Project description:Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem, we have predicted a detailed model for the nitrogen assimilation network in cyanobacterium Synechococcus sp. WH 8102 (WH8102) using a computational protocol based on comparative genomics analysis and mining experimental data from related organisms that are relatively well studied. This computational model is in excellent agreement with the microarray gene expression data collected under ammonium-rich versus nitrate-rich growth conditions, suggesting that our computational protocol is capable of predicting biological pathways/networks with high accuracy. We then refined the computational model using the microarray data, and proposed a new model for the nitrogen assimilation network in WH8102. An intriguing discovery from this study is that nitrogen assimilation affects the expression of many genes involved in photosynthesis, suggesting a tight coordination between nitrogen assimilation and photosynthesis processes. Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions.
Project description:We constructed a tiling microarray, covering nearly all of the intergenic regions larger than 50 bp on both strands of the genome of the marine picocyanobacterium Synechococcus WH7803. We analyzed transcript levels from cultures grown under ecologically relevant stress conditions. The investigated stress conditions were cold stress, high light stress, phosphate depletion and iron depletion. We identified several previously unknown small RNAs, partially differentially expressed. The detected RNAs provide a starting point for further investigations on the acclimatisation to different stresses for Synechococcus WH7803.
Project description:In wh-questions that form a syntactic dependency between the fronted wh-phrase and its thematic position, acceptability is severely degraded when the dependency crosses another wh-phrase. It is well known that the acceptability degradation in wh-island violation ameliorates in certain contexts, but the source of this variation remains poorly understood. In the syntax literature, an influential theory - Featural Relativized Minimality - has argued that the wh-island effect is modulated exclusively by the distinctness of morpho-syntactic features in the two wh-phrases, but psycholinguistic theories of memory encoding and retrieval mechanisms predict that semantic properties of wh-phrases should also contribute to wh-island amelioration. We report four acceptability judgment experiments that systematically investigate the role of morpho-syntactic and semantic features in wh-island violations. The results indicate that the distribution of wh-island amelioration is best explained by an account that incorporates the distinctness of morpho-syntactic features as well as the semantic denotation of the wh-phrases. We argue that an integration of syntactic theories and perspectives from psycholinguistics can enrich our understanding of acceptability variation in wh-dependencies.
