14 results on '"Gregory E. Jordan"'
Search Results
2. PhyloWidget: web-based visualizations for the tree of life.
- Author
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Gregory E. Jordan and William H. Piel
- Published
- 2008
- Full Text
- View/download PDF
3. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.
- Author
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Botond Sipos, Tim Massingham, Gregory E. Jordan, and Nick Goldman
- Published
- 2011
- Full Text
- View/download PDF
4. SMIM1 underlies the Vel blood group and influences red blood cell traits
- Author
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Dorine W. Swinkels, Heather Lloyd-Jones, Hendrik G. Stunnenberg, Graham Kiddle, Hindrik H. D. Kerstens, Gregory E. Jordan, Lonneke Haer-Wigman, Rudolf S N Fehrmann, Juha Karjalainen, Herman H W Silljé, Peter A. Smethurst, Cornelis A. Albers, Harm-Jan Westra, Hein Schepers, Jonathan Stephens, J. Poole, Willem H. Ouwehand, Mattia Frontini, Derek L. Stemple, Nicole Soranzo, Nicholas A. Watkins, Niek Verweij, Samantha Farrow, Augusto Rendon, Emile van den Akker, Vincent G. Haver, Alan Gray, C. Ellen van der Schoot, Ana Cvejic, Jennifer G. Sambrook, Myrto Kostadima, Nick Goldman, Ewa Bielczyk-Maczyńska, Botond Sipos, Malcolm Needs, Asif U. Tamuri, Aicha Ait Soussan, Lude Franke, Klaus Rieneck, Paul Bertone, Pim van der Harst, Masja de Haas, Damage and Repair in Cancer Development and Cancer Treatment (DARE), Guided Treatment in Optimal Selected Cancer Patients (GUTS), Stem Cell Aging Leukemia and Lymphoma (SALL), Cardiovascular Centre (CVC), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Landsteiner Laboratory, and Clinical Haematology
- Subjects
Erythrocytes ,Molecular Sequence Data ,Quantitative Trait Loci ,Iron metabolism Pathogenesis and modulation of inflammation [IGMD 7] ,GENOMES ,Electrophoretic Mobility Shift Assay ,030204 cardiovascular system & hematology ,Biology ,VARIANTS ,Article ,Frameshift mutation ,Genomic disorders and inherited multi-system disorders DCN MP - Plasticity and memory [IGMD 3] ,03 medical and health sciences ,0302 clinical medicine ,Isoantibodies ,Pregnancy ,Gene expression ,Genetics ,medicine ,Animals ,Humans ,Exome ,Gene Regulatory Networks ,Allele ,Gene ,Molecular Biology ,Alleles ,Zebrafish ,030304 developmental biology ,Oligonucleotide Array Sequence Analysis ,GENE-EXPRESSION ,0303 health sciences ,Gene knockdown ,Gene Expression Profiling ,Erythrocyte Membrane ,Homozygote ,Membrane Proteins ,Molecular biology ,3. Good health ,Gene expression profiling ,Red blood cell ,ALIGNMENT ,medicine.anatomical_structure ,biology.protein ,Blood Group Antigens ,Female ,Antibody ,Biomarkers ,Gene Deletion - Abstract
The blood group Vel was discovered 60 years ago(1), but the underlying gene is unknown. Individuals negative for the Vel antigen are rare and are required for the safe transfusion of patients with antibodies to Vel(2). To identify the responsible gene, we sequenced the exomes of five individuals negative for the Vel antigen and found that four were homozygous and one was heterozygous for a low-frequency 17-nucleotide frameshift deletion in the gene encoding the 78-amino-acid transmembrane protein SMIM1. A follow-up study showing that 59 of 64 Vel-negative individuals were homozygous for the same deletion and expression of the Vel antigen on SMIM1-transfected cells confirm SMIM1 as the gene underlying the Vel blood group. An expression quantitative trait locus (eQTL), the common SNP rs1175550 contributes to variable expression of the Vel antigen (P = 0.003) and influences the mean hemoglobin concentration of red blood cells (RBCs; P = 8.6 x 10(-15))(3). In vivo, zebrafish with smim1 knockdown showed a mild reduction in the number of RBCs, identifying SMIM1 as a new regulator of RBC formation. Our findings are of immediate relevance, as the homozygous presence of the deletion allows the unequivocal identification of Vel-negative blood donors.
- Published
- 2013
5. Insights into hominid evolution from the gorilla genome sequence
- Author
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Paul Flicek, Yong Gu, David Neil Cooper, Tuuli Lappalainen, Nicholas I. Mundy, Petra C. Schwalie, Bryndis Yngvadottir, Peter D. Stenson, Michelle C Ward, Stephen H. Montgomery, Linda Vigilant, Matthew Mort, Katy Shaw, Julien Y. Dutheil, Lars Nørvang Andersen, Wesley C. Warren, Paul Heath, Emmanouil T. Dermitzakis, Edward V. Ball, Kathryn Beal, LaDeana W. Hillier, Tomas Marques-Bonet, Yali Xue, Javier Herrero, Richard K. Wilson, Emre Karakoc, Andreas Heger, Michael A. Quail, Yuan Chen, Daniel J. Turner, Kasper Munch, Anja Kolb-Kokocinski, Aylwyn Scally, Gregory E. Jordan, Pieter J. de Jong, Saba Sajjadian, Timothy D. O’Connor, Duncan T. Odom, Richard Durbin, Chris P. Ponting, Oliver A. Ryder, Andrew David Phillips, James C. Mullikin, Anthony Rogers, Javier Prado-Martinez, Stephen Meader, Jared T. Simpson, Gavin K. Laird, Chris Tyler-Smith, Shane A. McCarthy, Qasim Ayub, Can Alkan, Chris Clee, Mikkel H. Schierup, Weldon Whitener, Evan E. Eichler, Tina Graves, Asger Hobolth, Gerton Lunter, Stephen M. J. Searle, Ian Goodhead, Zemin Ning, Y. Amy Tang, Brenda J. Bradley, Dominic Schmidt, Stephen Fitzgerald, Nick Goldman, Jane Rogers, Baoli Zhu, Albert J. Vilella, Thomas Mailund, Scally, Aylwyn [0000-0002-0807-1167], McCarthy, Shane [0000-0002-2715-4187], Montgomery, Stephen [0000-0002-5474-5695], Mundy, Nicholas [0000-0002-5545-1517], Odom, Duncan [0000-0001-6201-5599], Apollo - University of Cambridge Repository, Wellcome Trust, European Molecular Biology Laboratory, University of Cambridge, Lundbeck Foundation, Academy of Finland, Emil Aaltonen Foundation, European Commission, European Research Council, Ministerio de Educación (España), Biotechnology and Biological Sciences Research Council (UK), Medical Research Council (UK), National Human Genome Research Institute (US), Danish Council for Independent Research, Swiss National Science Foundation, Louis Jeantet Foundation, EMBO, BIOBASE, National Science Foundation (US), Howard Hughes Medical Institute, Lappalainen, Tuuli Emilia, and Dermitzakis, Emmanouil
- Subjects
0106 biological sciences ,Transcription, Genetic ,Gorilla ,01 natural sciences ,Genome ,ddc:576.5 ,Phylogeny ,Pongo/genetics ,Genetics ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Genomics ,Eastern gorilla ,3. Good health ,Genetic Variation/genetics ,Proteins/genetics ,Female ,Pan troglodytes ,Genetic Speciation ,Population ,Molecular Sequence Data ,Biology ,010603 evolutionary biology ,Article ,Evolution, Molecular ,03 medical and health sciences ,Western lowland gorilla ,Species Specificity ,biology.animal ,Animals ,Humans ,Gorilla gorilla/genetics ,Pan troglodytes/genetics ,education ,Gene ,030304 developmental biology ,Gorilla gorilla ,Pongo ,Genetic Variation ,Proteins ,biology.organism_classification ,Macaca mulatta ,Macaca mulatta/genetics ,Population bottleneck ,Gene Expression Regulation ,Evolutionary biology ,Genome/genetics ,Sequence Alignment - Abstract
Scally, A. et al., Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. © 2012 Macmillan Publishers Limited. All rights reserved., This research was supported in part by Wellcome Trust grants WT062023(toJ.H.,K.B.,S.F.,A.J.V.,P.F.),WT089066(toR.D.),WT077192(toR.D.,S.M., A.K.-K., J.T.S., W.W.), WT077009 (to Y.X., B.Y., Q.A., Y.C., C.T.-S.), WT077198 (to G.K.L.) and 075491/Z/04 (to G.L.); EMBL grants (to P.C.S., P.F.); scholarships from the Gates Cambridge Trust (to G.E.J. and T.D.O’C.); an MRC Special Fellowship in Biomedical Informatics (toA.S.);funding from the Lundbeck Foundation(toA.H.);the Academy of Finland and the Emil Aaltonen Foundation(toT.L.);a Marie Curie fellowship(toT.M.-B.); the European Community’s Seventh Framework Programme (FP7/2007-2013)/ ERC Starting Grant(StG_20091118)(toT.M.-B.);an FPI grant from the Spanish Ministry of Education (BES-2010-032251) (to J.P.-M.); a BBSRC Doctoral Training Grant (to S.H.M.); grants from the UK Medical Research Council (to A.H., S.M., C.P.P.); the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health(to J.C.M.);the Danish Council for Independent Research, Natural Sciences,grant no.09-062535(toK.M.,M.H.S.);a Commonwealth Scholarship (to M.C.W.); the Swiss National Science Foundation, Louis Jeantet Foundation (to E.T.D.); an ERC Starting Grant and an EMBO Young Investigator Award, Hutchinson Whampoa (to D.T.O.); NHGRI support (to W.C.W.); support from BIOBASE GmbH (to E.V.B., P.D.S., M.M., A.D.P., K.S., D.N.C.); US National Science Foundation grant DGE-0739133(toW.W.);NHGRIU54HG003079(toR.K.W.);NIHgrantHG002385(to E.E.E). E.E.E. is an investigator of the Howard Hughes Medical Institute.
- Published
- 2016
6. SWAMP: Sliding Window Alignment Masker for PAML
- Author
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Gregory E. Jordan, Stephen H. Montgomery, and Peter W. Harrison
- Subjects
0106 biological sciences ,Nonsynonymous substitution ,sequence analysis ,Sequence analysis ,Computer science ,lcsh:Evolution ,Genomics ,genome evolution ,computer.software_genre ,010603 evolutionary biology ,01 natural sciences ,Swamp ,Masking (Electronic Health Record) ,03 medical and health sciences ,Sliding window protocol ,Genetics ,False positive paradox ,lcsh:QH359-425 ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,geography ,adaptive evolution ,geography.geographical_feature_category ,Phylogenetic tree ,molecular evolution ,PAML ,Computer Science Applications ,phylogenetics ,Technical Advance ,Data mining ,computer - Abstract
With the greater availability of genetic data, large genome-wide scans for positive selection increasingly incorporate data from a range of sources. These data sets may be derived from different sequencing methods, each of which has potential sources of error. Sequencing errors, compounded by alignment errors, greatly increase the number of false positives in tests for adaptive evolution. Genome-wide analyses often fail to fully address these issues or to provide sufficient detail on postalignment masking/filtering. Here, we introduce a Sliding Window Alignment Masker for Phylogenetic Analysis by Maximum Likelihood (SWAMP) that scans multiple-sequence alignments for short regions enriched with unreasonably high rates of nonsynonymous substitutions caused, for example, by sequence or alignment errors. SWAMP prevents their inclusion in downstream evolutionary analyses and therefore increases the reliability of downstream analyses. It is able to effectively mask short stretches of erroneous sequence, particularly prevalent in low-coverage genomes, which may not be detected by existing methods based on filtering by sitewise conservation or alignment confidence. SWAMP offers a flexible masking approach, and the user can apply different masking regimens to specific branches or sequences in the phylogeny allowing the stringency of masking to vary according to branch length, expected divergence levels, or assembly quality. We exemplify SWAMPs effectiveness on a dataset of 6,379 protein-coding genes from primate species, including data of variable quality. Full reporting of the software parameters will further improve the reproducibility of genome-wide analyses, as well as reduce false-positive rates. Availability SWAMP is freely available, published under GNU GPL v3, including documentation and example test data from http://github.com/peterwharrison/SWAMP
- Published
- 2014
7. A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes
- Author
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Anna Ferrer-Admetlla, Matteo Fumagalli, Gregory E. Jordan, Emilia Huerta-Sanchez, Mehmet Somel, Rasmus Nielsen, and Melissa A. Wilson Sayres
- Subjects
Nonsynonymous substitution ,relaxation of constraints ,Balancing selection ,Genome ,Negative selection ,0302 clinical medicine ,Gene Frequency ,Genetics ,0303 health sciences ,education.field_of_study ,negative selection ,Single Nucleotide ,Human ,Biotechnology ,Proteasome Endopeptidase Complex ,Pan troglodytes ,Evolution ,1.1 Normal biological development and functioning ,Population ,Biology ,Polymorphism, Single Nucleotide ,Evolution, Molecular ,03 medical and health sciences ,human evolution ,Genetic ,Animals ,Humans ,Selection, Genetic ,Polymorphism ,education ,Molecular Biology ,Gene ,Selection ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,030304 developmental biology ,Evolutionary Biology ,Polymorphism, Genetic ,Genome, Human ,Human Genome ,Molecular ,proteasome ,Proteasome ,olfactory transduction ,Human genome ,Generic health relevance ,Biochemistry and Cell Biology ,030217 neurology & neurosurgery - Abstract
Environmental or genomic changes during evolution can relax negative selection pressure on specific loci, permitting high frequency polymorphisms at previously conserved sites. Here, we jointly analyze population genomic and comparative genomic data to search for functional processes showing relaxed negative selection specifically in the human lineage, whereas remaining evolutionarily conserved in other mammals. Consistent with previous studies, we find that olfactory receptor genes display such a signature of relaxation in humans. Intriguingly, proteasome genes also show a prominent signal of human-specific relaxation: multiple proteasome subunits, including four members of the catalytic core particle, contain high frequency nonsynonymous polymorphisms at sites conserved across mammals. Chimpanzee proteasome genes do not display a similar trend. Human proteasome genes also bear no evidence of recent positive or balancing selection. These results suggest human-specific relaxation of negative selection in proteasome subunits; the exact biological causes, however, remain unknown.
- Published
- 2013
8. The effects of alignment error and alignment filtering on the sitewise detection of positive selection
- Author
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Nick Goldman and Gregory E. Jordan
- Subjects
False positives and false negatives ,Biology ,Bioinformatics ,Evolution, Molecular ,INDEL Mutation ,Genetics ,False positive paradox ,Animals ,Humans ,Computer Simulation ,Selection, Genetic ,Divergence (statistics) ,Indel ,Codon ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Models, Genetic ,business.industry ,Positive selection ,Computational Biology ,Pattern recognition ,False positive rate ,Artificial intelligence ,business ,Sequence Alignment ,Algorithms - Abstract
When detecting positive selection in proteins, the prevalence of errors resulting from misalignment and the ability of alignment filters to mitigate such errors are not well understood, but filters are commonly applied to try to avoid false positive results. Focusing on the sitewise detection of positive selection across a wide range of divergence levels and indel rates, we performed simulation experiments to quantify the false positives and false negatives introduced by alignment error and the ability of alignment filters to improve performance. We found that some aligners led to many false positives, whereas others resulted in very few. False negatives were a problem for all aligners, increasing with sequence divergence. Of the aligners tested, PRANK’s codon-based alignments consistently performed the best and ClustalW performed the worst. Of the filters tested, GUIDANCE performed the best and Gblocks performed the worst. Although some filters showed good ability to reduce the error rates from ClustalW and MAFFT alignments, none were found to substantially improve the performance of PRANK alignments under most conditions. Our results revealed distinct trends in error rates and power levels for aligners and filters within a biologically plausible parameter space. With the best aligner, a low false positive rate was maintained even with extremely divergent indel-prone sequences. Controls using the true alignment and an optimal filtering method suggested that performance improvements could be gained by improving aligners or filters to reduce the prevalence of false negatives, especially at higher divergence levels and indel rates.
- Published
- 2011
9. Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome
- Author
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Augusto Rendon, Ana Cvejic, Paquita Nurden, Peter A. Smethurst, Ross Kettleborough, Randy J. Read, Willem H. Ouwehand, Katrin Voss, Rémi Favier, Graham Kiddle, Paul Bertone, Marie-Christine Alessi, Myrto Kostadima, Botond Sipos, Cornelis A. Albers, Alan T. Nurden, Evelien E. Bouwmans, Gregory E. Jordan, Jonathan Stephens, Suthesh Sivapalaratnam, Cvejic, Ana [0000-0003-3204-9311], Bertone, Paul [0000-0001-5059-4829], Read, Randy [0000-0001-8273-0047], Stephens, Jonathan [0000-0003-2020-9330], Rendon Restrepo, Augusto [0000-0001-8994-0039], Ouwehand, Willem [0000-0002-7744-1790], Apollo - University of Cambridge Repository, and Vascular Medicine
- Subjects
Adult ,Blood Platelets ,Male ,Embryo, Nonmammalian ,Platelet disorder ,Molecular Sequence Data ,Nerve Tissue Proteins ,030204 cardiovascular system & hematology ,Cytoplasmic Granules ,Gray Platelet Syndrome ,Article ,Gray platelet syndrome ,Animals, Genetically Modified ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,Sequence Homology, Nucleic Acid ,Genetics ,medicine ,Gene silencing ,Animals ,Humans ,Platelet ,Zebrafish ,Gene ,Exome sequencing ,030304 developmental biology ,Aged ,Regulation of gene expression ,0303 health sciences ,biology ,Base Sequence ,Secretory Vesicles ,Gene Expression Regulation, Developmental ,Sequence Analysis, DNA ,Middle Aged ,biology.organism_classification ,medicine.disease ,Pedigree ,Immunology ,Female - Abstract
Gray platelet syndrome (GPS) is a predominantly recessive platelet disorder that is characterized by mild thrombocytopenia with large platelets and a paucity of α-granules; these abnormalities cause mostly moderate but in rare cases severe bleeding. We sequenced the exomes of four unrelated individuals and identified NBEAL2 as the causative gene; it has no previously known function but is a member of a gene family that is involved in granule development. Silencing of nbeal2 in zebrafish abrogated thrombocyte formation.
- Published
- 2011
10. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
- Author
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Nick Goldman, Gregory E. Jordan, Botond Sipos, and Tim Massingham
- Subjects
Theoretical computer science ,Computer science ,Monte Carlo method ,Sequence alignment ,lcsh:Computer applications to medicine. Medical informatics ,Biochemistry ,Evolution, Molecular ,Software ,Structural Biology ,Molecular evolution ,Phylogenetics ,Computational statistics ,Sequence alignment algorithm ,Animals ,Humans ,Computer Simulation ,Indel ,Mathematical Computing ,Molecular Biology ,lcsh:QH301-705.5 ,Phylogeny ,Sequence ,Functional programming ,Base Sequence ,Models, Genetic ,business.industry ,Applied Mathematics ,Gillespie algorithm ,Computer Science Applications ,lcsh:Biology (General) ,lcsh:R858-859.7 ,DNA microarray ,business ,Monte Carlo Method ,Algorithms ,Monte Carlo molecular modeling - Abstract
Background The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity. Results PhyloSim is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, PhyloSim can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing PhyloSim to be adapted to specific needs. Conclusions Close integration with R and the wide range of features implemented offer unmatched flexibility, making it possible to simulate sequence evolution under a wide range of realistic settings. We believe that PhyloSim will be useful to future studies involving simulated alignments.
- Published
- 2011
11. Assigning strains to bacterial species via the internet
- Author
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Cynthia J. Bishop, Gregory E. Jordan, David M. Aanensen, Mogens Kilian, William P. Hanage, and Brian G. Spratt
- Subjects
Life Sciences & Biomedicine - Other Topics ,Physiology ,Sequence analysis ,Plant Science ,Computational biology ,General Biochemistry, Genetics and Molecular Biology ,Microbiology ,Tree (descriptive set theory) ,Type (biology) ,Species Specificity ,Structural Biology ,Databases, Genetic ,Cluster Analysis ,Biology ,lcsh:QH301-705.5 ,Ecology, Evolution, Behavior and Systematics ,Alleles ,Internet ,Science & Technology ,biology ,Agricultural and Biological Sciences(all) ,Bacteria ,business.industry ,Biochemistry, Genetics and Molecular Biology(all) ,Strain (biology) ,Genetic Variation ,Cell Biology ,Biological Sciences ,biology.organism_classification ,Classification ,Viridans Streptococci ,Phenotype ,lcsh:Biology (General) ,Viridans streptococci ,The Internet ,Identification (biology) ,Taxonomy (biology) ,General Agricultural and Biological Sciences ,business ,Life Sciences & Biomedicine ,Developmental Biology ,Biotechnology ,Research Article - Abstract
Background Methods for assigning strains to bacterial species are cumbersome and no longer fit for purpose. The concatenated sequences of multiple house-keeping genes have been shown to be able to define and circumscribe bacterial species as sequence clusters. The advantage of this approach (multilocus sequence analysis; MLSA) is that, for any group of related species, a strain database can be produced and combined with software that allows query strains to be assigned to species via the internet. As an exemplar of this approach, we have studied a group of species, the viridans streptococci, which are very difficult to assign to species using standard taxonomic procedures, and have developed a website that allows species assignment via the internet. Results Seven house-keeping gene sequences were obtained from 420 streptococcal strains to produce a viridans group database. The reference tree produced using the concatenated sequences identified sequence clusters which, by examining the position on the tree of the type strain of each viridans group species, could be equated with species clusters. MLSA also identified clusters that may correspond to new species, and previously described species whose status needs to be re-examined. A generic website and software for electronic taxonomy was developed. This site http://www.eMLSA.net allows the sequences of the seven gene fragments of a query strain to be entered and for the species assignment to be returned, according to its position within an assigned species cluster on the reference tree. Conclusion The MLSA approach resulted in the identification of well-resolved species clusters within this taxonomically challenging group and, using the software we have developed, allows unknown strains to be assigned to viridans species via the internet. Submission of new strains will provide a growing resource for the taxonomy of viridans group streptococci, allowing the recognition of potential new species and taxonomic anomalies. More generally, as the software at the MLSA website is generic, MLSA schemes and strain databases for other groups of related species can be hosted at this website, providing a portal for microbial electronic taxonomy.
- Published
- 2009
12. Minimally cationic cell-permeable miniature proteins via alpha-helical arginine display
- Author
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Gregory E. Jordan, Betsy A. Smith, Douglas S. Daniels, Lynn M. McGregor, Abigail Coplin, and Alanna Schepartz
- Subjects
Protein Folding ,Cell Membrane Permeability ,Time Factors ,Arginine ,Protein Conformation ,Cell ,Amino Acid Motifs ,Biochemistry ,Catalysis ,Protein Structure, Secondary ,Colloid and Surface Chemistry ,Protein structure ,Cations ,medicine ,Humans ,Amino Acid Sequence ,Peptide sequence ,Polyproline helix ,Chemistry ,Cationic polymerization ,Proteins ,General Chemistry ,medicine.anatomical_structure ,Membrane ,Biophysics ,Protein folding ,HeLa Cells - Abstract
Protein therapeutics are a blossoming industry, with revenues exceeding $51 billion in 2005 and a growth rate nearly three times that of the overall pharmaceutical industry. Although it has been known for decades that cationic polymers can transport molecular cargos across the plasma membrane, inefficient cellular delivery continues to impede the development of protein drugs. Our lab recently reported that small, folded proteins containing a minimal cationic motif embedded within a type II polyproline (PPII) helix efficiently cross the plasma membrane of eukaryotic cells. Here we demonstrate that an even smaller cationic motif can be embedded within the α-helix of a small, folded protein to generate molecules that penetrate cells significantly more efficiently than arginine-rich sequences or Tat. Our results suggest that the function of cell permeability can be encoded by judicious placement of as few as 2−3 additional arginine residues on a protein α-helix.
- Published
- 2008
13. Wind and Fire: St. Catherine of Siena and the North Wind in John Greenleaf Whittier's Snow-Bound
- Author
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Gregory E. Jordan
- Subjects
Cultural Studies ,History ,Literature and Literary Theory ,Snow ,Archaeology - Published
- 1995
14. PhyloWidget: web-based visualizations for the tree of life
- Author
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William H. Piel and Gregory E. Jordan
- Subjects
Statistics and Probability ,Source code ,Computer science ,Download ,media_common.quotation_subject ,Tree of life ,Biochemistry ,Evolution, Molecular ,World Wide Web ,Software Design ,Databases, Genetic ,Computer Graphics ,Animals ,Humans ,Web application ,Molecular Biology ,Phylogeny ,media_common ,Internet ,Phylogenetic tree ,SIMPLE (military communications protocol) ,Computers ,business.industry ,Computational Biology ,Biological Evolution ,Computer Science Applications ,Visualization ,Computational Mathematics ,Tree (data structure) ,Computational Theory and Mathematics ,Data Display ,Programming Languages ,business ,Algorithms ,Software - Abstract
Summary: PhyloWidget is a web-based tool for the visualization and manipulation of phylogenetic tree data. It can be accessed online or downloaded as a standalone application. A simple URL-based API allows databases to easily link to and customize PhyloWidget for interactively viewing medium- to large-sized trees. Availability: PhyloWidget is available for online use or download at http://www.phylowidget.org/. Its source code is released under the GNU General Public License. Contact: phylowidget@treebase.org
- Published
- 2008
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