Browsing by Autor "Carlos A. Jaramillo"

Filter results by typing the first few letters
Now showing 1 - 3 of 3
  • Thumbnail Image
    Item type: Item ,
    Analysis of Gromacs MPI Using the Opportunistic Cloud Infrastructure UnaCloud
    (2012) Nathalia Garcés; Harold Castro; Paula Delgado; Andres Gonz'lez; Carlos A. Jaramillo; Natalia Peñaranda; María del Pilar Delgado
    This paper shows and analyzes the execution of a molecular dynamic application that uses Message Passing Interface (MPI) mechanism-Gromacs MPI-over a cloud infrastructure (UnaCloud) supported by desktop computers. The main objective is to find a solution to support Gromacs-MPI on UnaCloud. This coupling was carried out in order to predict and to redefine the Helicobacter pylori Cag A protein 3D structure. Although the structure of eight indigenous sequences was obtained, the handle of resource discovery and failure recovery on the opportunistic infrastructure was achieved manually, restricting the application scope of the solution. To eliminate these restrictions, a mechanism to automate the process execution on UnaCloud was identified and proposed.
  • Thumbnail Image
    Item type: Item ,
    Genotipificación de cagA y de la región intermedia de vacA en cepas de Helicobacter pylori aisladas de pacientes adultos colombianos y asociación con enfermedades gástricas
    (2018) M. Camila Melo-Narváez; Diana F. Rojas-Rengifo; Luisa F. Jiménez‐Soto; María del Pilar Delgado Perafán; Belén Mendoza de Molano; Jose Fernando Vera‐Chamorro; Carlos A. Jaramillo
    Objetivo: este estudio caracteriza la diversidad de los genes de virulencia cagA (gen asociado con la citotoxina A) y vacA (citotoxina vacuolizante) en pacientes colombianos para determinar posibles asociaciones entre estos 2 genes y la severidad de los hallazgos endoscópicos teniendo en cuenta todos los genotipos reportados para el gen vacA (s, m e i).Materiales y métodos: Helicobacter pylori fue detectado por cultivo y por métodos moleculares en biopsias de 62 pacientes. Los genotipos de cagA y vacA (m/i/s) se determinaron por reacción en cadena de la polimerasa (PCR) y secuenciación. Resultados: se aislaron 124 cepas de 62 pacientes; de estas, el 48,5% (n = 48) fueron vacA s2/m2/i2-cagA (-) presente en su mayoría en pacientes con gastritis folicular; mientras el 32,3% (n = 32) fueron vacA s1/m1/i1-cagA (+) presentes mayormente en pacientes con gastritis folicular, gastritis crónica y posible metaplasia. Se encontró una asociación significativa entre la presencia de cagA y el genotipo vacA s1/m1/i1 y la ausencia de cagA y el genotipo vacA s2/m2/i2 (p <0,001). No se encontró una asociación significativa entre la severidad de los hallazgos endoscópicos y el estatus cagA-vacA de las cepas.Conclusión: se encontró una baja prevalencia de cepas cagA (+), el estatus cagA-vacA no es un predictor de riesgo en la población estudiada y la presencia de infecciones heterogéneas sin tropismo sugieren la necesidad de tomar biopsias tanto del cuerpo como del antro del estómago en la práctica clínica rutinaria.
  • Thumbnail Image
    Item type: Item ,
    Structural Analysis of Variability and Interaction of the N-Terminal of the Oncogenic Effector CagA of <em>Helicobacter pylori</em> with Phosphatidylserine
    (2018) Cindy P. Ulloa-Guerrero; María del Pilar Delgado; Carlos A. Jaramillo
    Helicobacter pylori cytotoxin-associated gene A protein (CagA) has been associated with the increase in virulence and risk of cancer. It has been demonstrated that CagA's translocation is dependent on its interaction with phosphatidylserine. We evaluated the variability of the N-terminal CagA in 127 sequences reported in NCBI, by referring to molecular interaction forces with the Phosphatidylserine and the docking of 3 mutations chosen from variations in specific positions. The major sites of conservation of the residues involved in CagA-Phosphatidylserine interaction were 617, 621 and 626 which had no amino acid variation. Position 636 had the lowest conservation score, so mutations in this position were evaluated to observe the differences in intermolecular forces of the CagA-Phosphatidylserine complex. We evaluated the docking of 3 mutations: K636A, K636R and K636N. The models of the crystal and mutations presented a ΔG of −8.919907, −8.665261, −8.701923, −8.515097 Kcal/mol, respectively, while mutations K636A, K636R, K636N and the crystal structure presented 0, 3, 4 and 1 H-bonds, respectively. Likewise, the bulk effect of the ΔG and amount of H-bonds was estimated in all of the docking models. The type of mutation affected both the ΔG (χ2(1) = 93.82, p-value < 2.2 × 10−16) and the H-bonds (χ2(1) = 91.93, p-value < 2.2 × 10−16). In all the data, 76.9% of the strains that exhibit the K636N mutation produced a severe pathology. The average H-bond count diminished when comparing the mutations with the crystal structure of all the docking models, which means that other molecular forces are involved in the CagA-Phosphatidylserine complex interaction.