Browsing by Author "Varela, C."

Now showing 1 - 5 of 5
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    Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
    (2006) Malig, R.; Varela, C.; Agosin T., Eduardo; Melo Ledermann, Francisco Javier
    Background In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE). The method relies on current genome information and annotation, incorporation of several new features, and key improvements over alternative methods, all of which are important to determine gene expression levels more accurately. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. Results We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. In addition, we report new insights from the analysis of existing SAGE data. First, we found that experimental SAGE tags mapping onto introns, intron-exon boundaries, and non-coding RNA elements are observed in all available SAGE data. Second, a significant fraction of experimental SAGE tags was found to map onto genomic regions currently annotated as intergenic. Third, a significant number of existing experimental SAGE tags for yeast has been derived from truncated cDNAs, which are synthesized through oligo-d(T) priming to internal poly-(A) regions during reverse transcription. Conclusion We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments. This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications.
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    Intermittent Hypoxia-Induced Carotid body chemosensory potentiation and hypertension are critically dependent on peroxynitrite formation
    (2016) Moya, E.; Arias, P.; Varela, C.; Oyarce, María Paz; Del Rio, Rodrigo; Iturriaga Agüera, Rodrigo
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    Percepción de cuidados parentales tempranos en consultantes a salud mental con intento e ideación suicida
    (2014) Morales Silva, Susana; Armijo Rodríguez, Iván Alejandro; Moya, C.; Echávarri, O.; Barros, J.; Varela, C.; Fischman, R.; Peñaloza, F.; Sánchez, G.
    Presentamos un estudio cuantitativo de sujetos con conducta suicida, realizado en 176 pacientes consultantes en servicios de salud mental. Se estudió la percepción que ellos tenían acerca del modo cómo habían sido cuidados por sus padres hasta los 16 años. Los resultados indican que el riesgo de un intento de suicidio de alta severidad, se asocia a una percepción de cuidado parental, definido como negligencia en el cuidado y en la protección. Esta asociación sería particularmente clara con la figura paterna. Un vínculo paterno que privilegia el sobre control, aún si presenta bajo niveles de cuidado, se asocia a menor riesgo de suicidio y/o a intentos más leves. Un rol materno de cuidado, pareciera ser un factor protector. Estos hallazgos abren preguntas importantes acerca de la necesidad de estudiar factores protectores o de riesgo, en los antecedentes biográficos de los pacientes con riesgo de suicidio.
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    Quantitative analysis of wine yeast gene expression profiles under winemaking conditions
    (2005) Varela, C.; Cárdenas, J.; Melo Ledermann, Francisco Javier; Agosin T., Eduardo
    Wine fermentation is a dynamic and complex process in which the yeast cell is subjected to multiple stress conditions. A successful adaptation involves changes in gene expression profiles where a large number of genes are up- or downregulated. Functional genomic approaches are commonly used to obtain global gene expression profiles, thereby providing a comprehensive view of yeast physiology. We used SAGE to quantify gene expression profiles in an industrial strain of Saccharomyces cerevisiae under winemaking conditions. The transcriptome of wine yeast was analysed at three stages during the fermentation process, mid-exponential phase, and early- and late-stationary phases. Upon correlation with the yeast genome, we found three classes of transcripts: (a) sequences that corresponded to ORFs; (b) expressed sequences from intergenic regions; and (c) messengers that did not match the published reference yeast genome. In all fermentation phases studied, the most highly expressed genes related to energy production and stress response. For many pathways, including glycolysis, different transcript levels were observed during each phase. Different isoenzymes, including hexose transporters (HXT), were differentially induced, depending on the growth phase. About 10% of transcripts matched non-annotated ORF regions within the yeast genome and could correspond to small novel genes originally omitted in the first gene annotation effort. Up to 22% of transcripts, particularly at late-stationary phase, did not match any known location within the genome. As the available reference yeast genome was obtained from a laboratory strain, these expressed sequences could represent genes only expressed by an industrial yeast strain. Further studies are necessary to identify the role of these potential genes during wine fermentation.
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    The application of non-Saccharomyces yeast in fermentations with limited aeration as a strategy for the production of wine with reduced alcohol content
    (ELSEVIER SCIENCE BV, 2015) Contreras, A.; Hidalgo, C.; Schmidt, S.; Henschke, P. A.; Curtin, C.; Varela, C.
    High alcohol concentrations reduce the complexity of wine sensory properties. In addition, health and economic drivers have the wine industry actively seeking technologies that facilitate the production of wines with lower alcohol content. One of the simplest approaches to achieve this aim would be the use of wine yeast strains which are less efficient at transforming grape sugars into ethanol, however commercially available wine yeasts produce very similar ethanol yields. Non-conventional yeast, in particular non-Saccharomyces species, have shown potential for producing wines with lower alcohol content. These yeasts are naturally present in the early stages of fermentation but in general are not capable of completing alcoholic fermentation. We have evaluated 48 non-Saccharomyces isolates to identify strains that, with limited aeration and in sequential inoculation regimes with S. cerevisiae, could be used for the production of wine with lower ethanol concentration. Two of these, Torulaspora delbrueckii AWRI1152 and Zygosaccharomyces bailii AWRI1578, enabled the production of wine with reduced ethanol concentration under limited aerobic conditions. Depending on the aeration regime T. delbrueckii AWRI1152 and Z bailii AWRI1578 showed a reduction in ethanol concentration of 1.5% (v/v) and 2.0% (v/v) respectively, compared to the S. cerevisiae anaerobic control. (C) 2015 Elsevier B.V. All rights reserved.