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Selected Posters

Remember that the acceptance of your poster presentation was notified by e-mail to the address you wrote when submitting your work.

 

Poster Presentations

Odd Numbered posters:

Monday, March 19, 5:30 PM to 7:00 PM.

Even Numbered posters:

Tuesday, March 20, 5:30 PM to 7:00 PM.

NOTE: Regardless of the day of presentation, all posters must be on display both days.

Poster Display Size: When preparing accepted posters please note that your poster should not exceed the following dimensions: 95 cm (37.4 inches) wide by 150 cm (59.0 inches) high.

 

List of accepted posters

Please note that each poster was assigned a unique ID (eg. PX, where X is a serial number). Note also that the posters in the list were grouped by topic session.

Comparative Genomics and Evolution
Genomics, Proteomics, Metagenomics and Metabolomics
Macromolecule Structure/Function Prediction
Computer Aided Drug Design and Docking/Molecular Dynamics Simulations
Biomedicine and Immunoinformatics
Functional Genomics and Systems Biology

Topic Session: Comparative Genomics and Evolution

P1 » Identification of transcription regulation associated proteins in plants and stramenopiles

Presenting Author: Diego Mauricio Riaño Pachón (Universidad de los Andes)

Co-authors: Francisco J. Buitrago-Florez (Universidad de los Andes, Biological Sciences); Silvia Restrepo-Restrepo (Universidad de los Andes, Biological Sciences); Bernd Mueller-Roeber (Universität Potsdam, Institute of Biochemistry and Biology)

Short Abstract: The generation of biodiversity is tied to the evolution and re-wiring of gene regulatory networks (GRNs). One component of these GRN are transcription factors and other transcriptional regulators. We have devised a pipeline for the identification of TFs and TRs, exploiting the domain architecture of these proteins. Currently we have a set of rules, representing 138 proteins families, that we have applied to the identification of ~20 different plant species and several species of Stramenopiles, where important plant pathogens are found. Results for plant species are available at http://plntfdb.uniandes.edu.co/; we are now developing a newer interface for Stramenopiles.

[Full Abstract]

P2 » Novel Classes of Eukaryotic Aspartic Proteases and the Identification of their Specificity Determining Residues

Presenting Author: María Revuelta (Universidad Nacional de Mar del Plata)

Short Abstract: Recent studies have indicated that fungi have a large number of APs in comparison to other taxonomic groups. We are interested in the functional diversification and redundancy of fungal APs. We performed a phylogenetic analysis of APs obtained by HMMer profiling of 107 sequenced eukaryotic genomes. The obtained phylogeny contains, besides the generally accepted A01A and A01B subfamilies, six subfamilies that are exclusive to fungi. Moreover, we identified a D and an E that are specific to the fungal subfamily of Yapsins, These residues are likely involved in monobasic sequence recognition and substrate processing of zymogens of various secreted hydrolases.

[Full Abstract]

P3 » Design-theoretical approach to homology assessment of DNA sequences

Presenting Author: Andrzej Brodzik (The MITRE Corporation)

Short Abstract: In this work we propose an approach for sequence comparison that relies on difference sets and their generalizations. Difference sets are special combinatorial objects, associated with sequences with ideal correlation properties. In the proposed DNA sequence comparison approach we use these objects as models for DNA sequence homology markers. These models are conceptually appropriate, as they quantify, in a certain sense, the degree of both sequence complexity and randomness. Moreover, the use of difference sets enables an algebraic analysis, which is advantageous in many applications, as statistics of DNA sequences vary significantly and reliable estimates are difficult to obtain.

[Full Abstract]

P4 » Shedding light into bacterial pathogenicity prediction: a machine learning approach

Presenting Author: Gregorio Iraola (Institut Pasteur Montevideo)

Co-authors: Lucía Spangenberg (Institut Pasteur Montevideo, Bioinformatics Unit); Gustavo Vazquez (Universidad Nacional del Sur, Departamento de Ciencias e Ingeniería de la Computación); Hugo Naya (Institut Pasteur Montevideo, Bioinformatics Unit)

Short Abstract: Accumulated sequencing information allows to study pathogenicity from a comparative genomics point of view. In particular, it is possible to envisage relevant differences based on presence/absence of virulence-genes in human-pathogenic and non-pathogenic species. We developed a model that can correctly classify as pathogens or non-pathogens 95% of 679 tested genomes, using 120 different genes.To date, pathogenicity prediction methods focus on particular groups. Our method showed a great performance with all available bacterial phyla, even outperforming more specialized classifiers. Finally, the biological information supporting our model is integrative over all bacteria, shedding some light into genetic basis of pathogenesis.

[Full Abstract]

P5 » Identifying associations between amino acid changes and meta information in alignments

Presenting Author: Lucía Spangenberg (Institut Pasteur de Montevideo)

Co-authors: Kay Nieselt (University of Tübingen, Center for Bioinformatics Tübingen); Florian Battke (University of Tübingen, Center for Bioinformatics Tübingen); Hugo Naya (Institut Pasteur de Montevideo, Bioinformatics Unit); Martín Graña (Institut Pasteur de Montevideo, Bioinformatics Unit)

Short Abstract: Next generation sequencing has dramatically increased the biological data available, particularly the identification of orthologous groups. We present a method that identifies associations between amino acid changes in potentially significant sites in an alignment with phenotypic data, through the phylogenetic mixed model. Previous studies show that the pathogenic aspect of many organisms may be associated with few changes in amino acids, which have strong structural impact on the protein. We used our method to predict significant sites in the RpoS protein from 209 bacteria. Several sites in biological relevant regions were found.

[Full Abstract]

P6 » A phylogenomic approach to understand genomic and metabolic diversity in extreme acidophilic environments

Presenting Author: Jorge Valdes (Fraunhofer Chile Research)

Short Abstract: Life in extreme acidic environments provide opportunities for studying genomic and metabolic diversity because the reduced biodiversity and the availability of genomic and metagenomic information. However, previous studies haven’t generated a comprehensive view of the potential processes responsible for the genomic and metabolic adaptations that these organisms have developed trough its evolutionary history. In this work we will show how a phylogenomic approach can help to unravel this processes in an organism specific way, and how it can provide some clues about the evolutionary processes that have impacted their physiology in order to survive in extreme acidic environments.

[Full Abstract]

P7 » Assessing the efficiency of multiple sequence alignment programs

Presenting Author: Patrícia Ruy (Oswaldo Cruz Foundation)

Co-authors: Fabiano Sviatopolk-Mirsky Pais (Oswaldo Cruz Foundation, Center for Excellence in Bioinformatics); Guilherme Oliveira (Oswaldo Cruz Foundation, Center for Excellence in Bioinformatics / Genomics and Computational Biology Group); Roney Santos Coimbra (Oswaldo Cruz Foundation, Center for Excellence in Bioinformatics / Genomics and Computational Biology Group)

Short Abstract: Multiple Sequence Alignment (MSA) plays an essential role in molecular biology and several programs and algorithms have been developed. Balance between accuracy and computational cost has become a critical indicator of the most suitable algorithm and program to each different dataset to be aligned. We compared the alignment accuracy and computational cost of eight MSA programs against the “gold standard” BAliBASE benchmark dataset. Consistency-based programs Probcons, T-Coffee, Probalign and MAFFT are recommended for high accuracy of MSAs, since their requirements of memory and time of execution did not exceed the capacity of low-cost available hardware and timelines of most projects.

[Full Abstract]

P8 » Conformational diversity: Relationship with protein evolution and designability

Presenting Author: Diego Zea (Universidad Nacional de Quilmes)

Co-authors: Gustavo Parisi (Universidad Nacional de Quilmes, Centro de Estudios e Investigaciones); Cristina Marino Buslje (Fundación Instituto Leloir, Bioinformatics Unit)

Short Abstract: The study of evolutionary rates is a central issue to understand the mechanisms underlying protein molecular evolution. In this work we study how the presence of conformational diversity in proteins could influence the rate of evolution. We have determined that the evolutionary rate positive correlates with the degree of conformational diversity measured by the maximum RMSD between conformers. Our results support the idea that proteins with larger native conformational space could have a higher average of inter residues contacts, a measure of protein designability, giving rise to an increased evolutionary rate.

[Full Abstract]

P9 » On the particularities of Protozoa: a comparative genomics approach

Presenting Author: Diogo Tschoeke (Oswaldo Cruz Institute)

Co-authors: Rodrigo Jardim (Computational and Systems Bology Lab, Oswaldo Cruz Institute, FIOCRU); Joana Lima (and Systems Bology Lab, Oswaldo Cruz Institute, FIOCRUZ); Sergio Serra (ICE / Federal Rural University of Rio de Janeiro, DEMAT ); Rafael Cuadrat (Computational and Systems Bology Lab, Oswaldo Cruz Institute, FIOCRUZ); Marta Mattoso (Federal University of Rio de Janeiro, COPPE/PESC ); Maria Luiza Campos (Federal University of Rio de Janeiro, PPGI); Alberto Dávila (Computational and Systems Bology Lab, Oswaldo Cruz Institute, FIOCRUZ)

Short Abstract: Protozoa is the common name given to unicellular Eukaryotes organisms that show an extremely diversity. After removing protein redundance with CD-HIT from Plasmodium, Entamoeba, Trypanosoma, Leishmania, Giardia, Theileria, Toxoplasma, Trichomonas and Cryptosporidium species we got 204,624 proteins from 22 proteomes, after that they were submitted to OrthoMCL and 26,101 homologs groups were generated (4,982 paralogs and 21,119 orthologs). 348 groups of orthologous proteins are shared by all the 22 organisms, representing the proteome core of Protozoa. In this study we discuss the distribution of these homologs genes (paralogs and orthologs) among the protozoa, his function and the functional categorization.

[Full Abstract]

P10 » Genomic characterization of Pseudomonas fluorescens NCIMB11764, a bacteria strain with unique cyanide metabolism capabilities

Presenting Author: Claudia Vilo (University of North Texas)

Co-authors: Michael Benedik (Texas A&M University, Biology); Daniel Kunz (University of North Texas, Biology); Qunfeng Dong (University of North Texas, Biology)

Short Abstract: Pseudomonas fluorescens NCIMB11764 (Pf11764) utilizes cyanide as a sole nitrogen source. However, the pathways of cyanide metabolism are not completely clear. Therefore, to understand Pf11764 adaptation to cyanide environments we characterized its genome using next-generation sequencing methodology. We found several components of the cyanide oxidase enzyme, which is essential for cyanide metabolism. Also, over-represented genes with metal ion binding and transport activity were found in Pf11764, indicating a direct relationship to cyanide metabolism since it often binds to metal ions. Additionally, a large number of genome rearrangements were observed in Pf11764 when compared with same species bacteria's genomes.

[Full Abstract]

P11 » Differential adaptive evolution in the Helicobacter pylori genome depending on human host population

Presenting Author: Maria Soto-Giron (University of Puerto Rico)

Short Abstract: H. pylori was the first bacterium identified as a class l carcinogen in 1994. H. pylori infection is associated with stomach ulcers and stomach cancer. Given that pathogenic factors are often under positive selection and correlated with a bacterial phenotype that produces specific manifestations of disease, we wished to identify novel pathogenic factors using this evolutionary perspective. The analysis revealed a larger number of genes under positive selection in Asian genomes (Korea: 50 and Japan: 27, Northwest Europe: 9 and Southern Europe: 12) potentially related with a high incidence of H. pylori associated pathogenicity present in East Asia.

[Full Abstract]

P12 » Evolution of 7SK RNA and Its Protein Partners in Metazoa

Presenting Author: Nina Verstraete (Institut de Biologie de l'Ecole Normale Supérieure)

Co-authors: Alexander Donath (University of Leipzig, Computer Science, and Interdisciplinary Center for Bioinformatics); Manja Marz (University of Leipzig, Computer Science, and Interdisciplinary Center for Bioinformatics); Peter F. Stadler (University of Leipzig, Computer Science, and Interdisciplinary Center for Bioinformatics); Van Trung Nguyen (Institut de Biologie de l'Ecole Normale Supérieure, Génomique Fonctionnelle); Olivier Bensaude (Institut de Biologie de l'Ecole Normale Supérieure, Génomique Fonctionnelle)

Short Abstract: 7SK ncRNA is a highly abundant non-coding RNA whose function in regulation of RNA Polymerase II transcription has only recently been elucidated. In mammals, 7SK plays a central scaffold role in the assembly of 7SK snRNP which allows sequestration and inhibition of the Positive Transcription Elongation Factor b. We present here a specialized search tool for 7SK and a comprehensive analysis of the coevolution of 7SK and its interacting-proteins in metazoa. We describe new 7SK homologues found in Caenorhabditis species and improve the secondary structure model of 7SK, showing the importance of structure conservation despite extreme divergence at sequence level.

[Full Abstract]

P13 » Expression evolution of prokaryotic organisms

Presenting Author: Pieter Meysman (KULeuven)

Co-authors: Kristof Engelen (KULeuven) Aminael Sánchez-Rodríguez (KULeuven, Department Of Microbial And Molecular Systems (M2S)); Qiang Fu (KULeuven, Department Of Microbial And Molecular Systems (M2S)); Kathleen Marchal (KULeuven, Department Of Microbial And Molecular Systems (M2S))

Short Abstract: Regulation of gene expression is one of the primary adaption techniques used by prokaryotic species to survive in a changing environment. In this work, we tried to assess how much the gene expression varies between three prokaryotic organisms, namely Escherichia coli, Salmonella entrica serovar Typhimurium and Bacillus subtilis. The variation in the gene expression behavior corresponded well with the general genomic variation: more distant organisms had a higher rate of gene expression divergence and genes with lower sequence conservation also had a more divergent gene expression. This could be the result of similar evolutionary pressure on both the expression and the sequence of a gene.

[Full Abstract]

P14 » Analysis of genomic regions with abundant repetitive sequences using high-throughput genomic data: Vibrio cholerae superintegron

Presenting Author: Michel Marín (Oswaldo Cruz Institute - Fiocruz)

Co-authors: Bas Dutilh (San Diego State University, Department of Biology and Department of Computer Science); Cristiane Thompson (Oswaldo Cruz Institute - Fiocruz, Laboratory of Molecular Genetics of Microorganisms); Robert Edwards (San Diego State University, Department of Computer Science)

Short Abstract: Comparative analysis of the Superintegron region (SI) has been carried out for 179 V. cholerae genomes of strains isolated around the world during the last six decades. We used raw sequencing reads from 39 V. cholerae genomes sequenced by us and added 139 publically available genomes. The results of the present work show that V. cholerae strains group into several discrete clusters corresponding to the V. cholerae lineages. The V. cholerae population structure based on the SI diversity show the SI stability and its coevolution with the host genome.

[Full Abstract]

P15 » Genomic and computational analysis used for bacterial taxonomy: streptococci species as a test case

Presenting Author: Michel Marín (Oswaldo Cruz Institute - Fiocruz)

Co-authors: Cristiane Thompson (Oswaldo Cruz Institute - Fiocruz) Vanessa Emmel (Oswaldo Cruz Institute - Fiocruz, Laboratory of Molecular Genetics of Microorganisms); Michel Marin (Oswaldo Cruz Institute - Fiocruz, Laboratory of Molecular Genetics of Microorganisms); Ana Carolina Vicente (Oswaldo Cruz Institute - Fiocruz, Laboratory of Molecular Genetics of Microorganisms)

Short Abstract: The aim of this study was to extract taxonomic information from streptococci genomes by means of a detailed genomic and computational analysis using Multilocus Sequence Analysis (MLSA), Average Amino Acid Identity (AAI), genomic signatures, Genome-to-Genome Distances (GGD) and codon usage. Our results showed that these genomic analysis are useful to identify streptococci species, resulting in a clear distinction of S. pneumoniae, S. mitis, and S. oralis. A streptococci species is defined as a group of strains that share ≥ 95% identity in MLSA and AAI, and > 70% identity in GGD, which are above the threshold for defining bacterial species.

[Full Abstract]

P16 » Identification of transcription factor genes and their correlation with the high diversity of Stramenopiles.

Presenting Author: Francisco Buitrago (Universidad de los Andes)

Co-authors: Francisco Buitrago-Florez (Universidad de los Andes) Silvia Restrepo (Universidad de los Andes, Biological Sciences); Diego Riaño-Pachon (Universidad de los Andes, Biological Sciences)

Short Abstract: We identify, and classify into families, transcription factors (TFs) and other transcriptional regulators (TRs) in genome sequences available from the Stramenopile group. We exploit the presence of protein domains and their combinations to build rules in the form of boolean rules, that are specific for each family of TFs and TRs. We found a correlation between the family size and some traits that has been described to be involved in the complexity of organisms. Furthermore, we found specific gains, losses and families that shows higher abundance, which may be involved in the regulation of specific traits for some Stramenopile species.

[Full Abstract]

P17 » The phylogenomics of carbohydrate metabolism in Protozoa

Presenting Author: Joana A. Lima Oliveira (Institute Oswaldo Cruz/Fiocruz)

Co-authors: Joana de Oliveira (Institute Oswaldo Cruz/Fiocruz) Diogo A. Tschoeke (Computational and Systems Biology Pole, Oswaldo Cruz Institute, FIOCRUZ); Alexandre Pittis (Center for Genomic Regulation/ CRG, CRG); Marina Marcet-Houben (Center for Genomic Regulation/ CRG, CRG); Toni Gabaldón (Center for Genomic Regulation/ CRG, CRG); Alberto M R Dávila (Computational and Systems Biology Pole, Oswaldo Cruz Institute, FIOCRUZ)

Short Abstract: Phylogenomic can be defined as the intersection between evolution and genomics. Protozoa are a phylogenetically-diverse assemblage of unicellular eukaryotes that spans different eukaryotic domains. The evolution of carbohydrate metabolism (CM) in Protozoa is related to energy production and development, which in turn are important processes for pathogenicity and obvious candidates for new drug targets. In this study, the proteome of 22 protozoan species obtained from NCBI and ProtozoaDB were compared to establish orthology and paralogy relationships in genes related to CM, with the aim of generating new information on the phylogenetic and evolutionary relationships of those genes.

[Full Abstract]

P18 » Analysis of the Pathogen-Host relationship of Orthomyxoviruses

Presenting Author: Mario Tello (Universidad de Santiago)

Co-authors: Jose Miguel Saavedra (Universidad de Santiago de Chile, Biología); Francisco Vergara (Universidad de Santiago de Chile, Biología); Eugenio Spencer (Universidad de Santiago de Chile, Biología)

Short Abstract: It’s widely accepted that main interspecies barrier is at cellular receptors level, however is unknown why some viruses can’t replicate in a new host. We proposed that viral host-codon adaptation is a key factor that precludes the protein determinants. Analyze of translational and codon adaptation of orthomyxoviruses showed that ISAV is the less host-adapted orthomyxovirus. In silico crossing of Interspecies Barrier showed that IAVs are better adapted to Chicken>Human>Duck>Swine. Pandemic viruses have high codon adaptation values that decrease across the time. Interestingly, an increment in adaptation to one host increased adaptation in to all others host.Grants: Project PDA20 and DICYT020943TR

[Full Abstract]

P19 » Comparative genomics of the oxidative stress response in acidophilic microorganisms

Presenting Author: Juan Pablo Cárdenas (Fundacion Ciencia para la Vida & Universidad Andres Bello)

Co-authors: Juan Cárdenas (Fundacion Ciencia para la Vida & Universidad Andres Bello) David Holmes (Fundacion Ciencia para la Vida & Universidad Andres Bello, Center of Bioinformatics and Genome Biology); Raquel Quatrini (Fundacion Ciencia para la Vida & Universidad Andres Bello, Laboratorio de Ecofisiologia Microbiana); Gloria Levican (Universidad de Santiago de Chile, Facultad de Quimica y Biologia)

Short Abstract: Oxidative stress, associated with extraordinarily high levels of soluble heavy metals, poses a major problem for life at extremely low pH (<2). High dimensional comparative genomics of over 50 sequenced acidophiles predicts molecular strategies that they use to combat oxidative stress. Strikingly, acidophiles lack typical stress response regulators and are significantly impoverished in mechanisms for classical reactive oxygen species (ROS) consumption. However, they exhibit an abundance of genes for macromolecule repair (DNA, lipids etc) and potential alternative regulators that it may play a novel role in the oxidative stress response.

[Full Abstract]

P20 » A phylogenomic approach to understand genomic and metabolic diversity in extreme acidophilic environments

Presenting Author: Jorge Valdes (Fraunhofer Chile Research)

Co-authors: Carolina Gonzalez (Center For Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Andrés Bello University, Departamento de Ciencias Biologicas); Paz Tapia (Fraunhofer Chile Research, Bio-Computing Division); O'car Campos (Fraunhofer Chile Research, Bio-Computing Division); David Holmes (Center For Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Andrés Bello University , Departamento de Ciencias Biologicas)

Short Abstract: Life in extreme acidic environments provide opportunities for studying genomic and metabolic diversity because the reduced biodiversity and the availability of genomic and metagenomic information. However, previous studies haven’t generated a comprehensive view of the potential processes responsible for the genomic and metabolic adaptations that these organisms have developed trough its evolutionary history. In this work we will show how a phylogenomic approach can help to unravel this processes in an organism specific way, and how it can provide some clues about the evolutionary processes that have impacted their physiology in order to survive in extreme acidic environments.

[Full Abstract]

P21 » Genome sequence analysis of Acinetobacter sp. Ver3 and Exiguobacterium sp. S17 isolated from High Altitude Andean Lakes

Presenting Author: Daniel Kurth (PROIMI-CONICET)

Co-authors: Omar Ordoñez (PROIMI-CONICET, LIMLA); Virginia Albarracin (PROIMI-CONICET, LIMLA); Nestor Cortez (UNR-IBR-CONICET, Biología Molecular); Adrian Turjanski (Facultad de Ciencias Exactas-UBA, Departamento de Química Inorgánica, Analítica, y Química Física); Martin Vazquez (INDEAR-CONICET, Plataforma de Secuenciación Genómica y Bioinformática); Maria Eugenia Farias (PROIMI-CONICET, LIMLA)

Short Abstract: The high-altitude Andean lakes (HAAL) in the Argentinean Puna-high Andes region represent an almost unexplored ecosystem exposed to extreme conditions, including high UV irradiation, hypersalinity, drastic temperature changes, desiccation, and high pH. So far, we have sequenced the genomes of three bacteria isolated from these environments. The analysis of these genomes reveals common mechanisms to survive in such hostile conditions, and also allows to identify unique systems that provide competitive advantages to each strain. The genomes sequences reported here include: Acinetobacter sp. Ver3, isolated from Verde lake, and Exiguobacterium sp. S17, isolated from Socompa lake.

[Full Abstract]

P22 » High dimensional multi-genomic investigation into the function and evolution of Eukaryotic single exon genes.

Presenting Author: Roddy Jorquera Cifuentes (Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago Chile)

Co-authors: David Holmes (Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago Chile) Rodrigo Ortiz Ortiz (Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas); Aucán Pedroso Rovira (Universidad de Talca, Facultad de Ingeniería)

Short Abstract: Eukaryotic genes are generally interrupted by introns. However, some of them lack introns and are termed single exon genes (SEGs). We have constructed a searchable database of SEGs predicted from 30 completely sequenced Eukaryotic genomes with representative species from yeast to human and including plants. High dimensional, multigenomic analyses of the information available in the database permits predictions of function and provides opportunities to address fundamental issues related to SEG origin and evolution. The database can also be mined for information linking SEGs with human disease.

[Full Abstract]

P23 » Distribution of Fur family of transcriptional regulators in species belonging to the Lactobacillales order

Presenting Author: Esteban Gárate (Universidad de Chile)

Co-authors: Mauricio González (Universidad de Chile, Laboratorio de Bioinformática y Expresión Génica, INTA); Angélica Reyes-Jara (Universidad de Chile, Laboratorio de Microbiología y Probióticos, INTA)

Short Abstract: The Fur protein acts as an iron sensing transcriptional factor and there are other factors with similar structure but different functions (like Zur and PerR), together associated as the Fur family.In this work we searched for Fur, Zur and PerR sequences in all the bacteria belonging to the Lactobacillales order and performed a phylogenetic analysis for these transcriptional factors. We found that Fur is present in most species while Zur or PerR are rarely found, suggesting that Fur is the most essential member of this family.

[Full Abstract]

P24 » Whole Genome Sequencing and Comparative Analysis of Yersinia pestis, the causative agent of a plague outbreak in northern Perú

Presenting Author: Heinner Guio (Peruvian National institute of Health)

Co-authors: Juan Montenegro (Peruvian National Institute of Health, Laboratorio de Biotecnología y Biología Molecular); Omar Cáceres (Peruvian National institute of Health, Laboratorio de Biotecnología y Biología Molecular); Carlos Padilla (Peruvian National institute of Health, Laboratorio de Biotecnología y Biología Molecular); Henri Bailón (Peruvian National institute of Health, Laboratorio de Biotecnología y Biología Molecular); David Tarazona (Peruvian National institute of Health, Laboratorio de Biotecnología y Biología Molecular); Patricia García (Peruvian National institute of Health, Laboratorio de Zoonosis Bacteriana); Manuel Céspedes (Peruvian National institute of Health, Centro Nacional de Salud Pública); Pedro Valencia (Peruvian National institute of Health, Centro Nacional de Salud Pública)

Short Abstract: The plague is a zoonotic disease caused by the bacterium Yersinia pestis which when untreated can kill up to 60% of infected patients. A strain of Y. pestis was isolated from a recent outbreak of pneumonic plague in Trujillo. This strain was sequenced with a Solid 3 sequencer and re-assembled to the CO92 reference genome (NCBI AL590842.1). The two genomes were 99.93% identical. We found 63 SNPs located in non-protein-coding loci. From these, 43 were located in UTRs of annotated genes and may influence gene expression. We also report the presence of three virulence plasmids: pCD1, pMT1 and pPCP1.

[Full Abstract]

P25 » Molecular characterization of kinetoplast of three Venezuelan isolates of Trypanosoma vivax.

Presenting Author: Alfredo Mijares (IVIC)

Co-authors: Iralis Cardozo (IVIC, CBB); Mary Isabel Gonzatti (Universidad Simon Bolivar, Departamento de Biología Celular)

Short Abstract: Trypanosomes are characterized by the presence of a Kinetoplast that contains mitochondrial DNA organized into a complex network of interlocked minicircles and maxicircles. Maxicircles contain typical mitochondrial genes most of which are translatable only after RNA editing, whereas minicircles encode small guide RNAs required for decrypting the maxicircle transcripts. In this study we amplified by PCR fragments of mini and maxicircles from three Venezuelan isolates of different degree of virulence of Trypanosoma vivax. We obtained partial sequences of minicircles containing the highly conserved origin of replication and established the presence of ATPase subunit 6 and NADH dehydrogenase subunit 8

[Full Abstract]

P26 » Evolutionary history of the Glucokinase/Phosphofructokinase activity in the ADP-dependent sugar kinases family.

Presenting Author: Victor-Hugo Castro (Universidad de Chile)

Co-authors: Victoria Guixe (Universidad de Chile, Departamento de Biología)

Short Abstract: The ADP-dependent sugar kinases family has two specificities; phosphofructokinase and glucokinase. Interestingly the enzyme from Methanococcus jannaschii is bi-functional. We reconstructed the phylogenetic tree for this family, analyzed the evolutionary history of the use of substrates and compared them with experimental evidence obtained from reconstruction of ancestral proteins. The results indicate that enzymes from Metanococales are not specific phosphofructokinases as are believed to date; they can utilize glucose and fructose-6P as substrates. We built models of the ancestral proteins structures and performed ligand-docking experiments which allow us to identify key residues for fructose-6P specialization in the Termococcales group (Fondecyt-1110137).

[Full Abstract]

P27 » Whole Genome Sequencing and Comparative Analysis of the Bartonella bacilliformis strain INS, the causative agent of Carrion's disease

Presenting Author: David Tarazona (Instituto Nacional de Salud)

Co-authors: Carlos Padilla (Instituto Nacional de Salud, Laboratorio de Biotecnologia y Biologia Molecular); Omar Caceres (Instituto Nacional de Salud, Laboratorio de Biotecnologia y Biologia Molecular); Juan Montenegro (Instituto Nacional de Salud, Laboratorio de Biotecnologia y Biologia Molecular); Henri Bailon (Instituto Nacional de Salud, Laboratorio de Biotecnologia y Biologia Molecular); Elizabeth Anaya (Instituto Nacional de Salud, Laboratorio de Metaxenicas Bacterianas); Giovanna Mendoza (Instituto Nacional de Salud, Laboratorio de Metaxenicas Bacterianas); Pedro Valencia (Instituto Nacional de Salud, Centro Nacional de Salud Pública); Heinner Guio (Instituto Nacional de Salud, Laboratorio de Biotecnologia y Biologia Molecular)

Short Abstract: Carrion's disease that is caused by Bartonella bacilliformis, has long been recognized in the Andean region of South America. The genome of B. bacilliformis strain INS consists of a single circular chromosome of 1,445,020bp in length, with a GC content of 38.2%. There are 1357 protein-coding sequences, 44 tRNAs, and 6 rRNA. The genome of B. bacilliformis strain INS contains 112 genes for virulence factors. In the comparative analysis of genomes of B. bacilliformis, B. henselae and B. quintana, we identified a genomic core of 898 genes and 355 unique genes .

[Full Abstract]

P28 » Looking for orthologs for the sodium K+-independent, ouabain-insensitive Na+-ATPase

Presenting Author: luz Thomas (Instituto Venezolano de Investigaciones Científicas)

Co-authors: Miguel Rocafull (Instituto Venezolano de Investigaciones Cientificas, Centro de Biofísica y Bioquímica); Jesús del Castillo (Instituto Venezolano de Investigaciones Cientificas, Centro de Biofísica y Bioquímica)

Short Abstract: Functional, biochemical and molecular evidences demonstrated the existence of a K+-independent, ouabain-insensitive Na+ pump, associated to a Na+-ATPase with similar characteristics to the classic Na+/K+ pump. Previously, the guinea-pig atna mRNA sequence (2787 bp) corresponding to this new ATPase was completed. Search for atna gene in guinea-pig genomic database reveals that atna and atp1a1 cDNAs are in the same genetic locus: atp1a1. Given that the ouabain-insensitive Na+-ATPase has been described in other specimens we decided explore the existence of a putative orthologue in human genome from ENSEMBL database using TBLASTN program and performed a phylogenetic analysis of ATNA protein.

[Full Abstract]

P29 » footprint-scan: Detecting conservation of regulatory interactions inside Gensor Units

Presenting Author: Alejandra Medina Rivera (Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México)

Co-authors: Jacques van Helden (Université d'Aix-Marseille (AMU), TAGC); Socorro Gama-Castro (Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Programa de Genómica Computacional); Julio Collado-Vides (Centro de Ciencias Genómicas-Universidad Nacional Autónoma de México, Programa de Genómica Computacional)

Short Abstract: Gensor Units describe regulatory mechanisms and pathways in the context of physiological sensing and response capabilities. The collection of genes conforming a GU subject to common regulation by a Transcription Factor (TF). We implemented the program footprint-scan, which obtains and scans promoters of orthologous genes with one or several PSSMS. On the basis of the results of this scanning, the program calculates the overrepresentation of TFBSs in a set of sequences, providing a score that indicates the phylogenetic conservation of cys-regulatory elements. This evolutionary conservation provides additional evidence for predicting TFBSs in apparently disconnected genes within GUs.

[Full Abstract]

P30 » Whole Genome Sequencing and Comparative Analysis of Yersinia pestis, the causative agent of a plague outbreak in northern Perú

Presenting Author: Juan D. Montenegro (Peruvian National institute of Health)

Co-authors: Heinner Guio (Peruvian National institute of Health) Juan D. Montenegro (Peruvian National Institute of Health, Laboratorio de Biotecnología y Biología Molecular); Omar Caceres (Peruvian National Institute of Health, Laboratorio de Biotecnología y Biología Molecular); Carlos Padilla (Peruvian National Institute of Health, Laboratorio de Biotecnología y Biología Molecular); Manuel Céspedes (Peruvian National Institute of Health, Peruvian National Public Health Centre); Henri Bailón (Peruvian National Institute of Health, Laboratorio de Biotecnología y Biología Molecular); David Tarazona (Peruvian National Institute of Health, Laboratorio de Biotecnología y Biología Molecular); Patricia García (Peruvian National Institute of Health, Laboratorio de Zoonosis Bacteriana); Pedro Valencia (Peruvian National Institute of Health, National Public Health Centre); Heinner Guio (Peruvian National Institute of Health, Laboratorio de Biotecnología y Biología Molecular)

Short Abstract: The plague is a zoonotic disease caused by the bacterium Yersinia pestis which when untreated can kill up to 60% of infected patients. A strain of Y. pestis was isolated from a recent outbreak of pneumonic plague in Trujillo. This strain was sequenced with a Solid 3 sequencer and re-assembled to the CO92 reference genome (NCBI AL590842.1). The two genomes were 99.93% identical. We found 63 SNPs located in non-protein-coding loci. From these, 43 were located in UTRs of annotated genes and may influence gene expression. We also report the presence of three virulence plasmids: pCD1, pMT1 and pPCP1.

[Full Abstract]

P31 » Mr.Cirrus: A Map-Reduce approach for High level Cloud Computing

Presenting Author: Oswaldo Trelles (University of Malaga)

Co-authors: Juan Lago (Fundación Iavante, ; Consejería de Salud de la Junta de Andalucia); Daniel Ramet (University of Malaga, Computer Architecture); Oscar Torreño (University of Malaga, Computer Architecture); Johan Karlsson (University of Malaga, Computer Architecture); Juan Falgueras (University of Malaga, Languages and Computer Sciences); Noura Chelbat (Johannes Kepler University, Institute for Bioinformatics); Michael Krieger (RISC Software GmbH, Co-Location Center)

Short Abstract: Mr.Cirrus, is a novel software, in the Map-Reduce direction, aimed to make easy an efficient the exploitation of Cloud resources. We have adapted our jORCA client software to simplify the registering, discovering, management, invocation and monitoring of services in the cloud, and then we address the cloudification of several tools for analysis of bio-sequences at genome level as a way to test different tasks scheduling approaches to make the exploitation of cloud resources efficient. Mr.Cirrus has been benchmarked in Amazon Elastic MapReduce, IBM InfoSphere BigInsights, MS-Azure, multiprocessors and cluster environments for porting legacy software in fast, economical and efficient way.

[Full Abstract]

Topic Session: Genomics, Proteomics, Metagenomics and Metabolomics

P32 » A Fast de novo Genome-Wide Tandem Repeat Discovery Algorithm

Presenting Author: Marcelo Gonçalves Narciso (Embrapa)

Co-authors: Michel Yamagishi (Embrapa) Marcelo Gonçalves Narciso (Embrapa, Bioinformatics)

Short Abstract: Tandem Repeats (TR) are sequences where the same pattern repeats consecutively. So far, they have been used as genomic markers, but new studies have associated them to important regulatory processes which increased their relevance. Although several TR discovery algorithms are available, genome-wide TR discovery is time consuming, and any improvement in computational performance may be significant. We present a new fast de novo genome-wide TR discovery algorithm, called ConvolutionTR. It deals with large genomes on average 30% to 50% faster than other approaches; furthermore, ConvolutionTR finds all the TRs while the most popular algorithms do not as will be shown

[Full Abstract]

P33 » Gene expression in Schistosoma mansoni schistosomula in the presence of hamster’s peripheral or portal serum

Presenting Author: Fabiano Pais (Oswaldo Cruz Foundation)

Co-authors: Wander J Jeremias (Oswaldo Cruz Foundation, Schistosomiasis Laboratory); Flavio M G Araujo (Oswaldo Cruz Foundation, Center for Excellence in Bioinformatics); Paulo M Coelho (Oswaldo Cruz Foundation, Schistosomiasis Laboratory); Guilherme Oliveira (Oswaldo Cruz Foundation, Center for Excellence in Bioinformatics - Genomics and Computational Biology Group); Anna C Salim (Oswaldo Cruz Foundation, Center for Excellence in Bioinformatics); Fernando L Kamitani (Oswaldo Cruz Foundation, Center for Excellence in Bioinformatics); Renata Guerra-Sa (Ouro Preto Federal University, Biochemistry and Molecular Biology Laboratory); Roney S Coimbra (Oswaldo Cruz Foundation, Center for Excellence in Bioinformatics - Genomics and Computational Biology Group); Elio H Babá (Oswaldo Cruz Foundation, Schistosomiasis Laboratory)

Short Abstract: Exploring the biochemical processes in the Schistosoma mansoni life cycle may aid the development of new drugs capable of eradicating the infection at an early stage. The development of schistosomula, which occurs in the hepatic system of the definitive host in the early infection, was simulated by exposing parasites to in vitro culture in the presence of the portal sera of hamster. Schistosomula exposed during 3 and 12 hours underwent massive mRNA extraction to construct the cDNA library that was sequenced with the SOLiD platform. Several gene expression patterns disclosed by Self-organizing maps were obtained after mapping reads.

[Full Abstract]

P34 » High-resolution community genomics of a hypersaline microbial ecosytem

Presenting Author: Juan Ugalde (University of California, San Diego)

Co-authors: Sheilla Podell (University of California, San Diego, Scripps Institution of Oceanography); Karla Heidelberg (University of Southern California, Department of Biological Sciences); Jill Banfield (University of California, Berkeley, Department of Earth and Planetary Sciences); Eric Allen (University of California, San Diego, Scripps Institution of Oceanography)

Short Abstract: The present work presents the comprehensive genetic analysis of a natural hypersaline microbial community using metagenomic deep-sequencing. We examined the accumulated metagenomic data via three complementary data analysis treatments. Foremost, raw sequencing reads were analyzed for phylogenetic and functional content (environmental gene-survey approach). Secondly, we reconstructed the genomes of the most abundant members of the microbial community (assembly-driven approach). Finally, we used the assembled genomes to dissect the genetic heterogeneity that is present in each microbial population (population genetic approach). The combination of different approaches provides a more detailed picture of the genetic and functional diversity of microbial communities.

[Full Abstract]

P35 » RNA-seq expression analyses in sweet cherries to try to understand cracking tolerance

Presenting Author: Jonathan Maldonado (University of Chile)

Co-authors: Herman Silva (University of Chile) Herman Silva (University of Chile, Agricultural Production); Juan Carlos Rios (University of Chile, Agricultural Production)

Short Abstract: Sweet cherries suffer a series of superficial problems such as the cracking that is one of the major reasons of losses in the worldwide production. The damage is produced when the cherry-fruit became in contact with water rain. We hypothesize that the susceptibility to cracking in these fruits could be related to differential expression of genes associated with this abiotic stress. We used 454 technology to sequence fruit and leaf total RNA from 3 varieties with different susceptibility to cracking obtaining 1.4 millions of reads (430Mb). 20,472 contigs were assembled from fruit reads and 20,264 contigs from leaf reads.

[Full Abstract]

P36 » COLOMBOS: an ever expanding collection of bacterial expression compendia

Presenting Author: Kristof Engelen (KULeuven)

Co-authors: Pieter Meysman (KULeuven, Department Of Microbial And Molecular Systems (M2S)); Aminael Sánchez-Rodríguez (KULeuven, Department Of Microbial And Molecular Systems (M2S)); Qiang Fu (KULeuven, Department Of Microbial And Molecular Systems (M2S)); Kathleen Marchal (KULeuven, Department Of Microbial And Molecular Systems (M2S))

Short Abstract: We have created cross-platform expression compendia for several bacterial model organisms and developed a complementary access port COLOMBOS, which also serves as a convenient expression analysis tool to extract useful biological information. A backend management system enables us to add compendia for new organisms in future releases, as well keep the existing ones up to date with more recent published expression data. This work is relevant to a large community of microbiologists by facilitating the use of publicly available microarray experiments to support their research.

[Full Abstract]

P37 » Revealing new perspectives on the regulation of gene expression by trans-splicing mechanism in S. mansoni

Presenting Author: Mainá Bitar (Universidade Federal de Minas Gerais)

Co-authors: Marina Mourão (Fiocruz, Centro de Pesquisas René Rachou); Francisco Lobo (EMBRAPA, Bioinformática); Priscila Grynberg (Universidade Federal de Minas Gerais, Bioquímica); Andréa Macedo (Universidade Federal de Minas Gerais, Bioquímica); Carlos Renato Machado (Universidade Federal de Minas Gerais, Bioquímica); Glória Franco (Universidade Federal de Minas Gerais, Bioquímica)

Short Abstract: Schistosomiasis is the second most prevalent neglected tropical disease caused by a trematode flatworm from the genus Schistosoma. Schistosomes possess a complex life cycle requiring numerous and intricate mechanisms to rule transcriptional and post-transcriptional gene regulation. It is believed that spliced leader (SL) trans-splicing could play an important role in the parasite biology. The purpose of this study was to shed light on the function of the trans-splicing mechanism in S. mansoni by searching gene categories that could be target of this process and attempting to silence transcripts harboring the SL sequence.

[Full Abstract]

P38 » The marine metagenomic databases and computational analysis for the environmental resistome exploration

Presenting Author: Michel Marin (Oswaldo Cruz Institute - Fiocruz)

Co-authors: Bruno Gabriel Andrade (Oswaldo Cruz Institute - Fiocruz) Erica Fonseca (Oswaldo Cruz Institute - Fiocruz, Laboratory of Molecular Genetics of Microorganisms); Michel Marín (Oswaldo Cruz Institute - Fiocruz, Laboratory of Molecular Genetics of Microorganisms); Ana Carolina Vicente (Oswaldo Cruz Institute - Fiocruz, Laboratory of Molecular Genetics of Microorganisms)

Short Abstract: The Metallo-β-Lactamase (MBL) genes belongs to a divergent and ancient family of enzymes that can hydrolyze the β-Lactams antibiotics. Studies have shown that the genes from clinical bacteria emerged in the natural environment. In this work we used the marine metagenomic projects to explore the marine resistome, searching for the clinical MBL GOB homologs using the Hmmer V3 software, Blastp+ and performing phylogenetic reconstruction with Mega5. Sequences related to GOB were found in oceans from the Global Ocean metagenomic project. For the first time, an in silico approach showed and mapped the dispersion of these genes in the oceans.

[Full Abstract]

P39 » MetaABC – an integrated Metagenomics platform for data Adjustment, Binning, and Clustering

Presenting Author: Cheng-Yan Kao (National Taiwan University)

Co-authors: Chien-Hao Su (National Taiwan University, Dept. of Computer Science & Information Engineering); Huai-Kuang Tsai (Academia Sinica, Institute of Information Science)

Short Abstract: MetaABC is a metagenomic platform that integrates several binning tools for removing artifacts, analyzing unassigned reads, and controlling sampling biases. It allows users to better interpret data by combining selected analysis methods. MetaABC can output data in various visual formats such as tables, pie and bar charts as well as clustering result diagrams. MetaABC also provides a stand-alone version of the software for dealing large datasets.

[Full Abstract]

P40 » Towards a comprehensive search of putative chitinases sequences in environmental metagenomic databases

Presenting Author: Aline Romao-Dumaresq (Fundação Oswaldo Cruz)

Co-authors: Rafael Cuadrat (Fundação Oswaldo Cruz, Instituto Oswaldo Cruz); Adriana Fróes (Fundação Oswaldo Cruz, Instituto Oswaldo Cruz); Floriano Silva Jr (Fundação Oswaldo Cruz, Instituto Oswaldo Cruz); Alberto Davila (Fundação Oswaldo Cruz, Instituto Oswaldo Cruz)

Short Abstract: This work aimed to test a profile Hidden Markov Model based strategy in identifying chitinases sequences in metagenomic databases and also to analyze the phylogenetic relationships of the retrieved sequences, the presence of chitinase signatures and the conserved domains variability. The Neighbor-Joining tree analysis showed some variability in the catalytic domain region of the metagenomic sequences and revealed common sequence patterns among all the trees. Additionally, the scanning of the retrieved metagenomic sequences for chitinase conserved domains/signatures using both an InterProScan and a RPS-BLAST search confirmed the efficacy of our HMM-based approach in detecting putative chitinases sequences.

[Full Abstract]

P41 » Analysis of non-canonical introns in the human transcriptome

Presenting Author: Guillermo Parada (Pontificia Universidad Católica de Chile)

Co-authors: Roberto Munita (Pontificia Universidad Católica de Chile, Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas); Katia Gysling (Pontificia Universidad Católica de Chile, Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas)

Short Abstract: Intron recognition relies on sequence-specific interactions between the intron terminal regions and the spliceosome ribonucleoprotein particles. Most of introns are of the U2-type with invariant GT-AG dinucleotides, while a minor group is of the U12-type that may also have AT-AC dinucleotides. There are only few cases of non-canonical introns reported. We have done a comprehensive analysis of non-canonical splice junctions present in EST, cDNA and RNA-Seq data from the human transcriptome, using different strategies to cope with artefactual splice sites. We have found novel non-canonical introns and validated them by RT-PCR.

[Full Abstract]

P42 » FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation

Presenting Author: David Urbina (Universidad de los Andes)

Co-authors: Diego Riaño-Pachón (Universidad de los Andes, Ciencias Biológicas)

Short Abstract: For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyze an available set of data from an assay of formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed. We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding Gene-Ontology (GO), for a evaluation of over-representate GO categories. Some genes, link with functions or locations, that have been previous described, indicating the success of the method finding carbon-metabolism related fragments.

[Full Abstract]

P43 » Bacterial Symbionts of the cochineal insect Dactylopius coccus, A Metagenomic Approach

Presenting Author: Shamayim Tabita Ramirez-Puebla (Center for Genomic Sciences. National Autonomous University of Mexico)

Co-authors: Esperanza Martínez-Romero (Center for Genomic Sciences. National Autonomous University of Mexico, Genomic Ecology); Monica Rosenblueth-Laguette (Center for Genomic Sciences. National Autonomous University of Mexico, Genomic Ecology)

Short Abstract: Class Insecta is the most abundant animal group on Earth. They have metabolic limitations so established mutulistic symbiosis with bacteria to compensate these deficiencies. The relationship is so close that influence their evolution. Bacteria commonly lose free-living genes, have reduced genomes (138 to 1500 Kb) and can not be cultured. The best approach to study is through metagenomics. Genomic analysis of those bacteria allow to know about evolution process and biological bases of the symbiosis. Insects of genus This study is about bacterial symbionts of Dactylopius coccus, the natural source for red crimson dye used in food, textile and cosmetics.

[Full Abstract]

P44 » Comparing the potential for identification of Lactobacillus spp of 16S rRNA variable regions

Presenting Author: LAURA GONZALEZ (UNIVERSIDAD DE LOS ANDES)

Co-authors: CONSUELO VANEGAS (UNIVERSIDAD DE LOS ANDES, BOGOTA D.C); DIEGO RIAÑO (UNIVERSIDAD DE LOS ANDES, BOGOTA D.C)

Short Abstract: The 16s rRNA is useful to classify bacterial strains into species. The identification of the minimal region of this gene that allows correct classification is important for metagenomic analyses. In this study we suggest using V1V3 region to classify Lactobacillus spp strains resulting from analysis with currently available tools, i.e., naïve Bayesian classifier, taxonomy assigning pipelines and phylogenetic inferences. The experimental data shows that this region gives the same information that shows the entire 16s rRNA. The proposed workflow could be employed to identify the minimal region of 16S rRNA to classify other species.

[Full Abstract]

P45 » Data Mining of Coffee Rust

Presenting Author: David Boter-Rozo (Universidad de Los Andes, Colombia)

Co-authors: David Boter-Rozo (Universidad de Los Andes, Colombia); William Giraldo (Cenicafé, Fitopatología); Álvaro Gaitán (Cenicafé, Biología); Marco Cristancho (Cenicafé, Fitopatología); Diego Riaño (Universidad de los Andes, Biología); Silvia Restrepo (Universidad de los Andes, Biología)

Short Abstract: The genomes of nine isolates of Hemileia vastatrix, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and de novo assemblies of data were performed. Since isolates were obtained from the field and it is not possible to produce axenic cultures of H. vastatrix, MEGAN software was used to evaluate contamination levels and to select contigs with fungal similarities. Mitochondrial contigs were identified and annotated by comparing this assembly against the Puccinia genome. Furthermore, two transcriptomes from isolates of H. vastatrix were assembled to complement the genomic data.

[Full Abstract]

P46 » Functional annotation pipeline for high-throughput sequencing microbiomes

Presenting Author: Estefania Mancini (INDEAR)

Co-authors: Santiago Revale (INDEAR, Genomics and Bioinformatics); Nicolas Rascovan (INDEAR, Genomics and Bioinformatics); M. Belen Carbonetto (INDEAR, Genomics and Bioinformatics); Martin Vazquez (INDEAR, Genomics and Bioinformatics)

Short Abstract: Microbial metagenomics and metatrancriptomics is a rapidly advancing field since the advent of next generation sequencing technologies. The major interests in the study of microbial communities are to discover the metabolic potential of an environmental sample and to know which ones are active at a specific condition. There is no single reference bioinformatics procedure to analyse these datasets. We herein introduce a pipeline for metatranscriptomes analysis that has been tested on our own datasets obtained from wheat rhizosphere samples from a semi-arid argentinean soil and sequenced using 454 technology. This pipeline allows sequence processing and analysis facilitating environmental functional studies.

[Full Abstract]

P47 » Data Merge Annotation Pipeline (DMAP); Utilizing a sequence coordinate based approach to Prokaryotic annotation.

Presenting Author: Maximo Rivarola (Instituto de Biotecnología, Instituto Nacional de Tecnologia Agropecuaria)

Co-authors: Sergio Gonzalez (Instituto Nacional de Tecnologia Agropecuaria, Instituto de Biotecnología); Bernanrdo Clavijo (Instituto Nacional de Tecnologia Agropecuaria, Instituto de Biotecnología); Paula Fernandez (Instituto Nacional de Tecnologia Agropecuaria, Instituto de Biotecnología); Maria Martinez (Instituto Nacional de Tecnologia Agropecuaria, Instituto de Biotecnología); Maria Ceron Cuchi (Instituto Nacional de Tecnologia Agropecuaria, Instituto de Patobiologia); Silvio Cravero (Instituto Nacional de Tecnologia Agropecuaria, Instituto de Biotecnologia); Joaquin Dopazo (Centro de Investigacion Principe Felipe , Department of Bioinformatics); Marisa Farber (Instituto Nacional de Tecnologia Agropecuaria, Instituto de Biotecnología); Norma Paniego (Instituto Nacional de Tecnologia Agropecuaria, Instituto de Biotecnología)

Short Abstract: We present a versatile and customizable approach to bacterial genome computational analysis, called DMAP. The pipeline works with NGS data and utilizes the Chado schema of GMOD database to analyze the functional annotation results. DMAP is capable of merging assemblies from different approaches, gene predictor combining and functional annotation of genes and gene products from different sources, while displaying all genomic data to the user in a customized Gbrowse with all its analysis in separate tracks. DMAP can query the merged data through the use of a coordinate based system through a web user interface.

[Full Abstract]

P48 » Bioinformatics analysis reveals the diverse and highly complex spinal cord regeneration transcriptome on Xenopus laevis

Presenting Author: Leonardo Almonacid (Pontificia Universidad Católica de Chile)

Co-authors: Dasfne Lee-Liu (Universidad de Chile, Center for Aging and Regeneration and Millenium Nucleus in Regenerative Biology); Francisco Melo (Pontificia Universidad Católica de Chile, Departamento de Genética Molecular y Microbiología); Juan Larrain (Pontificia Universidad Católica de Chile, Center for Aging and Regeneration and Millenium Nucleus in Regenerative Biology)

Short Abstract: Next-generation sequencing (NGS) has become one of the most preferred techniques to study complex biological process at the transcriptional level. In an integrative view, we have used the power of NGS analysis and bioinformatics resources to provide an enriched view of different pathways, novel transcripts and isoforms, and differential expression patterns of the spinal cord regeneration transcriptome for Xenopus laevis. Our analysis shows several groups of genes related with the biological function of cells proliferation, highlighting those related to regulation of transcription. These illustrate the level of signaling required to produce new differentiated cells to replace the damages ones.

[Full Abstract]

P49 » SNP discovery with fuzzy inference through computational model for decision making

Presenting Author: Wagner Arbex (Empresa Brasileira de Pesquisa Agropecuária)

Co-authors: Marta Martins (Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Gado de Leite); Marcos Vinícius Silva (Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Gado de Leite); Luís Alfredo Carvalho (Universidade Federal do Rio de Janeiro, Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia)

Short Abstract: SNPs discovery requires bioinformatics tools to be applied to different cases, with the ability to analyze “reads” from different sources and to establish reliable measures. These tools work with different methodologies concerning distinct attributes. However, similar results are expected, even when dealing with a same data set, but it’s not unusual to yield different results, which leads to uncertainty in decision making when the results are discordant. This text describes a fuzzy inference decision model applied to assist decision making in cases when information is conflicting and also in the confirmation of coincident information.

[Full Abstract]

Topic Session: Macromolecule Structure/Function Prediction

P50 » Modeling proteins using supersecondary structure library and NMR chemical shifts

Presenting Author: Andras Fiser (Albert Einstein College of Medicine)

Co-authors: Vilas Menon (Albert Einstein College of Medicine, Systems and Computational Biology); Joseph Dybas (Albert Einstein College of Medicine, Systems and Computational Biology)

Short Abstract: A new method is presented to generate theoretical protein structures for such remote homology modeling cases where sequence signal is not useful any more. The approach uses NMR chemical shift data and an exhaustive library of protein structure building blocks, Smotifs. The current modeling approach does not require any sequence information for modeling.

[Full Abstract]

P51 » Using correlation data and network decomposition to obtain sub-class determinants in protein families

Presenting Author: Lucas Bleicher (Universidade Federal de Minas Gerais)

Co-authors: Richard Garratt (Universidade de Sao Paulo, Instituto de Fisica de Sao Carlos); Ney Lemke (Universidade Estadual de Sao Paulo, Departamento de Fisica e Biofisica, Botucatu)

Short Abstract: Correlated mutation has been used mostly to detect structural contact pairs in protein families. Based on previous observations that it can also provide functional insights, we provide a framework devoted to this purpose, based on an amino acid specific correlation measure, used to build networks summarizing correlation and anti-correlation patterns in a protein family. Network decomposition results in subsets that can be further assessed by parameters and procedures, proposed for this methodology, having useful applications in protein family analysis. This framework is applied to the family of Fe/Mn superoxide dismutases, highlighting its potential use in protein characterization and gene annotation.

[Full Abstract]

P52 » Bacterial RNAs and host human cells interactions

Presenting Author: Amir Shmaryahu (Fundación Ciencia para la Vida)

Co-authors: Pablo DT Valenzuela (Fundación Ciencia para la Vida, Bioinformatics)

Short Abstract: We have developed a bioinformatic pipeline for possible miRNAs discovery generated from bacterial RNAs that may have potential to regulate gene expression of the host human cell, in case of infection. Given their versatile roles in transcriptional and translational control of gene expression and in quality control of macromolecular products, it is suggested that the study of these predicted miRNAs will yield important clues in the future as to how the host human fine tune cell processes possible human diseases like as cancer in response to changing bacterial environments.

[Full Abstract]

P53 » AFAL: a web service for profiling amino acids surrounding ligands in Protein Data Bank crystallographic data

Presenting Author: Mauricio Arenas (Universidad de Talca)

Co-authors: Samuel Ortega (Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Bioinformatica); Danilo Gonzalez-Nilo (Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Bioinformatica); David Holmes (Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Biology); Ehmke Pohl (Biophysical Sciences Institute, Durham University,, Chemistry); Raquel Quatrini (Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Biology)

Short Abstract: The advancement of crystallography technologies and the wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information.AFAL is a Web application for the analysis of crystallographic data stored in the Protein Database. This application determines the amino acid profile surrounding thousands of ligands that have been co-crystallized with proteins.The results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions, helping to compare the ligand-binding sites of different proteins and uncovering general as well as specific interaction patterns from existing data.

[Full Abstract]

P54 » Evolution of linear motifs within the intrinsically disordered and globular domains of the papillomavirus E7 oncoprotein

Presenting Author: Lucia Chemes (Fundación Instituto Leloir IIBBA-CONICET)

Co-authors: Juliana Glavina (Protein Physiology Laboratory, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, Departamento de Química Biológica); Julian Faivovich (División Herpetología, Museo Argentino de Ciencias Naturales-CONICET, Buenos Aires, Argentina, Museo Argentino de Ciencias Naturales); Leonardo Alonso (Fundacion Instituto Leloir , Buenos Aires Argentina, IIBBA-CONICET); Cristina Marino-Buslje (Fundacion Instituto Leloir, IIBBA CONICET, Buenos Aires Argentina, Structural Bioinformatics Laboratory); Gonzalo de Prat Gay (Fundacion Instituto Leloir IIBBA CONICET, Buenos AIres Argentina, Protein Structure-Function and Engineering Laboratory); Sanchez Ignacio (Protein Physiology Laboratory, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, Departamento de Quimica Biologica)

Short Abstract: Linear motifs mediate many protein functions. We studied conservation and evolution of eight linear motifs within the intrinsically disordered (E7N) and globular (E7C) domains of the papillomavirus E7 protein using 200 sequences. E7N and E7C show similar conservation, which is explained by the globular structure of E7C and by the conserved and coevolving linear motifs in E7N. Several motif pairs show high co-occurrence, suggesting that they form functional and evolutionary units. Multiple independent appearances of several motifs during papillomavirus evolution provide direct evidence for convergent evolution, which may play an adaptive role as shown by correlation with phenotype.

[Full Abstract]

P55 » Predicting Protein Function from Sequence and Structural Data: a Globin’s Family Case

Presenting Author: Juan Bustamante (University of Buenos Aires)

Co-authors: Dario Estrin (University of Buenos Aires, INQUIMAE); Marcelo Marti (University of Buenos Aires, INQUIMAE)

Short Abstract: Predicting function from sequence and/or structure are key issues in bioinformatics. Assuming that the protein function is coded in the structure through the determination of chemical properties, it is possible to predict a putative function if relevant properties can be computed. We has developed in-silico methods to determine functional processes based on structural information and applied them to the truncated hemoglobin family. Our results shows that predicting specific functional properties from sequence/structure is possible, also reveal interesting aspects about these globins family evolutionary history at molecular level.

[Full Abstract]

P56 » Cross talk between DNA and Transcription factors

Presenting Author: Matias Machado (Institut Pasteur de Montevideo)

Co-authors: Pablo Dans (Institut Pasteur de Montevideo, Biomolecular Simulation Group); Sergio Pantano (Institut Pasteur de Montevideo, Biomolecular Simulation Group)

Short Abstract: Transcription factors (TFs) regulate the gene expression by binding to cis-regulatory boxes at promoter regions of the DNA. On the other hand, DNA mutations away from regulatory boxes may modulate transcriptional efficiency. Using coarse grain simulations we studied the dynamics of different promoter regions in the timescale of the microsecond. Simulations performed in absence/presence of the TATA binding protein modify the structure and dynamics of DNA up to ~12 base pairs far from the binding site, suggesting a cross talk between different regulation boxes within the promoter region.

[Full Abstract]

P57 » Protein folding using a HP model based on an octahedral core and genetic algorithms.

Presenting Author: Darío José (Universidad Industrial de Santander)

Co-authors: Darío Delgado Quintero (Universidad Industrial de Santander) Henry Arguello Fuentes (Profesor titular, School of System Engineering); Rodrigo Gonzalo Torres Sáez (Profesor Titular, School of Chemistry)

Short Abstract: In this work, we develop a methodology to approximate the protein structure using genetic algorithms and a lattice model. To increase the accuracy in the structure aproximation, we use an octahedral lattice and developed an optimization function to increase the speed of convergence and reducing the search space. We showed step by step how develop a genetic algorithm that suits the problem of protein folding and how to adapt this problem to a combinatorial optimization problem.

[Full Abstract]

P58 » Sulfenamide formation is a conserved mechanism of autoprotection among protein folds.

Presenting Author: Lucas A. Defelipe (Universidad de Buenos Aires)

Co-authors: Adrián Turjanski (Universidad de Buenos Aires) Esteban Lanzarotti (Universidad de Buenos Aires, Departamento de Química Biológica/INQUIMAE-UBA-CONICET); Marcelo Marti (Universidad de Buenos Aires, Departamento de Química Biológica/INQUIMAE-UBA-CONICET)

Short Abstract: Cysteine oxidation is an important protein regulation mechanism. The first step in cysteine oxidation is the formation of sulfenic acid which can further oxidize into sulfinic and sulfonic acid or form in some cases reversible cyclic sulfenamides that are able to recover cysteine via selfregulation. We found a series of proteins with an anomalous cysteine psi dihedral angle and we correlate this finding with the ability to form a cyclic sulfenamide preventing to suffer irreversible oxidation. This structural motif is related to the ability to protect the protein from oxidative stress and is a more general mechanism than previously thought.

[Full Abstract]

P59 » Full-atom structure-based prediction of transcription factor binding sites

Presenting Author: Tomas Norambuena (Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile)

Co-authors: Francisco Melo (Pontificia Universidad Católica de Chile, Molecular Genetics and Microbiology)

Short Abstract: Protein-DNA binding is of paramount importance since it is involved in several cellular processes. Two main approaches to predict protein-binding sites in the DNA have been reported: Sequence-based methods and Structure-based methods. In this work, we present the development of novel statistical potentials that describe the protein-DNA interactions, used to estimate the stability of proteins-DNA complexes from the atomic coordinates of their 3D structures. Here we show that the combined use of these potentials and software for the 3D modelling of protein-DNA complexes allowed us to recover in a large degree the known experimental binding sites for several transcription factors.

[Full Abstract]

P60 » Annotation System based on Hydrophobic Cluster Analysis

Presenting Author: Dario Delgado (Universidad Industrial de Santander)

Co-authors: Cindy Solano (Universidad Industrial de Santander) Cindy Solano (researcher, School of Computer and System Engineering); Narmer Fernando Galeano Vanegas (Development and research, CENICAFE); Alvaro Leon Gaitán (Researcher, CENICAFE); Cristian Blanco Tirado (Associate Professor, School of Chemestry - Universidad Industrial de Santander )

Short Abstract: We developed a new online tool to compare and annotate protein sequences of coffee using HydrophobicCluster Analysis (HCA). The comparison tool is useful to ascertain molecular information of protein sequences not obtained using traditional approaches. Our comparison scheme is able to comparesystematically many proteins at once based on a prealignment of pairsof sequences using BLAST. Our set of tools has been successfullytried using well-known sets of proteins, such as those correspondingto the Arabidopsis thaliana genome sequence. Currently we arebuilding a database to annotate the Colombian coffee genomesequences using our set of online tools based on HCA analysis.

[Full Abstract]

P61 » Using protein conformational diversity increase protein stability estimation

Presenting Author: Ezequiel Juritz (Universidad Nacional de Quilmes)

Co-authors: Gustavo Parisi (Universidad Nacional de Quilmes) Maria Silvina Fornasari (Universidad Nacional de Quilmes, Ciencia y Tecnonlogia); Gustavo Parisi (Universidad Nacional de Quilmes, Ciencia y Tecnonlogia)

Short Abstract: Here we study the effect of considering conformational diversity of proteins to predict protein stability after single mutations. We evaluated 1993 mutations on 89 different proteins showing different degrees of conformational diversity. We found that using conformational diversity a given mutation could change their predicted stability as much as +-8 kcal/mol and that the correlation with experimental data increases notably. Interestingly, as conformers occur with different population accordingly to the thermodynamic equilibrium in solution, we found that in most proteins, 70% of the mutations that better correlate with experimental data are found in a given conformer.

[Full Abstract]

P62 » Structural bioinformatics on an enzyme involved in the synthesis of esters: The case of alcohol acyltransferase from the andean Vasconcellea pubescens.

Presenting Author: Luis Morales-Quintana (Universidad de Talca)

Co-authors: Raul Herrera (Universidad de Talca) Carlos Gaete (Universidad de Talca, IBVB); Lida Fuentes (Universidad de Talca, IBVB); Maria Moya-Leon (Universidad de Talca, IBVB)

Short Abstract: In Vasconcellea pubescens the aroma is formed mainly by esters, which are produced through an esterification reaction between alcohols and acyl-CoAs catalyzed by the enzyme acyl alcohol transferase (VpAAT1). A structural model for AAT was built by comparative modelling methodology. The results showed a protein structure composed of 15 β sheets and 14 α helix. Conformational interaction between the protein and several ligands was explored by molecular docking simulations, and the predictions obtained were tested through kinetic analysis. The favourable predicted substrate orientation was observed for benzyl alcohol and acetyl CoA, showing the coincidence between kinetic and molecular docking analysis.

[Full Abstract]

P63 » Sea Anemone Neurotoxins: A computational approach

Presenting Author: Samuel David Garcia (Pontificia Universidad Javeriana)

Co-authors: George Barreto (Pontificia Universidad Javeriana) Angelica Sabogal (Pontificia Universidad Javeriana, Nutrición y Bioquímica); Janneth Gonzalez (Pontificia Universidad Javeriana, Nutrición y Bioquímica); Ludis Morales (Pontificia Universidad Javeriana, Nutrición y Bioquímica)

Short Abstract: Sea anemone neurotoxins are peptides of which more than forty have been previously isolated and their atomic structures assessed. These toxins interact with Na+-K+ channels, resulting in specific alterations on their functions. These interactions are important for the treatment of nearly eighty autoimmune disorders. The aim of this study was to predict the interaction complex toxins-Kv1, by homology-modeling, molecular-docking, and computational alanine-scanning. Our results show three new predictive structural models of complex neurotoxins-Kv1 and binding-energy hot-spots in channel-neurotoxin interface. This knowledge may be useful to understand this interaction, and how this new information will serve as an input for the design of more promising drugs.

[Full Abstract]

P64 » Dissecting alpha helices in HIV proteins

Presenting Author: Hossein Fallahi (Raziuniversity)

Co-authors: Ali Bidmeshkipour (Razi University, Biology)

Short Abstract: Here a comparison was made between alpha helices in HIV and some other proteins to investigate if there are any differences between the content of amino acids in different positions of HIV proteins and those of other proteins. The results indicate that alpha helix number and size varies among the HIV proteins and between HIV proteins and other proteins in our dataset. Long alpha helices were found in HIV proteins, which could not be found in other proteins. On the other hand, some amino acids showed differential preferences toward HIV and other proteins in the dataset.

[Full Abstract]

P65 » Dissecting relationships between sequence, structure and functions in the ankyrin repeat protein family

Presenting Author: Rodrigo Gonzalo Parra (Universidad de Buenos Aires)

Co-authors: Diego Ferreiro (Universidad de Buenos Aires) Diego Ferreiro (Universidad de Buenos Aires, Química Biológica)

Short Abstract: Repeat-proteins are made up of tandem arrays of similar 20~40 amino acid stretches that usually fold up in elongated architectures mainly stabilized by local interactions. With a simple and linear structure that lacks of sequence-distant contacts, these proteins represent a useful model to study protein folding, dynamics and function.Ankyrin Repeat Proteins (ARPs) mediate protein-protein interactions and are widely distributed in nature. We have colected all available ARPs to build a database from which we have calculated and analyzed several parameters. We aim to establish correlations with experimental information and find simple descriptions that help to interpret their functional behaviour.

[Full Abstract]

P66 » Sequence dependent elasticity of DNA heteropolymer

Presenting Author: Sudipto Muhuri (Institute of Physics, Bhubaneswar, India)

Short Abstract: We study the ‘sequence’-distribution of thermally averaged global and local elastic properties of a DNA random heteropolymer, within the framework of a disordered Kratsky-Porod model. We arrive at a number of qualitative results on the form of the distribution function of the thermally averaged end-to-end distance, and its moments. For shorter chains, there is a crossover with the most probable end-to-end distance deviating significantly from the mean. Further, the distribution of local quantities related to thermally averaged tangent-tangent correlator are typically broad. We illustrate that scale dependent ‘sequence’ sensitivity should have implications for the binding of proteins to DNA.

[Full Abstract]

P67 » Computational analysis of the dominions CAH and FNIII of the Fosfacan DSD-1-PG and their union with the Tenascin R (TN-R)

Presenting Author: Guillermo Villamil Mora (Pontificia Universidad Javeriana)

Co-authors: George Barreto (Pontificia Universidad Javeriana, Biology); Janneth Gonzalez (Pontificia Universidad Javeriana, Biology)

Short Abstract: The proteoglycans are proteins involved in neuronal processes. The increment of these and the overexpression of the proteoglycan Fosfacan after a cerebral injury, leads towards inhibitory processes of the neuronal regeneration. This proteic function is mediated by unions at the dominion with proteins of the extracellular matrix. A computational structure was established by homology of the extracellular dominions of Fosfacan DSD-1-PG, which are FNIII and CAH. The objective was to study the place of union with the extracellular protein Tenascin R involved in the axonal regeneration. It was found that the DSD-1PG in complex with the Tenascin R is mediated by calcium atoms.

[Full Abstract]

P68 » VISUALDEP A TOOL TO VISUALIZE DIFFERENCES IN ELECTROSTATIC POTENTIALS

Presenting Author: Carlos Rios-Vera (Universidad de Concepcion)

Co-authors: Jose Martinez-Oyanedel (Universidad de Concepcion) Natalia Jaña-Perez (Universidad de Concepcion, Bioquimica y Biologia Molecular); Marta Bunster (Universidad de Concepcion, Bioquimica y Biologia Molecular)

Short Abstract: VisualDEP is a web application to compare and visualize differences in electrostatic potential (EP) between two proteins that have high structural similarity. In order to perform its workflow VisualDEP requires uploading the structures of both molecules to align it, calculate the difference in the electrostatic potential between both structures and a standarised difference and a similarity index are calculated. As final output, atoms strongly changing in EP are listed in a table and the differences in EP are colored on the reference structure.

[Full Abstract]

P69 » Prediction of Protein-Metal Binding Sites Using Machine Learning and Combining Diverse Types of Information

Presenting Author: José Reyes (Universidad de Talca)

Co-authors: Alfredo Pereira (Universidad de Talca, Centro de Bioinformática y Simulación Molecular); Mauricio Arenas (Universidad de Talca, Centro de Bioinformática y Simulación Molecular)

Short Abstract: Metalloproteins play an important role in many biological processes. It has been estimated that around one third of all proteins in an organism involved some kind of metal interaction. However, most of these interactions are yet to be discovered. Several computational methods for the inference of novel protein-metal binding sites have been recently developed. Here we undertake a comparative performance evaluation study of several machine learning algorithms for this task. Our approach is also based on the integration of diverse types of biological, structural and physicochemical information.

[Full Abstract]

P70 » Neural Network Detection of Viral Structural Proteins

Presenting Author: Victor Seguritan (San Diego State University)

Short Abstract: Phages are crucial for host survival and pathogenicity; their discovery may provide clues to the impact of viruses on microbes and humans. Viral structural protein function is challenging to detect from sequence data because of because of their high degree of diversity. Here, we trained Artificial Neural Networks (ANNs) to detect viral structural proteins by amino acid frequencies. Our ANNs correctly classified 76% of test sequences with 73% specificity and 84% sensitivity. Gene constructs of hypothetical proteins that are ANN-predicted structural proteins were expressed and visualized by transmission electron microscopy, which show self-assembled structures strongly resembling structural proteins.

[Full Abstract]

P71 » Potv2, a program that allows to plot the electrostatic potential of the minor groove of DNA.

Presenting Author: Fernando Gutierrez (P. Universidad Catolica de Chile)

Co-authors: Francisco Melo (P. Universidad Catolica de Chile); Tomas Norambuena (P. Universidad Catolica de Chile, Molecular Genetics and Microbiology)

Short Abstract: Electrostatic interactions play a central role in a variety of biological processes, and especially in the ability some proteins possess to recognize specific DNA sequences. Recent studies have highlighted the correlation exists between minor-groove width and electrostatic potential. Therefore, in this study we developed an application in C++ that displays 2D and calculate the electrostatic potential of DNA molecules attached to proteins, in addition to plotting the electrostatic potential of the minor groove. With the objective of studying the role that has the shape of the DNA in protein-DNA recognition.

[Full Abstract]

P72 » The salmonid selenotranscriptome: in silico and in vivo characterization.

Presenting Author: Francisco J. Altimiras (Universidad de Chile)

Co-authors: Verónica Cambiazo (Universidad de Chile, Laboratorio de Bioinformática y Expresión Génica, INTA.); Rodrigo Pulgar (Universidad de Chile, Laboratorio de Bioinformática y Expresión Génica, INTA.)

Short Abstract: The selenotranscriptome is the set of selenoprotein transcripts. Selenoproteins are a diverse group of proteins implicated in immune and oxidative responses that are present in all three domains of life: bacteria, archaea and eukaryota. Selenoproteins contain selenium (Se) in the form of the amino acid selenocysteine (Sec) which is encoded by the STOP codon (UGA). The presence of an RNA stem-loop structure, the Sec insertion sequence (SECIS) element in the 3' untranslated region (3'UTR) of eukaryotic mRNAs, differentiates the Sec or stop function of UGA codons. Here we applied a series of bioinformatics tools to predict the salmonid selenotranscriptome from large collections of EST sequences.

[Full Abstract]

P73 » Bioinformatic and Biophysical Characterization of Fur (Ferric Uptake Regulator) from an Extreme Acidophile Thriving in an Iron Rich Environment

Presenting Author: Mauricio Arenas (Universidad de Talca / Universidad Andres Bello)

Co-authors: ehmke pohl (Biophysical Sciences Institute, Durham University,, Chemistry); Narcizo Marquez (Laboratório Nacional de Luz Síncroton, XAFS); David S Holmes (Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, biologia); Raquel Quatrini (Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, biologia)

Short Abstract: Acidithiobacillus ferrooxidans lives at

[Full Abstract]

P74 » Comparative Modeling of B-DNA

Presenting Author: Ignacio Ibarra (P. Universidad Catolica de Chile)

Co-authors: Francisco Melo (P. Universidad Catolica de Chile); M.S. Madhusudhan (Bioinformatics Institute, Biomolecular Modeling and Design Division)

Short Abstract: An in silico protocol based in Comparative Modeling with MODELLER has been developed to obtain full-atom duplex B-DNA molecule models. The current approach takes into consideration physical restraints derived from a training set group of B-DNA structures and is assessed using a testing set of B-DNA structures. The created models for unknown DNA sequences that this protocol will give could be used to assess the interaction between them with other biomolecules, in cases such as protein-DNA complexes.

[Full Abstract]

P75 » FragProt, a database of short protein fragments clustered by structural similarity

Presenting Author: Felipe Rodríguez (P. Universidad Catolica de Chile)

Co-authors: Francisco Melo (P. Universidad Catolica de Chile) Alex Slater (P. Universidad Catolica de Chile, Molecular Genetics and Microbiology)

Short Abstract: Protein fragments play an essential role in many bioinformatics areas, like homology protein modeling, secondary and tertiary structure prediction and the study of sequence - structure relationships. In order to understand a little more about these building blocks, a repository containing thousands of protein fragments clustered by structural similarity was developed, also including data like accessible surface area per residue and hydrophobicity coefficients for each aminoacid. The major aim of this database, is to constitute a tool that allows to obtain information about groups of similar short conformations that could be of interest for the scientific community.

[Full Abstract]

P76 » Implementation of a new metodology for the 2D representation and visualization of 3D interfaces in protein-DNA complexes.

Presenting Author: Jaime Riquelme (P. Universidad Catolica de Chile)

Co-authors: Francisco Melo (P. Universidad Catolica de Chile)

Short Abstract: Modelling DNA protein complex in a 3D graphic representation has showed technical problems for distinguishing the protein-DNA interfaces. Considering this problem, new computer software has been developed to generate a 2D interface visualization. The software, named “iDNA”, uses as a template or reference frame the 2D projection of the DNA structure, locating the interactions based in the positions of the atoms in the nucleotides. The conclusion is that a 2D observation facilitates the visualization of the characteristics in a protein-DNA interface through the diagram provided by “iDNA”. The observation is more efficient than other 2D models like Nucplot.

[Full Abstract]

P77 » Using protein conformational diversity increase protein stability estimation

Presenting Author: Ezequiel Juritz (Universidad Nacional de Quilmes)

Co-authors: Silvina Fornasari (Universidad Nacional de Quilmes, Structural Bioinformatics Group); Gustavo Parisi (Universidad Nacional de Quilmes, Structural Bioinformatics Group)

Short Abstract: Here we study the effect of considering conformational diversity of proteins to predict protein stability after single mutations. We evaluated 1993 mutations on 89 different proteins showing different degrees of conformational diversity. We found that using conformational diversity a given mutation could change their predicted stability as much as +-8 kcal/mol and that the correlation with experimental data increases notably. Interestingly, as conformers occur with different population accordingly to the thermodynamic equilibrium in solution, we found that in most proteins, 70% of the mutations that better correlate with experimental data are found in a given conformer.

[Full Abstract]

P78 » On the conformational diversity of proteins and its relationship with biological properties

Presenting Author: Alexander Monzon (National University of Quilmes)

Co-authors: Ezequiel Juritz (National University of Quilmes, Departamento de Ciencia y Tecnologia); Gustavo Parisi (National University of Quilmes, Departamento de Ciencia y Tecnologia)

Short Abstract: We present an analysis of conformational diversity on proteins and its relation with biological and physical-chemical parameters. We recruited all available crystallographic structures of 3,600 proteins as derived from PDB, accounting 12,221 structures. As a measure of the conformational diversity we registered several structural similarity scores between different instances of crystallization of the same protein, using Mammoth, TM-Score and Profit. We registered an average RMSD of 0.7Å between conformers of the same protein; the maximum RMSD between conformers of the same protein shows an average value of 1.7Å. Interesting relationships between conformational diversity and protein function and taxonomy were found.

[Full Abstract]

P79 » BeEP and the BeEP Server: using evolutionary information to help in protein structure modeling and characterization

Presenting Author: Nicolás Palopoli (Universidad Nacional de Quilmes)

Co-authors: Gustavo Parisi (Universidad Nacional de Quilmes, Departamento de Ciencia y Tecnología)

Short Abstract: BeEP (Best Evolutionary Pattern) is a quality assessment program designed to validate protein 3D models through an explicit use of evolutionary information. Each proposed structural model is used to derive a model of protein evolution represented by a set of site-specific, structurally constrained substitution matrices. By means of maximum likelihood estimations it is possible to identify the best models as those that give the greatest correlation between the substitution pattern they generate and the information contained in a sequence alignment of homologous proteins. BeEP could be downloaded or accessed through a web server, with minor differences to suit particular needs.

[Full Abstract]

P80 » Modular anatomy of the Ribokinase family fold .

Presenting Author: Pablo Villalobos (Universidad de Chile)

Co-authors: Jorge Babul (Universidad de Chile, Bioquímica y Biología Molecular); Ricardo Cabrera (Universidad de Chile, Bioquímica y Biología Molecular); Mauricio Baez (Universidad de Chile, Bioquímica y Biología Molecular)

Short Abstract: We use the centripetal profile analysis to decompose the ribokinase family fold into modules. Using a non-redundant set of 32 members obtained from the PDB, we found 10 modules. We quantified how the residues from the protein core atomic interaction network are distributed along the different modules and this was correlated with their sequence similarity. We also observed correlated movements of modular nature in molecular simulations. Structural diversity distance trees were compared to the phylogenetic tree of the whole family. In this way we define differences between modules in regard to their content of residues important for folding and function.(Fondecyt,1090336)

[Full Abstract]

P81 » WebRASP: A novel web tool to assess and explore RNA structures based on the Ribonucleic Acids Statistical Potential

Presenting Author: Jorge Cares (P. Universidad Catolica de Chile)

Co-authors: Francisco Melo (P. Universidad Catolica de Chile) Tomas Norambuena (Pontificia Universidad Católica de Chile, Molecular Genetics and Microbiology); Francisco Melo (Pontificia Universidad Católica de Chile, Molecular Genetics and Microbiology)

Short Abstract: Understanding the three-dimensional structure of the RNA could give more insights about the function and evolution of these molecules which have a central role in a wide range of biological processes. In this work, we present a new web tool based on RASP, a statistical potential to assess the structure of RNA molecules. This server has a module for the assessment in terms of the energy given by the potential and a module to identify base pair interactions occurring in the structure. This web tool was developed in PHP and C++ programming languages.

[Full Abstract]

P82 » Clustering of Proteins based on their Three-dimensional Shape using Maximum Common Subgraph

Presenting Author: Cristian López (San Pablo Catholic University)

Co-authors: July Banda-Tapia (San Pablo Catholic University)

Short Abstract: Clustering is a technique of unsupervised learning widely used; in the case of clustering of proteins, one the main problems is given by the comparison method between them. This, to establish the value of similarity. In this sense, the present work propose the clustering of proteins using the maximum common subgraph, which is possible because a protein can be modeled as a graph and in consequence its value of similarity can be obtained through the extraction of the maximum common subgraph. The results will be validate with CATH, a free online tool that classify proteins in Class, Architecture, Topology and

[Full Abstract]

P83 » Curvature and Flexibility as Promoter Regions Classifiers in Gram-Negative Bacteria

Presenting Author: Ivaine Sauthier Sartor (University of Caxias do Sul)

Co-authors: Tahila Andrighetti (University of Caxias do Sul, Biotechnology Institute); Günther Gerhardt (University of Caxias do Sul, Biotechnology Institute); Sergio Echeverrigaray (University of Caxias do Sul, Biotechnology Institute); Scheila de Avila e Silva (University of Caxias do Sul, Biotechnology Institute)

Short Abstract: The promoters are recognized as one of the transcription regulatory regions, since recruit transcriptional machinery through the binding of regulatory proteins in their DNA sequences. The embedding of structural characteristics can increase the accuracy of prediction methods. This work aims to predict, recognize and characterize promoter regions recognized by sigma factor 28 employing an approach of artificial neural networks using as input parameter curvature and flexibility data. This approach performed 6400 simulations using curvature and flexibility values for promoter recognition and prediction. The results indicate that the flexibility is an important feature using as a parameter to classifying promoter regions.

[Full Abstract]

Topic Session: Computer Aided Drug Design and Docking/Molecular Dynamics Simulations

P84 » Molecular ordering of dotriacontane supported on silica surfaces

Presenting Author: Sebastián Gutiérrez-Maldonado (Computational Biology Lab (DLab), Centro de Modelamiento Matemático (CMM), Facultad de Ciencias Físicas y Matemáticas (FCFM), Universidad de Chile, Santiago, Chile)

Co-authors: Raul Araya-Secchi (Computational Biology Lab (DLab), Centro de Modelamiento Matemático (CMM), Facultad de Ciencias Físicas y Matemáticas (FCFM), Universidad de Chile, Santiago, Chile) Maria Jose Retamal (Laboratorio de Superficies (SurfLab), Facultad de Fisica, Pontificia Universidad Catolica de Chile, Santiago, Chile) Ulrich Volkmann (Laboratorio de Superficies (SurfLab), Facultad de Fisica, Pontificia Universidad Catolica de Chile, Santiago, Chile) Tomas Perez-Acle (Computational Biology Lab (DLab), Centro de Modelamiento Matemático (CMM), Facultad de Ciencias Físicas y Matemáticas (FCFM), Universidad de Chile, Santiago, Chile)

Short Abstract: In order to explore, at the atomic level, the dynamic behavior and packing of dotriacontane (C32) molecules supported over SiO2 surfaces, we have conducted the first all-atom MD simulations of C32 films considering different thicknesses and temperatures. Preliminary results show temperature-dependent density profiles with an oscillatory behavior, which suggests internal layering, while order profiles show preferential parallel ordering directly on the SiO2 surface. Further away from the surface there seems to be no preferential ordering.

[Full Abstract]

P85 » Study of the differences in activity between structurally similar protein kinase inhibitors by using docking, molecular dynamics, and fragment-based de novo design

Presenting Author: Julio Caballero (Universidad de Talca)

Short Abstract: Protein kinases (PKs) have been identified as drug targets in numerous diseases. Many PK inhibitors have been reported in the last two decades. The vast amount of structural information of PKs can help in the design of new PK inhibitors. We propose a protocol to investigate the differences in activity between structurally similar PK inhibitors using several structural bioinformatics methods. Inhibitors of B-Raf and VEGFR2 were selected for this study. We concluded that the analysis of the movement of the complexes, and the solvent environment allows to explain the large difference in activity between structurally similar inhibitors.

[Full Abstract]

P86 » Docking Studies of a New Series of Analgesic and Anti-inflammatory Compounds (NSAIDs) with Cyclooxygenase

Presenting Author: Lucas Saraiva (Federal University of Minas Gerais)

Co-authors: Ihosvany Camps (Federal University of Alfenas, Department of Exact Science); Raquel Melo-Minardi (Federal University of Minas Gerais, Department of Computer Science ); Marcia Veloso (Federal University of Alfenas, Faculty of Pharmaceutical Science); Rodrigo Sailva (Federal University of São Carlos, Department of Chemistry)

Short Abstract: Anti-inflammatory drugs (NSAIDs) have been widely used to treat inflammatory processes. Due to the potential side effects NSAIDs might produce in parallel with the need for new safer and more efficient anti-inflammatory drugs, this research aimed to characterize in a molecular level, a new series of analgesic and anti-inflammatory compounds synthesized by our laboratory. The structural studies of the new series of NSAIDs were conducted by molecular docking with COX-1 and COX-2. Our docking studies have demonstrated that all the compounds are able to interact to both COXs with good score and appropriate conformation, thus showing promissory in silico activity.

[Full Abstract]

P87 » HOW DOES A SPECIFIC DRUG BIND TO AN ION CHANNEL?

Presenting Author: Wendy Gonzalez (Universidad de Talca)

Short Abstract: We designed a strategy to study how does a specific drug bind to an ion channel. The strategy is applied in the study of two-pore domain potassium (K2P) channels. K2P channels have emerged as molecular candidates for the action of pharmacological agents.A specific antagonist and very similar K2P channels but with different IC50 values for this drug were selected. The putative binding sites for the antagonist are elucidated using multiple alignments, site-directed mutagenesis and electrophysiological analysis. Once the amino acids that bind the antagonist are determined, we used drug-receptor docking to explain how this drug binds to the channel.

[Full Abstract]

P88 » Efficient selection of flexible receptor snapshots applied in molecular docking simulations

Presenting Author: Karina Machado (Universidade Federal do Rio Grande)

Co-authors: Ana Winck (Pontifícia Universidade Católica do Rio Grande do Sul, GPIN-PPGCC-FACIN); Duncan Ruiz (Pontifícia Universidade Católica do Rio Grande do Sul, GPIN-PPGCC-FACIN); Osmar Norberto de Souza (Pontifícia Universidade Católica do Rio Grande do Sul, LABIO-PPGCC-FACIN)

Short Abstract: An alternative for considering the receptor flexibility in molecular docking is to perform a series of docking simulations, using in each one, one different snapshot obtained from a molecular dynamic trajectory (FFR model). This is very time consuming. In doing so, this work contributes to the selection of receptor snapshots from the FFR model aiming at execute faster and more realistic molecular docking simulations. To achieve this we applied a KDD process where we developed a specific database and performed classification, regression and clustering data mining experiments. We obtained promising results that will be considered in future virtual screening experiments.

[Full Abstract]

P89 » Semi-flexible Protein-Ligand Docking Using a Controlled Genetic Algorithm

Presenting Author: Paola Rondon-Villarreal (PhD Student-Universidad Industrial de Santander)

Co-authors: Rodrigo Torres (Professor - Universidad Industrial de Santander, School of Chemistry)

Short Abstract: This work describes the design and implementation of a controlled genetic algorithm for a molecular docking process between protein-ligand complexes. This algorithm was designed to keep a range of values for a selection pressure, and genotypic and phenotypic diversity, and aimed to prevent premature convergence or being trapped in a local minimum energy. Additionally this genetic algorithm allows a refinement in the search of the best protein-ligand complex. For validation of this algorithm, 10 simulations were performed for each one of the selected complexes and obtained values showed an average RMSD resolution lower than 2.5 Å.

[Full Abstract]

P90 » Structural databases: A way of improving knowledge-based docking

Presenting Author: Esteban Lanzarotti (Universidad de Buenos Aires)

Co-authors: Adrián Turjanski (Universidad de Buenos Aires) Lucas A. Defelipe (Universidad de Buenos Aires, Departamento de Química Biológica/INQUIMAE-UBA-CONICET); Marcelo Marti (Universidad de Buenos Aires, Departamento de Química Biológica/INQUIMAE-UBA-CONICET)

Short Abstract: Drug discovery through docking simulations has proven successful strategy but has its limitations Using our structural database2 and binding data from BindingDB3 we performed a search of structural similarity between the drugs with crystal structures in p38a.. Our results show that using this strategy improves the quality of obtained results and brings structural information on hundreds of drugs for which no crystal data is available. This methodology will be applied for all the drugs deposited in bindingDB in order to increase the available structural information for drug discovery.

[Full Abstract]

P91 » Molecular Docking Simulation of RILUZOLE complex with Structural Model of Human alpha subunit of voltage-gated sodium channel Nav 1.6.

Presenting Author: Omar Sierra Bello (Pontificia Universidad Javeriana)

Co-authors: Janeth Gonzalez (Pontificia Universidad Javeriana, Nutrition and Biochemistry); George Barreto (Pontificia Universidad Javeriana, Nutrition and Biochemistry)

Short Abstract: Amyotrophic Lateral Sclerosis is a neurodegenerative disorder characterized by a loss of motor neurons; glutamate excitotoxicity is the most likely cause by decreasing glutamate uptake in astrocytes. Riluzole interferes with glutamate-mediated transmission; it is thought these effects may be partly due to inactivation of voltage-dependent sodium channels. We report structural model of the interaction between Nav1.6 and Riluzole. The docked complexes were subjected to minimization and investigated the key interacting residues, binding free energies, bridge pairing determination, folding pattern, hydrogen bond formation, hydrophobic contacts and flexibilities; we observed that THY1787, LEU1843 and GLN1799 are the key residues for Riluzole recognitions.

[Full Abstract]

P92 » Molecular Modeling Interactions among Sea Anemone Toxins and Kv1 Channel

Presenting Author: Angélica Sabogal (Pontificia Universidad Javeriana)

Short Abstract: Sea anemone neurotoxins are peptides that can interact with Na+-K+ channels, resulting in specific alterations on their functions. These interactions are important for the treatment of nearly eighty autoimmune disorders, like Multiple Sclerosis. The aim of this study was to predict, the interaction complex toxins-Kv, by homology modeling, molecular-docking, and computational alanine scanning. Our results show sixteen new predictive structural models of neurotoxins and binding-energy hot-spots in channel-neurotoxin interface. This knowledge may be useful to understand this interaction complex, and how this new information will serve as an input for the design of more promising drugs.

[Full Abstract]

P93 » Topological constraints and challenges imposed by knots in proteins

Presenting Author: Cesar Ramirez (University of Chile)

Co-authors: Jeffrey K Noel (University of California San Diego, Center for Theoretical Biological Physics); Mauricio Baez (University of Chile, Department of Biology)

Short Abstract: Protein knots are intriguing structural motifs that have challenged both experimental and theoretical knowledge. We investigated thermodynamic and kinetic folding of the smallest knotted proteins known, VirC2 and MJ0366, from the ribbon-helix-helix (RHH) family of proteins, employing energy landscape theory and structure-based molecular dynamics using both coarse and all-atom graining. A preordered and looped, but unknotted, intermediate state is observed, and threading the loop by plugging or slipknotting is required to reach the knotted state. Moreover, we compared these results with Arc repressor, an unknotted dimer with similar architecture, showing that this topological constraint increases the free energy barrier severely.

[Full Abstract]

P94 » Molecular basis of the mechanism of thiol oxidation by hydrogen peroxide in aqueous solution: challenging the SN2 paradigm

Presenting Author: Ari Zeida (Facultad de Ciencias Exactas y Naurales, Universidad de Buenos Aires)

Co-authors: Ryan Babbush (Harvard University, Department of Chemistry ); Mariano C. González Lebrero (Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires , IQUIFIB-Dpto. Química Biológica ); Madia Trujillo (Facultad de Medicina, Universidad de la República , Departamento de Bioquímica and Center for Free Radical and Biomedical Research ); Rafael Radi (Facultad de Medicina, Universidad de la República , Departamento de Bioquímica and Center for Free Radical and Biomedical Research ); Dario Estrin (Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET)

Short Abstract: The oxidation of cellular thiol containing compounds hydrogen peroxide, is considered to play an important role in many biological processes. This reaction has been reported to proceedthrough a SN2 mechanism, but despite its importance, the mechanism is not completely understood at theatomic level. In this work we elucidate the reaction mechanism of thiol oxidation by H2O2 for a model methanethiolate system using state of the art hybrid QM-MM molecular dynamics simulations with an umbrella sampling scheme. The data reported herein provides a detailed microscopic view of this reaction in water, setting bases for future studies related to thiolate oxidation in different protein environments.

[Full Abstract]

P95 » Binding Studies and Quantitative Structure–Activity Relationship of 3-Amino-1H-Indazoles as Inhibitors of GSK3beta

Presenting Author: Julio Caballero (Universidad de Talca)

Co-authors: William Tiznado (Universidad Andres Bello, Facultad de Ecologia y Recursos Naturales)

Short Abstract: Docking of 3-amino-1H-indazoles complexed with GSK3beta was performed. The study was conducted on a selected set of 57 compounds with variation in structure and activity. The most active compounds established three hydrogen bonds with the residues of the hinge region of GSK3beta, but some of the less active compounds have other binding modes. In addition, models able to predict GSK3beta inhibitory activities (IC50) of the studied compounds were obtained by 3D-QSAR methods. Ligand-based and receptor-guided alignment methods were utilized. Each of the predictive models exhibited a similar ability to predict the activity of a test set.

[Full Abstract]

P96 » Molecular Dynamics Simulations of Cx26-Wt and deafness related mutants M34A, A40G and V37I.

Presenting Author: Raul Araya-Secchi (Computational Biology Lab, Center for Mathematical Modeling, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile)

Co-authors: Carlos Lagos (Departamento de Farmacia, Facultad de Quimica, P. Universidad Catolica de Chile, -); Fernando Abarca (Computational Biology Lab, Center for Mathematical Modeling, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, -); Agustin Martinez (Centro Interdisciplinario de Neurociencias de Valparaiso, -); Tomas Perez-Acle (Computational Biology Lab, Center for Mathematical Modeling, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, -)

Short Abstract: Gap junctions are specialized regions of the cellular membrane in which intercellular communication channels allow the exchange of small molecules up to ~1KDa. These channels are formed by the end-to-end docking of the extracellular portion of connexins. Mutations in connexin 26 (Cx26) have been associated to hereditary hearing loss. In this work we present results from molecular dynamics simulations of models of Cx26-Wt and deafness-associated mutants: M34A, V37I and A40G. Our results show that these mutations produce changes on the diameter of the pore and rearrangements on the electrostatic potential inside the channel.

[Full Abstract]

P97 » Multi template homology modeling improves the model for type II-NADH: menaquinone oxidoreductase from Mycobacterium tuberculosis: validation by antagonist docking.

Presenting Author: Nitin Chitranshi (Rameshwaram Institute of Technology & Management)

Co-authors: Shipra Gupta (Biotech Park, Bioinformatics); Pushpendra Tripathi (Rameshwaram Institute of Technology & Management, Pharmacy)

Short Abstract: Type II NADH: menaquinone oxidoreductase (NDH-2) is an essential respiratory enzyme of the pathogenic bacterium Mycobacterium tuberculosis (Mtb) and thus an important drug target for design of receptor specific antitubercular agents.To explore the binding conformations of phenothiazine analogs to NDH-2 an integrated homology modeling, and molecular docking was carried out. Availability of 3Dmodel of NDH-2 would significantly enhance the development of new drugs for tuberculosis. However, templates of NDH-2 with low sequence similarity increase the complexity in straightforward homology modeling, and hence there is a need to evaluate different modeling methodologies.

[Full Abstract]

P98 » De novo modeling and replica exchange molecular dynamic simulation of lipoprotein Licanantase of strain Licanantay: Acidithiobacillus thiooxidans DSM 17318.

Presenting Author: Fernando Abarca (Universidad de Chile)

Co-authors: Raul Araya-Secchi (Computational Biology Lab, Center for Mathematical Modeling (CMM), Facultad de Ciencias Fisicas y Matematicas (FCFM), Universidad de Chile, Santiago, Chile.) Pilar Parada (BioSigma ‘S.A.’, Loteo Los Libertadores, Lote 106, Colina, Chile.) Tomas Perez-Acle (Computational Biology Lab, Center for Mathematical Modeling (CMM), Facultad de Ciencias Fisicas y Matematicas (FCFM), Universidad de Chile, Santiago, Chile.)

Short Abstract: Licanantase is able to enhance chalcopyrite bioleaching rate. In this work a structure for Licanantase is proposed and evaluated. Our preliminary bioinformatics analyses show a great similarity with Lipoprotein of Escherichia coli which can form stable trimers in solution. Thus it is proposed that the more probable structure for Licanantase is a trimeric coiled-coil, which was predicted using de novo modeling. In addition, replica exchange molecular dynamics simulations were performed using Licanantase and Lipoprotein in its protonation states at acid and neutral pH. The unfolding process was analyzed, showing that Licanantase was more stable than Lipoproteín in both pH conditions.

[Full Abstract]

P99 » Study and molecular characterization of the hypothetical representative of a third subfamily of aquaporins, AqpF from Acidothiobacillus ferrooxidans.

Presenting Author: Sebastián Flores J (Centro de Modelamiento Matemático. Universidad de Chile.)

Co-authors: Raúl Araya-Secchi (Centro de Modelamiento Matemático. Universidad de Chile, Computational Biology Lab.); Tomás Perez-Acle (Centro de Modelamiento Matemático. Universidad de Chile, Computational Biology Lab); David Holmes (Fundación Ciencia para la Vida , Center for Bioinformatics and Genome Biology (CBBG))

Short Abstract: Aquaporins are a large family of ubiquitous trans-membrane channel proteins that allow passive but selective flow of water and other molecules across the cell membrane. Aquaporins can be divided into two sub-families: i) strict aquaporins that only allow the passage of water and ii) the less selective aquaglyceroporins that transport water and other neutral solutes, such as glycerol, CO2 or urea. In this work, we report the first molecular dynamics simulation of the aquaporin AqpF from the bacteria Acidothiobacillus ferrooxidans, hypothetical representative of a third subfamily of aquaporins.

[Full Abstract]

P100 » Theoretical study of the interaction between Zidovudine (and novel derivatives) and human serum albumin

Presenting Author: Ileana Tossolini (National University of Entre Ríos)

Co-authors: María Cecilia Gómez (National University of Entre Rios, Faculty of Engineering); Mario Alfredo Quevedo (National University of Córdoba, Department of Pharmacy)

Short Abstract: The acquired immunodeficiency syndrome (AIDS) is treated with antiretroviral cocktails, in which Zidovudine (AZT) is included. Despite its effectiveness, AZT has significant adverse effects, many of them associated to low plasma protein binding, including the human serum albumin (HSA). Hence, obtaining AZT prodrugs, with higher affinity for HSA, is a key strategy to increase the effectiveness of the drug.The present work is aimed at obtaining a theoretical-computational study of the complexes formed by AZT (and its derivatives) and HSA (in its pure form and complexed with fatty acids), applying molecular modeling methodologies, docking and molecular dynamics.

[Full Abstract]

P101 » 3D-QSAR and molecular docking studies of 2-Pyrimidinecarbonitrile derivatives as inhibitors against falcipain

Presenting Author: ANGAMBA POTSHANGBAM (UNIVERSITY OF HYDERABAD)

Short Abstract: 3D-QSAR and molecular docking studies were performed to understand intermolecular insights of 2-Pyrimidinecarbonitrile derivatives with falcipain cysteine protease active site. Stable and statistically reliable predictive models of CoMFA and CoMSIA have shown significant r2cv, r2 and r2pred, indicating a better statistical relationship between the activity and descriptors. Based on these models, activities of a set of 12 test set molecules have been predicted and these models exhibited good predicted correlation within an acceptable error range. The binding conformations and interactions were studied by docking the inhibitors into the active site of falcipain-3 using GOLD docking tool. Both molecular docking and 3D-QSAR studies rendered complementary information

[Full Abstract]

P102 » Discovering of small molecules designed to prevent ethanol-induced potentiation of GlyR by G-beta/gamma

Presenting Author: Fabián Cerda (University of Concepción)

Co-authors: Verónica Jimenez (University de Concepción, Group of computational Chemistry); José Guzmán (University of Concepcion, Departament of Physiology)

Short Abstract: Glycine Receptor (GlyR), a ligand gated ionic channel is an effector of the G-beta/gamma dimer. The binding region between G-beta/gamma and GlyR is located in a motif within the cytoplasmic domain wich has been used as a peptide (RQHc7) in electrophysiological assays demostrating to interfere with the binding of G-beta/gamma and GlyR. In this work we used bioinformatic tools to determine, first the modeled structure of RQHc7. Then, using docking and molecular dynamics, the interaction site in G-beta/gamma was determined. Finally a virtual screening was performed obtaining sixty one high affinity small molecules with potential drug activity.

[Full Abstract]

P103 » Docking study of LipL32-human plasminogen complex: insights contributing to knowledge of the host invasion by pathogenic leptospires

Presenting Author: Leidy Viviana Barreto (Pontificia Universidad Javeriana)

Co-authors: Janneth González (Pontificia Universidad Javeriana) George Barreto (Pontificia Universidad Javeriana, Nutrition and Biochemistry); Ludis Morales (Pontificia Universidad Javeriana, Nutrition and Biochemistry)

Short Abstract: Leptospirosis is a worldwide reemerging zoonosis caused by pathogenic Leptospira. The scarce knowledge about the molecular basis of its physiopathology led to a growing interest on the study of the lipoprotein LipL32 as a plasminogen (Plg) binding receptor from Leptospira interrogans. We generated the LipL32-Plg complex by molecular docking methods. The resulting complex reveals the involvement of lysine residues in the interaction, which agrees with previous experimental reports. This LipL32-Plg complex could facilitate the host invasion process by Leptospira through tissue degradation. Our result provides detailed insights about this possible invasion process allowing further researchon peptides for therapeutic purposes.

[Full Abstract]

P104 » Non-equilibrium molecular dynamics: An aproach to understand conductance in Shaker P475D potassium channel.

Presenting Author: Romina V. Sepúlveda (Universidad Andres Bello)

Co-authors: Romina Sepúlveda (Universidad Andres Bello) David Naranjo (CINV, Universidad de Valparaiso, CINV); Danilo González-Nilo (CINV - Universidad Andrés Bello, CBIB)

Short Abstract: The Shaker potassium channel is a specialized membrane protein that allows the conduction of K+ through cell membranes. Data from patch clamp recordings have showed that a single point mutation at residue 475, aminoacid located at the internal entrance, causes a 6-8 fold increase in the conductance in similar experimental conditions. To understand why this channel mutant transport K+ ions at such high rate, we made two molecular simulations of Shaker P475D subject to an external transmembrane electric field. With this method we obtained outward and inward K+ transport events in 100 ns of simulation.

[Full Abstract]

P105 » Studying binding free energies of protein kinase inhibitors combining molecular dynamic simulations and MM-GBSA methods.

Presenting Author: Camila Muñoz Gutierrez (Universidad de Talca)

Co-authors: Jans Alzate-Morales (Universidad de Talca) Julio Caballero (Universidad de Talca, Escuela de Ingeniería en Bioinformática, Centro de Bioinformática y Simulación Molecular.)

Short Abstract: Recently, some studies using MM-GBSA calculations on different complexes of protein-kinases inhibitors (CDK2-Aurora_A-p38) were performed, showing good correlations with respect to experimental data. In order to consider flexibility of the target binding sites, long molecular dynamics simulations were carried out for each model system. Then, a representative set of conformations was selected using an intermolecular-interactions-based clustering method, and finally perform MM-GBSA calculations. Whole process was done employing a custom automated workflow developed by us. Our approximation proved to be effective in the ranking of a diverse set of molecules, which potentially would predict future biological activity of novel inhibitors.

[Full Abstract]

P106 » Study of the Binding Strength and Selectivity of Inhibitors by CDK2/CDK4 Protein Systems: QM/MM Interaction Energy as a Descriptor of Biological Activity

Presenting Author: Ingrid Araya (Universidad de Talca)

Co-authors: Jans Alzate-Morales (Universidad de Talca)

Short Abstract: Cyclin-dependent-kinases (CDK) are enzymes involved in regulation of cell cycle. CDK2 is over-expressed in cancer cells; therefore it is important to inhibit it by inserting small molecules into its active site, which will compete against ATP. However, CDK2 shares high percentage of identity with CDK4 mainly in their binding site, which make difficult development of selective drugs. In this work, a computational model is proposed to gain insight about the selectivity of a set of aminoimidazo[1,2-a]pyridines inhibitors by CDK2/CDK4 systems. QM/MM approaches were used to obtain energy values of the complex interaction and correlate them with experimental biological activity data.

[Full Abstract]

P107 » Computational study of CDK2-ligand interactions: Search of new energy descriptors from MM-GBSA calculations

Presenting Author: Camila Navas (University of Talca)

Co-authors: Jans Alzate (University of Talca)

Short Abstract: This work presents several computational methods applied to the study of protein-inhibitor complexes between CDK2 (Cyclin Dependent Kinase 2) and a group of inhibitors, which have in common two chemical heterocycles nucleus named pyrazolopyrimidines and imidazopyrazines. All complexes have been already reported to have crystal structure and biological activity (IC50). The search for new descriptors is done applying molecular dynamics, and then performing MM-GBSA calculations on a defined set of structures. The free-binding energy results will be correlated against inhibitor’s IC50, to check if methodology gives rise to a descriptor that can be used as an index of biological-activity.

[Full Abstract]

P108 » Molecular modelling, docking simulations and substrate specificity of the protein alcohol acyltransferase from Vasconcellea pubescens

Presenting Author: Luis Morales-Quintana (Uiversidad de Talca)

Co-authors: Maria Alejandra Moya-León (Univeridad de Talca, Instituto de Biología Vegetal yBiotecnología); Raúl Herrera (Universidad de Talca, Instituto de Biología Vegetal y Biotecnología)

Short Abstract: In Vasconcellea pubescens the aroma is formed mainly by esters, which are produced by the enzyme acyl alcohol transferase (VpAAT1). To gain insight the mechanism of action at the molecular level, a structural model for VpAAT1 protein was built by comparative modelling methodology. The result showed that the protein structure is composed of 15 β sheets and 14 α helix. The conformational interaction between the protein and several ligands was explored by molecular docking, and the predictions obtained were tested through kinetic analysis. The favourable predicted substrate orientation was observed, showing a perfect coincidence between kinetic studies and molecular docking analysis.

[Full Abstract]

P109 » STRUCTURAL BASES OF P2X4R AND P2X2R ALLOSTERIC MODULATION

Presenting Author: Camilo Navarrete (CARE - Pontificia Universidad Católica de Chile)

Co-authors: Carlos F Lagos (Pontificia Universidad Católica de Chile, Farmacia); Natali Garcia (CARE-Pontificia Universidad Católica de Chile, Fisiologia); Juan Pablo Huidobro-Toro (CARE-Pontificia Universidad Católica de Chile, Fisiologia); Alex Slater ( Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy Pontificia Universidad Católica de Chile, Genética Molecular y Microbiología); Francisco Melo ( Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy Pontificia Universidad Católica de Chile, Genética Molecular y Microbiología); Paulina Bull (Pontificia Universidad Católica de Chile, Genética Molecular y Microbiología)

Short Abstract: P2XR are trimeric functional ATP gated channels involved in many critical physiological functions. In P2X4R from D. rerio, the ATP binding site is located on a pocket between two adjacent subunits. In P2X2R and P2X4R, ATP gated current can be modulated by different allosteric modulators. Zn2+ is a positive allosteric regulator of P2X2R or P2X4R, while Cu2+ is a negative allosteric modulator of only P2X4R. Additionally, several neurosteroids are positive or negative modulators of P2X4R. Here we will present results from our recent bioinformatics analyses and biochemical data oriented to better understand the function of P2XR.

[Full Abstract]

Topic Session: Biomedicine and Immunoinformatics

P110 » Analyzing Clinical data and Genetic data for the classification of Alzheimer's Disease using Bayesian networks

Presenting Author: Yomaira Guzmán Paredes (Universidad Nacional de Colombia)

Co-authors: Luis Fernando Niño Vásquez (Universidad Nacional de Colombia, Bogota D.C.); Humberto Arboleda Granados (Universidad Nacional de Colombia, Bogotá D.C); Ludwig Segura Bermúdez (Universidad Nacional de Colombia, Bogotá D.C.)

Short Abstract: This article presents the application of Bayesian networks to support the analysis of clinical characteristics and APOE genotypes in a sample of colombian patients with Alzheimer's disease (AD). The data analysis is based on the application of data mining techniques; particularly data cleaning,extraction and feature selection,and classification methods were applied. The data set included variables such as gender, education level, marital status, age, family history of dementia and the APOE genotype. In this sample, some genetic characteristics that are related to AD,such as genotype APOE 34 and the presence of family history of dementia of individuals with AD were identified.

[Full Abstract]

P111 » Bioinformatics software development in Central America: A growth alternative in education and computer technology on the molecular modeling of protein and DNA virtual structures field.

Presenting Author: Allan Orozco (University of Costa Rica)

Short Abstract: The present research is about an immersive visualization environment to model different molecular structures using virtual reality simultaneously with augmented reality, and can be used as an example to explore the possibilities to develop an emerging discipline like bioinformatics and computational biology on Central America. This would represent an opportunity to develop OMICS and biotechnology, epidemiology and biomedicine in the region as, for example, systems for virtual exploration the structure of proteins studied in the tropical region, as well as the design and programming of applications in increased reality for identification of markers (proteins and DNA) and genomic components.

[Full Abstract]

P112 » Systematic prediction of ligand-receptor pair across the immunoglobulin superfamily using a novel sequence homology measure

Presenting Author: Eng Hui Yap (Albert Einstein College of Medicine)

Co-authors: Andras Fiser (Albert Einstein College of Medicine, Systems and Computational Biology); Tyler Rosche (Albert Einstein College of Medicine, Systems and Computational Biology)

Short Abstract: The immunoglobulin superfamily (IgSF) is a large group of cell surface and soluble proteins that plays a key role in cell recognition, signaling and adhesion. We performed an IgSF-family wide prediction of new receptor-ligand relationships based on sequence homology to known IgSF receptor-ligand relationships. Our method measures sequence similarities via hidden Markov models (HMMs), and allows empirical information as part of the scoring scheme. We correctly predicted 40 out of 53 IgSF pairs that shared similar ligands from the STRING database. The method was then applied to 477 IgSF human proteins of interest, of which 380 IgSFs can be assigned.

[Full Abstract]

P113 » Modeling Cancer Metastasis by Using GGH Model in CompuCell3D

Presenting Author: ISMAEL FORTUNA (UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL)

Co-authors: RITA MARIA CUNHA DE ALMEIDA (UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL, INSTITUTO DE FÍSICA); GILBERTO LIMA THOMAS (UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL, INSTITUTO DE FÍSICA); FARES ZEIDÁN-CHULIÁ (UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL, INSTITUTO DE CIÊNCIAS BÁSICAS DA SAÚDE, DEPARTAMENTO DE BIOQUÍMICA); JOSÉ CLÁUDIO FONSECA MOREIRA (UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL, INSTITUTO DE CIÊNCIAS BÁSICAS DA SAÚDE, DEPARTAMENTO DE BIOQUÍMICA)

Short Abstract: Cancer is not a single disease, but a complicated set of diseases with bad consequences for the patient, relatives, friends, and even for the society. As a system, it is not well understood because of its complexity and micro-environmental high sensibility. By using GGH Model, which enable us to mimics mechanical behaviors for individual cells interactions with others cells or even with chemical fields, our contribution for knowledge about cancer consist in to construct a robust model to simulate the behavior of tumor evolution, aiming understand the gain of invasiveness of cancer cells that initiates the metastatic process.

[Full Abstract]

P114 » Developing new drugs and vaccines for schistosomiasis

Presenting Author: Guilherme Oliveira (Oswaldo Cruz Foundation)

Co-authors: Adhemar Zerlotini (Fiocruz, CEBio); Larissa Silva (Fiocruz, Genomics and Computational Biology Group); Luiza Andrade (Fiocruz, Genomics and Computational Biology Group); Marina Mourão (Fiocruz, Genomics and Computational Biology Group); Fernanda Ludolf (Fiocruz, Genomics and Computational Biology Group); Rômulo Morais (Fiocruz, Genomics and Computational Biology Group); Lívia Avelar (Fiocruz, Genomics and Computational Biology Group); Eric Aguiar (Fiocruz, CEBio); Rosângela Hickson (Inforium, Computer Science); Rosiane Pereira (Fiocruz, Genomics and Computational Biology Group); Raymond Pierce (Pasteur Institute, Lille, Centre d’Infection et d’Immunité de Lille); Franco Falcone (University of Nottingham, School of Pharmacy); Marina Marcet-Houben (Center for Genomic Regulation, Bioinformatics and Genomics Programme); Huayong Xu (Shanghai Center for Bioinformation Technology, Bioinformatics); Fudong Yu (Shanghai Center for Bioinformation Technology, Bioinformatics); Robin Gasser (University of Melbourne, Parasitology); Neil Young (University of Melbourne, Parasitology); Jessica Kissinger (University of Georgia, Genetics); Toni Gabaldon (Center for Genomic Regulation, Bioinformatics and Genomics Programme); Roney Coimbra (Fiocruz, CEBio); Laila Nahum (Fiocruz, Genomics and Computational Biology Group)

Short Abstract: The sequencing of parasitic species of schistosomes, Schistosoma mansoni and S. haematobium provided many opportunities the development of new control methods. In order to provide the community with a framework for the use of the genomic data we have developed SchistoDB hosting three schistosome genomes. We report on genomic strategies for the identification of antigens, drug targets and development of lead compounds. Combined computational and experimental approaches are being utilized for the study of histone modifying enzymes, kinases and docking on modeled proteins. Vaccine and diagnostic candidate antigens were identified by a mixed proteomic and immunoinformatics approach.

[Full Abstract]

P115 » Analysis of DNA Sequences of HIV Virus Using Information Theory

Presenting Author: Tahila Andrighetti (Universidade de Caxias do Sul)

Short Abstract: AIDS’ virus, has a great genetic diversity due to replication speed and evolution. So, to make comparisons between DNA sequences of different strains of HIV to elucidate aspects of the mutability of the virus and/or eventual deficiencies in its replication system, we used computational tools that allow analyzing the entropy of triplet and GC content of GAG and POL genes sequences. The graphic of values of GC content versus entropy measure shows the separation of two GAG gene groups and a higher triplet diversity in its composition.

[Full Abstract]

P116 » Using feature extraction to find biomarkers in Parkinson's disease

Presenting Author: Elinor Velasquez (University of California, Santa Cruz)

Short Abstract: We employed machine learning to identify plausible molecular biomarkers for Parkinson's disease. We compared traditional biomarker selection with recursive feature selection using logistic regression as well as support vector machines and found that these machine learning techniques outperform the traditional biomarker selection methods, using the NIPS 2003 feature selection criteria. We used a Naive Bayes algorithm as the baseline classifier. These results indicate that it may be possible to computationally identify novel biomarkers for Parkinson's disease using our approach.

[Full Abstract]

P117 » Characterizing the binding motifs of 11 common human HLA-DP and HLA-DQ molecules using NNAlign

Presenting Author: Massimo Andreatta (Technical University of Denmark)

Co-authors: Morten Nielsen (Technical University of Denmark, Center for Biological Sequence Analysis)

Short Abstract: Using the neural network-based method NNAlign, we characterized the binding specificities of 5 HLA-DP and 6 HLA-DQ among the most frequent in the human population. The DP molecules revealed a large overlap in the pattern of amino acid preferences at core positions, with conserved hydrophobic/aromatic anchors at P1 and P6, and an additional hydrophobic anchor at P9 in some variants. These results confirm the existence of a previously hypothesized supertype encompassing the most common DP alleles. Conversely, the binding motifs for DQ molecules appear more divergent, displaying unconventional anchor positions and in some cases rather unspecific amino acid preferences.

[Full Abstract]

P118 » Immune activation in Fragile X Mental Retardation 1 (FMR1) premutation carriers : Levels of IL-10 as a prognostic marker for Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) progression

Presenting Author: Diana Marek (University of Lausanne & Swiss Institute of Bioinformatics)

Co-authors: Stephanie Papin (University of Lausanne, Medical Genetics Department); Kim Ellefsen (Lausanne University Hospital, Division of Immunology and Allergy); Julien Niederhauser (Lausanne University Hospital, Department of Clinical Neuroscience); Nathalie Isidor (Lausanne University Hospital, Medical Genetics Service); Adriana Ransijn (University of Lausanne, Medical Genetics Department); Lucienne Poupon (Lausanne University Hospital, Division of Immunology and Allergy); Francois Spertini (Lausanne University Hospital, Division of Immunology and Allergy); Giuseppe Pantaleo (Lausanne University Hospital, Division of Immunology and Allergy); Sven Bergmann (University of Lausanne & Swiss Institute of Bioinformatics, Medical Genetics Department); Jacques S. Beckmann (University of Lausanne & Lausanne University Hospital, Medical Genetics Department & Service); Sebastien Jacquemont (Lausanne University Hospital, Medical Genetics Service); Goranka Tanackovic (University of Lausanne, Medical Genetics Department)

Short Abstract: FXTAS is an inherited late onset neurodegenerative disorder, caused by premutation expansions (CGG repeats) in the FMR1 gene. Since abnormal immunological patterns are often associated with neurodegenerative disorders and implicated in their etiology, interleukins 6, 8 and 10, from 15 FMR1 premutation carriers and 20 age-matched controls, were measured in peripheral blood mononuclear cells supernatants.We found that interleukin-10 levels significantly and postively correlated with CGG repeats (p-value=0.002) and that the mean interleukin-10 concentration was significantly higher in the premutation group (p-value=0.019). Therefore, interleukin-10 may be the first biomarker to follow the onset and progression of FXTAS.

[Full Abstract]

P119 » HIERARCHICAL CLUSTERING OF pMHC COMPLEXES BASED ON THE ELECTROSTATIC POTENTIAL OF THE TCR-INTERACTING SURFACE

Presenting Author: Dinler Amaral Antunes (Federal University of Rio Grande do Sul)

Co-authors: Danieli Forgiarini Figueiredo (Federal University of Rio Grande do Sul, Genetics); Mauricio Menegatti Rigo (Federal University of Rio Grande do Sul, Genetics); Jader Peres da Silva (Federal University of Rio Grande do Sul, Genetics); Jose Bogo Chies (Federal University of Rio Grande do Sul, Genetics); Marialva Sinigaglia (Federal University of Rio Grande do Sul, Genetics); Gustavo Fioravanti Vieira (Federal University of Rio Grande do Sul, Genetics)

Short Abstract: Our immune system is based in several molecular and cellular interactions. In this system, pattern recognition is essential to differentiate our own proteins from those of the several different pathogens that we are daily exposed to. Identification of such patterns can be useful to manipulate the immune system in order to induce protection against desired targets (vaccine design) and also to identify the impact of viral escape mutations. In this context, we used a structure based Hierarchical Cluster Analysis (HCA) to identify cross-reactive viral epitopes in the context of the human MHC allele HLA-A*02:01.

[Full Abstract]

P120 » ANALYSIS OF INTERACTION RESIDUES BETWEEN HLA-A*02:01 CLEFT AND EPITOPES

Presenting Author: Mauricio Menegatti Rigo (Federal University of Rio Grande do Sul)

Co-authors: MAURICIO MENEGATTI RIGO (Federal University of Rio Grande do Sul) Dinler Amaral Antunes (Federal University of Rio Grande do Sul, Genetics); Roberto Minozzo (Federal University of Rio Grande do Sul, Genetics); Jader Peres da Silva (Federal University of Rio Grande do Sul, Genetics); Danieli Forgiarini Figueiredo (Federal University of Rio Grande do Sul, Genetics); Jose Artur Bogo Chies (Federal University of Rio Grande do Sul, Genetics); Marialva Sinigaglia (Federal University of Rio Grande do Sul, Genetics); Gustavo Fioravanti Vieira (Federal University of Rio Grande do Sul, Genetics)

Short Abstract: The knowledge of issues regarding peptide affinity by MHC cleft and the stability of the resulting complex (peptide:MHC) is primordial, considering that this molecule is responsible for antigen recognition. In this work, we searched for peptide:HLA-A*02:01 crystal structures aiming to analyze the interaction pattern between the MHC and the epitope. Our results evidenced residues conservation and hydrogen bonds pattern lengths, mainly in two main residues - Tyr7 and Tyr99 – which are conserved in the floor of peptide-binding cleft of the MHC. These findings are unique and will be used as hallmarks in molecular modeling of non-solved MHC structures.

[Full Abstract]

P121 » Protein-disease association significance from candidate ranking lists

Presenting Author: Ariel Berenstein (University of Buenos Aires)

Co-authors: Irene Ibanez (University Buenos Aires, Physics); Ariel Chernomoretz (Fundacion Instituto Leloir, Integrative Systems Biology)

Short Abstract: In this contribution we show that gene-disease association predictions based on ranking candidate lists,as produced by graph-theoretic algorithms can be highly biased by network topology properties and produce inaccurate estimation of protein-disease association significances. We propose a boot-strapping technique in order to alleviate this problem.

[Full Abstract]

P122 » Gene expression profiling of human epithelial ovarian cancer

Presenting Author: Gladys Ramos (Universidad de Chile)

Co-authors: Ulises Urzúa (Universidad de Chile) Sandra Ampuero (Universidad de Chile, Programa de Virología); Nelson Peña (Universidad de Chile, Laboratorio de genómica aplicada); Ulises Urzua (Universidad de Chile, Laboratorio de genómica aplicada); Carmen Romero (Universidad de Chile, Laboratorio de endocrinología y reproducción)

Short Abstract: Ovarian cancer (OC) is the second cause of death by gynecological cancerin Chile. Due to the lack of early screening tests, OC is often diagnosedat late stages. Here, we performed a preliminary expression profiling ofovarian epithelial tumors using whole genome DNA-microarrays. Comparisonof OC to normal ovarian surface epithelial cells showed immune response(17 genes), lysosome (5 genes) and focal adhesion (6 genes) as enrichedup-regulated functions. Down-regulated functions were DNA repair (12genes), integrin binding (4 genes) and glycolisis/gluconeogenesis (5genes). Results are discussed in relation to known genetic and genome-wideassociations reported for this disease.

[Full Abstract]

P123 » Immunohistochemistry quantification using support vector machine

Presenting Author: Raquel Pezoa (Universidad Tecnica Federico Santa Maria)

Co-authors: Rodrigo Rojas-Moraleda (Universidad Tecnica Federico Santa Maria, Informatics)

Short Abstract: Immunohistochemistry (IHC) is a fundamental technique for the prognosis of certain cancers and for patient treatment. The present study is focused on the processing of IHC-stained breast tissue images, which present HER2 protein overexpression and is displayed by membrane staining. The goal of this study is to use the SVM to classify the pixels of the IHC-images into two classes: overexpressed or non-overexpressed, in order to obtain quantitative measurements of the stained elements for determination of overexpressed HER2 protein. The obtained results showed the SVM segmentation compared favorably with the manual segmentation criteria for a specific group.

[Full Abstract]

P124 » Integration of mRNA and miR profiles identified restricted and unique patterns in Breast & Colon cancer cell lines

Presenting Author: Benjamin Garcia (Pontificia Universidad Catolica de Chile)

Co-authors: Alejandro Corvalan (Pontificia Universidad Catolica de Chile); Alejandra Sandoval (Pontificia Universidad Catolica de Chile, Hematology and Oncology); Rodrigo Droguett (Pontificia Universidad Catolica de Chile, Hematology and Oncology); Jose Diaz (Pontificia Universidad Catolica de Chile, Hematology and Oncology)

Short Abstract: Genes are regulated by microRNA (miR). For both, a large amount of genomic information is available. However no integrative tools and biological significance has been developed. Here we present our Integrative Expression Signature (INES) tool and the analysis of 99 cancer cell lines, representing the four most common cancer types (breast, colon, lung and ovary). Our tool identified a restricted and unique pattern of miR and genes in specific tumor types (breast and colon) indicating a highly specific association in different cancer types.

[Full Abstract]

P125 » IN SILICO ISOLATION OF NATURAL PRODUCTS: OBTAINING 1H NMR SPECTRA OF PURE COMPOUNDS FROM SPECTRA OF MIXTURES THAT CONTAIN THEM

Presenting Author: Ivana Ayelen Ramallo (Universidad Nacional de Rosario)

Co-authors: Ivana Ramallo (Universidad Nacional de Rosario); Pablo Gatti (Facultad de Ciencias Exactas, Ingeniería y Agrimensura, CIFASIS); Ricardo Furlan (Facultad de Ciencias Bioquímicas y Farmacétuticas, Farmacognosia); Elizabeth Tapia (Facultad de Ciencias Exactas, Ingeniería y Agrimensura, CIFASIS); Gabriela Ibañez (Facultad de Ciencias Bioquímicas y Farmacétuticas, IQUIR); Alejandro Olivieri (Facultad de Ciencias Bioquímicas y Farmacétuticas, IQUIR)

Short Abstract: Natural products are a valuable source of molecular diversity with high therapeutic potential. However, their isolation from natural sources is an arduous task that doesn’t always lead with the identification of a new compound.A strategy to find out structures is to combine liquid chromatography (separative technique) with Nuclear Magnetic Resonance (spectroscopic method supplier of structural information). We present a novel MATLAB routine that extracts information from 1H NMR experiments of mixtures, and reconstructs the pure spectrum of each structure without completely physical separation. Also, number of present components and concentration profiles are acquired, without prior knowledge of the investigated-system.

[Full Abstract]

Topic Session: Functional Genomics and Systems Biology

P126 » Comparative Identification of Novel genes from Non Coding Regions of Plasmodium

Presenting Author: Anandakumar Shanmugam (Bharathiar University)

Short Abstract: The whole genome of all organisms comprises coding and non coding regions whereby functions of nocoding elements remains elusive. We have analyzed the non-coding regions of Plasmodium species. A total of 16231 non-coding sequences were extracted using PERL script, BLAST X analysis pointed out 530 coding sequences, allowing them to be designated as novel coding sequences. In order to find the coding potential of these regions, Coding Potential Calculator was deployed revealing 1107 coding regions whilst Geneid confirmed totally 1204 novel genes. Conclusively, PlasmoDB can effect re-annotation to incorporate the coding sequences revealed

[Full Abstract]

P127 » Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

Presenting Author: Kathleen Marchal (Ghent University)

Co-authors: Hong Sun (K.U.Leuven, Microbial and Molecular Systems); Tias Guns (K.U.Leuven, Computer Science); Ana Carolina Fierro (K.U.Leuven, Computer Science); Lieven Thorrez (K.U.Leuven, Interdepartmental Stem Cell Institute); Siegfried Nijssen (K.U.Leuven, Computer science)

Short Abstract: We developed CPModule, a novel approach for CRM detection with a performance that is competitive to that of other state-of-art tools, but that in contrast to previous tools can handle much larger datasets (such as 100 sequences in combination with a library of 517 PWMs). The flexible framework underlying CPModule in combination with its exhaustive search strategy allows to explicitly compare the feasibility of CRM detection in the presence and absence of ChIP-derived information. We good show on a real dataset that without ChIP-based information, CRM detection becomes an almost infeasible task.

[Full Abstract]

P128 » Integrative approaches for mode of action determination

Presenting Author: Ana Carolina Fierro Gutierrez (K.U. Leuven)

Co-authors: Riet De Smet (Ghent University, Plant Biotechnology and Bioinformatics); Yan Wu (Ghent University, Microbial and Molecular Systems); Lore Cloots (Ghent University, Microbial and Molecular Systems); Dries De Maeyer (Ghent University, Microbial and Molecular Systems); Peyman Zarrineh (Ghent University, Microbial and Molecular Systems); Qiang Fu (Ghent University, Microbial and Molecular Systems); Kristof Engelen (Ghent University, Microbial and Molecular Systems)

Short Abstract: High-throughput expression profiling techniques e.g. mRNA profiling often result in unstructured lists of differentially expressed genes. Computational analysis of unstructured lists will in most cases be restricted to a simple functional enrichment analysis to elucidate the potential pathways or functions the candidate genes belong to, but the interactions between the identified candidate genes or their role in the global molecular network of the cell remains unknown. In this work we present a suite of computational tools to analyse such data sets and to integrate them with publicly available omics data.

[Full Abstract]

P129 » An integrative methodology for the classification of genes into pathways using a novel text mining approach

Presenting Author: Julieta Dussaut (Universidad Nacional del Sur)

Co-authors: Ignacio Ponzoni (Universidad Nacional del Sur); Rocío Cecchini (Universidad Nacional del Sur, Laboratory of Research and Development in Scientific Computing (LIDeCC)); Ignacio Ponzoni (Universidad Nacional del Sur, Laboratory of Research and Development in Scientific Computing (LIDeCC)); Ana Maguitman (Universidad Nacional del Sur, Artificial Intelligence Research and Development Laboratory (LIDIA))

Short Abstract: In this work we present a text mining approach for the classification of genes into pathways. The first step consists in using ABNER to identify biological entity mentions in each of the publications. These entities are used to create a gene frequency matrix which is later adjusted using inverse pathway frequency information. The resulting matrix is then used to compute a co-occurrence weight for each pair of genes. The prediction is then made based on a novel voting scheme. In order to validate the proposed method, we contrast the resulting predictions with KEGG Pathway data using classical literature mining metrics.

[Full Abstract]

P130 » Network complexity evolves as an efficient mechanism for the acquisition of robustness in gene regulatory networks.

Presenting Author: Mario Pujato (Albert Einstein College of Medicine)

Co-authors: Thomas MacCarthy (Albert Einstein College of Medicine, Systems and Computational Biology); Andras Fiser (Albert Einstein College of Medicine, Systems and Computational Biology); Aviv Bergman (Albert Einstein College of Medicine, Systems and Computational Biology)

Short Abstract: Gene regulatory networks often show robustness to both genetic and environmental perturbations. Robustness is known to be an emergent property of network evolution, yet the underlying molecular mechanisms are still poorly understood. Using structural models of transcription factor-DNA complexes, we developed a tiered modeling approach that integrates molecular sequence and structure information with network architecture. We find that robustness evolves almost entirely via network rewiring, which is enabled by specific conditions like longer promoter lengths or greater binding discrimination of DNA motifs by transcription factors. These results suggest a mechanism for the acquisition of greater complexity in gene regulatory networks.

[Full Abstract]

P131 » LitProf – Gene Classifier: A text-mining gene function predictor for prokaryotes

Presenting Author: Roney Coimbra (FIOCRUZ-Minas)

Co-authors: Raul Torrieri (FIOCRUZ-Minas, Center for Excellence in Bioinformatics); Francislon Oliveira (FIOCRUZ-Minas, Center for Excellence in Bioinformatics); Guilherme Oliveira (FIOCRUZ-Minas, Center for Excellence in Bioinformatics)

Short Abstract: Most genome projects lack financial support to review annotations. Usually annotations are based solely on sequence similarity to a previously known gene, which was probably annotated in the same way. A large number of predicted genes remain unassigned to any functional category despite there is enough evidence in the literature to identify their function. We developed a classifier trained with term-frequency vectors automatically disclosed from text corpora of genes representative of functional categories of the JCVI ontology. The classifier unambiguously (confidence ≥ 0.7) assigned to functional categories 5,235 (from ~24k genes previously unclassified) for which there is literature in MEDLINE.

[Full Abstract]

P132 » Strategy for the Detection of Functional Clusters of Genes using Data Mining Techniques

Presenting Author: Liliana Olarte (Universidad Nacional de Colombia)

Co-authors: Luis Niño (Universidad Nacional de Colombia, Systems and Industrial Engineering); Liliana López (Universidad Nacional de Colombia, Statistics Department)

Short Abstract: The present work proposes a methodology to find gene groups, based on microarray and RNA_Seq expression data, highlighting relationships between genes and regulatory activities for expression experiments conducted in a condition of interest. In order to detect relationships between genes, we used data mining algorithms associated to biological knowledge on gene promoters. Once clusters were constructed, we searched for representative promoters to categorize and validate the obtained results. We were able to detect 3-5 interesting promoters that were related to pathogen resistance in plants. The proposed methodology is general and flexible to be applied to other organisms.

[Full Abstract]

P133 » Discriminative local subspaces in gene expression data for effective gene function prediction

Presenting Author: Tomas Puelma (Pontificia Universidad Católica de Chile)

Co-authors: Rodrigo Gutierrez (Pontificia Universidad Católica de Chile); Alvaro Soto (Pontificia Universidad Católica de Chile, Computer Science); Rodrigo Gutierrez (Pontificia Universidad Católica de Chile, Molecular Genetics and Microbiology)

Short Abstract: In this work we present Discriminative Local Subspaces (DLS), a novel supervised machine learning method designed to analyze gene expression data and predict new candidate genes associated to a biological process of interest. DLS uses the knowledge available in Gene Ontology (GO) to generate informative training sets that guide the discovery of expression signatures: expression patterns defined in subsets of experimental conditions that are distinctive to the process of interest. These signatures provide key information to make new functional connections and provide valuable insights to help biologists to understand the predictions and guide future experiments.

[Full Abstract]

P134 » Gene Functional Annotation beyond Enrichment Analysis: moving from gene lists to functional metagroups and gene networks

Presenting Author: Celia Fontanillo (Centro de Investigacion del Cancer)

Co-authors: Sara Aibar (Centro de Investigacion del Cancer, Bioinformatics and Functional Genomics Group); Javier De Las Rivas (Centro de Investigacion del Cancer, Bioinformatics and Functional Genomics Group)

Short Abstract: We present a computational method that filters the output of an Enrichment Analysis and finds significant coherent groups of genes and terms. These metagroups facilitate the interpretation of the biological functions and processes represented in a query gene list, inferring new associations among genes. The association of the genes to these “functional metagroups” is used to calculate a “functional score” for each gene. A comparison of these scores allows estimating a distance for each gene-pair. Using this method we build gene networks that reflect the proximity of each gene-pair based on a comprehensive analysis of their biological functional annotations.

[Full Abstract]

P135 » Computational Flux Balance Analysis (FBA) of new representative objective functions using a multiple compartmental objective approach and its application toSaccharomyces cerevisiae biological behavior

Presenting Author: Carlos García (Universidad Industrial de Santander)

Co-authors: Rodrigo Torres (Universidad Industrial de Santander); Carlos García (Universidad Industrial de Santander, Chemical Engineering); César Vargas (Universidad Industrial de Santander, System Engineering); Henry Argüello (Universidad Industrial de Santander, System Engineering)

Short Abstract: Flux Balance Analysis (FBA) is a methodology that enables to quantitatively predict the metabolic fluxes from a microorganism growing in determined environmental conditions, using the assumption that the cell tries to optimize certain objective function that represents its cellular behavior. Searching for new objective function describing cellular operation is critical in order to obtain good performance on application of FBA. In this work, several possible objective functions composed by linear combinations of objectives of the cell compartments from a genomic model of Saccharomyces cerevisiae were explored. Precision of the predictions obtained using those functions were also evaluated and analyzed.

[Full Abstract]

P136 » The just-in-time expression of yeast ribosomal proteins

Presenting Author: Andrzej Kudlicki (University of Texas Medical Branch)

Co-authors: Xueling Li (University of Texas Medical Branch, Institute of Translational Science); Gang Chen (Central South University, Computer Science)

Short Abstract: By model-based analysis of gene expression time course data, we reconstructed the precise timeline of transcription of yeast ribosomal genes, spanning a 20 minute interval. The time of expression is related to position within the yeast ribosome: proteins localized deeper inside the ribosome are expressed earlier than the ones on the outside, which suggests that timing of expression is optimized to facilitate the assembly of the complex. The expression times are correlated with distance between the Rap1 motif and coding sequence, which implies involvement of RAP1p in regulating the expression time, via a previously unknown mode of regulation.

[Full Abstract]

P137 » Deciphering human protein interactome using structural complexes

Presenting Author: Anna Panchenko (National Institutes of Health)

Co-authors: Manoj Tyagi (National Institutes of Health, NCBI); Kosuke Hashimoto (RIKEN, RIKEN); Benjamin Shoemaker (NIH, NCBI); Stefan Wuchty (NIH, NCBI)

Short Abstract: Although the identification of protein interactions by high-throughput methods progresses at a fast pace, ‘interactome’ datasets still suffer from high rates of false positives and low coverage. To map the human protein interactome, we describe a new framework that utilizes experimental evidence on structural complexes, the atomic details of binding interfaces and evolutionary conservation. The structurally-inferred interaction network is highly modular and more functionally coherent compared to experimental interaction networks derived from multiple literature citations. Moreover, structurally-inferred and high confidence high-throughput networks complement each other well, allowing us to construct the merged network to generate testable hypotheses and provide valuable experimental leads.

[Full Abstract]

P138 » SNPower, an integrative platform for the analysis and visualization of human disease-associated short mutations, genes, and protein interactions

Presenting Author: Cheng-Yan Kao (National Taiwan University)

Co-authors: Theresa Tsao (Department of Computer Science and Information Engineering & Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University); Sheng-An Lee (Department of Information Management, Kainan University)

Short Abstract: SNPower is an on-line platform for the analysis of human genetic diseases from a network biology perspective. It integrates the data of disease-associated genes, disease-related short mutations (SNPs), essential genes, predicted deleterious SNPs, and protein-protein interactions (PPIs) to assist the understanding of disease mechanisms and the identification of potential disease marker genes and treatment targets. Users can query for disease genes, calculate the number of experimentally identified and predicted deleterious SNPs within selected genes, and visualize the PPI network of disease genes. SNPower can also identify cliques and rank node centralities within PPI network. SNPower is available at http://SNPower.grid.tw.

[Full Abstract]

P139 » A search for probiotic yeast: comparison of transcriptional profile in S. cerevisiae strain W303 and S. boulardii using microarray

Presenting Author: Priscila Grynberg (Universidade Federal de Minas Gerais)

Co-authors: Leonardo Dias (Universidade Federal de Minas Gerais, Departamento de Bioquímica e Imunologia); Mariana Boroni (Universidade Federal de Minas Gerais, Departamento de Bioquímica e Imunologia); Daiane de Laat (Instituto Agronômico de Campinas, Divisão de Biologia Fitotécnica); Ieso Castro (Universidade Federal de Ouro Preto, Núcleo de Pesquisas em Ciências Biológicas - NUPEB); Gloria Franco (Universidade Federal de Minas Gerais, Departamento de Bioquímica e Imunologia)

Short Abstract: Recent studies have shown that S. boulardii (probiotic) and S. cerevisiae W303 (not probiotic) are strains of the same species, despite their metabolic and physiological differences, especially concerning growth and survival at 37oC and acid stress. Microarray analysis employing S. boulardii and S. cerevisiae W303 strains growing or not in pH 2,0 and 85 mM NaCl for 10 min and 30 min were carried out to characterize the gene expression profile of a probiotic and a common yeast strain. Results indicate variations in viability between both strains in control and 10 min treated cells.

[Full Abstract]

P140 » A Rule-based Model for a Stochastic Simulation of a Zombie Outbreak

Presenting Author: Felipe Nuñez (Universidad de Chile)

Co-authors: Cesar Ravello (Universidad de Chile, Computational Biology Lab. Center for Mathematical Modeling. Facultad de Ciencias Físicas y Matemáticas.); Hector Urbina (Universidad de Chile, Computational Biology Lab. Center for Mathematical Modeling. Facultad de Ciencias Físicas y Matemáticas.); Tomas Perez-Acle (Universidad de Chile, Computational Biology Lab. Center for Mathematical Modeling. Facultad de Ciencias Físicas y Matemáticas.)

Short Abstract: Zombies are elements from our collective imagination that have attracted much attention in the last years. They represent an object that generates chaos and shows similarities with events of disease outbreaks, leading to a state of catastrophe, affecting people both physically and emotionally.Accounting for the general rules that define a chaos situation, we present the description of a zombie outbreak using the kappa language. The result is a rule-based model that describes the dynamics of a group of cities under attack, describing the interactions between the elements in each city, as well as the rules of mobility between them.

[Full Abstract]

P141 » Another Tool for Genomic Comprehension (ATGC): an ontology driven database and web interface applied to Sunflower Microarray Project

Presenting Author: Paula Fernandez (Instituto Nacional de Tecnología Agropecuaria)

Co-authors: Sergio Gonzalez (Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología); Maximo Rivarola (Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología); Ruth Heinz (Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología); Marisa Farber (Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología); Norma Paniego (Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología); Bernardo Clavijo (Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología)

Short Abstract: The identification of candidate genes underlying agronomically important traits represents a key strategy for molecular breeding. In sunflower, the lack of genomic tools has limited functional studies. The development of comprehensive and well organized annotated unigene collections is a foundational step to generate a specific microarray and other tools. This collection allowed the generation of the first custom sunflower microarray under Agilent technology. This platform is currently being used to test sunflower gene expression under different conditions. In this work, we have approached the problem of building a database and web interface to this data based on GMOD Chado schema.

[Full Abstract]

P142 » Computational Flux Balance Analysis (FBA) of new representative objective functions using a multiple compartmental objective approach and its application to Saccharomyces cerevisiae biological behavior

Presenting Author: Carlos García Sánchez (Universidad Industrial de Santander)

Co-authors: César Augusto Vargas García (Universidad Industrial de Santander, Santander); Henry Argüello Fuentes (Universidad Industrial de Santander, Santander); Rodrigo Gonzalo Torres Sáez (Universidad Industrial de Santander, Santander)

Short Abstract: Flux Balance Analysis (FBA) is a methodology that enables to quantitatively predict the metabolic fluxes from a microorganism growing in determined environmental conditions, using the assumption that the cell tries to optimize certain objective function that represents its cellular behavior. Searching for new objective function describing cellular operation is critical in order to obtain good performance on application of FBA. In this work, several possible objective functions composed by linear combinations of objectives of the cell compartments from a genomic model of Saccharomyces cerevisiae were explored. Precision of the predictions obtained using those functions were also evaluated and analyzed.

[Full Abstract]

P143 » Comparing Stochastic Models of Gene Expression

Presenting Author: Pablo Gutierrez (Centro Regional de Estudios Genómicos - Universidad Nacional de La Plata)

Co-authors: Luis Diambra (Centro Regional de Estudios Genómicos - Universidad Nacional de La Plata, Laboratorio de Biología de Sistemas)

Short Abstract: Gene expression is intrinsically stochastic. In general, it shows sigmoid mean responses. Therefore, some functions of Hill type have been used to model noise in gene expression. These functions assume simultaneous binding of transcription factors and infinite energies of interaction between them. However, in previous studies we found dependency of gene expression fluctuations with the cooperative interaction energy. In our model, the promoter design includes several transcription factors binding sites and sequential binding of them. In this work, we explore similarities and differences in both approximations.

[Full Abstract]

P144 » Modeling the emergence of circadian rhythms in a clock network

Presenting Author: Luis Diambra (Universidad Nacional de La Plata)

Short Abstract: Circadian rhythms in pacemaker cells persist for weeks in constantdarkness, while in other types of cells the molecular oscillationsthat underlie circadian rhythms damp rapidly in the same condition. Although much progress has been made in understanding thebiochemical basis of circadian rhythms, the mechanismsleading to damped or self-sustained oscillationsremain unknown. In this work we have implemented a model for a network of interacting neurons to describe the emergence of circadian rhythms in Drosophila, in constant darkness.Our results indicate that the modulation of PER entrance into the nucleus allowsthe synchronization of clock neurons, leading to coherent circadianoscillations.

[Full Abstract]

Selected Orals

Remember that the acceptance of your oral presentation was notified by e-mail to the address you wrote when submitting your work.

 

List of accepted oral presentations

You will have a total time of 15 minutes for your presentation. Therefore, you should plan your presentation time for a maximum of 12 minutes, leaving 3 minutes for discussion and switch of speakers. Please be aware that session chairs will make a concentrated effort to keep sessions on a structured time schedule.

Please note that each presentation was assigned a unique ID of the form "DPX", where D is the day name (Monday, Tuesday or Wednesday), P is the period of time (Morning or Afternoon), and X is a serial number. Note also that the presentations in the list were grouped by topic session.

Comparative Genomics and Evolution
Genomics, Proteomics, Metagenomics and Metabolomics
Macromolecule Structure/Function Prediction
Computer Aided Drug Design and Docking/Molecular Dynamics Simulations
Biomedicine and Immunoinformatics
Functional Genomics and Systems Biology

Topic Session: Comparative Genomics and Evolution

MM1 » The PhyloFacts-SchistoDB Schistosoma Database

Presenting Author: Kimmen Sjolander (University of California Berkeley)

Co-authors: Yaoqing Shen (University of California Berkeley, QB3); Ajithkumar Warrier (University of California Berkeley, QB3); Laila Nahum (FIOCRUZ Minas, Genomics and Computational Biology Group); Guilherme Oliveira (FIOCRUZ Minas, Genomics and Computational Biology Group)

Short Abstract: We have performed a phylogenomic analysis of the Schistosoma mansoni proteome, classifying proteins into multi-domain architecture classes and constructing gene trees for proteins and for Pfam domains contained in these proteins. The resulting analyses are provided in the PhyloFacts-SchistoDB database. For each gene family in Schistosoma mansoni, the PhyloFacts-SchistoDB database contains a gene tree, multiple sequence alignment, predicted orthologs, hidden Markov model, identified Pfam domains and annotation data. A set of 1884 candidate sequence orphans in the S. mansoni genome has been identified, with the function of 259 of these orphans being potentially informed by matches to PhyloFacts families.

[Full Abstract]

MM2 » Identification of transcription regulation associated proteins in plants and stramenopiles

Presenting Author: Diego Mauricio Riaño Pachón (Universidad de los Andes)

Co-authors: Francisco J. Buitrago-Florez (Universidad de los Andes, Biological Sciences); Silvia Restrepo-Restrepo (Universidad de los Andes, Biological Sciences); Bernd Mueller-Roeber (Universität Potsdam, Institute of Biochemistry and Biology)

Short Abstract: The generation of biodiversity is tied to the evolution and re-wiring of gene regulatory networks (GRNs). One component of these GRN are transcription factors and other transcriptional regulators. We have devised a pipeline for the identification of TFs and TRs, exploiting the domain architecture of these proteins. Currently we have a set of rules, representing 138 proteins families, that we have applied to the identification of ~20 different plant species and several species of Stramenopiles, where important plant pathogens are found. Results for plant species are available at http://plntfdb.uniandes.edu.co/; we are now developing a newer interface for Stramenopiles.

[Full Abstract]

MM3 » Molecular Phylodynamics and Protein Modeling of Infectious Salmon Anemia Virus (ISAV)

Presenting Author: Eduardo Castro Nallar (Brigham Young University)

Co-authors: Marcelo Cortez-San Martín (Universidad de Santiago de Chile, Facultad de Química y Biología); Carolina Mascayano (Universidad de Santiago de Chile, Facultad de Química y Biología); Cristian Molina (Universidad de Santiago de Chile, Facultad de Química y Biología); Keith Crandall (Brigham Young University, Biology)

Short Abstract: Few studies have examined available data to test hypotheses associated with the phylogeographic partitioning of ISAV infecting viral population, the population dynamics, or evolutionary rates and demographic history. We addressed these questions using modern phylogenetic methods. A recombination breakpoint was consistently detected in the Hemagglutinin-Esterase gene around the Highly-Polymorphic Region (HPR). Evolutionary relationships of ISAV revealed the 2007 Chilean outbreak group as monophyletic for the fusion gene. Their tMRCA is consistent with epidemiological data and demographic history showed a profound bottleneck. Selection analyses detected ongoing diversifying selection in both genes associated with protease processing and the HPR region, respectively.

[Full Abstract]

MM4 » Evolutionary events involved in pathogenic trait acquisition in Ascomycetes

Presenting Author: Aminael Sanchez-Rodriguez (Katholieke Universiteit Leuven)

Co-authors: Riet De Smet (Ghent University, Plant Systems Biology); Kristof Engelen (Katholieke Universiteit Leuven, Molecular and Microbial Systems); Qiang Fu (Katholieke Universiteit Leuven, Molecular and Microbial Systems); Yan Wu (Katholieke Universiteit Leuven, Molecular and Microbial Systems); Kathleen Marchal (Katholieke Universiteit Leuven, Molecular and Microbial Systems)

Short Abstract: To unravel the genetics underlying pathogenicity in Ascomycetes, we reconstructed the evolutionary history of gene families and gene expression behavior using a sample of eight species. Both evolutionary events at coding sequence and regulatory network levels contributed to the acquisition of pathogenic traits in Ascomycetes. At the coding sequence level gene families with functions related to pathogenic host-fungus interactions showed an accelerated evolution rate. Also most pathogenicity related genes tend to be co-expressed with a different gene set than their orthologous counterparts in non-pathogens, indicating a considerable rewiring of the regulatory network during pathogenicity emergence.

[Full Abstract]

MM5 » Novel Classes of Eukaryotic Aspartic Proteases and the Identification of their Specificity Determining Residues

Presenting Author: María Revuelta (Universidad Nacional de Mar del Plata)

Short Abstract: Recent studies have indicated that fungi have a large number of APs in comparison to other taxonomic groups. We are interested in the functional diversification and redundancy of fungal APs. We performed a phylogenetic analysis of APs obtained by HMMer profiling of 107 sequenced eukaryotic genomes. The obtained phylogeny contains, besides the generally accepted A01A and A01B subfamilies, six subfamilies that are exclusive to fungi. Moreover, we identified a D and an E that are specific to the fungal subfamily of Yapsins, These residues are likely involved in monobasic sequence recognition and substrate processing of zymogens of various secreted hydrolases.

[Full Abstract]

MM6 » Conformational diversity: Relationship with protein evolution and designability

Presenting Author: Diego Zea (Universidad Nacional de Quilmes)

Co-authors: Gustavo Parisi (Universidad Nacional de Quilmes, Centro de Estudios e Investigaciones); Cristina Marino Buslje (Fundación Instituto Leloir, Bioinformatics Unit)

Short Abstract: The study of evolutionary rates is a central issue to understand the mechanisms underlying protein molecular evolution. In this work we study how the presence of conformational diversity in proteins could influence the rate of evolution. We have determined that the evolutionary rate positive correlates with the degree of conformational diversity measured by the maximum RMSD between conformers. Our results support the idea that proteins with larger native conformational space could have a higher average of inter residues contacts, a measure of protein designability, giving rise to an increased evolutionary rate.

[Full Abstract]

Topic Session: Genomics, Proteomics, Metagenomics and Metabolomics

MA1 » The ISA Commons – Towards interoperable data in bioscience

Presenting Author: Susanna-Assunta Sansone (University of Oxford)

Co-authors: Philippe Rocca-Serra (University of Oxford, Oxford e-Research Centre); Eamonn Maguire (University of Oxford, Oxford e-Research Centre)

Short Abstract: To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open ‘data commoning’ culture. Here we present the prerequisites for data commoning and describe an established and growing ecosystem of solutions using shared concepts to support that vision. The ISA commons is a growing exemplar ecosystem of data curation and sharing solutions built on a common metadata tracking framework, providing tools and resources to create and manage large, heterogeneous data sets in a coherent manner (Sansone*, Rocca-Serra* et al., Nature Genetics, in press).

[Full Abstract]

MA2 » A Fast de novo Genome-Wide Tandem Repeat Discovery Algorithm

Presenting Author: Marcelo Gonçalves Narciso (Embrapa)

Co-authors: Michel Yamagishi (Embrapa); Marcelo Gonçalves Narciso (Embrapa, Bioinformatics)

Short Abstract: Tandem Repeats (TR) are sequences where the same pattern repeats consecutively. So far, they have been used as genomic markers, but new studies have associated them to important regulatory processes which increased their relevance. Although several TR discovery algorithms are available, genome-wide TR discovery is time consuming, and any improvement in computational performance may be significant. We present a new fast de novo genome-wide TR discovery algorithm, called ConvolutionTR. It deals with large genomes on average 30% to 50% faster than other approaches; furthermore, ConvolutionTR finds all the TRs while the most popular algorithms do not as will be shown.

[Full Abstract]

MA3 » GOBOOT: testing set enrichment analysis robustness to background selectio

Presenting Author: Cristobal Fresno Rodríguez (Catholic University of Córdoba)

Co-authors: Andrea Llera (Leloir Institute, CONICET, Laboratory of Molecular and Cellular Therapy); María R Girotti (Leloir Institute, CONICET, Laboratory of Molecular and Cellular Therapy); María P Valacco (Leloir Institute, CONICET, Laboratory of Molecular and Cellular Therapy); Juan A López (National Center for Cardiovascular Research, Madrid); Osvaldo L Podhajcer (Leloir Institute, CONICET, Laboratory of Molecular and Cellular Therapy); Mónica G Balzarini (National University of Córdoba, Biometry Laboratory); Federico Prada (UADE, Institute of Technology, School of Engineering and Sciences); Elmer A Fernández (Catholic University of Córdoba, CONICET, BioScience Data Mining Group)

Short Abstract: Set enrichment analysis identifies enriched biological categories/terms by evaluating the proportion of differentially expressed genes against a background reference (BR) in high-throughput experiments. However, results will depend on BR choice. Currently there is no way to analyze enrichment robustness to BR choice. Bootstrapped versions of a given BR were carried out to provide robustness of enriched terms to BR selection. Thus, terms with a high stability are candidates to by explored leaving spurious enrichment out of the analysis. Results showed that stable terms were found to validate main experimental hypothesis and also new terms emerged providing new biological insight.

[Full Abstract]

MA4 » Computational Pattern Recognition for the Identification of Transposases in Prokaryotic Genomes: Challenges and Advances.

Presenting Author: Gonzalo Riadi (Talca University)

Co-authors: David Holmes (Fundacion Ciencia & Vida and Andres Bello University, Facultad Ciencias Biologicas); Gonzalo Riadi (Center of Bioinformatics and Molecular Simulation and Talca University, Engineering School)

Short Abstract: Transposases (Tnps) are enzymes that are encoded by Insertion Sequences (ISs). Tnps are one of the commonest proteins found in nature and play an important role in gene and genome evolution. However, they are difficult to predict bioinformatically and given the increasing availability of prokaryotic genomes and metagenomes, it is incumbent to develop rapid, high quality automatic annotation of Tnps. We have developed the most extensive and robust database of HMM Profiles for pattern recognition of Tnps in Prokaryote genomes. In this work we describe the novel biology revealed by high-dimensional analysis of over 210,000 Tnps.

[Full Abstract]

MA5 » Spinal Cord Regeneration in Xenopus: A Transcriptomics Analysis

Presenting Author: Dasfne Lee-Liu (Pontificia Universidad Catolica de Chile)

Co-authors: Juan Larrain (Pontificia Universidad Catolica de Chile); Leonardo Almonacid (Pontificia Universidad Catolica de Chile, Facultad de Ciencias Biologicas); Mauricio Moreno (Pontificia Universidad Catolica de Chile, Facultad de Ciencias Biologicas); Rosana Muñoz (Pontificia Universidad Catolica de Chile, Facultad de Ciencias Biologicas); Marcia Gaete (Pontificia Universidad Catolica de Chile, Facultad de Ciencias Biologicas); Francisco Melo (Pontificia Universidad Catolica de Chile, Facultad de Ciencias Biologicas)

Short Abstract: Spinal cord injury (SCI) results in motor and sensory loss. Xenopus is only able to regenerate after SCI before metamorphosis. Our hypothesis is: SCI induces a regenerative-permissive transcriptome in the X. laevis spinal cord, absent after metamorphosis. Overexpression or repression of key genes determines the regenerative abilities of pre-metamorphic stages. A bioinformatics analysis of our RNA-Seq study of the spinal cord transcriptome after injury in Xenopus regenerative and non-regenerative stages showed differential expression of genes related to neurogenesis, cell cycle and extracellular matrix. These differences may account for the regenerative abilities of pre-metamorphic stages, and the lack thereof after metamorphosis.

[Full Abstract]

MA6 » High-resolution community genomics of a hypersaline microbial ecosytem

Presenting Author: Juan Ugalde (University of California, San Diego)

Co-authors: Sheilla Podell (University of California, San Diego, Scripps Institution of Oceanography); Karla Heidelberg (University of Southern California, Department of Biological Sciences); Jill Banfield (University of California, Berkeley, Department of Earth and Planetary Sciences); Eric Allen (University of California, San Diego, Scripps Institution of Oceanography)

Short Abstract: The present work presents the comprehensive genetic analysis of a natural hypersaline microbial community using metagenomic deep-sequencing. We examined the accumulated metagenomic data via three complementary data analysis treatments. Foremost, raw sequencing reads were analyzed for phylogenetic and functional content (environmental gene-survey approach). Secondly, we reconstructed the genomes of the most abundant members of the microbial community (assembly-driven approach). Finally, we used the assembled genomes to dissect the genetic heterogeneity that is present in each microbial population (population genetic approach). The combination of different approaches provides a more detailed picture of the genetic and functional diversity of microbial communities.

[Full Abstract]

Topic Session: Macromolecule Structure/Function Prediction

TM1 » Modeling proteins using supersecondary structure library and NMR chemical shifts

Presenting Author: Andras Fiser (Albert Einstein College of Medicine)

Co-authors: Vilas Menon (Albert Einstein College of Medicine, Systems and Computational Biology); Joseph Dybas (Albert Einstein College of Medicine, Systems and Computational Biology)

Short Abstract: A new method is presented to generate theoretical protein structures for such remote homology modeling cases where sequence signal is not useful any more. The approach uses NMR chemical shift data and an exhaustive library of protein structure building blocks, Smotifs. The current modeling approach does not require any sequence information for modeling.

[Full Abstract]

TM2 » Using correlation data and network decomposition to obtain sub-class determinants in protein families

Presenting Author: Lucas Bleicher (Universidade Federal de Minas Gerais)

Co-authors: Richard Garratt (Universidade de Sao Paulo, Instituto de Fisica de Sao Carlos); Ney Lemke (Universidade Estadual de Sao Paulo, Departamento de Fisica e Biofisica, Botucatu)

Short Abstract: Correlated mutation has been used mostly to detect structural contact pairs in protein families. Based on previous observations that it can also provide functional insights, we provide a framework devoted to this purpose, based on an amino acid specific correlation measure, used to build networks summarizing correlation and anti-correlation patterns in a protein family. Network decomposition results in subsets that can be further assessed by parameters and procedures, proposed for this methodology, having useful applications in protein family analysis. This framework is applied to the family of Fe/Mn superoxide dismutases, highlighting its potential use in protein characterization and gene annotation.

[Full Abstract]

TM3 » Evolution of linear motifs within the intrinsically disordered and globular domains of the papillomavirus E7 oncoprotein

Presenting Author: Lucia Chemes (Fundación Instituto Leloir IIBBA-CONICET)

Co-authors: Juliana Glavina (Protein Physiology Laboratory, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, Departamento de Química Biológica); Julian Faivovich (División Herpetología, Museo Argentino de Ciencias Naturales-CONICET, Buenos Aires, Argentina, Museo Argentino de Ciencias Naturales); Leonardo Alonso (Fundacion Instituto Leloir , Buenos Aires Argentina, IIBBA-CONICET); Cristina Marino-Buslje (Fundacion Instituto Leloir, IIBBA CONICET, Buenos Aires Argentina, Structural Bioinformatics Laboratory); Gonzalo de Prat Gay (Fundacion Instituto Leloir IIBBA CONICET, Buenos AIres Argentina, Protein Structure-Function and Engineering Laboratory); Sanchez Ignacio (Protein Physiology Laboratory, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, Departamento de Quimica Biologica)

Short Abstract: Linear motifs mediate many protein functions. We studied conservation and evolution of eight linear motifs within the intrinsically disordered (E7N) and globular (E7C) domains of the papillomavirus E7 protein using 200 sequences. E7N and E7C show similar conservation, which is explained by the globular structure of E7C and by the conserved and coevolving linear motifs in E7N. Several motif pairs show high co-occurrence, suggesting that they form functional and evolutionary units. Multiple independent appearances of several motifs during papillomavirus evolution provide direct evidence for convergent evolution, which may play an adaptive role as shown by correlation with phenotype.

[Full Abstract]

TM4 » Cross talk between DNA and Transcription factors

Presenting Author: Matias Machado (Institut Pasteur de Montevideo)

Co-authors: Pablo Dans (Institut Pasteur de Montevideo, Biomolecular Simulation Group); Sergio Pantano (Institut Pasteur de Montevideo, Biomolecular Simulation Group)

Short Abstract: Transcription factors (TFs) regulate the gene expression by binding to cis-regulatory boxes at promoter regions of the DNA. On the other hand, DNA mutations away from regulatory boxes may modulate transcriptional efficiency. Using coarse grain simulations we studied the dynamics of different promoter regions in the timescale of the microsecond. Simulations performed in absence/presence of the TATA binding protein modify the structure and dynamics of DNA up to ~12 base pairs far from the binding site, suggesting a cross talk between different regulation boxes within the promoter region.

[Full Abstract]

TM5 » Standardized comparison of structural alignments of catalytic domains in DNA polymerases from different methods

Presenting Author: Alex Slater (Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy. Pontificia Universidad Católica de Chile)

Co-authors: Manfred Sippl (University of Salzburg); Francisco Melo (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología)

Short Abstract: We have implemented a new software based on dynamic programming that uses a previously computed optimal superposition of two structures to generate a new optimal alignment and to calculate structural similarity values that can be used as standard to select the best structural alignment from a set of solutions. We show several examples of structural misalignments in catalytic domains of DNA polymerases identified by our software. Our software allows the identification of biologically relevant alignments from a set calculated with different structural alignment programs.

[Full Abstract]

TM6 » A Multidisciplinary Strategy for Function Assignment: The Enzyme Function Initiative from a Bioinformatics Perspective

Presenting Author: Daniel Almonacid (University of California)

Co-authors: Shoshana Brown (University of California San Francisco, Bioengineering and Therapeutic Sciences); Patricia Babbitt (University of California San Francisco, Bioengineering and Therapeutic Sciences)

Short Abstract: The Enzyme Function Initiative aims at developing a large-scale strategy for function prediction. We present the work of the bioinformatics scientific cores (superfamily/genome and data/dissemination cores) of the strategy applied to one of five model systems: the isoprenoid synthase superfamily. All members of the superfamily conserve the catalytic machinery needed for carbocation formation, but each incorporates different mechanistic strategies generating 5 distinctive functional subgroups. We discuss the collection of sequence and associated functional data, the use of sequence similarity networks for visualization of entire superfamilies, target selection, data curation, annotation transfer, and data dissemination through our Structure-Function Linkage Database.

[Full Abstract]

Topic Session: Computer Aided Drug Design and Docking/Molecular Dynamics Simulations

TA1 » Confidence Assessment of Candidate Drug Property Predictions by Subspace Mapping Methods

Presenting Author: Axel Soto (Universidad Nacional del Sur)

Co-authors: Ignacio Ponzoni (Universidad Nacional del Sur) Gustavo Vazquez (Universidad Nacional del Sur, Laboratory of Research and Development in Scientific Computing (LIDeCC)); Marc Strickert (Siegen University, Institute for Vision and Graphics); Ignacio Ponzoni (Universidad Nacional del Sur, Laboratory of Research and Development in Scientific Computing (LIDeCC))

Short Abstract: We present a method for assisting virtual screening of drugs during the early stages of the drug development process. This methodology is proposed to improve the reliability of QSPR prediction. First, a transformation is sought for mapping a high-dimensional space defined by potentially redundant or irrelevant molecular descriptors into a low-dimensional target-related space. Second, we apply an applicability domain model on the low-dimensional space for assessing confidence of compound classification. By a probabilistic framework our approach identifies poorly represented compounds in the training set and space regions where the uncertainty about the predicted class is higher than normal.

[Full Abstract]

TA2 » Docking Studies of a New Series of Analgesic and Anti-inflammatory Compounds (NSAIDs) with Cyclooxygenase

Presenting Author: Lucas Saraiva (Federal University of Minas Gerais)

Co-authors: Ihosvany Camps (Federal University of Alfenas, Department of Exact Science); Raquel Melo-Minardi (Federal University of Minas Gerais, Department of Computer Science ); Marcia Veloso (Federal University of Alfenas, Faculty of Pharmaceutical Science); Rodrigo Sailva (Federal University of São Carlos, Department of Chemistry)

Short Abstract: Anti-inflammatory drugs (NSAIDs) have been widely used to treat inflammatory processes. Due to the potential side effects NSAIDs might produce in parallel with the need for new safer and more efficient anti-inflammatory drugs, this research aimed to characterize in a molecular level, a new series of analgesic and anti-inflammatory compounds synthesized by our laboratory. The structural studies of the new series of NSAIDs were conducted by molecular docking with COX-1 and COX-2. Our docking studies have demonstrated that all the compounds are able to interact to both COXs with good score and appropriate conformation, thus showing promissory in silico activity.

[Full Abstract]

TA3 » Desintegrin-like domains in computer aided drug design of integrin-specific inhibitors

Presenting Author: Jorge H. Fernandez (State University of North Fluminense)

Co-authors: Jorge Fernandez (State University of North Fluminense); Monika A. Coronado (UNESP-RP, Depto. de Física); Ana T.R. Vasconcelos (LNCC, BioInfo); Monica Lopes-Ferreira (Butantan Institute, LETA); Wilson Savino (Oswaldo Cruz Institute, Laboratory of Thymus Research)

Short Abstract: Integrins are membrane-spanning heterodimers composed of non covalently linked α and β subunits. Integrin-binding activity on adhesion proteins can be modulated by short synthetic peptides containing RGD, KTS or ECD motifs. As the integrin-mediated cell attachment influences and regulates migration, growth and apoptosis, small RGD/ECD-containig peptides can be used to probe integrin functions in various biological systems. Combining structural, “in silico”, “in vitro” and “in vivo” techniques, our group developed small peptide-based structures to target α6β1 integrins. Drug design based on these structures may provide new treatment possibilities for diseases such as metastasis and inflammation pathologies.

[Full Abstract]

TA4 » Using Computer Simulations to Understand Enzyme Mechanism: Application to Mycobacterium tuberculosis CYP121 Unusual Reaction

Presenting Author: Victoria Dumas (University of Buenos Aires)

Co-authors: Adrián Turjanski (University of Buenos Aires, Química Inorganica); Lucas Defelipe (University of Buenos Aires, Química Biologica); Marcelo Martí (University of Buenos Aires, Química Inorgánica)

Short Abstract: In this work, a combination of classical molecular dynamics and hybrid quantum-classical methodologies was used in order to elucidate the reaction mechanism carried out by CYP121, a cytochrome p450 essential to life of Mycobacterium tuberculosis. This protein is highly interesting not only because it is essential for the viability of the bacilli, but also because there is evidence that it catalyzes an unusual reaction. Our results allow for a better understanding of this enzyme and for the general reaction mechanism of CYPs proteins which could be of great value for anti-tuberculosis drug design.

[Full Abstract]

TA5 » Topological constraints and challenges imposed by knots in proteins

Presenting Author: Cesar Ramirez (University of Chile)

Co-authors: Jeffrey K Noel (University of California San Diego, Center for Theoretical Biological Physics); Mauricio Baez (University of Chile, Department of Biology)

Short Abstract: Protein knots are intriguing structural motifs that have challenged both experimental and theoretical knowledge. We investigated thermodynamic and kinetic folding of the smallest knotted proteins known, VirC2 and MJ0366, from the ribbon-helix-helix (RHH) family of proteins, employing energy landscape theory and structure-based molecular dynamics using both coarse and all-atom graining. A preordered and looped, but unknotted, intermediate state is observed, and threading the loop by plugging or slipknotting is required to reach the knotted state. Moreover, we compared these results with Arc repressor, an unknotted dimer with similar architecture, showing that this topological constraint increases the free energy barrier severely‬.

[Full Abstract]

TA6 » Combined structure- and ligand-based virtual screening in the search of novel 11beta-hydroxysteroid dehydrogenase inhibitors for the treatment of metabolic syndrome

Presenting Author: Carlos Lagos (Pontificia Universidad Catolica de Chile)

Co-authors: Andrea Vecchiola (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Fidel Allende (P. Universidad Catolica de Chile, Clinical Laboratory); Carolina Valdivia (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Cristobal A. Fuentes (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Sandra Solari (P. Universidad Catolica de Chile, Clinical Laboratory); Carmen Campino (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Rene Baudrand (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Cristian A. Carvajal (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Carlos E. Fardella (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Mariana Cifuentes (Universidad de Chile, Institute of Nutrition and Food Technology (INTA))

Short Abstract: 11beta-hydroxysteroid dehydrogenase type 1 (11BHSD1) catalyzes the interconversion of inactive cortisone to active cortisol in a NADPH dependent manner within cells of key metabolic tissues. Excess cortisol elevates blood glucose levels, leading to insulin resistance and metabolic syndrome. Recently solved crystal structures of 11BHSD1 enzymes provide a source of structural information that can be used in virtual screening, a technique widely used in drug discovery projects. In this work, we report a combined shape-based database searching and fast rigid docking approach to identify potential human 11BHSD1 inhibitor candidate compounds from a the NCI Open library of compounds.

[Full Abstract]

Topic Session: Biomedicine and Immunoinformatics

WM1 » MHCcluster, and method for functional clustering of MHC molecules

Presenting Author: Morten Nielsen (Center for Biological Sequence Analysis, BioCentrum, DTU)

Co-authors: Ole Lund (Center for Biological Sequence Analysis, BioCentrum, DTU, Department of Systems biology); Claus Lundegaard (Center for Biological Sequence Analysis, BioCentrum, DTU, Department of Systems biology)

Short Abstract: The MHC genomic region in most species is extremely polymorphic. The distinct specificity of the majority of the MHC molecules remains uncharacterized. Here, we describe a tool to functionally cluster MHC class I molecules (MHCI) based on their predicted binding specificity. The tool provides highly intuitive heat-map and graphical tree-based visualizations of the functional relationship between MHCI variants. The method has a flexible web interface that allows the use to include any MHCI of interest in the analysis. When applied to the HLA-A and B system, the method reproduces the conventional 12 HLA supertypes. MHCcluster is available at www.cbs.dtu.dk/services/MHCcluster.

[Full Abstract]

WM2 » A step towards pan-specific prediction methods for MHC class II molecules: a projection of HLA-DR on to HLA-DP and HLA-DQ

Presenting Author: Edita Karosiene (Technical University of Denmark)

Co-authors: Morten Nielsen (Technical University of Denmark, Department of Systems Biology)

Short Abstract: It has been demonstrated for MHC class I that a pan-specific predictor can benefit from being trained on cross-loci data, however the polymorphism of α and β chains of MHC class II molecules complicates the development of pan-specific methods and limits their specificity to HLA-DR molecules. In this study, using the predictions for HLA-DR, we demonstrated the first steps towards the development of pan-specific methods for HLA-DP and HLA-DQ. We have shown how the pseudosequence, defining MHC binding environment, can be shortened in order to reduce the input space for prediction methods without loosing or even increasing binding prediction accuracy.

[Full Abstract]

WM3 » Systematic prediction of ligand-receptor pair across the immunoglobulin superfamily using a novel sequence homology measure

Presenting Author: Eng Hui Yap (Albert Einstein College of Medicine)

Co-authors: Andras Fiser (Albert Einstein College of Medicine, Systems and Computational Biology); Tyler Rosche (Albert Einstein College of Medicine, Systems and Computational Biology)

Short Abstract: The immunoglobulin superfamily (IgSF) is a large group of cell surface and soluble proteins that plays a key role in cell recognition, signaling and adhesion. We performed an IgSF-family wide prediction of new receptor-ligand relationships based on sequence homology to known IgSF receptor-ligand relationships. Our method measures sequence similarities via hidden Markov models (HMMs), and allows empirical information as part of the scoring scheme. We correctly predicted 40 out of 53 IgSF pairs that shared similar ligands from the STRING database. The method was then applied to 477 IgSF human proteins of interest, of which 380 IgSFs can be assigned.

[Full Abstract]

WM4 » Common features in damaged DNA detection

Presenting Author: Juan José Cifuentes (Pontificia Universidad Católica de Chile)

Co-authors: Francisco Melo (Molecular Bioinformatics Laboratory, Depto. Genética Molecular y Microbiología. Pontificia Universidad Católica de Chile)

Short Abstract: DNA damage and repair play a central role in aging and cancer. It is currently unknown, how damage detection proteins (DDPs) recognize different adducts embedded in the genome and how distinct proteins can detect the same adduct. Through a comparative analysis of the known three-dimensional structures of protein–damaged-DNA complexes and isolated damaged-DNA structures, we show that the minor groove is widened at the lesion point. In this position DDPs insert a residue in stacking geometry into the minor groove of DNA. These findings suggest a common DNA minor groove shape readout mechanism for damage detection.

[Full Abstract]

WM5 » A bioinformatics strategy for the design of diagnostic epitope discovery tools: first generation peptide microarrays for Chagas Disease

Presenting Author: Santiago Carmona (Universidad Nacional de San Martín)

Co-authors: Fernán Agüero (Universidad Nacional de San Martín); Paula Sartor (UBA, Dept. of Microbiology-Fac.Med.); Maria Susana Leguizamón (UBA, Dept. of Microbiology-Fac.Med.); Oscar Campetella (UNSAM, IIB); Fernán Agüero (UNSAM, IIB);

Short Abstract: The increasing number of sequenced pathogen genomes provide great opportunities for the development of diagnostics, especially in the case of pathogens with complex genomes such as Trypanosoma cruzi. In this work we present a bioinformatic prioritization strategy to select peptides to be included in peptide microarrays, an excellent platform for large-scale screening of peptidic B-cell epitopes. The strategy integrates many feature predictors and experimental datasets, to propose candidate peptides for inclusion in the array. 200 candidate peptides were experimentally assayed against sera from patients, allowing the identification of 37 novel potential diagnostic epitopes.

[Full Abstract]

WM6 » Annotation of putative AraC/XylS-family transcription factors of known structure but unknown function

Presenting Author: Andreas Schüller (Pontificia Universidad Católica de Chile)

Co-authors: Alex W. Slater (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología); Tomás Norambuena (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología); Juan J. Cifuentes (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología); Francisco Melo (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología)

Short Abstract: With recent advances in structural genomics, a growing need for functional annotation of newly solved crystal structures is needed. Here we present a method that combines sequence-based relationships and structural similarity of transcriptional regulators with computer prediction of their cognate DNA binding sequences. We applied this method to the AraC/XylS family of transcription factors, which is a large family of transcriptional regulators found in many bacteria controlling the expression of genes involved in diverse biological functions. Three putative new members with known three-dimensional structure but unknown function were identified for which a probable functional classification is provided.

[Full Abstract]

Topic Session: Functional Genomics and Systems Biology

WA1 » Evolution of domain architectures and catalytic functions of enzymes in metabolic systems

Presenting Author: Chen-Hsiang Yeang (Academia Sinica)

Co-authors: Summit Suen (Academia Sinica, Institute of Statistical Science); Henry Horng-Shing Lu (National Chiao-Tung University, Institute of Statistics)

Short Abstract: Domain architectures and catalytic functions of enzymes in metabolic systems are formulated as a two-layered network consisting of domains, proteins and reactions. We propose an algorithm to reconstruct the evolutionary history of domain-protein-reaction networks across multiple species and categorize the mechanisms of metabolic systems evolution. The reconstructed history reveals distinct patterns of evolutionary mechanisms between prokaryotic and eukaryotic networks. Moreover, different metabolic pathways are enriched with distinct network evolution mechanisms. Finally we elicit and validate two general principles underlying the evolution of domain-protein-reaction networks. These results shed new lights on the evolution of metabolic systems.

[Full Abstract]

WA2 » Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

Presenting Author: Kathleen Marchal (Ghent University)

Co-authors: Hong Sun (K.U.Leuven, Microbial and Molecular Systems); Tias Guns (K.U.Leuven, Computer Science); Ana Carolina Fierro (K.U.Leuven, Computer Science); Lieven Thorrez (K.U.Leuven, Interdepartmental Stem Cell Institute); Siegfried Nijssen (K.U.Leuven, Computer science)

Short Abstract: We developed CPModule, a novel approach for CRM detection with a performance that is competitive to that of other state-of-art tools, but that in contrast to previous tools can handle much larger datasets (such as 100 sequences in combination with a library of 517 PWMs). The flexible framework underlying CPModule in combination with its exhaustive search strategy allows to explicitly compare the feasibility of CRM detection in the presence and absence of ChIP-derived information. We good show on a real dataset that without ChIP-based information, CRM detection becomes an almost infeasible task.

[Full Abstract]

WA3 » LitProf – Gene Classifier: A text-mining gene function predictor for prokaryotes

Presenting Author: Roney Coimbra (FIOCRUZ-Minas)

Co-authors: Raul Torrieri (FIOCRUZ-Minas, Center for Excellence in Bioinformatics); Francislon Oliveira (FIOCRUZ-Minas, Center for Excellence in Bioinformatics); Guilherme Oliveira (FIOCRUZ-Minas, Center for Excellence in Bioinformatics)

Short Abstract: Most genome projects lack financial support to review annotations. Usually annotations are based solely on sequence similarity to a previously known gene, which was probably annotated in the same way. A large number of predicted genes remain unassigned to any functional category despite there is enough evidence in the literature to identify their function. We developed a classifier trained with term-frequency vectors automatically disclosed from text corpora of genes representative of functional categories of the JCVI ontology. The classifier unambiguously (confidence ≥ 0.7) assigned to functional categories 5,235 (from ~24k genes previously unclassified) for which there is literature in MEDLINE.

[Full Abstract]

WA4 » Discriminative local subspaces in gene expression data for effective gene function prediction

Presenting Author: Tomas Puelma (Pontificia Universidad Católica de Chile)

Co-authors: Rodrigo Gutierrez (Pontificia Universidad Católica de Chile); Alvaro Soto (Pontificia Universidad Católica de Chile, Computer Science); Rodrigo Gutierrez (Pontificia Universidad Católica de Chile, Molecular Genetics and Microbiology)

Short Abstract: In this work we present Discriminative Local Subspaces (DLS), a novel supervised machine learning method designed to analyze gene expression data and predict new candidate genes associated to a biological process of interest. DLS uses the knowledge available in Gene Ontology (GO) to generate informative training sets that guide the discovery of expression signatures: expression patterns defined in subsets of experimental conditions that are distinctive to the process of interest. These signatures provide key information to make new functional connections and provide valuable insights to help biologists to understand the predictions and guide future experiments.

[Full Abstract]

WA5 » The just-in-time expression of yeast ribosomal proteins

Presenting Author: Andrzej Kudlicki (University of Texas Medical Branch)

Co-authors: Xueling Li (University of Texas Medical Branch, Institute of Translational Science); Gang Chen (Central South University, Computer Science)

Short Abstract: By model-based analysis of gene expression time course data, we reconstructed the precise timeline of transcription of yeast ribosomal genes, spanning a 20 minute interval. The time of expression is related to position within the yeast ribosome: proteins localized deeper inside the ribosome are expressed earlier than the ones on the outside, which suggests that timing of expression is optimized to facilitate the assembly of the complex. The expression times are correlated with distance between the Rap1 motif and coding sequence, which implies involvement of RAP1p in regulating the expression time, via a previously unknown mode of regulation.

[Full Abstract]

WA6 » Deciphering human protein interactome using structural complexes

Presenting Author: Anna Panchenko (National Institutes of Health)

Co-authors: Manoj Tyagi (National Institutes of Health, NCBI); Kosuke Hashimoto (RIKEN, RIKEN); Benjamin Shoemaker (NIH, NCBI); Stefan Wuchty (NIH, NCBI)

Short Abstract: Although the identification of protein interactions by high-throughput methods progresses at a fast pace, ‘interactome’ datasets still suffer from high rates of false positives and low coverage. To map the human protein interactome, we describe a new framework that utilizes experimental evidence on structural complexes, the atomic details of binding interfaces and evolutionary conservation. The structurally-inferred interaction network is highly modular and more functionally coherent compared to experimental interaction networks derived from multiple literature citations. Moreover, structurally-inferred and high confidence high-throughput networks complement each other well, allowing us to construct the merged network to generate testable hypotheses and provide valuable experimental leads.

[Full Abstract]

Detailed Agenda

Two days ISCB-LatinAmerica-2012 Practical Tutorials
Day 1: Saturday - March 17, 2012
8:30 AM - 9:00 AM Tutorial Registration
9:00 AM - 12:30 PM Practical Tutorials and Workshops (Morning Session)

Room Z06 FCBS

Analysis, Comparison and Classification of Protein Structures

Room CE1

Genome browsers with special emphasis in the ENSEMBL system

Room Z05 FCBS

Protein resources and tools: sequence, architecture and protein interactions

Room CC1D

Algorithms and tools for transcriptomics and multiple gene profiling using the open source platforms R and Bioconductor

12:30 PM - 2:00 PM Lunch
2:00 PM - 5:30 PM Practical Tutorials and Workshops (Afternoon Session)

Room Z06 FCBS

Analysis, Comparison and Classification of Protein Structures

Room CE1

Genome browsers with special emphasis in the ENSEMBL system

Room Z05 FCBS

Protein resources and tools: sequence, architecture and protein interactions

Room CC1D

Algorithms and tools for transcriptomics and multiple gene profiling using the open source platforms R and Bioconductor

Day 2: Sunday - March 18, 2012
8:30 AM - 9:00 AM Tutorial Registration
9:00 AM - 12:30 PM Practical Tutorials and Workshops (Morning Session)

Room CC1D

Immunoinformatics

Room Z06 FCBS

Next generation sequencing: an introduction for bioinformaticians

Room CE1

Functional Genomics

Room Z05 FCBS

Computer-Based Drug Design

12:30 PM - 2:00 PM Lunch
2:00 PM - 5:30 PM Practical Tutorials and Workshops (Afternoon Session)

Room CC1D

Immunoinformatics

Room Z06 FCBS

Next generation sequencing: an introduction for bioinformaticians

Room CE1

Functional Genomics

Room Z05 FCBS

Computer-Based Drug Design

Three days ISCB-LatinAmerica-2012 Main Conference
Day 3: Monday - March 19, 2012
8:00 AM - 5:30 PM Main Conference Registration
8:30 AM - 9:00 AM Welcome/Opening Main Conference

SESSION I. Comparative Genomics and Evolution.

Chair of Session: Cristina Marino (Instituto Leloir, Argentina)

Location: Auditorium Juan Francisco Fresno (ground floor)

9:00 AM - 9:40 AM Keynote Lecture I: "Function prediction at different spatial scales"
Peer Bork. EMBL, Heidelberg, Germany.
9:40 AM - 10:30 AM Oral Presentations MM1-MM3

MM1 » The PhyloFacts-SchistoDB Schistosoma Database

Presenting Author: Kimmen Sjolander (University of California Berkeley)

Co-authors: Yaoqing Shen (University of California Berkeley, QB3); Ajithkumar Warrier (University of California Berkeley, QB3); Laila Nahum (FIOCRUZ Minas, Genomics and Computational Biology Group); Guilherme Oliveira (FIOCRUZ Minas, Genomics and Computational Biology Group)

MM2 » Identification of transcription regulation associated proteins in plants and stramenopiles

Presenting Author: Diego Mauricio Riaño Pachón (Universidad de los Andes)

Co-authors: Francisco J. Buitrago-Florez (Universidad de los Andes, Biological Sciences); Silvia Restrepo-Restrepo (Universidad de los Andes, Biological Sciences); Bernd Mueller-Roeber (Universität Potsdam, Institute of Biochemistry and Biology)

MM3 » Molecular Phylodynamics and Protein Modeling of Infectious Salmon Anemia Virus (ISAV)

Presenting Author: Eduardo Castro Nallar (Brigham Young University)

Co-authors: Marcelo Cortez-San Martín (Universidad de Santiago de Chile, Facultad de Química y Biología); Carolina Mascayano (Universidad de Santiago de Chile, Facultad de Química y Biología); Cristian Molina (Universidad de Santiago de Chile, Facultad de Química y Biología); Keith Crandall (Brigham Young University, Biology)

10:30 AM - 11:00 AM Coffee Break
11:00 AM - 11:40 AM Keynote Lecture II: "Orphan Orfogenic ORFs in the genomes of African trypanosomes"
Fernando Alvarez. Universidad de la República, Uruguay.
11:40 AM - 12:30 PM Oral Presentations MM4-MM6

MM4 » Evolutionary events involved in pathogenic trait acquisition in Ascomycetes

Presenting Author: Aminael Sanchez-Rodriguez (Katholieke Universiteit Leuven)

Co-authors: Riet De Smet (Ghent University, Plant Systems Biology); Kristof Engelen (Katholieke Universiteit Leuven, Molecular and Microbial Systems); Qiang Fu (Katholieke Universiteit Leuven, Molecular and Microbial Systems); Yan Wu (Katholieke Universiteit Leuven, Molecular and Microbial Systems); Kathleen Marchal (Katholieke Universiteit Leuven, Molecular and Microbial Systems)

MM5 » Novel Classes of Eukaryotic Aspartic Proteases and the Identification of their Specificity Determining Residues

Presenting Author: María Revuelta (Universidad Nacional de Mar del Plata)

MM6 » Conformational diversity: Relationship with protein evolution and designability

Presenting Author: Diego Zea (Universidad Nacional de Quilmes)

Co-authors: Gustavo Parisi (Universidad Nacional de Quilmes, Centro de Estudios e Investigaciones); Cristina Marino Buslje (Fundación Instituto Leloir, Bioinformatics Unit)

12:30 PM - 2:00 PM Lunch
12:30 PM - 2:00 PM

Business Presentation with free Lunch Sponsored by Life Technologies (open to any interested people)

Location: Sala Colorada (ground floor)

SESSION II. Genomics, Proteomics, Metagenomics and Metabolomics.

Chair of Session: David Holmes (Fundación Ciencia & Vida; Universidad Andrés Bello, Chile)

Location: Auditorium Juan Francisco Fresno (ground floor)

2:00 PM - 2:40 PM Keynote Lecture III: "Challenges of Assembling Genomes from the Second Generation Sequencing data"
Aleksey Zimin. University of Maryland, USA.
2:40 PM - 3:30 PM Oral Presentations MA1-MA3

MA1 » The ISA Commons – Towards interoperable data in bioscience

Presenting Author: Susanna-Assunta Sansone (University of Oxford)

Co-authors: Philippe Rocca-Serra (University of Oxford, Oxford e-Research Centre); Eamonn Maguire (University of Oxford, Oxford e-Research Centre)

MA2 » A Fast de novo Genome-Wide Tandem Repeat Discovery Algorithm

Presenting Author: Marcelo Gonçalves Narciso (Embrapa)

Co-authors: Michel Yamagishi (Embrapa); Marcelo Gonçalves Narciso (Embrapa, Bioinformatics)

MA3 » GOBOOT: testing set enrichment analysis robustness to background selection

Presenting Author: Cristobal Fresno Rodríguez (Catholic University of Córdoba)

Co-authors: Andrea Llera (Leloir Institute, CONICET, Laboratory of Molecular and Cellular Therapy); María R Girotti (Leloir Institute, CONICET, Laboratory of Molecular and Cellular Therapy); María P Valacco (Leloir Institute, CONICET, Laboratory of Molecular and Cellular Therapy); Juan A López (National Center for Cardiovascular Research, Madrid); Osvaldo L Podhajcer (Leloir Institute, CONICET, Laboratory of Molecular and Cellular Therapy); Mónica G Balzarini (National University of Córdoba, Biometry Laboratory); Federico Prada (UADE, Institute of Technology, School of Engineering and Sciences); Elmer A Fernández (Catholic University of Córdoba, CONICET, BioScience Data Mining Group)

3:30 PM - 4:00 PM Coffee Break
4:00 PM - 4:40 PM Keynote Lecture IV: "SABIA: A new version for next generation sequencing platforms"
Ana Teresa Ribeiro de Vasconcelos. National Laboratory of Scientific Computation, Brazil.
4:40 PM - 5:30 PM Oral Presentations MA4-MA6

MA4 » Computational Pattern Recognition for the Identification of Transposases in Prokaryotic Genomes: Challenges and Advances

Presenting Author: Gonzalo Riadi (Universidad de Talca)

Co-authors: David Holmes (Fundación Ciencia & Vida and Universidad Andrés Bello, Facultad Ciencias Biológicas); Gonzalo Riadi (Center of Bioinformatics and Molecular Simulation and Universidad de Talca, Engineering School)

MA5 » Spinal Cord Regeneration in Xenopus: A Transcriptomics Analysis

Presenting Author: Dasfne Lee-Liu (Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas)

Co-authors: Juan Larrain (Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas) Leonardo Almonacid (Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas); Mauricio Moreno (Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas); Rosana Muñoz (Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas); Marcia Gaete (Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas); Francisco Melo (Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas)

MA6 » High-resolution community genomics of a hypersaline microbial ecosytem

Presenting Author: Juan Ugalde (University of California, San Diego)

Co-authors: Sheilla Podell (University of California, San Diego, Scripps Institution of Oceanography); Karla Heidelberg (University of Southern California, Department of Biological Sciences); Jill Banfield (University of California, Berkeley, Department of Earth and Planetary Sciences); Eric Allen (University of California, San Diego, Scripps Institution of Oceanography)

5:30 PM - 7:00 PM

Poster Session I (Odd numbers)

Location: Central Square (ground floor)

6:30 PM - 8:30 PM

Meeting of SoIBio and FreeBIT/CYTED: Societies and Networks promoting Bioinformatics for Life Sciences and Biomedicine in IberoAmerica.

Location: Sala Colorada (ground floor)

Day 4: Tuesday - March 20, 2012
8:00 AM - 5:30 PM Main Conference Registration

SESSION III. Macromolecule Structure/Function Prediction.

Chair of Session: Diego Ferreiro (Universidad de Buenos Aires, Argentina)

Location: Auditorium Juan Francisco Fresno (ground floor)

9:00 AM - 9:40 AM Keynote Lecture V: "Amazing Protein Folds"
Manfred Sippl. University of Salzburg, Austria.
9:40 AM - 10:30 AM Oral Presentations TM1-TM3

TM1 » Modeling proteins using supersecondary structure library and NMR chemical shifts

Presenting Author: Andras Fiser (Albert Einstein College of Medicine)

Co-authors: Vilas Menon (Albert Einstein College of Medicine, Systems and Computational Biology); Joseph Dybas (Albert Einstein College of Medicine, Systems and Computational Biology)

TM2 » Using correlation data and network decomposition to obtain sub-class determinants in protein families

Presenting Author: Lucas Bleicher (Universidade Federal de Minas Gerais)

Co-authors: Richard Garratt (Universidade de Sao Paulo, Instituto de Fisica de Sao Carlos); Ney Lemke (Universidade Estadual de Sao Paulo, Departamento de Fisica e Biofisica, Botucatu)

TM3 » Evolution of linear motifs within the intrinsically disordered and globular domains of the papillomavirus E7 oncoprotein

Presenting Author: Lucia Chemes (Fundación Instituto Leloir IIBBA-CONICET)

Co-authors: Juliana Glavina (Protein Physiology Laboratory, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, Departamento de Química Biológica); Julian Faivovich (División Herpetología, Museo Argentino de Ciencias Naturales-CONICET, Buenos Aires, Argentina, Museo Argentino de Ciencias Naturales); Leonardo Alonso (Fundacion Instituto Leloir , Buenos Aires Argentina, IIBBA-CONICET); Cristina Marino-Buslje (Fundacion Instituto Leloir, IIBBA CONICET, Buenos Aires Argentina, Structural Bioinformatics Laboratory); Gonzalo de Prat Gay (Fundacion Instituto Leloir IIBBA CONICET, Buenos AIres Argentina, Protein Structure-Function and Engineering Laboratory); Sanchez Ignacio (Protein Physiology Laboratory, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, Departamento de Quimica Biologica)

10:30 AM - 11:00 AM Coffee Break
11:00 AM - 11:40 AM Keynote Lecture VI: "Conformational diversity and the development of new tools in bioinformatics"
Gustavo Parisi. Universidad Nacional de Quilmes, Argentina.
11:40 AM - 12:30 PM Oral Presentations TM4-TM6

TM4 » Cross talk between DNA and Transcription factors

Presenting Author: Matias Machado (Institut Pasteur de Montevideo)

Co-authors: Pablo Dans (Institut Pasteur de Montevideo, Biomolecular Simulation Group); Sergio Pantano (Institut Pasteur de Montevideo, Biomolecular Simulation Group)

TM5 » Standardized comparison of structural alignments of catalytic domains in DNA polymerases from different methods

Presenting Author: Alex Slater (Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy. Pontificia Universidad Católica de Chile)

Co-authors: Manfred Sippl (University of Salzburg); Francisco Melo (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología)

TM6 » A Multidisciplinary Strategy for Function Assignment: The Enzyme Function Initiative from a Bioinformatics Perspective

Presenting Author: Daniel Almonacid (University of California)

Co-authors: Shoshana Brown (University of California San Francisco, Bioengineering and Therapeutic Sciences); Patricia Babbitt (University of California San Francisco, Bioengineering and Therapeutic Sciences)

12:30 PM - 2:00 PM Lunch
12:40 PM - 2:00 PM

Business Presentation with free Lunch Sponsored by Roche (open to any interested people)

Location: Sala Colorada (ground floor)

SESSION IV. Computer Aided Drug Design and Docking/Molecular Dynamics Simulations.

Chair of Session: Tomás Pérez-Acle (Universidad de Chile, Chile)

Location: Auditorium Juan Francisco Fresno (ground floor)

2:00 PM - 2:40 PM Keynote Lecture VII: "Coarse-Grain methods for molecular dynamics simulations: Actually bridging the gap between simulations and biological scales"
Sergio Pantano. Instituto Pasteur de Montevideo, Uruguay.
2:40 PM - 3:30 PM Oral Presentations TA1-TA3

TA1 » Confidence Assessment of Candidate Drug Property Predictions by Subspace Mapping Methods

Presenting Author: Axel Soto (Universidad Nacional del Sur)

Co-authors: Ignacio Ponzoni (Universidad Nacional del Sur) Gustavo Vazquez (Universidad Nacional del Sur, Laboratory of Research and Development in Scientific Computing (LIDeCC)); Marc Strickert (Siegen University, Institute for Vision and Graphics); Ignacio Ponzoni (Universidad Nacional del Sur, Laboratory of Research and Development in Scientific Computing (LIDeCC))

TA2 » Docking Studies of a New Series of Analgesic and Anti-inflammatory Compounds (NSAIDs) with Cyclooxygenase

Presenting Author: Lucas Saraiva (Federal University of Minas Gerais)

Co-authors: Ihosvany Camps (Federal University of Alfenas, Department of Exact Science); Raquel Melo-Minardi (Federal University of Minas Gerais, Department of Computer Science ); Marcia Veloso (Federal University of Alfenas, Faculty of Pharmaceutical Science); Rodrigo Sailva (Federal University of São Carlos, Department of Chemistry)

TA3 » Desintegrin-like domains in computer aided drug design of integrin-specific inhibitors

Presenting Author: Jorge H. Fernandez (State University of North Fluminense)

Co-authors: Jorge Fernandez (State University of North Fluminense) Monika A. Coronado (UNESP-RP, Depto. de Física); Ana T.R. Vasconcelos (LNCC, BioInfo); Monica Lopes-Ferreira (Butantan Institute, LETA); Wilson Savino (Oswaldo Cruz Institute, Laboratory of Thymus Research)

3:30 PM - 4:00 PM Coffee Break
4:00 PM - 4:40 PM Keynote Lecture VIII: "Molecular Simulation of Non-equilibrium Systems: The Dance of ions across the membrane"
Danilo González. Universidad Andres Bello, Chile.
4:40 PM - 5:30 PM Oral Presentations TA4-TA6

TA4 » Using Computer Simulations to Understand Enzyme Mechanism: Application to Mycobacterium tuberculosis CYP121 Unusual Reaction

Presenting Author: Victoria Dumas (University of Buenos Aires)

Co-authors: Adrián Turjanski (University of Buenos Aires, Química Inorganica); Lucas Defelipe (University of Buenos Aires, Química Biologica); Marcelo Martí (University of Buenos Aires, Química Inorgánica)

TA5 » Topological constraints and challenges imposed by knots in proteins

Presenting Author: César Ramírez (University of Chile)

Co-authors: Jeffrey K. Noel (University of California San Diego, Center for Theoretical Biological Physics); Mauricio Baez (University of Chile, Department of Biology)

TA6 » Combined structure- and ligand-based virtual screening in the search of novel 11beta-hydroxysteroid dehydrogenase inhibitors for the treatment of metabolic syndrome

Presenting Author: Carlos Lagos (Pontificia Universidad Católica de Chile)

Co-authors: Andrea Vecchiola (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Fidel Allende (P. Universidad Catolica de Chile, Clinical Laboratory); Carolina Valdivia (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Cristobal A. Fuentes (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Sandra Solari (P. Universidad Catolica de Chile, Clinical Laboratory); Carmen Campino (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Rene Baudrand (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Cristian A. Carvajal (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Carlos E. Fardella (P. Universidad Catolica de Chile, Molecular Endocrinology Laboratory); Mariana Cifuentes (Universidad de Chile, Institute of Nutrition and Food Technology (INTA))

5:30 PM - 7:00 PM

Poster Session II (Even numbers)

Location: Central Square (ground floor)

Day 5: Wednesday - March 21, 2012

SESSION V. Biomedicine and Immunoinformatics.

Chair of Session: Alexis Kalergis (Pontificia Universidad Católica de Chile)

Location: Auditorium Juan Francisco Fresno (ground floor)

9:00 AM - 9:40 AM Keynote Lecture IX: "Immune Epitope Database and Analysis Resource Program: Proving Intuitive Access To Comprehensive Epitope Data And Tools"
Alessandro Sette. La Jolla Institute for Allergy and Immunology, USA.
9:40 AM - 10:30 AM Oral Presentations WM1-WM3

WM1 » MHCcluster, and method for functional clustering of MHC molecules

Presenting Author: Morten Nielsen (Center for Biological Sequence Analysis, BioCentrum, DTU)

Co-authors: Ole Lund (Center for Biological Sequence Analysis, BioCentrum, DTU, Department of Systems biology); Claus Lundegaard (Center for Biological Sequence Analysis, BioCentrum, DTU, Department of Systems biology)

WM2 » A step towards pan-specific prediction methods for MHC class II molecules: a projection of HLA-DR on to HLA-DP and HLA-DQ

Presenting Author: Edita Karosiene (Technical University of Denmark)

Co-authors: Morten Nielsen (Technical University of Denmark, Department of Systems Biology)

WM3 » Systematic prediction of ligand-receptor pair across the immunoglobulin superfamily using a novel sequence homology measure

Presenting Author: Eng Hui Yap (Albert Einstein College of Medicine)

Co-authors: Andras Fiser (Albert Einstein College of Medicine, Systems and Computational Biology); Tyler Rosche (Albert Einstein College of Medicine, Systems and Computational Biology)

10:30 AM - 11:00 AM Coffee Break
11:00 AM - 11:40 AM Keynote Lecture X: "Using Genomics to Improve Response to Neoadjuvant Therapy in Patients with Rectal Cancer"
Anamaría Camargo. Ludwig Institute for Cancer Research, Brazil.
11:40 AM - 12:30 PM Oral Presentations WM4-WM6

WM4 » Common features in damaged DNA detection

Presenting Author: Juan José Cifuentes (Pontificia Universidad Católica de Chile)

Co-authors: Francisco Melo (Molecular Bioinformatics Laboratory, Depto. Genética Molecular y Microbiología. Pontificia Universidad Católica de Chile)

WM5 » A bioinformatics strategy for the design of diagnostic epitope discovery tools: first generation peptide microarrays for Chagas Disease

Presenting Author: Santiago Carmona (Universidad Nacional de San Martín)

Co-authors: Fernán Agüero (Universidad Nacional de San Martín) Paula Sartor (UBA, Dept. of Microbiology-Fac.Med.); Maria Susana Leguizamón (UBA, Dept. of Microbiology-Fac.Med.); Oscar Campetella (UNSAM, IIB); Fernán Agüero (UNSAM, IIB)

WM6 » Annotation of putative AraC/XylS-family transcription factors of known structure but unknown function

Presenting Author: Andreas Schüller (Pontificia Universidad Católica de Chile)

Co-authors: Alex W. Slater (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología); Tomás Norambuena (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología); Juan José Cifuentes (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología); Francisco Melo (Pontificia Universidad Católica de Chile, Depto. Genética Molecular y Microbiología)

12:30 PM - 2:00 PM Lunch
12:45 PM - 1:45 PM

The ISCB Open Member Meeting (open to any interested people)

Location: Sala Colorada (ground floor)

SESSION VI. Functional Genomics and Systems Biology.

Chair of Session: Rodrigo Gutiérrez (Pontificia Universidad Católica de Chile)

Location: Auditorium Juan Francisco Fresno (ground floor)

2:00 PM - 2:40 PM Keynote Lecture XI: "Using ‘omics’ data to study regulator-target interactions and organizational principles in networks"
Yves van de Peer. University of Ghent, Belgium.
2:40 PM - 3:30 PM Oral Presentations WA1-WA3

WA1 » Evolution of domain architectures and catalytic functions of enzymes in metabolic systems

Presenting Author: Chen-Hsiang Yeang (Academia Sinica)

Co-authors: Summit Suen (Academia Sinica, Institute of Statistical Science); Henry Horng-Shing Lu (National Chiao-Tung University, Institute of Statistics)

WA2 » Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

Presenting Author: Kathleen Marchal (Ghent University)

Co-authors: Hong Sun (K.U.Leuven, Microbial and Molecular Systems); Tias Guns (K.U.Leuven, Computer Science); Ana Carolina Fierro (K.U.Leuven, Computer Science); Lieven Thorrez (K.U.Leuven, Interdepartmental Stem Cell Institute); Siegfried Nijssen (K.U.Leuven, Computer science)

WA3 » LitProf – Gene Classifier: A text-mining gene function predictor for prokaryotes

Presenting Author: Roney Coimbra (FIOCRUZ-Minas)

Co-authors: Raul Torrieri (FIOCRUZ-Minas, Center for Excellence in Bioinformatics); Francislon Oliveira (FIOCRUZ-Minas, Center for Excellence in Bioinformatics); Guilherme Oliveira (FIOCRUZ-Minas, Center for Excellence in Bioinformatics)

3:30 PM - 4:00 PM Coffee Break
4:00 PM - 4:40 PM Keynote Lecture XII: "On the evolution of PPI networks"
Sandro José de Souza. Ludwig Institute for Cancer Research, Brazil.
4:40 PM - 5:30 PM Oral Presentations WA4-WA6

WA4 » Discriminative local subspaces in gene expression data for effective gene function prediction

Presenting Author: Tomás Puelma (Pontificia Universidad Católica de Chile)

Co-authors: Rodrigo Gutiérrez (Pontificia Universidad Católica de Chile); Alvaro Soto (Pontificia Universidad Católica de Chile, Computer Science); Rodrigo Gutierrez (Pontificia Universidad Católica de Chile, Molecular Genetics and Microbiology)

WA5 » The just-in-time expression of yeast ribosomal proteins

Presenting Author: Andrzej Kudlicki (University of Texas Medical Branch)

Co-authors: Xueling Li (University of Texas Medical Branch, Institute of Translational Science); Gang Chen (Central South University, Computer Science)

WA6 » Deciphering human protein interactome using structural complexes

Presenting Author: Anna Panchenko (National Institutes of Health)

Co-authors: Manoj Tyagi (National Institutes of Health, NCBI); Kosuke Hashimoto (RIKEN, RIKEN); Benjamin Shoemaker (NIH, NCBI); Stefan Wuchty (NIH, NCBI)

5:30 PM - 6:00 PM Awards Ceremony
6:00 PM – 6:30 PM Closing Remarks
7:00 PM – 11:30 PM

Conference Banquet

Location: Castillo Hidalgo, Cerro Santa Lucía, Santiago [SEE MAP HERE]

One day satellite Workshops and Round Tables
Day 6: Thursday - March 22, 2012

SESSION VII. WorkShops on Next Generation Sequencing Technologies and GRID Computing.

Chair of Session: Romilio Espejo (Omics Solutions, Chile)

Location: Auditorium Aula Magna Eleodoro Matte Ossa (second floor)

10:00 AM - 11:15 AM "Ion Torrent – Open, Accessible, and Enabling"
Matt Dyer. Life Technologies, USA.
11:15 AM - 11:30 AM Coffee Break
11:30 AM - 12:45 PM "Introducing GS FLX+ System"
Xuemin Liu. 454 Sequencing/Roche, USA.
12:45 PM - 2:00 PM Lunch
2:00 PM - 3:00 PM "Optimization of bioinformatics applications to be executed on GRID platforms"
Manuel A. Rodríguez-Pascual and Rafael Mayo-García (CIEMAT, Spain; SoIBio, CYTED and FreeBIT).
3:00 PM - 3:20 PM Coffee Break

SESSION VIII. Round Tables on Bioinformatics Research, Training and Education in Iberoamerica.

Chair of Session: Danilo González (Universidad Andrés Bello, Chile)

Location: Auditorium Aula Magna Eleodoro Matte Ossa (second floor)

3:20 PM – 4:20 PM "Bioinformatics Education in Iberoamerica"
Alejandra Medina-Rivera and Juan Pablo Bustamante (SoIBio Student Council), Daniel Almonacid and Priscila Grynberg (ISCB Student Council).
4:20 PM – 4:40 PM Coffee Break
4:40 PM – 5:40 PM "Bioinformatics Research and Training in Iberoamerica"
Guilherme de Oliveira (Brazil), Fernán Aguero (Argentina), Javier de las Rivas (Spain), Julio Collado-Vides (México), Allan Orozco (Costa Rica) and Francisco Melo (Chile).

Call for Oral/Poster presentations

Call for Late Poster presentations for ISCB-LatinAmerica 2012 is now open!

Oral Presentation submission deadline is November 28, 2011 CLOSED

Poster Presentation submission deadline is January 13, 2012 CLOSED

Late Poster Presentation submission deadline is February 7, 2012 CLOSED

Before submitting your work, please be aware that you will be required to provide a title, a short abstract (100 words to be pasted in the form) and a long abstract (1-2 pages to be uploaded as a PDF file). All submissions must be in English, and incomplete submissions will not be considered.

To submit your work, please fill in the following SUBMISSION FORM.

Also, you will be required to categorize your Oral/Poster presentation into one of the following six categories:

SESSION I. Comparative Genomics and Evolution

This session will include the analysis and comparison of genomic data from different species, as well as sequence variation and evolution.

SESSION II. Genomics, Proteomics, Metagenomics and Metabolomics

This session will include large-scale sequencing, genome assembling, analysis of gene expression data, pattern recognition and data mining.

SESSION III. Macromolecule Structure/Function Prediction

This session will include protein, DNA (chromatin) and RNA structure and function prediction, classification.

SESSION IV. Computer Aided Drug Design and Docking/Molecular Dynamics Simulations

This session will include specific cases of structure-based molecular dynamics and docking simulations.

SESSION V. Biomedicine and Immunoinformatics

This session will include development of biomarkers, vaccines, analysis of polimorfisms in humans or pathogens, pattern recognition and data mining; all oriented to human health and disease.

SESSION VI. Functional Genomics and Systems Biology

This session will include the analysis and modeling of metabolic networks, gene expression networks, signal transduction networks and population networks, pattern recognition and data mining.

 

If you have any problem or questions with the submission process, please send your inquiries to: This email address is being protected from spambots. You need JavaScript enabled to view it.

Program Committee of ISCB-Latin America 2012

 

 

  • Juan Opazo, Universidad Austral, Chile.
  • Gustavo Parisi, Universidad de Quilmes, Argentina.
  • Damien Devos, EMBL, Germany.
  • David Holmes, Universidad Andrés Bello, Chile.
  • Mauricio González, INTA, Chile.
  • Elmer Fernández, Universidad Católica de Córdoba, Argentina.
  • Diego Ferreiro, Universidad de Buenos Aires, Argentina.
  • Ignacio Sánchez, Intituto Leloir, Argentina.
  • Marc Marti-Renom, Instituto de Investigación Príncipe Felipe, Spain.
  • Andreas Schüller, P. Universidad Católica de Chile, Chile.
  • Tomás Pérez Acle, Universidad de Chile, Chile.
  • Sergio Pantano, Intituto Pasteur, Uruguay.
  • Morten Nielsen, Technical University of Denmark, Denmark.
  • Andras Fiser, Albert Einstein Medical School, USA.
  • Fernan Aguero, Universidad Nacional de San Martín, Argentina.
  • Rodrigo Gutiérrez, P. Universidad Católica de Chile, Chile.
  • Luis Larrondo, P. Universidad Católica de Chile, Chile.
  • Alberto Dávila, Instituto Oswaldo Cruz, Brazil.

 

 

Steering Committee of ISCB-Latin America 2012

  • Francisco Melo, Pontificia Universidad Católica de Chile, Conference Chair
  • Cristina Marino, Instituto Leloir, Argentina
  • Alejandro Maass, Universidad de Chile, Chile
  • Guilherme Oliveira, CEBio, Brazil
  • Hugo Naya, Institut Pasteur de Montevideo, Uruguay
  • Burkhard Rost, ISCB President
  • Janet Kelso, ISCB Conference Committee Chair
  • Reinhard Schneider, ISCB Treasurer
  • BJ Morrison McKay, ISCB Executive Officer

Call for Oral/Poster presentations

Call for Oral/Poster presentations for ISCB-LatinAmerica-2012 is now open!

Before submitting your work, please be aware that you will be required to provide a title, a short abstract (100 words to be pasted in the form) and a long abstract (1-2 pages to be uploaded as a PDF file). Incomplete submissions will not be considered.

To submit your work, please fill in the following FORM.

Also, you will be required to categorize your Oral/Poster presentation into one of the following six categories:

SESSION I. Comparative Genomics and Evolution

This session will include the analysis and comparison of genomic data from different species, as well as sequence variation and evolution.

SESSION II. Genomics, Proteomics, Metagenomics and Metabolomics

This session will include large-scale sequencing, genome assembling, analysis of gene expression data, pattern recognition and data mining.

SESSION III. Macromolecule Structure/Function Prediction

This session will include protein, DNA (chromatin) and RNA structure and function prediction, classification.

SESSION IV. Computer Aided Drug Design and Docking/Molecular Dynamics Simulations

This session will include specific cases of structure-based molecular dynamics and docking simulations.

SESSION V. Biomedicine and Immunoinformatics

This session will include development of biomarkers, vaccines, analysis of polimorfisms in humans or pathogens, pattern recognition and data mining; all oriented to human health and disease.

SESSION VI. Functional Genomics and Systems Biology

This session will include the analysis and modeling of metabolic networks, gene expression networks, signal transduction networks and population networks, pattern recognition and data mining.

 

If you have any problem or questions with the submission process, please send your inquiries to: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 

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  • Member Discount

    ISCB Members enjoy discounts on conference registration (up to $150), journal subscriptions, book (25% off), and job center postings (free).

  • Why Belong

    Connecting, Collaborating, Training, the Lifeblood of Science. ISCB, the professional society for computational biology!

     

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