19 research outputs found

    Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

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    <p>Abstract</p> <p>Background</p> <p><it>Candida parapsilosis </it>is one of the most common causes of <it>Candida </it>infection worldwide. However, the genome sequence annotation was made without experimental validation and little is known about the transcriptional landscape. The transcriptional response of <it>C. parapsilosis </it>to hypoxic (low oxygen) conditions, such as those encountered in the host, is also relatively unexplored.</p> <p>Results</p> <p>We used next generation sequencing (RNA-seq) to determine the transcriptional profile of <it>C. parapsilosis </it>growing in several conditions including different media, temperatures and oxygen concentrations. We identified 395 novel protein-coding sequences that had not previously been annotated. We removed > 300 unsupported gene models, and corrected approximately 900. We mapped the 5' and 3' UTR for thousands of genes. We also identified 422 introns, including two introns in the 3' UTR of one gene. This is the first report of 3' UTR introns in the Saccharomycotina. Comparing the introns in coding sequences with other species shows that small numbers have been gained and lost throughout evolution. Our analysis also identified a number of novel transcriptional active regions (nTARs). We used both RNA-seq and microarray analysis to determine the transcriptional profile of cells grown in normoxic and hypoxic conditions in rich media, and we showed that there was a high correlation between the approaches. We also generated a knockout of the <it>UPC2 </it>transcriptional regulator, and we found that similar to <it>C. albicans</it>, Upc2 is required for conferring resistance to azole drugs, and for regulation of expression of the ergosterol pathway in hypoxia.</p> <p>Conclusion</p> <p>We provide the first detailed annotation of the <it>C. parapsilosis </it>genome, based on gene predictions and transcriptional analysis. We identified a number of novel ORFs and other transcribed regions, and detected transcripts from approximately 90% of the annotated protein coding genes. We found that the transcription factor Upc2 role has a conserved role as a major regulator of the hypoxic response in <it>C. parapsilosis </it>and <it>C. albicans</it>.</p

    Valuing Others’ Information under Imperfect Expectations

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    Sometimes we believe that others receive harmful information. However, Marschak’s value of information framework always assigns non-negative value under expected utility: it starts from the decision maker’s beliefs – and one can never anticipate information’s harmfulness for oneself. The impact of decision makers’ capabilities to process information and of their expectations remains hidden behind the individual and subjective perspective Marschak’s framework assumes. By introducing a second decision maker as a point of reference, this paper introduces a way for evaluating others’ information from a cross-individual, imperfect expectations perspective for agents maximising expected utility. We define the cross-value of information that can become negative – then the information is “harmfulâ€\x9D from a cross-individual perspective – and we define (mutual) cost of limited information processing capabilities and imperfect expectations as an opportunity cost from this same point of reference. The simple relationship between these two expected utility-based concepts and Marschak’s framework is shown, and we discuss evaluating short-term reactions of stock market prices to new information as an important domain of valuing others’ information. Copyright Springer Science+Business Media, LLC 2007value of information, decision under risk, imperfect expectations, cross-value of information, harmful information, stock market prices, D80, D82, D83,
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