Cyclotella katiana sp. nov. from la reina swamp, parque nacional natural los katíos, Colombia

Fil: Sala, Silvia Estela. División Ficología. Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Ramirez Restrepo, John Jairo. Instituto de Biologia. Facultad de Ciencias Exactas y Naturales. Universidad de Antioquia. Medellin; Colombi

Data Mining of the Coffee Rust Genome

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

Genetic diversity of Phytophthora infestans in the Northern Andean region.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana) and tree tomato (Solanum betaceum), all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, β-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. RESULTS: Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. CONCLUSIONS: The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a

Development of a genetic tool for functional screening of anti-malarial bioactive extracts in metagenomic libraries

Ajuts: Departamento Administrativo de Ciencias, Tecnología e Innovación (Colciencias), República de Colombia; Convocatoria 489 - 2009, Código 657048925406, Contrato de financiación RC. 427 - 2009 Colciencias - CorpoGen; Programa de Asistencias Graduadas de Universidad de los Andes, Bogotá, Colombia; i Programa Jóvenes Investigadores de ColcienciasBACKGROUND: The chemical treatment of Plasmodium falciparum for human infections is losing efficacy each year due to the rise of resistance. One possible strategy to find novel anti-malarial drugs is to access the largest reservoir of genomic biodiversity source on earth present in metagenomes of environmental microbial communities. METHODS: A bioluminescent P. falciparum parasite was used to quickly detect shifts in viability of microcultures grown in 96-well plates. A synthetic gene encoding the Dermaseptin 4 peptide was designed and cloned under tight transcriptional control in a large metagenomic insert context (30 kb) to serve as proof-of-principle for the screening platform. RESULTS: Decrease in parasite viability consistently correlated with bioluminescence emitted from parasite microcultures, after their exposure to bacterial extracts containing a plasmid or fosmid engineered to encode the Dermaseptin 4 anti-malarial peptide. Here, a new technical platform to access the anti-malarial potential in microbial environmental metagenomes has been develope

Development of a genetic tool for functional screening of anti-malarial bioactive extracts in metagenomic libraries

BACKGROUND: The chemical treatment of Plasmodium falciparum for human infections is losing efficacy each year due to the rise of resistance. One possible strategy to find novel anti-malarial drugs is to access the largest reservoir of genomic biodiversity source on earth present in metagenomes of environmental microbial communities. METHODS: A bioluminescent P. falciparum parasite was used to quickly detect shifts in viability of microcultures grown in 96-well plates. A synthetic gene encoding the Dermaseptin 4 peptide was designed and cloned under tight transcriptional control in a large metagenomic insert context (30 kb) to serve as proof-of-principle for the screening platform. RESULTS: Decrease in parasite viability consistently correlated with bioluminescence emitted from parasite microcultures, after their exposure to bacterial extracts containing a plasmid or fosmid engineered to encode the Dermaseptin 4 anti-malarial peptide. CONCLUSIONS: Here, a new technical platform to access the anti-malarial potential in microbial environmental metagenomes has been developed

Identification and Evolution of Transcription Factors in Stramenopiles

Background. 
Many transcriptional regulatory proteins have been identified and classified into several families on the basis of sequence similarity (Fukami, 2003), these families usually regulate important biological processes, such as development and responses to external stimuli. Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing the action of RNA polymerases (Latchman, 2004); in addition to TFs, other Transcriptional regulators (TRs) participate in transcriptional modulation by e.g., chromatin remodeling. With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the entire set of Transcription factors (TFs) and Transcription regulators (TRs) can be identified, described, and compared between species and lineages. The diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they are present in freshwater, marine and terrestrial habitats and embrace many ecologically important algal (e.g. diatoms, brown algae, chrysophytes), and heterotrophic (e.g., Oomycetes) groups.

Methods. 
In order to find TF and TR genes in the deduced proteomes of Stramenopile we followed the approach developed in Perez et al. 2010. Briefly, it exploits the presence of protein domains and their combinations, in the form of boolean rules, that are specific for different families of TFs and TRs. Such rules are represented as a bipartite graph in which a set of nodes represent gene families and the other set of nodes, protein domains. Edges are drawn between nodes of different types indicating whether a protein domain is required in the gene family or it is forbidden.

Results. 
We applied an enlarged set of rules to the deduced proteomes of 8 different Stramenopiles, identifying more than 400 different regulatory genes in each species belonging to up to 59 different gene families.

Conclusions. 
The identification of this class of regulatory genes will constitute and important resource that could be exploited in gene functional characterization and evolutionary analyses. All TFs and TRs families found will be publicly released via a web database.

References.
Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B. 2010. Nucleic Acids Res. 38(Database issue):D822-

Phytophthora infestans population structure: a worldwide scale

Phytophthora infestans, the causal agent of late blight disease in potato and other members of the Solanaceae family, is responsible for causing the Irish potato famine and, even today, it causes enormous economic losses all over the world. For the establishment of an adequate pest management strategy, the determination of population structure is required. To characterize P. infestans populations worldwide two allozymes, Gpi (Glucose-6-phospate isomerase) and Pep (Peptidase), the RG57 DNA RFLP fingerprinting probe, as well as resistance to the fungicide metalaxyl and the mating type, have been used as markers. P. infestans populations in Mexico have been one of the main focuses of research in the population biology of this pathogen because this country has been considered as one of the possible centers of origin of this oomycete. In this review we present the population structure of P. infestans in Mexico, Europe, Africa, Asia, North America, and South America expanding on the present situation of P. infestans in Colombia. Finally, we will discuss different lines of research that are being carried out today with respect to P. infestans in Colombia, which have shown the importance of continuing the study of this devastating plant pathogen in our country.Phytophthora infestans, el agente causal del tizón tardío de la papa y otros miembros de la familia de las Solanáceas, es el responsable de la gran hambruna irlandesa y aún hoy sigue causando grandes pérdidas económicas alrededor del planeta. Para establecer estrategias de control adecuadas contra este patógeno se requiere comprender la estructura poblacional del mismo. Mundialmente se han utilizado como marcadores las aloenzimas, Gpi (Glucosa-6-fosfato isomerasa) y Pep (Peptidasa) y la sonda de fingerprinting de RFLP (Polimorfismos de la Longitud de los Fragmentos de Restricción), RG57. De igual forma, la resistencia al fungicida metalaxyl y el tipo de apareamiento, han sido empleados para caracterizar las poblaciones de P. infestans. Las poblaciones de P. infestans en México han sido uno de los focos principales de investigación en la biología poblacional de este patógeno debido a que este país ha sido considerado como uno de los posibles centros de origen de este oomiceto. En esta revisión se presentará la estructura poblacional de P. infestans en México, Europa, África, Asia, Norte América y Sur América, profundizando en la situación actual de P. infestans en Colombia. Finalmente, se discutirá las diferentes líneas de investigación que se llevan a cabo hoy respecto a P. infestans en Colombia, las cuales han mostrado la importancia de continuar con el estudio de este devastador patógeno de plantas en nuestro país

Modelo de Inteligencia Ambiental basado en la integración de Redes de Sensores Inalámbricas y Agentes Inteligentes

La Inteligencia Ambiental o AmI (Ambient Intelligence), es un área de las Ciencias Computacionales que integra aspectos novedosos como computación ubicua, interfaces inteligentes, sistemas adaptativos, Smart WSN, entre otros. Sin embargo, no existe un modelo genérico para diseñar y desarrollar aplicaciones reales de AmI. El objetivo de esta tesis de maestría es proponer un meta-modelo de AmI que incluya los modelos más relevantes que deben ser tenidos en cuenta para el diseño e implementación de tales sistemas, definidos como modelo de contexto, modelo de adaptación, modelo del usuario y modelo del dominio. Adicional a estos modelos, es necesario especificar un módulo con los servicios adaptados que pueden ser ofrecidos por agentes inteligentes quienes utilizan para ello el conocimiento almacenado en los diferentes modelos./ Abstract. The Ambient Intelligence (AmI) is a Computer Science field that integrates new research topics such as ubiquitous computing, intelligent interfaces, adaptive systems, Smart WSN, among others. However, there is not a generic model to design and develop real AmI applications. The aim of this master thesis is to propose an AmI meta-model that includes the more relevant models that should be considered to the design and implementation of such systems, defined as context model, adaptation model, user model, and domain model. In addition to these models, a module comprised by intelligent-agent-based adaptive services must be specified which use the knowledge stored within different models.Maestrí