RESUMO
Hi-C enables the characterization of the 0conformation of the genome in the three-dimensional nuclear space. This technique has revolutionized our ability to detect interactions between linearly distant genomic sites on a genome-wide scale. Here, we detail a protocol to carry out in situ Hi-C in plants and describe a straightforward bioinformatics pipeline for the analysis of such data, in particular for comparing samples from different organs or conditions.
Assuntos
Cromatina , Biologia Computacional , Núcleo Celular/genética , Biologia Computacional/métodos , Genoma , Genômica/métodos , Plantas/genéticaRESUMO
After Candida albicans, Candida glabrata is one of the most common fungal species associated with candidemia in nosocomial infections. Rapid acquisition of nutrients from the host is important for the survival of pathogens which possess the metabolic flexibility to assimilate different carbon and nitrogen compounds. In Saccharomyces cerevisiae, nitrogen assimilation is controlled through a mechanism known as Nitrogen Catabolite Repression (NCR). NCR is coordinated by the action of four GATA factors; two positive regulators, Gat1 and Gln3, and two negative regulators, Gzf3 and Dal80. A mechanism in C. glabrata similar to NCR in S. cerevisiae has not been broadly studied. We previously showed that in C. glabrata, Gln3, and not Gat1, has a major role in nitrogen assimilation as opposed to what has been observed in S. cerevisiae in which both factors regulate NCR-sensitive genes. Here, we expand the knowledge about the role of Gln3 from C. glabrata through the transcriptional analysis of BG14 and gln3Δ strains. Approximately, 53.5% of the detected genes were differentially expressed (DEG). From these DEG, amino acid metabolism and ABC transporters were two of the most enriched KEGG categories in our analysis (Up-DEG and Down-DEG, respectively). Furthermore, a positive role of Gln3 in AAA assimilation was described, as was its role in the transcriptional regulation of ARO8. Finally, an unexpected negative role of Gln3 in the gene regulation of ABC transporters CDR1 and CDR2 and its associated transcriptional regulator PDR1 was found. This observation was confirmed by a decreased susceptibility of the gln3Δ strain to fluconazole.
Assuntos
Aminoácidos/biossíntese , Candida glabrata/fisiologia , Farmacorresistência Fúngica/genética , Fluconazol/metabolismo , Fatores de Transcrição GATA/metabolismo , Transportadores de Cassetes de Ligação de ATP/genética , Compostos de Amônio/metabolismo , Antifúngicos/metabolismo , Antifúngicos/farmacologia , Candida glabrata/efeitos dos fármacos , Candida glabrata/genética , Candida glabrata/metabolismo , Repressão Catabólica , Farmacorresistência Fúngica/efeitos dos fármacos , Fluconazol/farmacologia , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Fatores de Transcrição GATA/genética , Perfilação da Expressão Gênica , Regulação Fúngica da Expressão Gênica , MutaçãoRESUMO
A primitive-equation model has been used to investigate the meteorologically-driven circulation of the Bay of Algeciras. It is shown that the mean circulation of Atlantic Water (AW) is characterized by an anticyclonic cell, while Mediterranean Water (MW) follows a preferred cyclonic pathway. Meteorological forcing distorts substantially the AW mean circulation pattern, and only modulates that of the MW. Winds drive a vertical circulation cell in the Atlantic layer consistent with Ekman dynamics, whereas the horizontal circulation pattern is markedly dependent on the swift Atlantic jet entering the Mediterranean and changes from clearly anticyclonic to cyclonic as the jet separates or approaches the strait's northern shoreline. This occurs through atmospheric pressure-driven acceleration/deceleration of the jet, in agreement with internal hydraulics theory predictions. It is also found that the renewal of AW is largely modulated by tides, with meteorological forcing playing a secondary role. The opposite applies to the renewal of MW.
