Repositorio Institucional Universidad EAFIT ::Examinando por Materia "chemistry"

Examinando por Materia "chemistry"

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Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
(BioMed Central Ltd., 2018-01-17) Molano, E.P.L.; Cabrera, O.G.; Jose, J.; do Nascimento, L.C.; Carazzolle, M.F.; Teixeira, P.J.P.L.; Alvarez, J.C.; Tiburcio, R.A.; Tokimatu Filho, P.M.; de Lima, G.M.A.; Guido, R.V.C.; Corrêa, T.L.R.; Leme, A.F.P.; Mieczkowski, P.; Pereira, G.A.G.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Background: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. Results: We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Conclusion: Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity. © 2018 The Author(s).
Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
(BioMed Central Ltd., 2018-01-17) Molano, E.P.L.; Cabrera, O.G.; Jose, J.; do Nascimento, L.C.; Carazzolle, M.F.; Teixeira, P.J.P.L.; Alvarez, J.C.; Tiburcio, R.A.; Tokimatu Filho, P.M.; de Lima, G.M.A.; Guido, R.V.C.; Corrêa, T.L.R.; Leme, A.F.P.; Mieczkowski, P.; Pereira, G.A.G.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)
Background: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. Results: We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Conclusion: Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity. © 2018 The Author(s).
Effect of chemical composition and microstructure on the mechanical behavior of fish scales from Megalops Atlanticus
(ELSEVIER SCIENCE BV, 2016-03-01) Gil-Duran, S.; Arola, D.; Ossa, E.A.; Gil-Duran, S.; Arola, D.; Ossa, E.A.; Universidad EAFIT. Departamento de Ingeniería de Producción; Materiales de Ingeniería
This paper presents an experimental study of the composition, microstructure and mechanical behavior of scales from the Megalops Atlanticus (Atlantic tarpon). The microstructure and composition were evaluated by Scanning Electron Microscopy (SEM) and RAMAN spectroscopy, respectively. The mechanical properties were evaluated in uniaxial tension as a function of position along the length of the fish (head, mid-length and tail). Results showed that the scales are composed of collagen and hydroxyapatite, and these constituents are distributed within three well-defined layers from the bottom to the top of the scale. The proportion of these layers with respect to the total scale thickness varies radially. The collagen fibers are arranged in plies with different orientations and with preferred orientation in the longitudinal direction of the fish. Results from the tensile tests showed that scales from Megalops Atlanticus exhibit variations in the elastic modulus as a function of body position. Additional testing performed with and without the highly mineralized top layers of the scale revealed that the mechanical behavior is anisotropic and that the highest strength was exhibited along the fish length. Furthermore, removing the top mineralized layers resulted in an increase in the tensile strength of the scale. © 2015 Elsevier Ltd.
Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases
(BioMed Central Ltd., 2014-01-01) Mosquera-Rendón, J.; Cárdenas-Brito, S.; Pineda, J.D.; Corredor, M.; Benítez-Páez, A.; Mosquera-Rendón, J.; Cárdenas-Brito, S.; Pineda, J.D.; Corredor, M.; Benítez-Páez, A.; Universidad EAFIT. Departamento de Ingeniería de Sistemas; I+D+I en Tecnologías de la Información y las Comunicaciones
Background: RNA post-transcriptional modification is an exciting field of research that has evidenced this editing process as a sophisticated epigenetic mechanism to fine tune the ribosome function and to control gene expression. Although tRNA modifications seem to be more relevant for the ribosome function and cell physiology as a whole, some rRNA modifications have also been seen to play pivotal roles, essentially those located in central ribosome regions. RNA methylation at nucleobases and ribose moieties of nucleotides appear to frequently modulate its chemistry and structure. RNA methyltransferases comprise a superfamily of highly specialized enzymes that accomplish a wide variety of modifications. These enzymes exhibit a poor degree of sequence similarity in spite of using a common reaction cofactor and modifying the same substrate type. Results: Relationships and lineages of RNA methyltransferases have been extensively discussed, but no consensus has been reached. To shed light on this topic, we performed amino acid and codon-based sequence analyses to determine phylogenetic relationships and molecular evolution. We found that most Class I RNA MTases are evolutionarily related to protein and cofactor/vitamin biosynthesis methyltransferases. Additionally, we found that at least nine lineages explain the diversity of RNA MTases. We evidenced that RNA methyltransferases have high content of polar and positively charged amino acid, which coincides with the electrochemistry of their substrates. Conclusions: After studying almost 12,000 bacterial genomes and 2,000 patho-pangenomes, we revealed that molecular evolution of Class I methyltransferases matches the different rates of synonymous and non-synonymous substitutions along the coding region. Consequently, evolution on Class I methyltransferases selects against amino acid changes affecting the structure conformation. © 2014 Mosquera-Rendón et al.; licensee BioMed Central Ltd.
Insights into the structure and stability of the carbonic acid dimer
(ROYAL SOC CHEMISTRY, 2010-01-01) Murillo, Juliana; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
In this paper we report the geometries and properties of 40 structural isomers located on the MP2/6-311++G** PES of the carbonic acid dimer. All six possible combinations of carbonic acid monomers were considered. The dimers are divided into six geometrical motifs. Our data suggests that combinations of anti-anti monomers do not necessarily lead to larger stabilization energies in the formation of the dimers. MP2 underestimates the relative binding energies with respect to CCSD(T) by as much as 3.2 kcal mol-1. At least 3 different dimers which may contribute to the stability of carbonic acid are predicted to have significant populations. Binding energy is only directly related to relative stability when comparing dimers formed from the same monomers. Overall stabilization is mainly dictated by attractive electrostatic interactions via cooperative polarization by virtue of the spatial arrangement of the dipole moment components along the polar bonds. Shorter O…H bond distances and larger bond orders predicted for the hydrogen bonds directed towards carbonyl groups make for stronger hydrogen bonding than in O…H bonds directed towards hydroxyl groups. © the Owner Societies.
Microsolvation of dimethylphosphate: A molecular model for the interaction of cell membranes with water
(ROYAL SOC CHEMISTRY, 2013-01-01) Ibargueen, Cesar; Manrique-Moreno, Marcela; Hadad, C. Z.; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
We present an exhaustive stochastic search of the quantum conformational spaces of the (CH3O)2PO2 - + nH 2O (n = 1,2,3) systems. We uncover structural, conformational and energetic features of the problem. As in the isolated species, clusters containing the gauche-gauche (gg) conformation of dimethylphosphate (DMP -) are energetically preferred, however, contributions from hydrated gauche-anti (ga) and anti-anti (aa) monomers cannot be neglected because such structures are quite common and because they are close in energy to those containing the gg monomer. At least seven distinct types of O?H-O-H contacts lead to DMP- ? water interactions that are always stabilizing, but not strong enough to induce significant changes in the geometries of either DMP- or water units. Our results lead us to postulate DMP- to be a suitable model to study explicit and detailed aspects of microsolvation of cell membranes. This journal is © 2013 the Owner Societies.
Paracoccidioides spp. catalases and their role in antioxidant defense against host defense responses
(Elsevier, 2017-03-01) Tamayo, D.; Muñoz, J.F.; Almeida, A.J.; Puerta, J.D.; Restrepo, Á.; Cuomo, C.A.; McEwen, J.G.; Hernández, O.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)
Dimorphic human pathogenic fungi interact with host effector cells resisting their microbicidal mechanisms. Yeast cells are able of surviving within the tough environment of the phagolysosome by expressing an antioxidant defense system that provides protection against host-derived reactive oxygen species (ROS). This includes the production of catalases (CATs). Here we identified and analyzed the role of CAT isoforms in Paracoccidioides, the etiological agent of paracoccidioidomycosis. Firstly, we found that one of these isoforms was absent in the closely related dimorphic pathogen Coccidioides and dermatophytes, but all of them were conserved in Paracoccidioides, Histoplasma and Blastomyces species. We probed the contribution of CATs in Paracoccidioides by determining the gene expression levels of each isoform through quantitative RT-qPCR, in both the yeast and mycelia phases, and during the morphological switch (transition and germination), as well as in response to oxidative agents and during interaction with neutrophils. PbCATP was preferentially expressed in the pathogenic yeast phase, and was associated to the response against exogenous H2O2. Therefore, we created and analyzed the virulence defects of a knockdown strain for this isoform, and found that CATP protects yeast cells from H2O2 generated in vitro and is relevant during lung infection. On the other hand, CATA and CATB seem to contribute to ROS homeostasis in Paracoccidioides cells, during endogenous oxidative stress. CAT isoforms in Paracoccidioides might be coordinately regulated during development and dimorphism, and differentially expressed in response to different stresses to control ROS homeostasis during the infectious process, contributing to the virulence of Paracoccidioides. © 2017 Elsevier Inc.
Structural characterization of the (MeSH)4 potential energy surface
(SPRINGER, 2013-05-01) Gomez, Sara; Guerra, Doris; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
A random walk on the PES for (MeSH)4 clusters produced 50 structural isomers held together by hydrogenbonding networks according to calculations performed at the B3LYP/6-311++G* * andMP2/6-311++G* * levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted. © Springer-Verlag Berlin Heidelberg 2012.
Structural characterization of the (methanol)4 potential energy surface
(AMER CHEMICAL SOC, 2009-09-24) David, Jorge; Guerra, Doris; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
In this paper, we report the geometries and properties of the structural isomers obtained from a random walk of the potential energy surface (PES) of the methanol tetramer. Thirty-three structures were obtained after B3LYP/6-31+g* optimization of 94 candidate structures generated from a stochastic search of the PM3 conformational space. The random search was carried out using a recently proposed modified Metropolis acceptance test in the simulated annealing (SA) procedure. Corrections for the basis set superposition error (BSSE) show improvements on the binding energies of the clusters in an average of approximately 2.0 kcal/mol, while geometries are predicted to be less sensitive to BSSE corrections. MP2/aug-cc-pvdz calculations on representative structures did not change the geometries but predicted better binding energies. Highly correlated CCSD(T) energies were calculated on the B3LYP and MP2 stationary points and used to establish relative stabilities. We report several new conformations and group the structures into six distinct geometrical motifs. Only the cyclic tetramers with four primary hydrogen bonds in the same plane are predicted to have significant populations. Secondary hydrogen bonds, those for which the donated proton comes from an alkyl group, lead to a rich conformational space.
Structures, energies, and bonding in the water heptamer
(AMER INST PHYSICS, 2013-07-28) Acelas, Nancy; Hincapie, Gina; Guerra, Doris; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
In this paper we report the geometries and properties of 38 distinct geometrical motifs located on the B3LYP/6-31+G(d), MP2/6-311++G(d, p) potential energy surfaces of the water heptamer. Binding energies of up to 45 kcal/mol are calculated. All motifs fall within 10 kcal/mol of the most stable conformation, with at least 13 structural patterns located no more than 3 kcal/mol above, leading to a very complex potential energy surface, populated by a multitude of motifs each one allowing large numbers of conformations. Cluster stability does not seem to be correlated with the number of hydrogen bonds. Compact structures are energetically favored by electronic energies with zero-point energy corrections, while more open structures are preferred when temperature and entropy are accounted for. The molecular interactions holding the clusters as discrete units lead to large binding energies but are not strong enough to cause significant changes in the geometries of the interacting monomers. Our results indicate that bonding in the water heptamers can be considered as largely non-shared interactions with contributions from intermediate character of increasing covalency. © 2013 AIP Publishing LLC.
Time dependent deformation behavior of dentin
(PERGAMON-ELSEVIER SCIENCE LTD, 2017-04-01) Montoya C; Arola D; Ossa EA; Montoya C; Arola D; Ossa EA; Universidad EAFIT. Departamento de Ingeniería de Producción; Materiales de Ingeniería
Objective The viscoelastic behavior of dentin and its ability to undergo time dependent deformation are considered to be important to oral functions and its capacity to resist fracture. There are spatial variations in the microstructure of dentin within the crown, which could be important to the viscous behavior. However, a spatially resolved description for the viscoelastic behavior of coronal dentin has not been reported. Methods In this investigation spherical indentations were made in three regions of coronal dentin including the outer, middle and inner regions. Power law relations were developed to quantitatively describe the stress-strain responses of the tissue. Results Results showed that the deformation behavior was strongly dependent on the composition (mineral to collagen ratio) and microstructure (tubule density), which contributed to an increase in the rate of viscous deformation with increasing proximity to the pulp. Conclusions A model accounting for spatial variations in composition and microstructure was developed to describe the steady-state time dependent deformation behavior of coronal dentin, and a good agreement was found with the experimental results. © 2017 Elsevier Ltd
Treatment of automotive industry oily wastewater by electrocoagulation: statistical optimization of the operational parameters.
(IWA PUBLISHING, 2009-11-01) GilPavas, Edison; Molina-Tirado, Kevin; Angel Gomez-Garcia, Miguel; GilPavas, Edison; Molina-Tirado, Kevin; Angel Gomez-Garcia, Miguel; Universidad EAFIT. Departamento de Ingeniería de Procesos; Procesos Ambientales (GIPAB)
An electrocoagulation process was used for the treatment of oily wastewater generated from an automotive industry in Medellin (Colombia). An electrochemical cell consisting of four parallel electrodes (Fe and Al) in bipolar configuration was implemented. A multifactorial experimental design was used for evaluating the influence of several parameters including: type and arrangement of electrodes, pH, and current density. Oil and grease removal was defined as the response variable for the statistical analysis. Additionally, the BOD(5), COD, and TOC were monitored during the treatment process. According to the results, at the optimum parameter values (current density = 4.3 mA/cm(2), distance between electrodes = 1.5 cm, Fe as anode, and pH = 12) it was possible to reach a c.a. 95% oils removal, COD and mineralization of 87.4% and 70.6%, respectively. A final biodegradability (BOD(5)/COD) of 0.54 was reached.

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