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Including transcription factor information in the superparamagnetic clustering of microarray data
Get PDF"In this work, we modify the superparamagnetic clustering algorithm (SPC) by adding an extra weight to the interaction formula that considers which genes are regulated by the same transcription factor. With this modified algorithm that we call SPCTF, we analyze Spellman et al. microarray data for cell cycle genes in yeast, and find clusters with a higher number of elements compared with those obtained with the SPC algorithm. Some of the incorporated genes by using SPCFT were not detected at first by Spellman et al. but were later identified by other studies, whereas several genes still remain unclassified. The clusters composed by unidentified genes were analyzed with MUSA, the motif finding using an unsupervised approach algorithm, and this allow us to select the clusters whose elements contain cell cycle transcription factor binding sites as clusters worth of further experimental studies because they would probably lead to new cell cycle genes. Finally, our idea of introducing available infor-mation about transcription factors to optimize the gene classification could be implemented for other distance-based clustering algorithms.
Efecto de Neuropéptidos QRFP sobre la adipogénesis in vitro y su expresión en depositos grasos de rata.
Get PDFTesis (Maestría en Ciencias en Biología Molecular)"Los péptidos RFamida son producidos en el hipotálamo y ejercen efectos anorexigénicos y orexigénicos cuando se inyectan intracerebroventricularmente. Resultados de nuestro laboratorio mostraron que los péptidos RFamida anorexigénicos NPAF, NPFF y NPSF bloquean la adipogénesis in vitro. Los péptidos RFamida QRFP (pyroglutamylated arginine-phenylalanineamide peptide) son orexigénicos inyectados en el hipotálamo pero se desconoce si ejercen efectos periféricos. Nosotros evaluamos el efecto de los péptidos QRFP h26RFa, r26RFa, r26RFa1-16, r26RFa20-26 y r43RFa sobre la adipogénesis in vitro de la línea celular 3T3-F442A y encontramos que éstos incrementaron la acumulación lipídica en función de la concentración. Asimismo, determinamos mediante RT-PCR que los mRNAs de QRFP y de su receptor, GPR103, se expresan en preadipocitos 3T3-F442A pero no en los adipocitos de esta línea celular. Los mRNAs y las proteínas de QRFP se expresaron también en depósitos grasos de epiplón, epidídimo, subcutáneo y perirenal provenientes de ratas macho Wistar. Nuestros resultados sugieren que los péptidos QRFP juegan un papel importante en la regulación del metabolismo y la diferenciación del tejido adiposo actuando directamente sobre este tejido, ya sea de forma endocrina o autocrina. Nuestro trabajo futuro estudiará los mecanismos moleculares por los cuales los péptidos QRFP favorecen la acumulación lipídica en células adiposas y caracterizará la expresión de estos péptidos en depósitos grasos de ratas sometidas a diferentes regímenes alimenticios.""Hypothalamic RFamide peptides exert both anorexigenic and orexigenic effects injected intracerebroventricularly. Results from our laboratory showed that anorexigenic RFamide peptides, NPAF, NPFF and NPSF block the in vitro adipogenesis. RFamide QRFP (Pyroglutamylated arginine-phenylalanineamide peptide) peptides are centrally orexigenic but it is unknown whether they exert peripheral effects. We evaluated the effect of the QRFP peptides h26RFa, r26RFa, r26RFa(1-16), r26RFa(20-26) and r43RFa on 3T3-F442A adipogenesis and found that they increased lipid accumulation in a concentration-dependent manner. We also determined by RT-PCR that mRNAs for QRFP and its receptor, GPR103, were expressed in 3T3-F442A preadipocytes but not in mature adipocytes of this cell line. QRFP mRNAs and proteins are also expressed in omental, epididymal, perirenal and subcutaneous fat depots of Wistar rats. Our results suggest that QRFP peptides play an important role in regulating metabolism and differentiation of adipose tissue by acting directly on this tissue, either endocrinally or autocrinally. Our future work will study the molecular mechanisms by which peptides QRFP favor lipid accumulation in fat cells and will characterize the expression of these peptides in fat depots of rats subjected to different diets.
Antagonism of two ascomycetes against Phytophthora capsici Leonian, causing wilt of pepper (Capsicum annuum L.)
Get PDFoai:repositorio.ipicyt.edu.mx:11627/3730"En esta investigación se evaluó la actividad antagónica y protección de plántulas in vitro del ascomiceto Xylaria poitei, y la actividad antagónica de éste en combinación con un ascomiceto desconocido (AD) contra P. capsici, causante de la marchitez del chile. Xylaria poitei protegió plántulas de chile y permitió la sobrevivencia de un 58.3% de las plántulas, mientras que el oomiceto causó 100% de mortandad; además este hongo inhibió el crecimiento micelial de P. capsici hasta un 49.6% en uno de los experimentos donde se establecieron confrontaciones duales. En confrontaciones triples ambos ascomicetos incrementan ligeramente su inhibición a los 12 días de establecida la confrontación contra P. capsici; y aún mantienen la inhibición del oomiceto cuatro días después. Ambos ascomicetos estimulan o inhiben su crecimiento en alguna fecha de evaluación durante la confrontación entre ellos. El medio líquido papa dextrosa expuesto al crecimiento de X. poitei (filtrado) tiene baja actividad contra el crecimiento micelial de P. capsici. Los resultados anteriores indican que la actividad antagónica de ambos ascomicetos contra P. capsici se incrementa cuando ambos crecen en forma combinada respecto a las confrontaciones duales, y sugieren que la actividad antagónica de X. poitei es estimulada por la presencia del oomicete.""In this study we evaluated the antagonistic activity and protection of seedlings in vitro of the ascomycete Xylaria poitei, and its antagonistic activity in combination with an unknown ascomycete (AD) against P. capsici, the cause of wilt in pepper. Xylariapoitei protected pepper seedlings and allowed 58.3% survival of seedlings, while the oomycete caused 100% mortality, besides this fungus inhibited the mycelial growth of P. capsici up to 49.6% in one of the experiments where they settled dual confrontations. In triple confrontations both ascomycetes increase slightly their inhibition at 12 days of confortation against P. capsici, and still maintain the inhibition of the oomycete four days later. It was observed that both ascomycetes stimulare or inhibit each other growth at some time during the evaluation of confortation. The potato dextrose liquid medium exposed to the growth of X. poitei (filtrate) has low activity against the mycelial growth of P. capsici. The above results indicate that the antagonistic activity of both ascomycetes againstbP. capsici increases when they grow in combination with respect to the dual confrontations, and suggest that the antagonistic activity of X. poitei is stimulated by the presence of the oomycete.
Oligonucleotides of Candida parapsilosis, detection method and kit comprising same
No full text"The invention discloses an in vitro method for the identification of Candida parapsilosis, the sequences associated to said identification, as well as diagnosis kits for identifying Candida parapsilosis.""La invención describe un método in vitro de identificación de Candida parapsilosis , las secuencias asociadas a dicha identificación, así como kits de diagnóstico para identificar Candida parapsilosis.
El Factor GATA Gln3 está involucrado en la regulación de los genes TDH1,TDH2 Y TDH3 en Saccharomyces cerevisiae.
Get PDFTesis (Maestría en Ciencias en Biología Molecular)"Saccharomyces cerevisiae es una levadura que posee un genoma relativamente pequeño, distribuido en 16 cromosomas, que contienen aproximadamente 6000 marcos de lectura abierta (ORFs). Se sabe que el carbono y el nitrógeno son nutrientes esenciales para los organismos unicelulares. La levadura S. cerevisiae es capaz de utilizar una amplia variedad de compuestos como fuente de nitrógeno. Estos compuestos se pueden clasificar como buenas fuentes (como glutamina o asparagina) o malas fuentes (como prolina o GABA). Cuando la levadura crece en buenas fuentes de nitrógeno mantiene reprimidos genes que codifican para transportadores y enzimas catabólicas de malas fuentes. A este mecanismo se le conoce como represión catabólica nitrogenada (NCR). La NCR se encuentra coordinada por cuatro factores transcripcionales: dos activadores Gln3 y Gat1 y dos represores Gzf3 y Dal80. Los activadores Gat1 y Gln3 son más activos cuando las células crecen en malas fuentes de nitrógeno, por lo que incrementan la expresión de sus genes blanco, que en buenas fuentes se encuentran reprimidos. Sin embargo, existen genes cuya expresión depende de Gln3, pero no de NCR: GDH3, UGA3 y GLT1. Para determinar qué otros genes son activados por Gln3 en una buena fuente de nitrógeno, se diseñaron microarreglos en medios que contenían glutamina como fuente de nitrógeno. Se encontró la sobreexpresión de 15 genes en una cepa parental con respecto de una cepa gln3Δ. De estos genes se seleccionaron los genes TDH1, TDH2 y TDH3 para analizar su expresión. Estos genes tienen secuencias consenso de tipo GATA (5’-GATWA-3’) en sus regiones intergénicas. Al evaluar la expresión dependiente de Gln3, se observó que estos tres genes sí están regulados por dicho activador, tanto en glutamina como en prolina.""Saccharomyces cerevisiae is an organism that contains a relatively small genome, comprised in 16 chromosomes containing around 6000 open reading frames (ORFs). It’s accepted that carbon and nitrogen compounds are the basic nutrients of the cellular living forms. The yeast S. cerevisiae is able to use a broad variety of nitrogen compounds as nitrogen sources, these compounds can be classified as good sources (glutamine, asparagine) or bad sources (proline, GABA). When yeasts are grown in a good nitrogen source, genes encoding proteins involved in transport and catabolism of bad nitrogen sources are repressed. This mechanism is known as nitrogen catabolite repression (NCR). NCR is coordinated by four transcripcional factors: two activators, Gln3 and Gat1; and two repressors, Gzf3 and Dal80. Gat1 and Gln3 are active when cells are grown in bad nitrogen sources; consequently, the expression of their target genes is de-repressed. However, there are some genes which expression depends on Gln3, but not necessary on NCR (e.g. GDH3, UGA3 and GLT1). To determine the genes that are activated by Gln3 in a good nitrogen source, we designed and performed microarray experiments in minimal medium with glutamine as nitrogen source. The expression profile of a wild type strain was compared with the one obtained from a gln3Δ mutant strain. Noteworthy, we found the over-expression of 15 genes among which we chose the genes TDH1, TDH2 and TDH3 to analyze their expression by RT-PCR. These genes contain, in their intergenic region, consensus sequences of the GATA core (5’-GATWA-3’). Our results show that these genes certainly depend on Gln3 for its expression when glutamine or proline are used as nitrogen sources.
Magnetocaloric effect in nanostructured Pr2Fe17 and Nd2Fe17 synthesized by high-energy ball-milling
No full text"Nanocrystalline Pr2Fe17 and Nd2Fe17 powders with rhombohedral Th2Zn17-type crystal structure and average particle sizes around 20 nm have been obtained by high-energy ball milling While the bulk alloys show a well-defined and sharp drop in the low-field magnetization curve at the Curie temperature, T-C = 285 K (Pr) and 335 K (Nd), the ball-milled samples exhibit a substantial broadening of the ferro-to-paramagnetic transition due to a considerable augmentation of the disordered inter-grain boundaries The latter results in an increase of more than 25% in the values of the full width at half maximum of the temperature dependence of the magnetic entropy change maintaining almost unchanged the relative cooling power
Mediadores redox inmovilizados para tratamiento de aguas contaminadas y emisiones de gas
No full text"The present invention relates to a treatment process applicable to degrade or transform organic and inorganic pollutants, commonly found in industrial wastewaters, contaminated aquifers and gas emissions, in which reduction or oxidation reactions (e.g. redox reactions) are involved. The treatment concept comprises reactors in which catalysts, with redox mediating properties, have been immobilized on ion exchange resins in order to improve and accelerate the transformation of priority pollutants by chemical or biological means.""La presente invención se relaciona con un proceso de tratamiento aplicable para degradar o transformar contaminantes orgánicos e inorgánicos, comúnmente encontrados en aguas residuales industriales, acuíferos contaminados y emisiones de gas, en el cual se involucran reacciones de reducción u oxidación (por ej. reacciones redox). El concepto de tratamiento comprende reactores en los cuales los catalizadores, con propiedades mediadas por redox, han sido inmovilizados en resinas de intercambio iónico para mejorar y acelerar la transformación de contaminantes prioritarios por medios químicos o biológicos.
Braid solutions to the action of the Gin enzyme
Get PDF"The topological analysis of enzymes, an active research topic, has allowed the application of the tangle model of Ernst and Sumners to deduce the action mechanism of several enzymes, modeled as 2-string tangles. By first deriving some results in the theory of 3-braids, in this paper we analyze knotted and linked products of site-specific recombination mediated by the Gin DNA invertase, an enzyme that involves 3-string tangles. Provided that the 3-tangles involved are 3-braids, we determine four families of solutions to its action, two families for each of the directly and inversely repeated site cases. For each case, one of the given solutions had not previously been reported in the related literature. These solutions were found using a computer algorithm, based on our theoretical results, which allows one to solve tangle equations under the assumption that the product of two or more rounds of recombinations is known.
Observation of magnetic edge state in graphene nanoribbons
Get PDF"The electronic structure and spin magnetism for few-layer-graphene nanoribbons synthesized by chemical vapor deposition have been investigated using near-edge x-ray absorption fine structure (NEXAFS) and electron-spin resonance (ESR). For the pristine sample, a prepeak was observed below the pi* peak close to the Fermi level in NEXAFS, indicating the presence of additional electronic states close to the Fermi level. The intensity of this prepeak decreased with increasing annealing temperature and disappeared after annealing above 1500 degrees C. The ESR spectra, which proved the presence of localized spins, tracked the annealing-temperature-dependent behavior of the prepeak with fidelity. The NEXAFS and ESR results jointly confirm the existence of a magnetic edge state that originates from open nanographene edges. The disappearance of the edge state after annealing at higher temperatures is explained by the decrease in the population of open edges owing to loop formation of adjacent graphene edges.
Ablation and optical third-order nonlinearities in Ag nanoparticles
Get PDF"The optical damage associated with high intensity laser excitation of silver nanoparticles (NPs) was studied. In order to investigate the mechanisms of optical nonlinearity of a nanocomposite and their relation with its ablation threshold, a high-purity silica sample implanted with Ag ions was exposed to different nanosecond and picosecond laser irradiations. The magnitude and sign of picosecond refractive and absorptive nonlinearities were measured near and far from the surface plasmon resonance (SPR) of the Ag NPs with a self-diffraction technique. Saturable optical absorption and electronic polarization related to self-focusing were identified. Linear absorption is the main process involved in nanosecond laser ablation, but nonlinearities are important for ultrashort picosecond pulses when the absorptive process become significantly dependent on the irradiance. We estimated that near the resonance, picosecond intraband transitions allow an expanded distribution of energy among the NPs, in comparison to the energy distribution resulting in a case of far from resonance, when the most important absorption takes place in silica. We measured important differences in the ablation threshold and we estimated that the high selectiveness of the SPR of Ag NPs as well as their corresponding optical nonlinearities can be strongly significant for laser-induced controlled explosions, with potential applications for biomedical photothermal processes.