeer El-Showk,Arto Annila
Quantitative Biology , 2008,
Abstract: Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of increasing entropy. According to thermodynamics of open systems, genomes evolve toward diversity by various mechanisms that increase, decrease and distribute genomic material in response to thermodynamic driving forces. Evolution results in an excessive genome, a high-entropy ecosystem of its own, where copious non-coding segments associate with low-level functions and conserved sequences code coordinated activities. The rate of entropy increase, equivalent to the rate of free energy decrease, is identified with the universal fitness criterion of natural selection that governs populations of genomic entities as well as other species.
Genomic Diversity and Evolution of the Lyssaviruses  [PDF]
Olivier Delmas, Edward C. Holmes, Chiraz Talbi, Florence Larrous, Laurent Dacheux, Christiane Bouchier, Hervé Bourhy
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002057
Abstract: Lyssaviruses are RNA viruses with single-strand, negative-sense genomes responsible for rabies-like diseases in mammals. To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution. Herein, we report the first genomic and evolutionary analysis using complete genome sequences of all recognised lyssavirus genotypes, including 14 new complete genomes of field isolates from 6 genotypes and one genotype that is completely sequenced for the first time. In doing so we significantly increase the extent of genome sequence data available for these important viruses. Our analysis of these genome sequence data reveals that all lyssaviruses have the same genomic organization. A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats. We also suggest that multiple genotypes may exist within the diversity of viruses currently classified as ‘Lagos Bat’. In sum, we show that rigorous phylogenetic techniques based on full length genome sequence provide the best discriminatory power for genotype classification within the lyssaviruses.
The use of entropy to measure structural diversity  [PDF]
L. Masisi,V. Nelwamondo,T. Marwala
Computer Science , 2008,
Abstract: In this paper entropy based methods are compared and used to measure structural diversity of an ensemble of 21 classifiers. This measure is mostly applied in ecology, whereby species counts are used as a measure of diversity. The measures used were Shannon entropy, Simpsons and the Berger Parker diversity indexes. As the diversity indexes increased so did the accuracy of the ensemble. An ensemble dominated by classifiers with the same structure produced poor accuracy. Uncertainty rule from information theory was also used to further define diversity. Genetic algorithms were used to find the optimal ensemble by using the diversity indices as the cost function. The method of voting was used to aggregate the decisions.
Genomic approaches to research in pulmonary hypertension
Mark W Geraci, Bifeng Gao, Yasushi Hoshikawa, Michael E Yeager, Rubin M Tuder, Norbert F Voelkel
Respiratory Research , 2001, DOI: 10.1186/rr59
Abstract: Pulmonary hypertension (PH) refers to a spectrum of diseases where the pulmonary artery pressure is elevated. A new classification of PH has recently been proposed [1]. No cause can be elucidated in primary (or sporadic, idiopathic) pulmonary hypertension (PPH). Secondary forms of PH can occur in association with congenital heart disease, thromboembolic disease, HIV, anorexigen usage, and a variety of connective tissue disorders. Familial primary pulmonary hypertension (FPPH) has been associated with heterozygous germline mutations in the bone morphogenetic protein type II receptor gene (BMPR2) [2,3]. While this recent discovery has generated extreme interest, the pathobiology of severe PH remains enigmatic. Recent genomic approaches to investigate PH are reviewed. Early studies investigated the alterations of vasoactive and growth factor related genes. Animal models, using either pharmaceutical approaches, transgenics, or targeted disruption of genes, have allowed for whole animal modeling of specific pathways in the development of PH. Progress in medical genetic investigations has lead to the discovery of a gene (BMPR2) associated with FPPH. Finally, microarray expression analysis has been utilized to investigate animal models, and has shown to be a useful tool providing novel information and better characterization of the molecular pathobiology of distinct clinical phenotypes of PH.Most investigations of the role of specific genes in the pathobiology of PH have focused either on the balance of vasoconstriction and vasodilation or on specific growth factors, inflammatory mediators, or ion channels. Another approach has been to compartmentalize the vasculature, and focus the investigations on the endothelium, smooth muscle cells, and the adventitia/extracellular matrix. Christman et al initially reported an imbalance of prostacyclin (PGI2) and thromboxane metabolites in the urine of patients with both primary and secondary forms of PH, with more vasoconstrictor thr
Pseudomonas aeruginosa Genomic Structure and Diversity  [PDF]
Jens Klockgether,Burkhard Tümmler
Frontiers in Microbiology , 2011, DOI: 10.3389/fmicb.2011.00150
Abstract: The Pseudomonas aeruginosa genome (G + C content 65–67%, size 5.5–7 Mbp) is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators, and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5–0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNALys or tRNAGly genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. One hundred ninety-eight of the 231 single nucleotide substitutions (SNPs) were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport, and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer.
Unraveling the genomic diversity of small eukaryotes
Gilles Fischer, Dawn Thompson, Jennifer Wortman, Cécile Fairhead
Genome Biology , 2009, DOI: 10.1186/gb-2009-10-12-318
Abstract: The first meeting in a new series of EMBO meetings aimed at bringing together those working on genome-enabled research encompassing the great diversity of eukaryotic microorganisms was held recently in Spain. New technology such as high-throughput sequencing now allows less well studied eukaryotic microbes to come into the limelight, providing some fascinating glimpses into the eukaryotic world that lies outside multicellular plants and animals. Some of the highlights of the meeting are presented here.In celebration of the 150th anniversary of the publication of Charles Darwin's On the Origin of Species, the meeting opened with 'The Darwin Lecture' delivered by Bernard Dujon (Institut Pasteur, Paris, France), who highlighted the fact that our current knowledge of eukaryotic genomes is highly biased towards the two supergroups of Unikonts (the animals and fungi) and Plantae (red and green algae and plants) and to a lesser extent towards the Chromalveolates (ciliates, brown algae, diatoms, and dinoflagellates, for example). Dujon pointed out the need for more genomics data representing the other two eukaryotic supergroups - the Excavata (which contains some important parasites of humans) and the Rhizaria (the pseudopodial amoeboids) - to foster a clearer understanding of eukaryotic diversity. A spectacular illustration of this diversity was presented by Gertraud Burger (University of Montreal, Canada), whose research on the mitochondrial genome of diplonemids (members of the Excavates) has shown that each core gene is split into several small modules scattered across multiple circular chromosomes. The concatenation of these modules occurs at the RNA level via an unusual trans-splicing mechanism, along with RNA editing at the junctions, in order to reconstruct a full transcript of each gene.The vast majority of eukaryotic taxa are composed of unicellular organisms that, with the exception of yeasts, have largely been overlooked until recent advances in genomic technolo
Entropy Diversity in Multi-Objective Particle Swarm Optimization  [PDF]
Eduardo J. Solteiro Pires,José A. Tenreiro Machado,Paulo B. de Moura Oliveira
Entropy , 2013, DOI: 10.3390/e15125475
Abstract: Multi-objective particle swarm optimization (MOPSO) is a search algorithm based on social behavior. Most of the existing multi-objective particle swarm optimization schemes are based on Pareto optimality and aim to obtain a representative non-dominated Pareto front for a given problem. Several approaches have been proposed to study the convergence and performance of the algorithm, particularly by accessing the final results. In the present paper, a different approach is proposed, by using Shannon entropy to analyze the MOPSO dynamics along the algorithm execution. The results indicate that Shannon entropy can be used as an indicator of diversity and convergence for MOPSO problems.
Maximum entropy models for antibody diversity  [PDF]
Thierry Mora,Aleksandra Walczak,William Bialek,Curtis G. Callan Jr
Quantitative Biology , 2009, DOI: 10.1073/pnas.1001705107
Abstract: Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM sequences in zebrafish. These models are based solely on pairwise correlations between residue positions, but correctly capture the higher order statistical properties of the repertoire. Exploiting the interpretation of these models as statistical physics problems, we make several predictions for the collective properties of the sequence ensemble: the distribution of sequences obeys Zipf's law, the repertoire decomposes into several clusters, and there is a massive restriction of diversity due to the correlations. These predictions are completely inconsistent with models in which amino acid substitutions are made independently at each site, and are in good agreement with the data. Our results suggest that antibody diversity is not limited by the sequences encoded in the genome, and may reflect rapid adaptation to antigenic challenges. This approach should be applicable to the study of the global properties of other protein families.
Genomic diversity of citrate fermentation in Klebsiella pneumoniae
Ying-Tsong Chen, Tsai-Lien Liao, Keh-Ming Wu, Tsai-Ling Lauderdale, Jing-Jou Yan, I-Wen Huang, Min-Chi Lu, Yi-Chyi Lai, Yen-Ming Liu, Hung-Yu Shu, Jin-Town Wang, Ih-Jen Su, Shih-Feng Tsai
BMC Microbiology , 2009, DOI: 10.1186/1471-2180-9-168
Abstract: Using a genomic microarray containing probe sequences from multiple K. pneumoniae strains, we investigated genetic diversity among K. pneumoniae clinical isolates and found that a genomic region containing the citrate fermentation genes was not universally present in all strains. We confirmed by PCR analysis that the gene cluster was detectable in about half of the strains tested. To demonstrate the metabolic function of the genomic region, anaerobic growth of K. pneumoniae in artificial urine medium (AUM) was examined for ten strains with different clinical histories and genomic backgrounds, and the citrate fermentation potential was found correlated with the genomic region. PCR detection of the genomic region yielded high positive rates among a variety of clinical isolates collected from urine, blood, wound infection, and pneumonia. Conserved genetic organizations in the vicinity of the citrate fermentation gene clusters among K. pneumoniae, Salmonella enterica, and Escherichia coli suggest that the13-kb genomic region were not independently acquired.Not all, but nearly half of the K. pneumoniae clinical isolates carry the genes responsible for anaerobic growth on citrate. Genomic variation of citrate fermentation genes in K. pneumoniae may contribute to metabolic diversity and adaptation to variable nutrient conditions in different environments.Citrate, a ubiquitous natural compound that exists in all living cells, can be used by several enterobacterial species as a carbon and energy source. Klebsiella pneumoniae has been known to be able to grow anaerobically with citrate as the sole carbon source. During the past decade, the physiology, biochemistry, and regulation of this pathway have been extensively studied in K. pneumoniae [1-4]. The fermentation process involves uptake of citrate by a Na+ -dependent citrate carrier, cleavage into oxaloacetate and acetate by citrate lyase, and decarboxylation of oxaloacetate to pyruvate by oxaloacetate decarboxylase. Finall
Correlation exploration of metabolic and genomic diversity in rice
Keiichi Mochida, Taku Furuta, Kaworu Ebana, Kazuo Shinozaki, Jun Kikuchi
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-568
Abstract: We selected 18 accessions from the world rice collection based on their population structure. To determine the genomic diversity of the rice genome, we genotyped 128 restriction fragment length polymorphism (RFLP) markers to calculate the genetic distance among the accessions. To identify the variations in the metabolic fingerprint, a soluble extract from the seed grain of each accession was analyzed with one dimensional 1H-nuclear magnetic resonance (NMR). We found no correlation between global metabolic diversity and the phylogenetic relationships among the rice accessions (rs = 0.14) by analyzing the distance matrices (calculated from the pattern of the metabolic fingerprint in the 4.29- to 0.71-ppm 1H chemical shift) and the genetic distance on the basis of the RFLP markers. However, local correlation analysis between the distance matrices (derived from each 0.04-ppm integral region of the 1H chemical shift) against genetic distance matrices (derived from sets of 3 adjacent markers along each chromosome), generated clear correlations (rs > 0.4, p < 0.001) at 34 RFLP markers.This combinatorial approach will be valuable for exploring the correlative relationships between metabolic and genomic diversity. It will facilitate the elucidation of complex regulatory networks and those of evolutionary significance in plant metabolic systems.It is essential to elucidate the relationships between metabolic and genomic diversity to understand the genetic causes of phenotypic variation among natural populations. Visible and chemical variations associated with genomic diversity provide the information required to identify key genes associated with such phenotypic changes [1]. Patterns of nucleotide polymorphisms and a population structure figured in a natural population have allowed us to understand the evolutionary significance of genetic variation under the influence of geographic factors or different environments [2,3].The technical development of metabolite profiling has p
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