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Search Results: 1 - 10 of 174709 matches for " Juan Rincon F. "
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Estructura y diversidad genética en vacas Holstein de Antioquia usando un polimorfismo del gen bGH
Juan Rincon F.,Albeiro Lopez H.,Julian Echeverri Z.
Revista MVZ Córdoba , 2013,
Abstract: Objetivo. Determinar las frecuencias alélicas y genotípicas del polimorfismo del intrón 3 del gen bGH y estimar algunos parámetros de estructura poblacional en ganado Holstein. Materiales y métodos. El estudio se realizó con 1366 vacas Holstein en 120 hatos de 11 municipios del departamento de Antioquia. Se extrajo DNA por el método de Salting out y la genotipificación se realizó usando la técnica de PCR-RFLPs. La diversidad genética se determinó mediante la comparación de las heterocigosidades, El equilibrio de Hardy-Weinberg (HW) y la diferenciación genética entre las poblaciones se realizó usando el software Arlequín 2.0 Las frecuencias alélicas y genotípicas se evaluaron mediante el paquete estadístico SAS . Resultados. Las frecuencias genotípicas encontradas fueron 0.764 (+/+), 0.223 (+/-) y 0.013 (-/-) y las frecuencias alélicas 0.876 (+) y 0.124 (-). No se encontraron desviaciones del Equilibrio de Hardy Weinberg en ninguna de las subpoblaciones. La diversidad genética determinada mediante la comparación de las heterocigosidades fue relativamente baja entre poblaciones pero al interior de estas no. El valor de FST de toda la población fue de 0.0068 y significativo (p<0.05), algunos FST pareados también lo fueron, tomando valores desde 0.0 a 0.13. Los estadísticos FIT y FIS no fueron significativos. Conclusiones. El gen bGH es un candidato interesante para evaluar características de importancia económica ya que no parece haber sido sometido a selección directa, presenta una variabilidad media en las poblaciones, observándose diferenciación genética significativa entre distintos municipios, producto de los diferentes sistemas de producción y acceso a las biotecnologías.
Transcriptional profiling of bovine milk using RNA sequencing
Saumya Wickramasinghe, Gonzalo Rincon, Alma Islas-Trejo, Juan F Medrano
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-45
Abstract: A total of 16,892 genes were expressed in transition lactation, 19,094 genes were expressed in peak lactation and 18,070 genes were expressed in late lactation. Regardless of the lactation stage approximately 9,000 genes showed ubiquitous expression. Genes encoding caseins, whey proteins and enzymes in lactose synthesis pathway showed higher expression in early lactation. The majority of genes in the fat metabolism pathway had high expression in transition and peak lactation milk. Most of the genes encoding for endogenous proteases and enzymes in ubiquitin-proteasome pathway showed higher expression along the course of lactation.This is the first study to describe the comprehensive bovine milk transcriptome in Holstein cows. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells. Most of the genes were ubiquitously expressed in all three stages of lactation. However, a fraction of the milk transcriptome has genes devoted to specific functions unique to the lactation stage. This indicates the ability of milk somatic cells to adapt to different molecular functions according to the biological need of the animal. This study provides a valuable insight into the biology of lactation in the cow, as well as many avenues for future research on the bovine lactome.Milk is a unique biological fluid consumed by mammalian infants. It contains many macro- and micro-nutrients that are essential for the growth and development of the newborn [1,2]. In addition, a diverse cocktail of bioactive factors, such as antibodies, oligosaccharides and nucleotides in milk, play immune, pre-biotic and protective functions in the infant gut [1,3,4].Cow milk has an important role in human nutrition because cow milk-based infant formula is the most available substitute for human breast milk and cow milk is consumed beyond infancy in human populations around the world. However, there are significant differences between the physicochemical properties
Transcriptome Profiling of Bovine Milk Oligosaccharide Metabolism Genes Using RNA-Sequencing
Saumya Wickramasinghe,Serenus Hua,Gonzalo Rincon,Alma Islas-Trejo,J. Bruce German,Carlito B. Lebrilla,Juan F. Medrano
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0018895
Abstract: This study examines the genes coding for enzymes involved in bovine milk oligosaccharide metabolism by comparing the oligosaccharide profiles with the expressions of glycosylation-related genes. Fresh milk samples (n = 32) were collected from four Holstein and Jersey cows at days 1, 15, 90 and 250 of lactation and free milk oligosaccharide profiles were analyzed. RNA was extracted from milk somatic cells at days 15 and 250 of lactation (n = 12) and gene expression analysis was conducted by RNA-Sequencing. A list was created of 121 glycosylation-related genes involved in oligosaccharide metabolism pathways in bovine by analyzing the oligosaccharide profiles and performing an extensive literature search. No significant differences were observed in either oligosaccharide profiles or expressions of glycosylation-related genes between Holstein and Jersey cows. The highest concentrations of free oligosaccharides were observed in the colostrum samples and a sharp decrease was observed in the concentration of free oligosaccharides on day 15, followed by progressive decrease on days 90 and 250. Ninety-two glycosylation-related genes were expressed in milk somatic cells. Most of these genes exhibited higher expression in day 250 samples indicating increases in net glycosylation-related metabolism in spite of decreases in free milk oligosaccharides in late lactation milk. Even though fucosylated free oligosaccharides were not identified, gene expression indicated the likely presence of fucosylated oligosaccharides in bovine milk. Fucosidase genes were expressed in milk and a possible explanation for not detecting fucosylated free oligosaccharides is the degradation of large fucosylated free oligosaccharides by the fucosidases. Detailed characterization of enzymes encoded by the 92 glycosylation-related genes identified in this study will provide the basic knowledge for metabolic network analysis of oligosaccharides in mammalian milk. These candidate genes will guide the design of a targeted breeding strategy to optimize the content of beneficial oligosaccharides in bovine milk.
Hadronic Transport Coefficients from Effective Field Theories
Juan M. Torres-Rincon
Physics , 2012,
Abstract: This dissertation focuses on the calculation of transport coefficients in the matter created in a relativistic heavy-ion collision after the chemical freeze-out. This matter can be well approximated by a pion gas out of equilibrium. We describe the theoretical framework to obtain the shear and bulk viscosities, the thermal and electrical conductivities and the flavor diffusion coefficients of a meson gas at low temperatures. To describe the interactions of the degrees of freedom, we use effective field theories with chiral and heavy quark symmetries. We introduce the unitarization methods in order to obtain a scattering amplitude that satisfies the unitarity condition exactly. We perform the calculation of the transport properties of the low temperature phase of quantum chromodynamics -the hadronic medium- that can be used in the hydrodynamic simulations of a relativistic heavy-ion collision and its subsequent evolution. We show that the shear viscosity over entropy density exhibits a minimum in a phase transition by studying this coefficient in atomic Argon (around the liquid-gas phase transition) and in the linear sigma model in the limit of large number of scalar fields (that presents a chiral phase transition). Finally, we provide an experimental method to estimate the bulk viscosity in relativistic heavy-ion collisions by performing correlations of the fluctuating components of the stress-energy tensor.
Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies
Gonzalo Rincon, Katarina Tengvall, Janelle M Belanger, Laetitia Lagoutte, Juan F Medrano, Catherine André, Anne Thomas, Cynthia Lawley, Mark ST Hansen, Kerstin Lindblad-Toh, Anita M Oberbauer
BMC Research Notes , 2011, DOI: 10.1186/1756-0500-4-226
Abstract: In both buccal and blood samples, whether whole genome amplified or not, 97% of the samples had SNP call rates in excess of 80% indicating that the vast majority of the SNPs would be suitable to perform association studies regardless of the DNA source. Similarly, there were no significant differences in marker intensity measurements between buccal and blood samples for copy number variations (CNV) analysis.All DNA samples assayed, buccal or blood, native or whole genome amplified, are appropriate for use in array-based genome-wide association studies. The concordance between subsets of dogs for which both buccal and blood samples, or those samples whole genome amplified, was shown to average >99%. Thus, the two DNA sources were comparable in the generation of SNP genotypes and intensity values to estimate structural variation indicating the utility for the use of buccal cytobrush samples and the reliability of whole genome amplification for genome-wide association and CNV studies.The present study was undertaken to assess the utility of buccal cytobrush derived DNA and whole genome amplified (WGA) blood or buccal-derived DNA for use on the most recent iteration of the canine SNP GWA platform. Buccal-derived DNA has been suggested as insufficient in quantity and quality for application to the high-throughput SNP array platforms [1]. Whole blood DNA and buccal-derived DNA, as well as DNA samples (from both sources) subjected to WGA, were compared using the Illumina Infinium CanineHD Genotyping BeadChip containing 173,662 SNPs. Copy number variations (CNV), while shown to account for a significant proportion of human genetic polymorphism and have been suggested to play a role in genetic causes of disease [2], is complex and technically challenging to analyze. Specifically CNV analysis is uniquely different to GWA-SNP analysis because the data is based on the intensity measurement of the SNP. Despite the technical issues, the opportunity exists to examine this important
Overexpression of Scg5 increases enzymatic activity of PCSK2 and is inversely correlated with body weight in congenic mice
Charles R Farber, James Chitwood, Sang-Nam Lee, Ricardo A Verdugo, Alma Islas-Trejo, Gonzalo Rincon, Iris Lindberg, Juan F Medrano
BMC Genetics , 2008, DOI: 10.1186/1471-2156-9-34
Abstract: Through a combination of DNA microarray analysis and quantitative PCR we identified a strong expression quantitative trait locus (eQTL) regulating Scg5 expression in two mouse chromosome 2 congenic strains and three additional F2 intercrosses. More importantly, the eQTL was coincident with a body weight QTL in congenic mice and Scg5 expression was negatively correlated with body weight in two of the F2 intercrosses. Analysis of haplotype blocks and genomic sequencing of Scg5 in high (C3H/HeJ, DBA/2J, BALB/cByJ, CAST/EiJ) and low (C57BL/6J) expressing strains revealed mutations unique to C57BL/6J and possibly responsible for the difference in mRNA abundance. To evaluate the functional consequence of Scg5 overexpression we measured the pituitary levels of 7B2 protein and PCSK2 activity and found both to be increased. In spite of this increase, the level of pituitary α-MSH, a PCSK2 processing product, was unaltered.Together, these data support a role for Scg5 in the modulation of body weight.Body weight, as with all complex traits, is partially regulated by the coordinate action of individual genes. One common approach for dissecting the genetics of growth is the mapping of quantitative trait loci (QTL). In the last decade numerous human and mouse growth QTL have been identified [1]; however, while this progress is important, few if any of the loci have been unequivocally resolved to the effects of a single quantitative trait gene (QTG).Several studies involving many different mouse inbred strains have demonstrated an enrichment of growth and obesity QTL on chromosome 2 [2,3]. In our laboratory, we have developed a number of genomic resources with the goal of discerning the molecular basis of chromosome 2 QTL segregating between the C57BL/6J (B6), C57BL/6J-hg/hg (HG) and CAST/EiJ (CAST) strains [4,5]. These include two congenic strains, B6.CAST-(D2Mit329-D2Mit457)N(6) (B62D) and HG.CAST-(D2Mit329-D2Mit457)N(6) (HG2D), constructed by introgressing an identical congenic
Dynamical evolution of the chiral magnetic effect: Applications to the quark-gluon plasma
Cristina Manuel,Juan M. Torres-Rincon
Physics , 2015, DOI: 10.1103/PhysRevD.92.074018
Abstract: We study the dynamical evolution of the so-called chiral magnetic effect in an electromagnetic conductor. To this end, we consider the coupled set of corresponding Maxwell and chiral anomaly equations, and we prove that these can be derived from chiral kinetic theory. After integrating the chiral anomaly equation over space in a closed volume, it leads to a quantum conservation law of the total helicity of the system. A change in the magnetic helicity density comes together with a modification of the chiral fermion density. We study in Fourier space the coupled set of anomalous equations and we obtain the dynamical evolution of the magnetic fields, magnetic helicity density, and chiral fermion imbalance. Depending on the initial conditions we observe how the helicity might be transferred from the fermions to the magnetic fields, or vice versa, and find that the rate of this transfer also depends on the scale of wavelengths of the gauge fields in consideration. We then focus our attention on the quark-gluon plasma phase, and analyze the dynamical evolution of the chiral magnetic effect in a very simple toy model. We conclude that an existing chiral fermion imbalance in peripheral heavy ion collisions would affect the magnetic field dynamics, and consequently, the charge dependent correlations measured in these experiments.
Kinetic theory of chiral relativistic plasmas and energy density of their gauge collective excitations
Cristina Manuel,Juan M. Torres-Rincon
Physics , 2013, DOI: 10.1103/PhysRevD.89.096002
Abstract: We use the recently developed kinetic theory with Berry curvature to describe the fermions and antifermions of a chiral relativistic plasma. We check that this transport approach allows to reproduce the chiral anomaly equation of relativistic quantum field theory at finite temperature. We also check that it allows to describe the anomalous gauge polarization tensor that appears in the Hard Thermal (and/or Dense) effective field theory. We also construct an energy density associated to the gauge collective modes of the chiral relativistic plasma, valid in the case of small couplings or weak fields, which can be the basis for the study of their dynamical evolution.
D-meson propagation in hot dense matter
Laura Tolos,Juan M. Torres-Rincon
Physics , 2013, DOI: 10.1103/PhysRevD.88.074019
Abstract: The drag force and diffusion coefficients for a D meson are calculated in hot dense matter composed of light mesons and baryons, such as it is formed in heavy-ion collisions. We use a unitarized approach based on effective models for the interaction of a D meson with hadrons, which are compatible with chiral and heavy quark symmetries. We study the propagation of the D meson in the hadron matter in two distinct cases. On the one hand, we analyze the propagation of D mesons in matter at vanishing baryochemical potential, which is relevant for high-energetic collisions at LHC or RHIC. On the other hand, we show the propagation of D mesons in the hadronic medium following isentropic trajectories, appropiate at FAIR and NICA heavy-ion experiments. We find a negligible baryon contribution to the transport coefficients at vanishing chemical potential. However at finite baryochemical potential we obtain a large correction to the transport coefficients with the inclusion of nucleons and Delta baryons. The relaxation time for D mesons is reduced a factor 2-3 in the later case, producing a more thermalized D meson-spectrum for FAIR physics than for the typical LHC energies. We finally present results for the spatial diffusion coefficient of a D meson in hadronic matter and the possible existence of a minimum near the phase transition to the quark-gluon plasma at zero and finite baryochemical potential.
Chiral transport equation from the quantum Dirac Hamiltonian and the on-shell effective field theory
Cristina Manuel,Juan M. Torres-Rincon
Physics , 2014, DOI: 10.1103/PhysRevD.90.076007
Abstract: We derive the relativistic chiral transport equation for massless fermions and antifermions by performing a semiclassical Foldy-Wouthuysen diagonalization of the quantum Dirac Hamiltonian. The Berry connection naturally emerges in the diagonalization process to modify the classical equations of motion of a fermion in an electromagnetic field. We also see that the fermion and antifermion dispersion relations are corrected at first order in the Planck constant by the Berry curvature, as previously derived by Son and Yamamoto for the particular case of vanishing temperature. Our approach does not require knowledge of the state of the system, and thus it can also be applied at high temperature. We provide support for our result by an alternative computation using an effective field theory for fermions and antifermions: the on-shell effective field theory. In this formalism, the off-shell fermionic modes are integrated out to generate an effective Lagrangian for the quasi-on-shell fermions/antifermions. The dispersion relation at leading order exactly matches the result from the semiclassical diagonalization. From the transport equation, we explicitly show how the axial and gauge anomalies are not modified at finite temperature and density despite the incorporation of the new dispersion relation into the distribution function.
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