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Mapping Genetic Variants Underlying Differences in the Central Nitrogen Metabolism in Fermenter Yeasts
Matías Jara, Francisco A. Cubillos, Verónica García, Francisco Salinas, Omayra Aguilera, Gianni Liti, Claudio Martínez
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086533
Abstract: Different populations within a species represent a rich reservoir of allelic variants, corresponding to an evolutionary signature of withstood environmental constraints. Saccharomyces cerevisiae strains are widely utilised in the fermentation of different kinds of alcoholic beverages, such as, wine and sake, each of them derived from must with distinct nutrient composition. Importantly, adequate nitrogen levels in the medium are essential for the fermentation process, however, a comprehensive understanding of the genetic variants determining variation in nitrogen consumption is lacking. Here, we assessed the genetic factors underlying variation in nitrogen consumption in a segregating population derived from a cross between two main fermenter yeasts, a Wine/European and a Sake isolate. By linkage analysis we identified 18 main effect QTLs for ammonium and amino acids sources. Interestingly, majority of QTLs were involved in more than a single trait, grouped based on amino acid structure and indicating high levels of pleiotropy across nitrogen sources, in agreement with the observed patterns of phenotypic co-variation. Accordingly, we performed reciprocal hemizygosity analysis validating an effect for three genes, GLT1, ASI1 and AGP1. Furthermore, we detected a widespread pleiotropic effect on these genes, with AGP1 affecting seven amino acids and nine in the case of GLT1 and ASI1. Based on sequence and comparative analysis, candidate causative mutations within these genes were also predicted. Altogether, the identification of these variants demonstrate how Sake and Wine/European genetic backgrounds differentially consume nitrogen sources, in part explaining independently evolved preferences for nitrogen assimilation and representing a niche of genetic diversity for the implementation of practical approaches towards more efficient strains for nitrogen metabolism.
Dehydration of Agro Products in a Hybrid Solar Dryer Controlled through a Fuzzy Logic System  [PDF]
Alejandro Reyes, Francisco Cubillos, Andrea Mahn, José Vásquez
International Journal of Modern Nonlinear Theory and Application (IJMNTA) , 2014, DOI: 10.4236/ijmnta.2014.33009
Abstract:

Drying is one of the most energy-intensive processes in agro-products industry. For this reason, using solar energy appears as an attractive not polluting alternative to be used in drying processes. However, the daily and seasonal fluctuations in the radiation level require using energy accumulators with phase change materials (paraffin wax), to have a continuous drying processes. In hybrid solar dryers with energy accumulation system, a control system is essential to coordinate the control valves that allow the income of air that comes from the solar panel or from the energy accumulator. In this work, we implemented an advances multivariable control system that uses fuzzy logic in the hybrid solar dryer. The dryer includes an energy accumulator panel with paraffin wax as phase change material. The input variables were ambient temperature and solar radiation, both not controllable. The controlled variables were the opening level of the solar panel and accumulator energy valves. The control program consisted in an algorithm implemented with the “Fuzzy” toolbox in Matlab. Data were acquired with OPTO 22. The control system performed adequately when used to dehydrate mushroom slices and plums. Closing or opening the respective valves as a response to the variations of solar radiation and ambient air temperature allowed optimizing the use of solar energy.

 

SHOOT GROWTH1 Maintains Arabidopsis Epigenomes by Regulating IBM1
Vincent Coustham, Daniela Vlad, Aurélie Deremetz, Isabelle Gy, Francisco A. Cubillos, Envel Kerdaffrec, Olivier Loudet, Nicolas Bouché
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0084687
Abstract: Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1), a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH) domain found in several chromatin regulators and an RNA-Recognition Motif (RRM). The sg1 mutations are associated with drastic pleiotropic phenotypes. The mutants degenerate after few generations and are similar to mutants of the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1). A methylome analysis of sg1 mutants revealed a large number of gene bodies hypermethylated in the cytosine CHG context, associated with an increase in di-methylation of lysine 9 on histone H3 tail (H3K9me2), an epigenetic mark normally found in silenced transposons. The sg1 phenotype is suppressed by mutations in genes encoding the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) or the histone methyltransferase KRYPTONITE (KYP), indicating that SG1 functions antagonistically to CMT3 or KYP. We further show that the IBM1 transcript is not correctly processed in sg1, and that the functional IBM1 transcript complements sg1. Altogether, our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1.
The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae
Francisco Salinas, Francisco A. Cubillos, Daniela Soto, Verónica Garcia, Anders Bergstr?m, Jonas Warringer, M. Angélica Ganga, Edward J. Louis, Gianni Liti, Claudio Martinez
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049640
Abstract: Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs) that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories.
Segregating YKU80 and TLC1 Alleles Underlying Natural Variation in Telomere Properties in Wild Yeast
Gianni Liti ,Svasti Haricharan,Francisco A. Cubillos,Anna L. Tierney,Sarah Sharp,Alison A. Bertuch,Leopold Parts,Elizabeth Bailes,Edward J. Louis
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000659
Abstract: In yeast, as in humans, telomere length varies among individuals and is controlled by multiple loci. In a quest to define the extent of variation in telomere length, we screened 112 wild-type Saccharomyces sensu stricto isolates. We found extensive telomere length variation in S. paradoxus isolates. This phenotype correlated with their geographic origin: European strains were observed to have extremely short telomeres (<150 bp), whereas American isolates had telomeres approximately three times as long (>400 bp). Insertions of a URA3 gene near telomeres allowed accurate analysis of individual telomere lengths and telomere position effect (TPE). Crossing the American and European strains resulted in F1 spores with a continuum of telomere lengths consistent with what would be predicted if many quantitative trait loci (QTLs) were involved in length maintenance. Variation in TPE is similarly quantitative but only weakly correlated with telomere length. Genotyping F1 segregants indicated several QTLs associated with telomere length and silencing variation. These QTLs include likely candidate genes but also map to regions where there are no known genes involved in telomeric properties. We detected transgressive segregation for both phenotypes. We validated by reciprocal hemizygosity that YKU80 and TLC1 are telomere-length QTLs in the two S. paradoxus subpopulations. Furthermore, we propose that sequence divergence within the Ku heterodimer generates negative epistasis within one of the allelic combinations (American-YKU70 and European-YKU80) resulting in very short telomeres.
Análisis de los cambios de abundancia de sardina común (Strangomera bentincki): estructura a?o calendario versus a?o biológico
Arteaga,Marcos; Cubillos,Luis A;
Latin american journal of aquatic research , 2008,
Abstract: two indirect stock assessment models are implemented in order to analyze changes in the common sardine abundance. one model uses a calendar-year configuration (january-december year t) and the other a biological-year configuration (july year t - june year t+1). each model is contrasted with catch-at-length data, total catch in weight, catch per unit effort from 1990 to 2002, and biomass from acoustic surveys done every january from 2000 to 2002 off central-southern chile. the two applied population dynamics models (calendar and biological year approaches) differ structurally only in the treatment of the data that reveal the annual changes. the changes observed in the common sardine abundance, per calendar or biological year, indícate similar trends as those reported in earlier studies. nevertheless, differences were registered in the esti-mations for both assessments, with the biological year showing lower abundance levéis that are closely related to recruitment; this, considers the magnitude of the real composition of the annual class/cohort. on the other hand, the calendar year assessment incorporates the remaining annual classes/cohorts, thereby generating an erroneous estimation of the annual class/cohort abundance. the two models are compared with a likelihood indicator, finding that the assessment using the biological configuration was the best model, with a better fit to the data and greater degrees of explanation.
Cuando el vino dice algo más sobre la sociedad: Otra visión de Roma Imperial
Cubillos Poblete,Marcela A. E;
Universum (Talca) , 2005, DOI: 10.4067/S0718-23762005000200002
Abstract: the present investigation comprises of a work greater than we have developed during last the six years. from some passages of the satires of juvenal we delineated the vision of the poet on the roman society. in individual, we were centered in the commentaries related to the wine world and the kitchen, under the understood one that these contexts also reflect the roman mentality and, in special, the noticeable existing social differences in imperial rome. the conceptual frame follows the ways of the thought established by social history and the marginality history, whose objective looks for to offer new perspective to know other "angles" the mentality of the greco-roman man
Análisis de los cambios de abundancia de sardina común (Strangomera bentincki): estructura a o calendario versus a o biológico An analysis of changes in sardine (Strangomera bentincki) abundance: calendar versus biological year structure
Marcos Arteaga,Luis A Cubillos
Latin american journal of aquatic research , 2008,
Abstract: Se implementa dos modelos de evaluación de stock indirecta para analizar los cambios de abundancia en sardina común. Un modelo utiliza una asignación a o calendario (enero-diciembre del a o t), y el segundo un a o biológico (julio del a o t a junio del a o siguiente, t + 1). El modelo se contrasta con datos de captura en número a la talla, capturas totales en peso, captura por unidad de esfuerzo en el periodo 1990-2002, y biomasa acústica evaluada en enero de 2000 al 2002 en la zona centro-sur de Chile. El modelo de dinámica poblacional aplicado, se diferencia estructuralmente sólo en el tratamiento de los datos para reflejar cambios anuales, tanto bajo el enfoque a o calendario como biológico. Los cambios observados en el stock de sardina común, según a o calendario o biológico, indican tendencias similares a los que han sido reportadas en evaluaciones previas. Sin embargo, se observan diferencias en los estimados de ambas evaluaciones, donde la estructura a o biológico, presenta índices de abundancia de menor magnitud y estrechamente ligados al reclutamiento, esto considerando la real composición en magnitud que posee la clase anual. En contraste, la evaluación a o calendario incorpora la presencia de clases anuales remanentes, generando de esta manera un escenario erróneo en la fuerza de la clase anual. Ambos modelos se contrastan con un indicador que utiliza la composición de la verosimilitud, encontrándose a la evaluación a o biológico el mejor modelo basado en un mayor ajuste frente a los datos y mayor grado de explicación. Two indirect stock assessment models are implemented in order to analyze changes in the common sardine abundance. One model uses a calendar-year configuration (January-December year t) and the other a biological-year configuration (July year t - June year t+1). Each model is contrasted with catch-at-length data, total catch in weight, catch per unit effort from 1990 to 2002, and biomass from acoustic surveys done every January from 2000 to 2002 off central-southern Chile. The two applied population dynamics models (calendar and biological year approaches) differ structurally only in the treatment of the data that reveal the annual changes. The changes observed in the common sardine abundance, per calendar or biological year, indícate similar trends as those reported in earlier studies. Nevertheless, differences were registered in the esti-mations for both assessments, with the biological year showing lower abundance levéis that are closely related to recruitment; this, considers the magnitude of the real composition of the annu
Cuando el vino dice algo más sobre la sociedad: Otra visión de Roma Imperial
Marcela A. E Cubillos Poblete
Universum : Revista de Humanidades y Ciencias Sociales , 2005,
Abstract: La presente investigación forma parte de un trabajo mayor que hemos desarrollado durante los últimos seis a os. A partir de algunos pasajes de las Sátiras de Juvenal delineamos la visión del poeta sobre la sociedad romana. En particular, nos centramos en los comentarios relacionados con el mundo vitivinícola y la cocina, bajo el entendido que dichos contextos también reflejan la mentalidad romana y, en especial, las marcadas diferencias sociales existentes en Roma Imperial. El marco conceptual sigue los lineamientos establecidos por la Historia Social y la Historia de la Marginalidad, cuyo objetivo busca ofrecer nuevas perspectivas para conocer otros "ángulos" de la mentalidad del hombre greco-romano. The present investigation comprises of a work greater than we have developed during last the six years. From some passages of the Satires of Juvenal we delineated the vision of the poet on the Roman society. In individual, we were centered in the commentaries related to the wine world and the kitchen, under the understood one that these contexts also reflect the Roman mentality and, in special, the noticeable existing social differences in Imperial Rome. The conceptual frame follows the ways of the thought established by Social History and the Marginality History, whose objective looks for to offer new perspective to know other "angles" the mentality of the greco-Roman man
Estudio enzimático y anatomopatológico de ponedoras alimentadas con semilla de Lupinus albus (dulce y amarga) durante 22 semanas Enzymatic and anatomopathological study of laying hens feeding on Lupinus albus seeds (sweet and bitter) for 22 weeks
J.C. LOPEZ,V. CUBILLOS,A. CUBILLOS,I. MOLINA
Archivos de medicina veterinaria , 1997,
Abstract: Se estudió el efecto de la incorporación de semilla de Lupinus albus var. Multolupa en la ración de gallinas ponedoras. Un total de 160 gallinas White Leghorn (línea Shaver Starcross 288), de 34 semanas de edad, divididas al azar en 4 grupos, fueron alimentadas en forma controlada durante 22 semanas con una dieta basal más un 10% de semilla de lupino con diferentes porcentajes de alcaloides. Las aves fueron divididas en 4 grupos de 40 aves cada uno, a las que se les administró 0.0105, 0.0421, 0.106 y 0.148 g% de alcaloide, respectivamente. El estudio enzimático consideró las enzimas as-partato-aminotransferasa, alanino-aminotrans-ferasa y fosfatasa alcalina. Se recolectaron muestras de hígado, cerebro y ri ón para estudio macro y microscópico, y se llevó un registro de mortalidad. No se encontraron valores enzimáticos que indiquen alteraciones a nivel hepático atribuibles al lupino. Las principales alteraciones morfoló-gicas encontradas fueron trastornos degenerativos y necróticos en cerebro, en igual proporción en los 4 grupos. A nivel renal, en los túbulos se observaron trastornos degenerativos de carácter vacuolar. Las lesiones encontradas en hígado no mostraron un claro compromiso de este órgano. Se concluye que la semilla de lupino amargo con 2.63% de alcaloides, incorporada hasta en un 10% de la ración de ponedoras durante su primera fase de postura, no produce efectos nocivos en la salud de las aves. The effect produced by the incorporation of Lupinus albus var. Multolupa seeds in the rations of laying hens was studied. One hundred and sixty (34 week old) White Leghorn hens (Shaver Starcross 288) were divided into 4 groups. These hens were fed with a basal diet plus 10% lupine seeds, with different percentages of alkaloids, for 22 weeks. The hens were kept in individual coops. They were fed daily with 112.5 g/fowl and water was given ad-libitum. The enzymatic study was carried out by measuring the activity of aspartate-aminotransferase, alanine-aminotransferase and alkaline phosphatase enzimes. Liver, brain and kidney samples were collected in order to perform macro and microscopic analysis. A mortality record was kept. There were no enzymatic values indicating disorder in the hepatic functions due to the lupine seeds. The main morphological alterations were degenerative and necrotic changes in the brain. Degenerative changes were observed in the tubular portions of the kidney. In similar proportions, within the groups, degenerative changes were observed in the liver. In conclusion, the bitter lupine seeds (2.63% of total alkaloids), incorporated
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