<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Zengler, Karsten</style></author><author><style face="normal" font="default" size="100%">Barrett, Christian L</style></author><author><style face="normal" font="default" size="100%">Qiu, Yu</style></author><author><style face="normal" font="default" size="100%">Palsson, Bernhard O</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutagenesis, Insertional</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Riboswitch</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">13-23</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The stimulation of subsurface microbial metabolism often associated with engineered bioremediation of groundwater contaminants presents subsurface microorganisms, which are adapted for slow growth and metabolism in the subsurface, with new selective pressures. In order to better understand how Geobacter species might adapt to selective pressure for faster metal reduction in the subsurface, Geobacter sulfurreducens was put under selective pressure for rapid Fe(III) oxide reduction. The genomes of two resultant strains with rates of Fe(III) oxide reduction that were 10-fold higher than those of the parent strain were resequenced. Both strains contain either a single base-pair change or a 1 nucleotide insertion in a GEMM riboswitch upstream of GSU1761, a gene coding for the periplasmic c-type cytochrome designated PgcA. GSU1771, a gene coding for a SARP regulator, was also mutated in both strains. Introduction of either of the GEMM riboswitch mutations upstream of pgcA in the wild-type increased the abundance of pgcA transcripts, consistent with increased expression of pgcA in the adapted strains. One of the mutations doubled the rate of Fe(III) oxide reduction. Interruption of GSU1771 doubled the Fe(III) oxide reduction rate. This was associated with an increased in expression of pilA, the gene encoding the structural protein for the pili thought to function as microbial nanowires. The combination of the GSU1771 interruption with either of the pgcA mutations resulted in a strain that reduced Fe(III) as fast as the comparable adapted strain. These results suggest that the accumulation of a small number of beneficial mutations under selective pressure, similar to that potentially present during bioremediation, can greatly enhance the capacity for Fe(III) oxide reduction in G. sulfurreducens. Furthermore, the results emphasize the importance of the c-type cytochrome PgcA and pili in Fe(III) oxide reduction and demonstrate how adaptive evolution studies can aid in the elucidation of complex mechanisms, such as extracellular electron transfer.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20636372?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rich, Stephen M</style></author><author><style face="normal" font="default" size="100%">Xu, Guang</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Resolving the phylogeny of malaria parasites.</style></title><secondary-title><style face="normal" font="default" size="100%">Proc Natl Acad Sci U S A</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Malaria</style></keyword><keyword><style  face="normal" font="default" size="100%">Parasites</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Aug 9</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">108</style></volume><pages><style face="normal" font="default" size="100%">12973-4</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">32</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21804030?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ashkenazy, Haim</style></author><author><style face="normal" font="default" size="100%">Erez, Elana</style></author><author><style face="normal" font="default" size="100%">Martz, Eric</style></author><author><style face="normal" font="default" size="100%">Pupko, Tal</style></author><author><style face="normal" font="default" size="100%">Ben-Tal, Nir</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Conserved Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid Conformation</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Conformation</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Amino Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">38</style></volume><pages><style face="normal" font="default" size="100%">W529-33</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new version of the ConSurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/.</style></abstract><issue><style face="normal" font="default" size="100%">Web Server issue</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20478830?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Young, Nelson D</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proton-Translocating ATPases</style></keyword><keyword><style  face="normal" font="default" size="100%">Citric Acid Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">Cluster Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Comparative Genomic Hybridization</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Duplication</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Transfer, Horizontal</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">NADH Dehydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">40</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Geobacter species grow by transferring electrons out of the cell--either to Fe(III)-oxides or to man-made substances like energy-harvesting electrodes. Study of Geobacter sulfurreducens has shown that TCA cycle enzymes, inner-membrane respiratory enzymes, and periplasmic and outer-membrane cytochromes are required. Here we present comparative analysis of six Geobacter genomes, including species from the clade that predominates in the subsurface. Conservation of proteins across the genomes was determined to better understand the evolution of Geobacter species and to create a metabolic model applicable to subsurface environments.

RESULTS: The results showed that enzymes for acetate transport and oxidation, and for proton transport across the inner membrane were well conserved. An NADH dehydrogenase, the ATP synthase, and several TCA cycle enzymes were among the best conserved in the genomes. However, most of the cytochromes required for Fe(III)-reduction were not, including many of the outer-membrane cytochromes. While conservation of cytochromes was poor, an abundance and diversity of cytochromes were found in every genome, with duplications apparent in several species.

CONCLUSIONS: These results indicate there is a common pathway for acetate oxidation and energy generation across the family and in the last common ancestor. They also suggest that while cytochromes are important for extracellular electron transport, the path of electrons across the periplasm and outer membrane is variable. This combination of abundant cytochromes with weak sequence conservation suggests they may not be specific terminal reductases, but rather may be important in their heme-bearing capacity, as sinks for electrons between the inner-membrane electron transport chain and the extracellular acceptor.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20078895?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Evol Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Evol. Biol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Comparative Genomic Hybridization</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Intergenic</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacillus</style></keyword><keyword><style  face="normal" font="default" size="100%">Histidine-tRNA Ligase</style></keyword><keyword><style  face="normal" font="default" size="100%">Inverted Repeat Sequences</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">230</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Pelobacter carbinolicus, a bacterium of the family Geobacteraceae, cannot reduce Fe(III) directly or produce electricity like its relatives. How P. carbinolicus evolved is an intriguing problem. The genome of P. carbinolicus contains clustered regularly interspaced short palindromic repeats (CRISPR) separated by unique spacer sequences, which recent studies have shown to produce RNA molecules that interfere with genes containing identical sequences.

RESULTS: CRISPR spacer #1, which matches a sequence within hisS, the histidyl-tRNA synthetase gene of P. carbinolicus, was shown to be expressed. Phylogenetic analysis and genetics demonstrated that a gene paralogous to hisS in the genomes of Geobacteraceae is unlikely to compensate for interference with hisS. Spacer #1 inhibited growth of a transgenic strain of Geobacter sulfurreducens in which the native hisS was replaced with that of P. carbinolicus. The prediction that interference with hisS would result in an attenuated histidyl-tRNA pool insufficient for translation of proteins with multiple closely spaced histidines, predisposing them to mutation and elimination during evolution, was investigated by comparative genomics of P. carbinolicus and related species. Several ancestral genes with high histidine demand have been lost or modified in the P. carbinolicus lineage, providing an explanation for its physiological differences from other Geobacteraceae.

CONCLUSIONS: The disappearance of multiheme c-type cytochromes and other genes typical of a metal-respiring ancestor from the P. carbinolicus lineage may be the consequence of spacer #1 interfering with hisS, a condition that can be reproduced in a heterologous host. This is the first successful co-introduction of an active CRISPR spacer and its target in the same cell, the first application of a chimeric CRISPR construct consisting of a spacer from one species in the context of repeats of another species, and the first report of a potential impact of CRISPR on genome-scale evolution by interference with an essential gene.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20667132?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chen, Meng</style></author><author><style face="normal" font="default" size="100%">Lopes, John M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Multiple basic helix-loop-helix proteins regulate expression of the ENO1 gene of Saccharomyces cerevisiae.</style></title><secondary-title><style face="normal" font="default" size="100%">Eukaryot Cell</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Eukaryotic Cell</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Basic Helix-Loop-Helix Transcription Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">beta-Galactosidase</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromatin Immunoprecipitation</style></keyword><keyword><style  face="normal" font="default" size="100%">E-Box Elements</style></keyword><keyword><style  face="normal" font="default" size="100%">Epistasis, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Fungal</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Dominant</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Phosphopyruvate Hydratase</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombinant Fusion Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Saccharomyces cerevisiae</style></keyword><keyword><style  face="normal" font="default" size="100%">Saccharomyces cerevisiae Proteins</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">786-96</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The basic helix-loop-helix (bHLH) eukaryotic transcription factors have the ability to form multiple dimer combinations. This property, together with limited DNA-binding specificity for the E box (CANNTG), makes them ideally suited for combinatorial control of gene expression. We tested the ability of all nine Saccharomyces cerevisiae bHLH proteins to regulate the enolase-encoding gene ENO1. ENO1 was known to be activated by the bHLH protein Sgc1p. Here we show that expression of an ENO1-lacZ reporter was also regulated by the other eight bHLH proteins, namely, Ino2p, Ino4p, Cbf1p, Rtg1p, Rtg3p, Pho4p, Hms1p, and Ygr290wp. ENO1-lacZ expression was also repressed by growth in inositol-choline-containing medium. Epistatic analysis and chromatin immunoprecipitation experiments showed that regulation by Sgc1p, Ino2p, Ino4p, and Cbf1p and repression by inositol-choline required three distal E boxes, E1, E2, and E3. The pattern of bHLH binding to the three E boxes and experiments with two dominant-negative mutant alleles of INO4 and INO2 support the model that bHLH dimer selection affects ENO1-lacZ expression. These results support the general model that bHLH proteins can coordinate different biological pathways via multiple mechanisms.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17351075?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Landau, Meytal</style></author><author><style face="normal" font="default" size="100%">Mayrose, Itay</style></author><author><style face="normal" font="default" size="100%">Rosenberg, Yossi</style></author><author><style face="normal" font="default" size="100%">Glaser, Fabian</style></author><author><style face="normal" font="default" size="100%">Martz, Eric</style></author><author><style face="normal" font="default" size="100%">Pupko, Tal</style></author><author><style face="normal" font="default" size="100%">Ben-Tal, Nir</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Substitution</style></keyword><keyword><style  face="normal" font="default" size="100%">Amino Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bayes Theorem</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Potassium Channels</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Conformation</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Jul 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">33</style></volume><pages><style face="normal" font="default" size="100%">W299-302</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under strong evolutionary constraints. Thus, the biological importance of a residue often correlates with its level of evolutionary conservation within the protein family. ConSurf (http://consurf.tau.ac.il/) is a web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. Structurally and functionally important regions in the protein typically appear as patches of evolutionarily conserved residues that are spatially close to each other. We present here version 3.0 of ConSurf. This new version includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release. Various additional steps in the calculation can now be controlled by a number of advanced options, thus further improving the accuracy of the calculation. Moreover, ConSurf version 3.0 also includes a measure of confidence for the inferred amino acid conservation scores.</style></abstract><issue><style face="normal" font="default" size="100%">Web Server issue</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15980475?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Glaser, Fabian</style></author><author><style face="normal" font="default" size="100%">Pupko, Tal</style></author><author><style face="normal" font="default" size="100%">Paz, Inbal</style></author><author><style face="normal" font="default" size="100%">Bell, Rachel E</style></author><author><style face="normal" font="default" size="100%">Bechor-Shental, Dalit</style></author><author><style face="normal" font="default" size="100%">Martz, Eric</style></author><author><style face="normal" font="default" size="100%">Ben-Tal, Nir</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioinformatics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">bcl-X Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">Conserved Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Conformation</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Proto-Oncogene Proteins c-bcl-2</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">19</style></volume><pages><style face="normal" font="default" size="100%">163-4</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We recently developed algorithmic tools for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence homologues. Projecting the conservation grades onto the molecular surface of these proteins reveals patches of highly conserved (or occasionally highly variable) residues that are often of important biological function. We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins. AVAILABILITY: The ConSurf web server is available at:http://consurf.tau.ac.il. SUPPLEMENTARY INFORMATION: A set of examples is available at http://consurf.tau.ac.il under 'GALLERY'.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12499312?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rich, Stephen M</style></author><author><style face="normal" font="default" size="100%">Ayala, Francisco J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Progress in malaria research: the case for phylogenetics.</style></title><secondary-title><style face="normal" font="default" size="100%">Adv Parasitol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Adv. Parasitol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Biomedical Research</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome</style></keyword><keyword><style  face="normal" font="default" size="100%">Malaria</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmodium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">54</style></volume><pages><style face="normal" font="default" size="100%">255-80</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Malaria, from the Italian for &quot;bad air&quot;, is a term used to describe a human disease caused by any of four parasites of the genus, Plasmodium. There are in fact over 200 described species of Plasmodium that parasitize reptiles, birds, and mammals, and may or may not cause disease in these various hosts. In this chapter, we highlight important evolutionary studies that have been undertaken to determine the relatedness among these species and their place in the taxonomic hierarchy. We begin by providing an overview of our present understanding of the phylum to which malaria parasites belong--Apicomplexa. The unique characteristics of these parasites reflect both their adaptation to the parasitic life style as well as some vestigial remnants of their pre-parasitic evolutionary past. Phylogenetic analyses provide the means for discerning the means by which these characteristics have come into existence. We next discuss the systematics of the genus Plasmodium. Morphology, genomic structure and content as well as host affiliation of these parasites are all traits that have been used for establishing taxonomic arrangements. Molecular phylogenetics has proven to be an invaluable tool in this regard and so we discuss the current phylogenetic picture of the genus as well as the correspondence among the various datasets (morphology, molecules, and host-preference). Lastly, we present a detailed account of our current understanding of the evolutionary past of the most deadly of the human malaria species--P. falciparum.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/14711087?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ferreira, Marcelo U</style></author><author><style face="normal" font="default" size="100%">Ribeiro, Weber L</style></author><author><style face="normal" font="default" size="100%">Tonon, Angela P</style></author><author><style face="normal" font="default" size="100%">Kawamoto, Fumihiko</style></author><author><style face="normal" font="default" size="100%">Rich, Stephen M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-1 (MSP-1) of Plasmodium falciparum.</style></title><secondary-title><style face="normal" font="default" size="100%">Gene</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Gene</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Alleles</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Brazil</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Protozoan</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Variation</style></keyword><keyword><style  face="normal" font="default" size="100%">Haplotypes</style></keyword><keyword><style  face="normal" font="default" size="100%">Linkage Disequilibrium</style></keyword><keyword><style  face="normal" font="default" size="100%">Malaria Vaccines</style></keyword><keyword><style  face="normal" font="default" size="100%">Merozoite Surface Protein 1</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmodium falciparum</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Single Nucleotide</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombination, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Tanzania</style></keyword><keyword><style  face="normal" font="default" size="100%">Thailand</style></keyword><keyword><style  face="normal" font="default" size="100%">Vietnam</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Jan 30</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">304</style></volume><pages><style face="normal" font="default" size="100%">65-75</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The merozoite surface protein-1 (MSP-1) of the malaria parasite Plasmodium falciparum is a major blood-stage antigen containing highly polymorphic tripeptide repeats in the domain known as block 2 and several non-repetitive domains that are essentially dimorphic. We have analyzed sequence variation in block 2 repeats and in non-repetitive block 17, as well as other polymorphisms within the MSP-1 gene, in clinical isolates of P. falciparum. Repeat haplotypes were defined as unique combinations of repeat motifs within block 2, whereas block 17 haplotypes were defined as unique combinations of single nucleotide replacements in this domain. A new block 17 haplotype, E-TNG-L, was found in one isolate from Vietnam. MSP-1 alleles, defined as unique combinations of haplotypes in blocks 2 and 17 and other polymorphisms within the molecule, were characterized in 60 isolates from hypoendemic Brazil and 37 isolates from mesoendemic Vietnam. Extensive diversity has been created in block 2 and elsewhere in the molecule, while maintaining significant linkage disequilibrium between polymorphisms across the non-telomeric MSP-1 locus separated by a map distance of more than 4 kb, suggesting that low meiotic recombination rates occur in both parasite populations. These results indicate a role for non-homologous recombination, such as strand-slippage mispairing during mitosis and gene conversion, in creating variation in a malarial antigen under strong diversifying selection.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12568716?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Burke, William D</style></author><author><style face="normal" font="default" size="100%">Malik, Harmit S</style></author><author><style face="normal" font="default" size="100%">Rich, Stephen M</style></author><author><style face="normal" font="default" size="100%">Eickbush, Thomas H</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia.</style></title><secondary-title><style face="normal" font="default" size="100%">Mol Biol Evol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mol. Biol. Evol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Protozoan</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Giardia lamblia</style></keyword><keyword><style  face="normal" font="default" size="100%">Long Interspersed Nucleotide Elements</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Open Reading Frames</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Repetitive Sequences, Nucleic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Nucleic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Telomere</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">19</style></volume><pages><style face="normal" font="default" size="100%">619-30</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Mobile elements that use reverse transcriptase to make new copies of themselves are found in all major lineages of eukaryotes. The non-long terminal repeat (non-LTR) retrotransposons have been suggested to be the oldest of these eukaryotic elements. Phylogenetic analysis of non-LTR elements suggests that they have predominantly undergone vertical transmission, as opposed to the frequent horizontal transmissions found for other mobile elements. One prediction of this vertical model of inheritance is that the oldest lineages of eukaryotes should exclusively harbor the oldest lineages of non-LTR retrotransposons. Here we characterize the non-LTR retrotransposons present in one of the most primitive eukaryotes, the diplomonad Giardia lamblia. Two families of elements were detected in the WB isolate of G. lamblia currently being used for the genome sequencing project. These elements are clearly distinct from all other previously described non-LTR lineages. Phylogenetic analysis indicates that these Genie elements (for Giardia early non-LTR insertion element) are among the oldest known lineages of non-LTR elements consistent with strict vertical descent. Genie elements encode a single open reading frame with a carboxyl terminal endonuclease domain. Genie 1 is site specific, as seven to eight copies are present in a single tandem array of a 771-bp repeat near the telomere of one chromosome. The function of this repeat is not known. One additional, highly divergent, element within the Genie 1 lineage is not located in this tandem array but is near a second telomere. Four different telomere addition sites could be identified within or near the Genie elements on each of these chromosomes. The second lineage of non-LTR elements, Genie 2, is composed of about 10 degenerate copies. Genie 2 elements do not appear to be site specific in their insertion. An unusual aspect of Genie 2 is that all copies contain inverted repeats up to 172 bp in length.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11961096?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Martz, Eric</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Protein Explorer: easy yet powerful macromolecular visualization.</style></title><secondary-title><style face="normal" font="default" size="100%">Trends Biochem Sci</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Trends Biochem. Sci.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Macromolecular Substances</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Structure, Secondary</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">27</style></volume><pages><style face="normal" font="default" size="100%">107-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Protein Explorer (PE, http://www.proteinexplorer.org) enables students, educators and other nonspecialists to visualize macromolecular structures easily. It also offers several advanced capabilities useful to protein structure specialists. Great attention has been given to making PE easy to use. Explanations, color keys and troubleshooting information are displayed automatically. There are also 'Frequently Asked Questions', a one-hour 'Quick-Tour', an alphabetical 'Help/Index/Glossary', and a detailed 'Tutorial'; all making PE much easier to use than either Chime or RasMol. Moreover, it is much more powerful; in addition to basic macromolecular visualization capabilities common to most similar programs, it offers one-click visualization of interfaces between moieties ('contacts'), cation-pi interactions and salt bridges, as well as easy-to-use routines to visualize regions of conservation in three-dimensional protein structures based on multiple sequence alignments.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11852249?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sandler, S J</style></author><author><style face="normal" font="default" size="100%">Hugenholtz, P</style></author><author><style face="normal" font="default" size="100%">Schleper, C</style></author><author><style face="normal" font="default" size="100%">DeLong, E F</style></author><author><style face="normal" font="default" size="100%">Pace, N R</style></author><author><style face="normal" font="default" size="100%">Clark, A J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Diversity of radA genes from cultured and uncultured archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Archaeal Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cloning, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Primers</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Repair</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombinant Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Saccharomyces cerevisiae</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1999</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1999 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">181</style></volume><pages><style face="normal" font="default" size="100%">907-15</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 radA genes from uncultured natural sources. Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species of Crenarcheota. The two most deeply branching archaeal radA genes found had some amino acid deletion and insertion patterns characteristic of bacterial recA genes. Possible explanations are discussed. Finally, signature codons are presented to distinguish among RecA protein family members.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/9922255?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ayala, F J</style></author><author><style face="normal" font="default" size="100%">Escalante, A A</style></author><author><style face="normal" font="default" size="100%">Rich, S M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolution of Plasmodium and the recent origin of the world populations of Plasmodium falciparum.</style></title><secondary-title><style face="normal" font="default" size="100%">Parassitologia</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Parassitologia</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Protozoan</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Hominidae</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Merozoite Surface Protein 1</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmodium</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmodium falciparum</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1999</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1999 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">41</style></volume><pages><style face="normal" font="default" size="100%">55-68</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We have investigated the evolution of Plasmodium parasites by analyzing DNA sequences of several genes. We reach the following conclusions: (1) The four human parasites, P. falciparum, P. malariae, P. ovale, and P. vivax are very remotely related to each other, so that their evolutionary divergence predates the origin of the hominids; several of these parasites became associated with the human lineage by lateral transfer from other hosts. (2) P. falciparum diverged from P. reichenowi about 8 million years ago, consistently with the time of divergence of the human lineage from the apes; a parsimonious inference is that falciparum has been associated with humans since the origin of the hominids. (3) P. malariae is genetically indistinguishable from P. brasilianum, a parasite of New World monkeys; and, similarly. (4) P. vivax is genetically indistinguishable from the New World monkey parasite P. simium. We infer in each of these two cases a very recent lateral transfer between the human and monkey hosts, and explore alternative hypotheses about the direction of the transfer. We have also investigated the population structure of P. falciparum by analyzing 10 genes and conclude that the extant world populations of this parasite have evolved from a single strain within the last several thousand years. The extensive polymorphisms observed in the highly repetitive central region of the Csp gene, as well as the apparently very divergent two classes of alleles at the Msa-1 gene, are consistent with this conclusion.</style></abstract><issue><style face="normal" font="default" size="100%">1-3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/10697834?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rich, S M</style></author><author><style face="normal" font="default" size="100%">Licht, M C</style></author><author><style face="normal" font="default" size="100%">Hudson, R R</style></author><author><style face="normal" font="default" size="100%">Ayala, F J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum.</style></title><secondary-title><style face="normal" font="default" size="100%">Proc Natl Acad Sci U S A</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Africa</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Asia</style></keyword><keyword><style  face="normal" font="default" size="100%">Climate</style></keyword><keyword><style  face="normal" font="default" size="100%">Demography</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Protozoan</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Protozoan</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Life Cycle Stages</style></keyword><keyword><style  face="normal" font="default" size="100%">Malaria</style></keyword><keyword><style  face="normal" font="default" size="100%">Malaria, Falciparum</style></keyword><keyword><style  face="normal" font="default" size="100%">Netherlands</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmodium</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmodium falciparum</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">South America</style></keyword><keyword><style  face="normal" font="default" size="100%">Tetrahydrofolate Dehydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Time</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1998</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1998 Apr 14</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">95</style></volume><pages><style face="normal" font="default" size="100%">4425-30</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We have analyzed DNA sequences from world-wide geographic strains of Plasmodium falciparum and found a complete absence of synonymous DNA polymorphism at 10 gene loci. We hypothesize that all extant world populations of the parasite have recently derived (within several thousand years) from a single ancestral strain. The upper limit of the 95% confidence interval for the time when this most recent common ancestor lived is between 24,500 and 57,500 years ago (depending on different estimates of the nucleotide substitution rate); the actual time is likely to be much more recent. The recent origin of the P. falciparum populations could have resulted from either a demographic sweep (P. falciparum has only recently spread throughout the world from a small geographically confined population) or a selective sweep (one strain favored by natural selection has recently replaced all others). The selective sweep hypothesis requires that populations of P. falciparum be effectively clonal, despite the obligate sexual stage of the parasite life cycle. A demographic sweep that started several thousand years ago is consistent with worldwide climatic changes ensuing the last glaciation, increased anthropophilia of the mosquito vectors, and the spread of agriculture. P. falciparum may have rapidly spread from its African tropical origins to the tropical and subtropical regions of the world only within the last 6,000 years. The recent origin of the world-wide P. falciparum populations may account for its virulence, as the most malignant of human malarial parasites.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/9539753?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Brendel, V</style></author><author><style face="normal" font="default" size="100%">Brocchieri, L</style></author><author><style face="normal" font="default" size="100%">Sandler, S J</style></author><author><style face="normal" font="default" size="100%">Clark, A J</style></author><author><style face="normal" font="default" size="100%">Karlin, S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms.</style></title><secondary-title><style face="normal" font="default" size="100%">J Mol Evol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Mol. Evol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Archaeal Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Cycle Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Consensus Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Conserved Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Rad51 Recombinase</style></keyword><keyword><style  face="normal" font="default" size="100%">Rec A Recombinases</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1997</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1997 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">44</style></volume><pages><style face="normal" font="default" size="100%">528-41</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Protein sequences with similarities to Escherichia coli RecA were compared across the major kingdoms of eubacteria, archaebacteria, and eukaryotes. The archaeal sequences branch monophyletically and are most closely related to the eukaryotic paralogous Rad51 and Dmc1 groups. A multiple alignment of the sequences suggests a modular structure of RecA-like proteins consisting of distinct segments, some of which are conserved only within subgroups of sequences. The eukaryotic and archaeal sequences share an N-terminal domain which may play a role in interactions with other factors and nucleic acids. Several positions in the alignment blocks are highly conserved within the eubacteria as one group and within the eukaryotes and archaebacteria as a second group, but compared between the groups these positions display nonconservative amino acid substitutions. Conservation within the RecA-like core domain identifies possible key residues involved in ATP-induced conformational changes. We propose that RecA-like proteins derive evolutionarily from an assortment of independent domains and that the functional homologs of RecA in noneubacteria comprise an array of RecA-like proteins acting in series or cooperatively.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/9115177?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Boyd, E F</style></author><author><style face="normal" font="default" size="100%">Hill, C W</style></author><author><style face="normal" font="default" size="100%">Rich, S M</style></author><author><style face="normal" font="default" size="100%">Hartl, D L</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mosaic structure of plasmids from natural populations of Escherichia coli.</style></title><secondary-title><style face="normal" font="default" size="100%">Genetics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genetics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Helicases</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Mosaicism</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid Hybridization</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmids</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombination, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Repressor Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Trans-Activators</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1996</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1996 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">143</style></volume><pages><style face="normal" font="default" size="100%">1091-100</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The distribution of plasmids related to the fertility factor F was examined in the ECOR reference collection of Escherichia coli. Probes specific for four F-related genes were isolated and used to survey the collection by DNA hybridization. To estimate the genetic diversity of genes in F-like plasmids, DNA sequences were obtained for four plasmid genes. The phylogenetic relationships among the plasmids in the ECOR strains is very different from that of the strains themselves. This finding supports the view that plasmid transfer has been frequent within and between the major groups of ECOR. Furthermore, the sequences indicate that recombination between genes in plasmids takes place at a considerably higher frequency than that observed for chromosomal genes. The plasmid genes, and by inference the plasmids themselves, are mosaic in structure with different regions acquired from different sources. Comparison of gene sequences from a variety of naturally occurring plasmids suggested a plausible donor of some of the recombinant regions as well as implicating a chi site in the mechanism of genetic exchange. The relatively high rate of recombination in F-plasmid genes suggests that conjugational gene transfer may play a greater role in bacterial population structure than previously appreciated.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/8807284?dopt=Abstract</style></custom1></record></records></xml>