Sequence Analysis, Comparative Genomics and Evolution
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27
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In silico testing of 23S rRNA primers for further use in cyanobacterial mats biodiversity studies
Cristian Coman, Adriana Bica, Bogdan Druga, Ana Nicoara and Nicolae Dragos
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This study presents the importance of computational biology in microbial biodiversity studies in the crucial step of primer design and in silico testing. After the primers were constructed, they were tested on more than 2500 bacterial 23S rRNA sequences (ARB-SILVA) to test their specificity and their possible application in phylogenetic studies.
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28
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Protein Data Integration for Phylogenetic Data Mining
Humberto Razente, Antonio Braz, Luis Scott
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In order to investigate a hypothesis, a researcher must deal with thousands of sequences. The work includes the classification, selection, and linkage of sequence names from different sources. Data integration is fundamental to phylogenetic studies, allowing structures, transcription and translation levels to be used for a single objective.
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29
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Genomic Ecology: genes competing for a metabolic niche?
Marcos Catanho, Ana Carolina Ramos Guimarães, Thomas Dan Otto, Fernando Alvarez-Valin, Wim Degrave & Antonio Basílio de Miranda
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Previous works performed by other groups suggest that the fraction of enzymatic activities in which multiple events of independent origin have occurred may be substantial. Here, we investigate the variability/evolution of metabolic pathways in prokaryotes, analyzing the frequency, distribution and extinction patterns of putative analogous enzymes in the glycolysis/gluconeogenesis pathway.
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30
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A computational pipeline for diagnostic biomarker discovery in the human pathogen Trypanosoma cruzi
Santiago Carmona, Paula Sartor, Susana Leguizamón, Oscar Campetella and Fernán Agüero
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A bioinformatic strategy was developed to identify peptidic antigens in the genome of Trypanosoma cruzi. A 12-residue sliding window assigned scores to each peptide based on a number of properties. The highest scoring peptides were synthesized and tested as candidate serodiagnostic biomarkers for Chagas disease.
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31
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Compositional Profile of the Human Genome at the Chromosome Level
Victor Sabbia, Hector Romero, Hector Musto, Hugo Naya
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We studied the compositional differences among chromosomes, considering structural and functional aspects using the chromosomes as the units of analysis.The results support the existence of a link between composition and spatial/structural/functional features of entire chromosomes.
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32
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Analogous enzymes inside the Tritryps genomes
Ana Carolina Ramos Guimarães, Wim Maurits Degrave, Antonio Basílio de Miranda
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The existence of alternative forms to perform the same enzymatic function as a result of multiple events of independent origin had been previously described and called as analogous enzymes. However, the possibility of occurrence of functional analogues inside the genome of single organism had not been observed.
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33
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Comparative microbial genomics in Pasteurellaceae family using second generation sequencing
Isabelle da Piedade, Timothy J Johnson, Anders M Bojesen
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Pasteurellaceae is an increasing and diverse family of Gram-negative bacteria that include primary pathogens, such as Haemophilus influenza, Pasteurella multocida and Actinobacillus pleuropneumoniae, as well as several potential pathogens. In this study, we present an extensive comparative analysis of different clades of the Pasteurellaceae family using second generation sequencing.
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34
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The Genome Comparison Project and the Protein World Database
Thomas Dan Otto, Marcos Catanho, Cristian Tristão, Márcia Bezerra, Renan Mathias Fernandes, Guilherme Steinberger Elias, Alexandre Capeletto Scaglia, Bill Bovermann, Viktors Berstis, Sergio Lifschitz, Antonio Basílio de Miranda & Wim Degrave
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Many analyses in modern research are based on biological sequence comparisons, resulting in functional, evolutionary, and structural inferences. ProteinWorldDB represents a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach.
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35
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Searching for signals in the Tritryps genomes
Pablo Smircich, Gustavo Cerqueira, Najib El-Sayed, Beatriz Garat
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The Tritryps present unique biological features. Particularly, the search for transcription initiation sites has been elusive so far. We aim to determine structural characteristics of already described sites to establish a prediction system for putative binding sites. We have recognized conserved features in ARNPI promoters that may serve this purpose.
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36
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Comparative proteome analysis of protozoan parasites: tandem repeat proteins and epitope predictions
Tiago Mendes, Frascisco Lobo, Leandro Freitas, Tiago Rodrigues, Daniella Bartholomeu
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We have performed in silico analysis searching for perfect and degenerated repeats in the predicted proteome of nine parasites. The repetitive content of B cell and T cell predicted epitopes and the subcellular location of the corresponding proteins were also analyzed. The results show differences between extracellular and intracellular parasites.
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37
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Codon usage analysis in Enterobacteriaceae: towards the detection of ancestral optimal triplets
Juan Baraibar, Andrés Iriarte, Héctor Romero, Héctor Musto
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We tracked the influence of natural selection in the history of Enterobacteriaceae and map the dynamic of optimal codons in the lineage. We propose: 1) natural selection is one of the main evolutive forces affecting synonymous codon usage; 2) 16 codons may have been optimal in the common ancestor.
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38
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Selection to less thymine dimmers content in the DNA of resistant UV bacteria and archaea
Jorge Bresciano
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I research on the hypothesis of a selection to less thymine dimmers content in the DNA of bacteria and archaea. The formation of the dymmers cause an important damage,so i count them in the genomes of resistant UV bacteria and i compare them with a group representing the total bacteria.
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39
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Sequence analysis of class 1 integron's integrase gene and the associated attI1 recombination site
María Paula Quiroga, Maximiliano Nardelli, María Soledad Ramírez, Daniela Centrón
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We evaluated the variability of the type 1 integrase gene and the attI1 recombination site, plus the attI1's dispersion. We found various intI1 alleles among the nosocomial samples although the attI1 shows a remarkable stability, and that a specific portion of the attI1 is highly dispersed in the bacterial genomes.
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40
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Lifestyle, gene repertory and base composition bias in spirochetes
Natalia Rego, Martín Graña, Guillermo Lamolle, Fernando Alvarez-Valin, Hugo Naya
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Spirochetes display different lifestyles even at the intragenus level. While highly variable, decrease of G+C content accompanying changes to a host-obligated cycle is not observed. We discuss this behaviour as related to modifications of the mutational bias associated to changes in DNA-repair enzyme repertory.
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41
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An easy way to incorporate phylogenetic uncertainty in the comparative model
Lucía Spangenberg, Natalia Rego, Hector Romero, Hugo Naya
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We present an easy way to incorporate phylogenetic uncertainty in the comparative model. We run the mixed model of Lynch in a Bayesian manner for several sampled trees and integrate the different posterior distributions ("model-averaging"). No "true" evolutionary model has to be assumed, since the inference can be performed with trees constructed under different evolutionary.
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42
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Integrated in silico-wet biology approach for improving the annotation of Babesia bigemina perforin family
Romina Petrigh, Natalia Rego, Beatriz Valentini, Ignacio Echaide, Hugo Naya, Marisa Farber
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Babesia bigemina is an apicomplexan haemoparasite that causes babesiosis in cattle. Currently, B. bigemina genome assembly and annotation is still in progress. In this work, we performed the annotation of a B. bigemina secreted protein family containing membrane- attack complex/ perforin (MACPF) - like domain using bioinformatic and biochemical tools.
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43
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A Combinatorial-Analytic Approach to Indel and Single Nucleotide Polymorphism Detection
Andrzej K. Brodzik
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A new approach for the analysis of DNA sequences, based on combinatorial-analytic concepts, is proposed. In this approach the DNA sequence is represented by its subsampled version derived from the distribution of cyclic difference sets. The approach permits rapid identification of single nucleotide polymorphisms.
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44
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Molecular Evolution and Functional Divergence of Alcohol Dehydrogenases in Animals, Fungi and Plants
Thompson, C.E.; Freitas, L.B.; Salzano, F.M.
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The alcohol dehydrogenase enzyme belongs to the large superfamily of medium- chain dehydrogenases/reductases, which have been characterized in animals, fungi, plants, protozoan, and bacteria. The phylogeny of 192 sequences of animals, fungi and plants were considered. Amino acid residues responsible for functional divergence between ADH types and among fungi, plant and animals were identified.
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45
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Discovery of a new conserved tandem motif upstream of outer membrane hemin transporters in alpha and beta-proteobacteria
Uriel Koziol, Vanesa Amarelle, Federico Rosconi, Francisco Noya, Mark R. O'Brian and Elena Fabiano
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A conserved tandem motif is described upstream of genes that code for outer membrane hemin transporters in alpha and beta-proteobacteria. This motif is not found upstream of other iron uptake related genes, and its presence is associated with the presence of orthologs of the hmuP gene in the same genome.
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46
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Bioinformatic insight into eisosomes' molecular function
Agustina Olivera-Couto and Pablo S. Aguilar
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Eisosomes are novel cellular structures that organize the plasma membrane. Not a single eisosomal protein bear an obvious structural domain. We have described the evolutionary distribution of different eisosomal proteins and predicted previously unrecognized protein domains of them. This study is highly valuable for the comprehension of eisosomes' molecular function.
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47
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Identifier (ID) elements inserted into non-coding regions of pol II-primary transcripts are not related to the regulation of tissue-specific gene expression in rat
Andrés Goldman, Evangelina González-López, Carlos A. Capoano and Adriana Geisinger
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We hereby show that IDs, short interspersed repetitive sequences (SINEs) from rodents, that had a suspected role in brain-specific gene expression are equally distributed among brain-specific, other tissue-specific, and housekeeping genes. All the data indicate that IDs are randomly distributed and do not exert a role in tissue-specific gene regulation.
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48
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12D3 gene sequence conservation in Mexican isolates of Babesia bovis
Jocelin Perez, Javier Pérez, Patricia Vargas, Antonio Alvarez, Carmen Rojas, Julio V. Figueroa
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Comparative analysis of the consensus nucleotide sequences obtained for the 12d3 alleles present in 19 out of 20 B. bovis Mexican isolates revealed a high degree of conservation (99% sequence identity) when compared to the 12d3 reference sequences from the Texan and Australian B. bovis isolates.
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49
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Initial Babesia bigemina gene identification by Expressed Sequence Tags analysis of the intraerythrocytic stage
Javier Perez, Patricia Vargas, Antonio Alvarez, Carmen Rojas, Julio V. Figueroa
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Blast search for 1904 ESTs of Babesia bigemina showed 470 ESTs (267 clusters) had no significant sequence identity with Apicomplexan genes; 21 ESTs corresponded to 6 known B. bigemina antigen coding genes; 1285 ESTs (159 clusters) had identity with B. bovis coding genes; 112 ESTs corresponded to 59 non-Babesia genes.
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