| Accepted Posters |
| Category 'F'- Evolution' |
| Poster F02 |
| Horizontal gene transfer evidences on a dual target protein, the tRNA synthetase family. |
| Marcelo Brandão- ESALQ - University of São Paulo |
| Marcio Silva Filho (ESALQ, Genetics); |
| Short Abstract: The aim of this work was to propose a phylogenetic hypotheses for all dual target aminoacyl-tRNA synthetase and to identify the possible bacterial ancestor for each protein. To accomplish this we develop the BIOSPHA, a new suite of scripts that automate all pre-phylogenetics analyses tasks with great accuracy. |
| Long Abstract: Click Here |
| Poster F03 |
| Correlated mutations analysis reveals tRNA binding and recognition sites of amino-acyl tRNA synthetases |
| Milana Morgenstern- Weizmann Institute of Science |
| No additional authors |
| Short Abstract: The aminoacyl-tRNA-synthetases (aaRSs) family comprises twenty enzymes that covalently attach amino acids to the corresponding nucleic acid adaptor molecules, tRNA. We addressed the question of tRNA binding by aaRSs, and tRNA-recognition site adaptation using the correlated mutation analysis inside the aaRS molecules. The physical nature of correlated mutations found as preserved-forces of aaRSs functional sites. |
| Long Abstract: Click Here |
| Poster F04 |
| Estimation of error in rRNA sequences using a maximum likelihood approach. |
| James Cole- Michigan State University |
| Adithya Bandela (Michigan State University, Center for Microbial Ecology); Qiong Wang (Michigan State University, Center for Microbial Ecology); |
| Short Abstract: By making use of the natural variation in the evolutionary rates of substitution at different residues, we estimated the amount of sequencing error in 16S rRNA sequences. Using models incorporating position-dependent rates with and without sequencing error, we determined that 0.3% of the tested rRNA sequences were significantly noisy. |
| Long Abstract: Click Here |
| Poster F05 |
| Protein evolution driven by symmetric structural repeats |
| Anne-Laure Abraham- Institut Pasteur |
| Joël Pothier (UPMC Univ Paris 06, Atelier de BioInformatique); Eduardo P.C. Rocha (Institut Pasteur, Microbial Evolutionary Genomics group); |
| Short Abstract: Duplications play major roles in protein evolution and in functional innovation. We developed a program to detect repeats in DNA and protein sequences, and in 3D structures. Surprisingly we found many symmetrical repeats in 3D structures which we suspect reveals a trend to replace homodimers with a single protein sequence. |
| Long Abstract: Click Here |
| Poster F06 |
| Choice of Distance Measures for Detecting Horizontal Gene Transfer |
| Hua Li- Stowers Institute for Medical Research |
| Lavanya Kannan (Stowers Institute for Medical Research, Bioinformatics Center); Arcady Mushegian (Stowers Institute for Medical Research, Bioinformatics Center); |
| Short Abstract: We investigate statistical properties of four widely used tree distance measures and evaluate their power in detecting Horizontal Gene Transfer (HGT) by a simulation study using perturbed phylogenetic trees. We propose to use Fisher's combined p-values from multiple tests of different distance measures to improve the power of HGT identification. |
| Long Abstract: Click Here |
| Poster F07 |
| Evolutionary analysis of expanded gene families in Mycobacterium Tuberculosis. |
| Venu Vuppu- IIDMM |
| Nicky Mulder (IIDMM, NBN UCT Medical School, UCT); |
| Short Abstract: Genomes are subject to modifications depending upon the life style of the organism. The modifications may be due to gene duplications, mutations, recombination, deletion, insertion, or horizontal gene transfer. The project aims to identify and characterize duplicate genes in Mycobacterium tuberculosis H37Rv. |
| Long Abstract: Click Here |
| Poster F08 |
| Systematic Evaluation of Phylogenetic Incongruence Tests |
| Michael Lo- Dalhousie University |
| Christian Blouin (Dalhousie University, Computer Science); |
| Short Abstract: We propose a method to systematically evaluate tests that detect incongruence between the phylogeny of genes, such as the likelihood ratio and incongruence length difference tests. Rigorous testing of the power of these methods is an important step in interpreting complex phylogenies, specifically those of the influenza A virus. |
| Long Abstract: Click Here |
| Poster F09 |
| R/Mesquite: Interoperability of Comparative Methods And Visualization between R and Mesquite |
| Hilmar Lapp- National Evolutionary Synthesis Center (NESCent) |
| Wayne Maddison (University of British Columbia, Departments of Zoology and Botany); |
| Short Abstract: We present the R/Mesquite project, which aims to make features and methods implemented in either R or Mesquite, two rich platforms for comparative phylogenetic analysis, available to the other in a transparent fashion. In addition we report on the 2007 Comparative Methods in R Hackathon, where this work started. |
| Long Abstract: Click Here |
| Poster F10 |
| Structural heterogeneity and turnover of transcript start sites contribute to rapid divergence in expression between duplicate genes |
| Chungoo Park- The Pennsylvania State University |
| Kateryna Makova (The Pennsylvania State University, Biology); |
| Short Abstract: Because of the importance of gene duplication in evolution, it is crucial to know how duplicate genes have diverged and which factors determine their destiny. We revealed that structural difference of duplicate genes is predominant in human, and the turnover of TSSs can also provide evidence of the expression divergence. |
| Long Abstract: Click Here |
| Poster F11 |
| SPHINGOMYELINASE-D (SMASED) OCCURRENCE IN FUNGI, BACTERIA AND ARACHNIDS AND THEIR EVOLUTIVE RELATION |
| Izabella Pena- UFMG - Universidade Federal de Minas Gerais |
| Oto S Coelho-Júnior (UFMG, Bioquímica e Imunologia); J. Miguel Ortega (UFMG, Bioquímica e Imunologia); |
| Short Abstract: A Lateral Gene Transfer of SMaseD between spider and bacteria was previsiously discussed in some works. Now, we show that this history gains another characters: eleven fungi species have proteins very similar to bacteria and spider SmaseD, and maybe the Lateral Gene Transfer includes the fungi proteins in the game. |
| Long Abstract: Click Here |
| Poster F12 |
| An Alignment-Free Approach for Inferring Phylogenies |
| Christopher Bun- Loyola University Chicago |
| No additional authors |
| Short Abstract: Herein we present a set of specialized data structures and metrics for an alignment-free method of comparing sequences and deriving phylogenies. As an example, these tools were used to determine the phylogenic relationship between the diverse, multi-segmented Bunyaviridae virus family as well as the twelve completely sequenced species Drosophila. |
| Long Abstract: Click Here |
| Poster F13 |
| Expansion of the beta-trefoil family by repetition of sub-domain elements |
| Andrew Doxey- University of Waterloo |
| Elizabeth Meiering (University of Waterloo, Chemistry); Brendan McConkey (University of Waterloo, Biology); |
| Short Abstract: An analysis of repeats occurring in the beta-trefoil family was performed to elucidate mechanisms of beta-trefoil family expansion. Through phylogenetic analysis of predicted repeats, we have detected over 30 separate instances of beta-trefoils having arisen by repetition of smaller precursor repeats as opposed to domain duplication. |
| Long Abstract: Click Here |
| Poster F14 |
| Functional specificity and coevolution: a correlated story? |
| Saikat Chakrabarti- National Institutes of Health |
| Stephen Bryant (National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine); Anna Panchenko (National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine); |
| Short Abstract: It is important to identify the sites that are responsible for functional specification within proteins. To address this critical problem a method named SPEER is developed to distinguish specificity determining sites. We also found that specificity determining sites more often participate in coevolutionary relationships with each other and other sites. |
| Long Abstract: Click Here |
| Poster F15 |
| Unraveling protein universe using self consistency grouping |
| Bong-Hyun Kim- UT Southwestern Medical Center at Dallas |
| Lisa Kinch (UT Southwestern Medical Center at Dallas, HHMI); Hua Cheng (UT Southwestern Medical Center at Dallas, HHMI); Nick Grishin (UT Southwestern Medical Center at Dallas, HHMI, Department of Biochemistry); |
| Short Abstract: We clustered proteins into evolutionary groups using both sequence and structure by a fully automated method. We developed a stringent algorithm, self-consistency grouping (SCG) method. Comparison of SCG and other commonly used clustering methods to a widely accepted manual classification scheme showed SCG groups to better reflect the reference classification. |
| Long Abstract: Click Here |
| Poster F16 |
| Codon Usage Reduces Frameshifting Errors in Saccharomyces cerevisiae |
| Yang Huang- NCBI/NLM/NIH |
| Teresa Przytycka (NCBI/NLM/NIH, Computational Biology Branch); David Lipman (NIH, NCBI); |
| Short Abstract: Little is known about the relationship between codon usage and frameshifting errors, an important form of processivity errors. We studied this relation for Saccharomyces cerevisiae gene sequences. Based on a recently proposed frameshifting model, we directly showed that the pattern of codon usage bias indicates a certain level of optimization against frameshifting errors. |
| Long Abstract: Click Here |
| Poster F17 |
| Analysis of Heterogeneous Genome Evolution across the Universal Tree of Life |
| Wataru Iwasaki- University of Tokyo |
| Toshihisa Takagi (University of Tokyo, Department of Computational Biology, Graduate School of Frontier Sciences); |
| Short Abstract: At the previous conference, we presented an effective and efficient method for reconstructing highly heterogeneous history of gene-content evolution with hundreds of genomes (Iwasaki W. and Takagi T., ISMB/ECCB2007). Here, we will introduce what we observed by applying our method to actual genome data across the universal tree of life. |
| Long Abstract: Click Here |
| Poster F18 |
| Diversity of structure and evolutionary reconstruction of the BTB superfamily |
| Peter Stogios- University of Toronto |
| Jose-Antonio Cuesta-Seijo (University Health Network, Cancer Genomics and Proteomics); Lu Chen (University Health Network, Cancer Genomics and Proteomics); Neil Pomroy (University Health Network, Cancer Genomics and Proteomics); Gilbert Prive (University Health Network, Cancer Genomics and Proteomics); |
| Short Abstract: Examples of the BTB fold average 4-35% pairwise sequence identity. We determined the crystal structures of four BTB domains and reconstructed the evolutionary history. The fold is very well-preserved, with variation in domain-swapping, movement of a particular strand, and high diversity in the nature of surface residues. |
| Long Abstract: Click Here |
| Poster F19 |
| Evidence of bias towards buffered codons in human transcripts |
| Eric Rouchka- University of Louisville |
| Rami Mahdi (University of Louisville, Comp. Eng. & Comp. Sci.); |
| Short Abstract: Codon usage bias is considered given selection is expected to act to favor codons more buffered, or protected, from mutation. Buffering capacities of coding sequences are shown to be higher than randomly generated sequences and shifted reading frames. In addition, housekeeping genes are shown to have higher buffering capacities. |
| Long Abstract: Click Here |
| Poster F20 |
| The Effect of Cellular Location and Solvent Exposure to Protein Evolution |
| Joshua Mackaluso- Michigan State University |
| Shin-Han Shiu (Michigan State University, Dept. of Plant Biology); Maria Zavodszky (Michigan State University, Dept. of Bichemistry and Molecular Biology); |
| Short Abstract: We compared the rate of evolution of extracellular and intracellular proteins using a dataset of 100 orthologous human and mouse proteins with known 3-dimensional structures and known cellular locations. The results indicate that extracellular proteins tend to evolve faster, especially in the solvent exposed regions. |
| Long Abstract: Click Here |
| Poster F21 |
| Investigating the modular properties of precursor microRNAs |
| Miler Lee- University of Pennsylvania School of Medicine |
| Junhyong Kim (University of Pennsylvania, Biology); |
| Short Abstract: We investigate the modular properties of precursor microRNAs and show that they are structurally robust to changes in genomic context, in contrast to other classes of non-coding RNAs. We propose that pre-miRNAs can be characterized as modular building-block units, with an evolutionary history marked by rapid combination and rearrangement. |
| Long Abstract: Click Here |
| Accepted Posters |
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