Saccharomycotin transcriptomics by next-generation sequencing

The non-standard decoding of the CUG codon in Candida cylindracea raises a number of questions about the evolutionary process of this organism and other species Candida clade for which the codon is ambiguous. In order to find some answers we studied the transcriptome of C. cylindracea, comparing its behavior with that of Saccharomyces cerevisiae (standard decoder) and Candida albicans (ambiguous decoder). The transcriptome characterization was performed using RNA-seq. This approach has several advantages over microarrays and its application is booming. TopHat and Cufflinks were the software used to build the protocol that allowed for gene quantification. About 95% of the reads were mapped on the genome. 3693 genes were analyzed, of which 1338 had a non-standard start codon (TTG/CTG) and the percentage of expressed genes was 99.4%. Most genes have intermediate levels of expression, some have little or no expression and a minority is highly expressed. The distribution profile of the CUG between the three species is different, but it can be significantly associated to gene expression levels: genes with fewer CUGs are the most highly expressed. However, CUG content is not related to the conservation level: more and less conserved genes have, on average, an equal number of CUGs. The most conserved genes are the most expressed. The lipase genes corroborate the results obtained for most genes of C. cylindracea since they are very rich in CUGs and nothing conserved. The reduced amount of CUG codons that was observed in highly expressed genes may be due, possibly, to an insufficient number of tRNA genes to cope with more CUGs without compromising translational efficiency. From the enrichment analysis, it was confirmed that the most conserved genes are associated with basic functions such as translation, pathogenesis and metabolism. From this set, genes with more or less CUGs seem to have different functions. The key issues on the evolutionary phenomenon remain unclear. However, the results are consistent with previous observations and shows a variety of conclusions that in future analyzes should be taken into consideration, since it was the first time that such a study was conducted.

Endowing NoSQL DBMS with SQL features through standard Call Level Interfaces

To store, update and retrieve data from database management systems (DBMS), software architects use tools, like call-level interfaces (CLI), which provide standard functionalities to interact with DBMS. However, the emerging of NoSQL paradigm, and particularly new NoSQL DBMS providers, lead to situations where some of the standard functionalities provided by CLI are not supported, very often due to their distance from the relational model or due to design constraints. As such, when a system architect needs to evolve, namely from a relational DBMS to a NoSQL DBMS, he must overcome the difficulties conveyed by the features not provided by NoSQL DBMS. Choosing the wrong NoSQL DBMS risks major issues with components requesting non-supported features. This paper focuses on how to deploy features that are not so commonly supported by NoSQL DBMS (like Stored Procedures, Transactions, Save Points and interactions with local memory structures) by implementing them in standard CLI.