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Dive into the research topics where Camilo López is active.

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Featured researches published by Camilo López.


BMC Plant Biology | 2010

Plant microRNAs and their role in defense against viruses: a bioinformatics approach

Álvaro Luis Pérez-Quintero; Rafik Neme; Andrés Zapata; Camilo López

BackgroundmicroRNAs (miRNAs) are non-coding short RNAs that regulate gene expression in eukaryotes by translational inhibition or cleavage of complementary mRNAs. In plants, miRNAs are known to target mostly transcription factors and are implicated in diverse aspects of plant growth and development. A role has been suggested for the miRNA pathway in antiviral defense in plants. In this work, a bioinformatics approach was taken to test whether plant miRNAs from six species could have antiviral activity by targeting the genomes of plant infecting viruses.ResultsAll plants showed a repertoire of miRNAs with potential for targeting viral genomes. The viruses were targeted by abundant and conserved miRNA families in regions coding for cylindrical inclusion proteins, capsid proteins, and nuclear inclusion body proteins. The parameters for our predicted miRNA:target pairings in the viral genomes were similar to those for validated targets in the plant genomes, indicating that our predicted pairings might behave in-vivo as natural miRNa-target pairings. Our screening was compared with negative controls comprising randomly generated miRNAs, animal miRNAs, and genomes of animal-infecting viruses. We found that plant miRNAs target plant viruses more efficiently than any other sequences, but also, miRNAs can either preferentially target plant-infecting viruses or target any virus without preference.ConclusionsOur results show a strong potential for antiviral activity of plant miRNAs and suggest that the miRNA pathway may be a support mechanism to the siRNA pathway in antiviral defense.


PLOS ONE | 2013

An Improved Method for TAL Effectors DNA-Binding Sites Prediction Reveals Functional Convergence in TAL Repertoires of Xanthomonas oryzae Strains

Álvaro Luis Pérez-Quintero; Luis M. Rodriguez-R; Alexis Dereeper; Camilo López; Ralf Koebnik; Boris Szurek; Sébastien Cunnac

Transcription Activators-Like Effectors (TALEs) belong to a family of virulence proteins from the Xanthomonas genus of bacterial plant pathogens that are translocated into the plant cell. In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures of TALE-DNA complexes were recently reported. Accurate prediction of TAL Effector Binding Elements (EBEs) is essential to elucidate the biological functions of the many sequenced TALEs as well as for robust design of artificial TALE DNA-binding domains in biotechnological applications. In this work a program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions. To gain a systems perspective on the large TALE repertoires from X. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs.


Biochemical and Biophysical Research Communications | 2011

Artificial microRNAs (amiRNAs) engineering - On how microRNA-based silencing methods have affected current plant silencing research.

Gaurav Sablok; Álvaro Luis Pérez-Quintero; Mehedi Hassan; Tatiana V. Tatarinova; Camilo López

In recent years, endogenous microRNAs have been described as important regulators of gene expression in eukaryotes. Artificial microRNAs (amiRNAs) represent a recently developed miRNA-based strategy to silence endogenous genes. amiRNAs can be created by exchanging the miRNA/miRNA(∗) sequence within a miRNA precursor with a sequence designed to match the target gene, this is possible as long as the secondary RNA structure of the precursor is kept intact. In this review, we summarize the basic methodologies to design amiRNAs and detail their applications in plants genetic functional studies as well as their potential for crops genetic improvement.


Briefings in Functional Genomics | 2013

Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data

Liliana López-Kleine; Luis Guillermo Leal; Camilo López

Techniques in molecular biology have permitted the gathering of an extremely large amount of information relating organisms and their genes. The current challenge is assigning a putative function to thousands of genes that have been detected in different organisms. One of the most informative types of genomic data to achieve a better knowledge of protein function is gene expression data. Based on gene expression data and assuming that genes involved in the same function should have a similar or correlated expression pattern, a function can be attributed to those genes with unknown functions when they appear to be linked in a gene co-expression network (GCN). Several tools for the construction of GCNs have been proposed and applied to plant gene expression data. Here, we review recent methodologies used for plant gene expression data and compare the results, advantages and disadvantages in order to help researchers in their choice of a method for the construction of GCNs.


BMC Genomics | 2015

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

Johana Carolina Soto; Juan Felipe Ortiz; Laura Perlaza-Jiménez; Andrea Vásquez; Luis Augusto Becerra Lopez-Lavalle; Boby Mathew; Jens Léon; Adriana Bernal; Agim Ballvora; Camilo López

BackgroundCassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome.ResultsA high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs.ConclusionsThis is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.


Tropical Plant Biology | 2012

Cassava Bacterial Blight: Using Genomics for the Elucidation and Management of an Old Problem

Camilo López; Adriana Bernal

Bacterial Blight is an important disease of cassava, causing losses that have resulted in historical famines in certain growing zones. The disease is caused by Xanthomonas axonopodis pv. manihotis, a gram-negative rod that belongs to the gammaproteobacteria. In this review, we describe the pathosystem and the recent studies that have been undertaken to elucidate both susceptibility and resistance mechanisms in cassava, with the hope of generating resistant plants using biotechnology. We first describe studies of the pathogen, including pathogen population changes through time as well as genomic tools that have recently been generated to determine pathogenicity factors. Secondly, we discuss mechanisms of disease resistance that have been elucidated in recent years and how these mechanisms could be used for the generation of improved plants resistant to CBB.


Frontiers in Plant Science | 2015

MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility

Mathilde Hutin; Alvaro L. Pérez-Quintero; Camilo López; Boris Szurek

Many plant-pathogenic xanthomonads rely on Transcription Activator-Like (TAL) effectors to colonize their host. This particular family of type III effectors functions as specific plant transcription factors via a programmable DNA-binding domain. Upon binding to the promoters of plant disease susceptibility genes in a sequence-specific manner, the expression of these host genes is induced. However, plants have evolved specific strategies to counter the action of TAL effectors and confer resistance. One mechanism is to avoid the binding of TAL effectors by mutations of their DNA binding sites, resulting in resistance by loss-of-susceptibility. This article reviews our current knowledge of the susceptibility hubs targeted by Xanthomonas TAL effectors, possible evolutionary scenarios for plants to combat the pathogen with loss-of-function alleles, and how this knowledge can be used overall to develop new pathogen-informed breeding strategies and improve crop resistance.


Molecular Biotechnology | 2013

Tell Me a Tale of TALEs

Alejandra Muñoz Bodnar; Adriana Bernal; Boris Szurek; Camilo López

Pathogenic bacteria of the Xanthomonas and Ralstonia genus have developed resourceful strategies creating a favorable environment to multiply and colonize their host plants. One of these strategies involves the secretion and translocation of several families of effector proteins into the host cell. The transcription activator-like effector (TALE) family forms a subset of proteins involved in the direct modulation of host gene expression. TALEs include a number of tandem 34-amino acid repeats in their central part, where specific residues variable in two adjacent positions determine DNA-binding in the host genome. The specificity of this binding and its predictable nature make TALEs a revolutionary tool for gene editing, functional analysis, modification of target gene expression, and directed mutagenesis. Several examples have been reported in higher organisms as diverse as plants, Drosophila, zebrafish, mouse, and even human cells. Here, we summarize the functions of TALEs in their natural context and the biotechnological perspectives of their use.


Genomics, Proteomics & Bioinformatics | 2013

Identification of ta-siRNAs and Cis-nat-siRNAs in Cassava and Their Roles in Response to Cassava Bacterial Blight

Andrés Quintero; Álvaro Luis Pérez-Quintero; Camilo López

Trans-acting small interfering RNAs (ta-siRNAs) and natural cis-antisense siRNAs (cis-nat-siRNAs) are recently discovered small RNAs (sRNAs) involved in post-transcriptional gene silencing. ta-siRNAs are transcribed from genomic loci and require processing by microRNAs (miRNAs). cis-nat-siRNAs are derived from antisense RNAs produced by the simultaneous transcription of overlapping antisense genes. Their roles in many plant processes, including pathogen response, are mostly unknown. In this work, we employed a bioinformatic approach to identify ta-siRNAs and cis-nat-siRNAs in cassava from two sRNA libraries, one constructed from healthy cassava plants and one from plants inoculated with the bacterium Xanthomonas axonopodis pv. manihotis (Xam). A total of 54 possible ta-siRNA loci were identified in cassava, including a homolog of TAS3, the best studied plant ta-siRNA. Fifteen of these loci were induced, while 39 were repressed in response to Xam infection. In addition, 15 possible cis-natural antisense transcript (cis-NAT) loci producing siRNAs were identified from overlapping antisense regions in the genome, and were found to be differentially expressed upon Xam infection. Roles of sRNAs were predicted by sequence complementarity and our results showed that many sRNAs identified in this work might be directed against various transcription factors. This work represents a significant step toward understanding the roles of sRNAs in the immune response of cassava.


PLOS ONE | 2013

Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen Xanthomonas axonopodis pv. Manihotis Strain CIO151

Mario L Arrieta-Ortiz; Luis M. Rodríguez-R; Álvaro Luis Pérez-Quintero; Lucie Poulin; Ana Díaz; Nathalia Arias Rojas; Cesar Trujillo; Mariana Restrepo Benavides; Rebecca Bart; Jens Boch; Tristan Boureau; Armelle Darrasse; Perrine David; Thomas Dugé de Bernonville; Paula Fontanilla; Lionel Gagnevin; Fabien Guérin; Marie-Agnès Jacques; Emmanuelle Lauber; Pierre Lefeuvre; Cesar Medina; Edgar M. Medina; Nathaly Montenegro; Alejandra Muñoz Bodnar; Laurent D. Noël; Juan F. Ortiz Quiñones; Daniela Osorio; Carolina Pardo; Prabhu B. Patil; Stéphane Poussier

Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.

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Andrés Zapata

National University of Colombia

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Liliana López-Kleine

National University of Colombia

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Simón Cortés

National University of Colombia

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Boris Szurek

Institut de recherche pour le développement

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Andrea Vásquez

National University of Colombia

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Luis Guillermo Leal

National University of Colombia

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Paul Chavarriaga

International Center for Tropical Agriculture

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Andrés Quintero

National University of Colombia

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Simón Cortés Sierra

National University of Colombia

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